galaxy-commits October 2013

galaxy-commits@lists.galaxyproject.org

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226 discussions

commit/galaxy-central: greg: (1) enhance the 'Manage installed tool shed repositories' grid to mark repositories that contain exported workflows, (2) Set the tool_shed_status column value when installing a new repository or reinstalling an uninstalled repository, (3) On the 'Manage installed tool shed repositories' gird, display installed repositories ordered by tool_shed, name, owner, ctx_rev.
by commits-noreply＠bitbucket.org 02 Oct '13

02 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5aef59e68411/ Changeset: 5aef59e68411 User: greg Date: 2013-10-01 20:31:40 Summary: (1) enhance the 'Manage installed tool shed repositories' grid to mark repositories that contain exported workflows, (2) Set the tool_shed_status column value when installing a new repository or reinstalling an uninstalled repository, (3) On the 'Manage installed tool shed repositories' gird, display installed repositories ordered by tool_shed, name, owner, ctx_rev. Affected #: 2 files diff -r da46b521540df29f936aa51cd03e75068eff1204 -r 5aef59e6841170aa6e21794d78f709b17738595e lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py --- a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py +++ b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py @@ -15,6 +15,13 @@ deprecated_tip_str = '' return '<img src="/static/images/icon_error_sml.gif" %s/>' % deprecated_tip_str +def generate_includes_workflows_img_str( include_mouse_over=False ): + if include_mouse_over: + deprecated_tip_str = 'class="icon-button" title="This repository contains exported workflows"' + else: + deprecated_tip_str = '' + return '<img src="/static/images/fugue/gear.png" %s/>' % deprecated_tip_str + def generate_latest_revision_img_str( include_mouse_over=False ): if include_mouse_over: latest_revision_tip_str = 'class="icon-button" title="This is the latest installable revision of this repository"' @@ -60,6 +67,8 @@ tool_shed_status_str += generate_revision_updates_img_str( include_mouse_over=True ) if tool_shed_repository.upgrade_available: tool_shed_status_str += generate_revision_upgrades_img_str( include_mouse_over=True ) + if tool_shed_repository.includes_workflows: + tool_shed_status_str += generate_includes_workflows_img_str( include_mouse_over=True ) else: tool_shed_status_str = generate_unknown_img_str( include_mouse_over=True ) return tool_shed_status_str @@ -211,7 +220,11 @@ use_paging = False def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( self.model_class ) + return trans.sa_session.query( self.model_class ) \ + .order_by( self.model_class.table.c.tool_shed, + self.model_class.table.c.name, + self.model_class.table.c.owner, + self.model_class.table.c.ctx_rev ) @property def legend( self ): @@ -219,6 +232,7 @@ legend_str += '%s  A newer installable revision is available for this repository<br/>' % generate_revision_upgrades_img_str() legend_str += '%s  This is the latest installable revision of this repository<br/>' % generate_latest_revision_img_str() legend_str += '%s  This repository is deprecated in the Tool Shed<br/>' % generate_deprecated_repository_img_str() + legend_str += '%s  This repository contains exported workflows<br/>' % generate_includes_workflows_img_str() legend_str += '%s  Unable to get information from the Tool Shed<br/>' % generate_unknown_img_str() return legend_str diff -r da46b521540df29f936aa51cd03e75068eff1204 -r 5aef59e6841170aa6e21794d78f709b17738595e lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -352,6 +352,10 @@ updating_installed_repository=False, persist=True ) tool_shed_repository.metadata = metadata_dict + # Update the tool_shed_repository.tool_shed_status column in the database. + tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( trans.app, tool_shed_repository ) + if tool_shed_status_dict: + tool_shed_repository.tool_shed_status = tool_shed_status_dict trans.sa_session.add( tool_shed_repository ) trans.sa_session.flush() if 'tool_dependencies' in metadata_dict and not reinstalling: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 02 Oct '13

02 Oct '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5019491835c7/ Changeset: 5019491835c7 User: Dave Bouvier Date: 2013-10-01 19:54:57 Summary: Migrate cuffcompare, cuffdiff, cufflinks, and cuffmerge from the distribution to the tool shed. Update the 'Review migration stages' layout. Affected #: 38 files diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py --- a/lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py +++ b/lib/tool_shed/galaxy_install/migrate/versions/0008_tools.py @@ -6,45 +6,49 @@ 3: Compute Motif Frequencies For All Motifs motif by motif 4: Compute Motif Frequencies in indel flanking regions 5: CTD analysis of chemicals, diseases, or genes -6: Delete Overlapping Indels from a chromosome indels file -7: Separate pgSnp alleles into columns -8: Draw Stacked Bar Plots for different categories and different criteria -9: Length Distribution chart -10: FASTA Width formatter -11: RNA/DNA converter -12: Draw quality score boxplot -13: Quality format converter (ASCII-Numeric) -14: Filter by quality -15: FASTQ to FASTA converter -16: Remove sequencing artifacts -17: Barcode Splitter -18: Clip adapter sequences -19: Collapse sequences -20: Draw nucleotides distribution chart -21: Compute quality statistics -22: Rename sequences -23: Reverse- Complement -24: Trim sequences -25: FunDO human genes associated with disease terms -26: HVIS visualization of genomic data with the Hilbert curve -27: Fetch Indels from 3-way alignments -28: Identify microsatellite births and deaths -29: Extract orthologous microsatellites for multiple (>2) species alignments -30: Mutate Codons with SNPs -31: Pileup-to-Interval condenses pileup format into ranges of bases -32: Filter pileup on coverage and SNPs -33: Filter SAM on bitwise flag values -34: Merge BAM Files merges BAM files together -35: Generate pileup from BAM dataset -36: SAM-to-BAM converts SAM format to BAM format -37: Convert SAM to interval -38: flagstat provides simple stats on BAM files -39: MPileup SNP and indel caller -40: rmdup remove PCR duplicates -41: Slice BAM by provided regions -42: Split paired end reads -43: T Test for Two Samples -44: Plotting tool for multiple series and graph types. +6: Cuffcompare +7: Cuffdiff +8: Cufflinks +9: Cuffmerge +10: Delete Overlapping Indels from a chromosome indels file +11: Separate pgSnp alleles into columns +12: Draw Stacked Bar Plots for different categories and different criteria +13: Length Distribution chart +14: FASTA Width formatter +15: RNA/DNA converter +16: Draw quality score boxplot +17: Quality format converter (ASCII-Numeric) +18: Filter by quality +19: FASTQ to FASTA converter +20: Remove sequencing artifacts +21: Barcode Splitter +22: Clip adapter sequences +23: Collapse sequences +24: Draw nucleotides distribution chart +25: Compute quality statistics +26: Rename sequences +27: Reverse- Complement +28: Trim sequences +29: FunDO human genes associated with disease terms +30: HVIS visualization of genomic data with the Hilbert curve +31: Fetch Indels from 3-way alignments +32: Identify microsatellite births and deaths +33: Extract orthologous microsatellites for multiple (>2) species alignments +34: Mutate Codons with SNPs +35: Pileup-to-Interval condenses pileup format into ranges of bases +36: Filter pileup on coverage and SNPs +37: Filter SAM on bitwise flag values +38: Merge BAM Files merges BAM files together +39: Generate pileup from BAM dataset +40: SAM-to-BAM converts SAM format to BAM format +41: Convert SAM to interval +42: flagstat provides simple stats on BAM files +43: MPileup SNP and indel caller +44: rmdup remove PCR duplicates +45: Slice BAM by provided regions +46: Split paired end reads +47: T Test for Two Samples +48: Plotting tool for multiple series and graph types. The tools are now available in the repositories respectively: @@ -53,45 +57,49 @@ 3: compute_motif_frequencies_for_all_motifs 4: compute_motifs_frequency 5: ctd_batch -6: delete_overlapping_indels -7: divide_pg_snp -8: draw_stacked_barplots -9: fasta_clipping_histogram -10: fasta_formatter -11: fasta_nucleotide_changer -12: fastq_quality_boxplot -13: fastq_quality_converter -14: fastq_quality_filter -15: fastq_to_fasta -16: fastx_artifacts_filter -17: fastx_barcode_splitter -18: fastx_clipper -19: fastx_collapser -20: fastx_nucleotides_distribution -21: fastx_quality_statistics -22: fastx_renamer -23: fastx_reverse_complement -24: fastx_trimmer -25: hgv_fundo -26: hgv_hilbertvis -27: indels_3way -28: microsatellite_birthdeath -29: multispecies_orthologous_microsats -30: mutate_snp_codon -31: pileup_interval -32: pileup_parser -33: sam_bitwise_flag_filter -34: sam_merge -35: sam_pileup -36: sam_to_bam -37: sam2interval -38: samtools_flagstat -39: samtools_mpileup -40: samtools_rmdup -41: samtools_slice_bam -42: split_paired_reads -43: t_test_two_samples -44: xy_plot +6: cuffcompare +7: cuffdiff +8: cufflinks +9: cuffmerge +10: delete_overlapping_indels +11: divide_pg_snp +12: draw_stacked_barplots +13: fasta_clipping_histogram +14: fasta_formatter +15: fasta_nucleotide_changer +16: fastq_quality_boxplot +17: fastq_quality_converter +18: fastq_quality_filter +19: fastq_to_fasta +20: fastx_artifacts_filter +21: fastx_barcode_splitter +22: fastx_clipper +23: fastx_collapser +24: fastx_nucleotides_distribution +25: fastx_quality_statistics +26: fastx_renamer +27: fastx_reverse_complement +28: fastx_trimmer +29: hgv_fundo +30: hgv_hilbertvis +31: indels_3way +32: microsatellite_birthdeath +33: multispecies_orthologous_microsats +34: mutate_snp_codon +35: pileup_interval +36: pileup_parser +37: sam_bitwise_flag_filter +38: sam_merge +39: sam_pileup +40: sam_to_bam +41: sam2interval +42: samtools_flagstat +43: samtools_mpileup +44: samtools_rmdup +45: samtools_slice_bam +46: split_paired_reads +47: t_test_two_samples +48: xy_plot from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu and will be installed into your local Galaxy instance at the diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 scripts/migrate_tools/0008_tools.xml --- a/scripts/migrate_tools/0008_tools.xml +++ b/scripts/migrate_tools/0008_tools.xml @@ -15,6 +15,18 @@ <repository owner="devteam" changeset_revision="4a32700dcaa2" name="ctd_batch" description="Galaxy wrappers for the tool CTD: analysis of chemicals, diseases, or genes"><tool id="ctdBatch_1" version="1.0.0" file="ctd.xml" /></repository> + <repository owner="devteam" changeset_revision="9d35cf35634e" name="cuffcompare" description="Galaxy wrappers for the Cuffcompare tool."> + <tool id="cuffcompare" version="0.0.5" file="cuffcompare_wrapper.xml" /> + </repository> + <repository owner="devteam" changeset_revision="0dabb2ed6eb1" name="cuffdiff" description="Galaxy wrappers for the Cuffdiff tool."> + <tool id="cuffdiff" version="0.0.6" file="cuffdiff_wrapper.xml" /> + </repository> + <repository owner="devteam" changeset_revision="b50aacc8ae49" name="cufflinks" description="Galaxy wrappers for the Cufflinks tool."> + <tool id="cufflinks" version="0.0.6" file="cufflinks_wrapper.xml" /> + </repository> + <repository owner="devteam" changeset_revision="dbbd37e013aa" name="cuffmerge" description="Galaxy wrappers for the Cuffmerge tool."> + <tool id="cuffmerge" version="0.0.5" file="cuffmerge_wrapper.xml" /> + </repository><repository owner="devteam" changeset_revision="f16000dc644b" name="delete_overlapping_indels" description="Galaxy wrappers for the tool Delete Overlapping Indels: from a chromosome indels file"><tool id="delete_overlapping_indels" version="1.0.0" file="delete_overlapping_indels.xml" /></repository> diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 templates/admin/review_tool_migration_stages.mako --- a/templates/admin/review_tool_migration_stages.mako +++ b/templates/admin/review_tool_migration_stages.mako @@ -35,6 +35,7 @@ </p></div><table class="grid"> + <% from tool_shed.util.shed_util_common import to_html_string %> %for stage in migration_stages_dict.keys(): <% migration_command = 'sh ./scripts/migrate_tools/%04d_tools.sh' % stage @@ -54,7 +55,7 @@ <tr><td bgcolor="#FFFFCC"><div class="form-row"> - <p>${migration_info} <b>Run commands from the Galaxy installation directory!</b></p> + <p>${to_html_string(migration_info)} <b>Run commands from the Galaxy installation directory!</b></p><p> %if tool_dependencies: This migration stage includes tools that have tool dependencies that can be automatically installed. To install them, run:<br/> diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffcompare_in2.gtf --- a/test-data/cuffcompare_in2.gtf +++ /dev/null @@ -1,100 +0,0 @@ -chr1 Cufflinks transcript 3174766 3174792 1000 . . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3174766 3174792 1000 . . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3187402 3187428 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3187402 3187428 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3188522 3188548 1000 . . gene_id "CUFF.5"; transcript_id "CUFF.5.1"; FPKM "21.2266273824"; frac "1.000000"; conf_lo "0.000000"; conf_hi "59.889707"; cov "1.205672"; -chr1 Cufflinks exon 3188522 3188548 1000 . . gene_id "CUFF.5"; transcript_id "CUFF.5.1"; exon_number "1"; FPKM "21.2266273824"; frac "1.000000"; conf_lo "0.000000"; conf_hi "59.889707"; cov "1.205672"; -chr1 Cufflinks transcript 3190859 3191434 1000 . . gene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "19.806349"; conf_hi "39.612698"; cov "1.687500"; -chr1 Cufflinks exon 3190859 3191434 1000 . . gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "19.806349"; conf_hi "39.612698"; cov "1.687500"; -chr1 Cufflinks transcript 3191513 3192077 1000 . . gene_id "CUFF.9"; transcript_id "CUFF.9.1"; FPKM "34.0729325807"; frac "1.000000"; conf_lo "23.364686"; conf_hi "44.781179"; cov "1.935341"; -chr1 Cufflinks exon 3191513 3192077 1000 . . gene_id "CUFF.9"; transcript_id "CUFF.9.1"; exon_number "1"; FPKM "34.0729325807"; frac "1.000000"; conf_lo "23.364686"; conf_hi "44.781179"; cov "1.935341"; -chr1 Cufflinks transcript 3189811 3190789 1000 . . gene_id "CUFF.11"; transcript_id "CUFF.11.1"; FPKM "32.5317765567"; frac "1.000000"; conf_lo "24.582998"; conf_hi "40.480555"; cov "1.847804"; -chr1 Cufflinks exon 3189811 3190789 1000 . . gene_id "CUFF.11"; transcript_id "CUFF.11.1"; exon_number "1"; FPKM "32.5317765567"; frac "1.000000"; conf_lo "24.582998"; conf_hi "40.480555"; cov "1.847804"; -chr1 Cufflinks transcript 3192251 3192336 1000 . . gene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "16.5820596576"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.729373"; cov "0.941860"; -chr1 Cufflinks exon 3192251 3192336 1000 . . gene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "16.5820596576"; frac "1.000000"; conf_lo "0.000000"; conf_hi "35.729373"; cov "0.941860"; -chr1 Cufflinks transcript 3192650 3192676 1000 . . gene_id "CUFF.15"; transcript_id "CUFF.15.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3192650 3192676 1000 . . gene_id "CUFF.15"; transcript_id "CUFF.15.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3194707 3194733 1000 . . gene_id "CUFF.17"; transcript_id "CUFF.17.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3194707 3194733 1000 . . gene_id "CUFF.17"; transcript_id "CUFF.17.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3197426 3197452 1000 . . gene_id "CUFF.19"; transcript_id "CUFF.19.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3197426 3197452 1000 . . gene_id "CUFF.19"; transcript_id "CUFF.19.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3200431 3200457 1000 . . gene_id "CUFF.21"; transcript_id "CUFF.21.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3200431 3200457 1000 . . gene_id "CUFF.21"; transcript_id "CUFF.21.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3200057 3200144 1000 . . gene_id "CUFF.23"; transcript_id "CUFF.23.1"; FPKM "16.2051946653"; frac "1.000000"; conf_lo "0.000000"; conf_hi "34.917342"; cov "0.920455"; -chr1 Cufflinks exon 3200057 3200144 1000 . . gene_id "CUFF.23"; transcript_id "CUFF.23.1"; exon_number "1"; FPKM "16.2051946653"; frac "1.000000"; conf_lo "0.000000"; conf_hi "34.917342"; cov "0.920455"; -chr1 Cufflinks transcript 3201161 3201187 1000 . . gene_id "CUFF.25"; transcript_id "CUFF.25.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3201161 3201187 1000 . . gene_id "CUFF.25"; transcript_id "CUFF.25.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3201008 3201039 1000 . . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "71.725135"; cov "1.687500"; -chr1 Cufflinks exon 3201008 3201039 1000 . . gene_id "CUFF.26"; transcript_id "CUFF.26.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "71.725135"; cov "1.687500"; -chr1 Cufflinks transcript 3201597 3201666 1000 . . gene_id "CUFF.29"; transcript_id "CUFF.29.1"; FPKM "13.5814964814"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.788633"; cov "0.771429"; -chr1 Cufflinks exon 3201597 3201666 1000 . . gene_id "CUFF.29"; transcript_id "CUFF.29.1"; exon_number "1"; FPKM "13.5814964814"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.788633"; cov "0.771429"; -chr1 Cufflinks transcript 3201726 3201809 1000 . . gene_id "CUFF.31"; transcript_id "CUFF.31.1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "45.271655"; cov "1.285714"; -chr1 Cufflinks exon 3201726 3201809 1000 . . gene_id "CUFF.31"; transcript_id "CUFF.31.1"; exon_number "1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "45.271655"; cov "1.285714"; -chr1 Cufflinks transcript 3211522 3211561 1000 . . gene_id "CUFF.33"; transcript_id "CUFF.33.1"; FPKM "23.7676188425"; frac "1.000000"; conf_lo "0.000000"; conf_hi "57.380108"; cov "1.350000"; -chr1 Cufflinks exon 3211522 3211561 1000 . . gene_id "CUFF.33"; transcript_id "CUFF.33.1"; exon_number "1"; FPKM "23.7676188425"; frac "1.000000"; conf_lo "0.000000"; conf_hi "57.380108"; cov "1.350000"; -chr1 Cufflinks transcript 3212718 3212801 1000 . . gene_id "CUFF.35"; transcript_id "CUFF.35.1"; FPKM "11.3179137345"; frac "1.000000"; conf_lo "0.000000"; conf_hi "27.323861"; cov "0.642857"; -chr1 Cufflinks exon 3212718 3212801 1000 . . gene_id "CUFF.35"; transcript_id "CUFF.35.1"; exon_number "1"; FPKM "11.3179137345"; frac "1.000000"; conf_lo "0.000000"; conf_hi "27.323861"; cov "0.642857"; -chr1 Cufflinks transcript 3213119 3213242 1000 . . gene_id "CUFF.37"; transcript_id "CUFF.37.1"; FPKM "11.5004607302"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.780049"; cov "0.653226"; -chr1 Cufflinks exon 3213119 3213242 1000 . . gene_id "CUFF.37"; transcript_id "CUFF.37.1"; exon_number "1"; FPKM "11.5004607302"; frac "1.000000"; conf_lo "0.000000"; conf_hi "24.780049"; cov "0.653226"; -chr1 Cufflinks transcript 3240607 3240633 1000 . . gene_id "CUFF.39"; transcript_id "CUFF.39.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; -chr1 Cufflinks exon 3240607 3240633 1000 . . gene_id "CUFF.39"; transcript_id "CUFF.39.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; -chr1 Cufflinks transcript 3242480 3242512 1000 . . gene_id "CUFF.41"; transcript_id "CUFF.41.1"; FPKM "43.2138524409"; frac "1.000000"; conf_lo "0.000000"; conf_hi "93.112911"; cov "2.454545"; -chr1 Cufflinks exon 3242480 3242512 1000 . . gene_id "CUFF.41"; transcript_id "CUFF.41.1"; exon_number "1"; FPKM "43.2138524409"; frac "1.000000"; conf_lo "0.000000"; conf_hi "93.112911"; cov "2.454545"; -chr1 Cufflinks transcript 3242925 3243005 1000 . . gene_id "CUFF.43"; transcript_id "CUFF.43.1"; FPKM "23.4741914494"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.948383"; cov "1.333333"; -chr1 Cufflinks exon 3242925 3243005 1000 . . gene_id "CUFF.43"; transcript_id "CUFF.43.1"; exon_number "1"; FPKM "23.4741914494"; frac "1.000000"; conf_lo "0.000000"; conf_hi "46.948383"; cov "1.333333"; -chr1 Cufflinks transcript 3243109 3243154 1000 . . gene_id "CUFF.45"; transcript_id "CUFF.45.1"; FPKM "20.6674946457"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.895746"; cov "1.173913"; -chr1 Cufflinks exon 3243109 3243154 1000 . . gene_id "CUFF.45"; transcript_id "CUFF.45.1"; exon_number "1"; FPKM "20.6674946457"; frac "1.000000"; conf_lo "0.000000"; conf_hi "49.895746"; cov "1.173913"; -chr1 Cufflinks transcript 3254080 3254106 1000 . . gene_id "CUFF.47"; transcript_id "CUFF.47.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3254080 3254106 1000 . . gene_id "CUFF.47"; transcript_id "CUFF.47.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3277156 3277182 1000 . . gene_id "CUFF.49"; transcript_id "CUFF.49.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3277156 3277182 1000 . . gene_id "CUFF.49"; transcript_id "CUFF.49.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3277914 3278390 1000 . . gene_id "CUFF.51"; transcript_id "CUFF.51.1"; FPKM "14.9481879513"; frac "1.000000"; conf_lo "7.228977"; conf_hi "22.667399"; cov "0.849057"; -chr1 Cufflinks exon 3277914 3278390 1000 . . gene_id "CUFF.51"; transcript_id "CUFF.51.1"; exon_number "1"; FPKM "14.9481879513"; frac "1.000000"; conf_lo "7.228977"; conf_hi "22.667399"; cov "0.849057"; -chr1 Cufflinks transcript 3280118 3280144 1000 . . gene_id "CUFF.53"; transcript_id "CUFF.53.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; -chr1 Cufflinks exon 3280118 3280144 1000 . . gene_id "CUFF.53"; transcript_id "CUFF.53.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; -chr1 Cufflinks transcript 3280499 3280525 1000 . . gene_id "CUFF.55"; transcript_id "CUFF.55.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3280499 3280525 1000 . . gene_id "CUFF.55"; transcript_id "CUFF.55.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3282505 3282531 1000 . . gene_id "CUFF.57"; transcript_id "CUFF.57.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3282505 3282531 1000 . . gene_id "CUFF.57"; transcript_id "CUFF.57.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3282651 3282677 1000 . . gene_id "CUFF.59"; transcript_id "CUFF.59.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3282651 3282677 1000 . . gene_id "CUFF.59"; transcript_id "CUFF.59.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3282761 3282832 1000 . . gene_id "CUFF.61"; transcript_id "CUFF.61.1"; FPKM "13.2042326903"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.877838"; cov "0.750000"; -chr1 Cufflinks exon 3282761 3282832 1000 . . gene_id "CUFF.61"; transcript_id "CUFF.61.1"; exon_number "1"; FPKM "13.2042326903"; frac "1.000000"; conf_lo "0.000000"; conf_hi "31.877838"; cov "0.750000"; -chr1 Cufflinks transcript 3284967 3284993 1000 . . gene_id "CUFF.63"; transcript_id "CUFF.63.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3284967 3284993 1000 . . gene_id "CUFF.63"; transcript_id "CUFF.63.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3290799 3290859 1000 . . gene_id "CUFF.65"; transcript_id "CUFF.65.1"; FPKM "31.1706476623"; frac "1.000000"; conf_lo "0.000000"; conf_hi "62.341295"; cov "1.770492"; -chr1 Cufflinks exon 3290799 3290859 1000 . . gene_id "CUFF.65"; transcript_id "CUFF.65.1"; exon_number "1"; FPKM "31.1706476623"; frac "1.000000"; conf_lo "0.000000"; conf_hi "62.341295"; cov "1.770492"; -chr1 Cufflinks transcript 3299444 3299640 1000 . . gene_id "CUFF.67"; transcript_id "CUFF.67.1"; FPKM "15.6813507371"; frac "1.000000"; conf_lo "3.378764"; conf_hi "27.983938"; cov "0.890700"; -chr1 Cufflinks exon 3299444 3299640 1000 . . gene_id "CUFF.67"; transcript_id "CUFF.67.1"; exon_number "1"; FPKM "15.6813507371"; frac "1.000000"; conf_lo "3.378764"; conf_hi "27.983938"; cov "0.890700"; -chr1 Cufflinks transcript 3290920 3291273 1000 . . gene_id "CUFF.69"; transcript_id "CUFF.69.1"; FPKM "18.7992465421"; frac "1.000000"; conf_lo "8.750627"; conf_hi "28.847866"; cov "1.067797"; -chr1 Cufflinks exon 3290920 3291273 1000 . . gene_id "CUFF.69"; transcript_id "CUFF.69.1"; exon_number "1"; FPKM "18.7992465421"; frac "1.000000"; conf_lo "8.750627"; conf_hi "28.847866"; cov "1.067797"; -chr1 Cufflinks transcript 3299692 3299733 1000 . . gene_id "CUFF.71"; transcript_id "CUFF.71.1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "54.647722"; cov "1.285714"; -chr1 Cufflinks exon 3299692 3299733 1000 . . gene_id "CUFF.71"; transcript_id "CUFF.71.1"; exon_number "1"; FPKM "22.6358274691"; frac "1.000000"; conf_lo "0.000000"; conf_hi "54.647722"; cov "1.285714"; -chr1 Cufflinks transcript 3307749 3307775 1000 . . gene_id "CUFF.73"; transcript_id "CUFF.73.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3307749 3307775 1000 . . gene_id "CUFF.73"; transcript_id "CUFF.73.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3318621 3318647 1000 . . gene_id "CUFF.75"; transcript_id "CUFF.75.1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; -chr1 Cufflinks exon 3318621 3318647 1000 . . gene_id "CUFF.75"; transcript_id "CUFF.75.1"; exon_number "1"; FPKM "52.8169307611"; frac "1.000000"; conf_lo "0.000000"; conf_hi "113.804669"; cov "3.000000"; -chr1 Cufflinks transcript 3330528 3330554 1000 . . gene_id "CUFF.77"; transcript_id "CUFF.77.1"; FPKM "17.6056435870"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.816931"; cov "1.000000"; -chr1 Cufflinks exon 3330528 3330554 1000 . . gene_id "CUFF.77"; transcript_id "CUFF.77.1"; exon_number "1"; FPKM "17.6056435870"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.816931"; cov "1.000000"; -chr1 Cufflinks transcript 3351241 3351311 1000 . . gene_id "CUFF.79"; transcript_id "CUFF.79.1"; FPKM "13.3902077986"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.326821"; cov "0.760563"; -chr1 Cufflinks exon 3351241 3351311 1000 . . gene_id "CUFF.79"; transcript_id "CUFF.79.1"; exon_number "1"; FPKM "13.3902077986"; frac "1.000000"; conf_lo "0.000000"; conf_hi "32.326821"; cov "0.760563"; -chr1 Cufflinks transcript 3355908 3356119 1000 . . gene_id "CUFF.81"; transcript_id "CUFF.81.1"; FPKM "11.2111409634"; frac "1.000000"; conf_lo "1.183592"; conf_hi "21.238690"; cov "0.636792"; -chr1 Cufflinks exon 3355908 3356119 1000 . . gene_id "CUFF.81"; transcript_id "CUFF.81.1"; exon_number "1"; FPKM "11.2111409634"; frac "1.000000"; conf_lo "1.183592"; conf_hi "21.238690"; cov "0.636792"; -chr1 Cufflinks transcript 3356181 3356225 1000 . . gene_id "CUFF.83"; transcript_id "CUFF.83.1"; FPKM "21.1267723045"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.004540"; cov "1.200000"; -chr1 Cufflinks exon 3356181 3356225 1000 . . gene_id "CUFF.83"; transcript_id "CUFF.83.1"; exon_number "1"; FPKM "21.1267723045"; frac "1.000000"; conf_lo "0.000000"; conf_hi "51.004540"; cov "1.200000"; -chr1 Cufflinks transcript 3363077 3363176 1000 . . gene_id "CUFF.85"; transcript_id "CUFF.85.1"; FPKM "19.0140950740"; frac "1.000000"; conf_lo "0.000000"; conf_hi "38.028190"; cov "1.080000"; -chr1 Cufflinks exon 3363077 3363176 1000 . . gene_id "CUFF.85"; transcript_id "CUFF.85.1"; exon_number "1"; FPKM "19.0140950740"; frac "1.000000"; conf_lo "0.000000"; conf_hi "38.028190"; cov "1.080000"; -chr1 Cufflinks transcript 3363388 3363446 1000 . . gene_id "CUFF.87"; transcript_id "CUFF.87.1"; FPKM "24.1704598398"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.080103"; cov "1.372881"; -chr1 Cufflinks exon 3363388 3363446 1000 . . gene_id "CUFF.87"; transcript_id "CUFF.87.1"; exon_number "1"; FPKM "24.1704598398"; frac "1.000000"; conf_lo "0.000000"; conf_hi "52.080103"; cov "1.372881"; -chr1 Cufflinks transcript 3364872 3364919 1000 . . gene_id "CUFF.89"; transcript_id "CUFF.89.1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "64.015126"; cov "1.687500"; -chr1 Cufflinks exon 3364872 3364919 1000 . . gene_id "CUFF.89"; transcript_id "CUFF.89.1"; exon_number "1"; FPKM "29.7095235531"; frac "1.000000"; conf_lo "0.000000"; conf_hi "64.015126"; cov "1.687500"; -chr1 Cufflinks transcript 3367211 3367237 1000 . . gene_id "CUFF.91"; transcript_id "CUFF.91.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3367211 3367237 1000 . . gene_id "CUFF.91"; transcript_id "CUFF.91.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3369581 3369607 1000 . . gene_id "CUFF.93"; transcript_id "CUFF.93.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3369581 3369607 1000 . . gene_id "CUFF.93"; transcript_id "CUFF.93.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3375002 3375028 1000 . . gene_id "CUFF.95"; transcript_id "CUFF.95.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3375002 3375028 1000 . . gene_id "CUFF.95"; transcript_id "CUFF.95.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3379889 3379915 1000 . . gene_id "CUFF.97"; transcript_id "CUFF.97.1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks exon 3379889 3379915 1000 . . gene_id "CUFF.97"; transcript_id "CUFF.97.1"; exon_number "1"; FPKM "35.2112871741"; frac "1.000000"; conf_lo "0.000000"; conf_hi "85.007567"; cov "2.000000"; -chr1 Cufflinks transcript 3386740 3386836 1000 . . gene_id "CUFF.99"; transcript_id "CUFF.99.1"; FPKM "19.6021598701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.204320"; cov "1.113402"; -chr1 Cufflinks exon 3386740 3386836 1000 . . gene_id "CUFF.99"; transcript_id "CUFF.99.1"; exon_number "1"; FPKM "19.6021598701"; frac "1.000000"; conf_lo "0.000000"; conf_hi "39.204320"; cov "1.113402"; diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffcompare_in3.gtf --- a/test-data/cuffcompare_in3.gtf +++ /dev/null @@ -1,100 +0,0 @@ -chr1 mm9_refFlat stop_codon 3206103 3206105 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat CDS 3206106 3207049 0.000000 - 2 gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat exon 3204563 3207049 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat CDS 3411783 3411982 0.000000 - 1 gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat exon 3411783 3411982 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat CDS 3660633 3661429 0.000000 - 0 gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat start_codon 3661427 3661429 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat exon 3660633 3661579 0.000000 - . gene_id "Xkr4"; transcript_id "Xkr4"; -chr1 mm9_refFlat stop_codon 4334681 4334683 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat CDS 4334684 4340172 0.000000 - 2 gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat exon 4334224 4340172 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat CDS 4341991 4342162 0.000000 - 0 gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat exon 4341991 4342162 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat CDS 4342283 4342906 0.000000 - 0 gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat start_codon 4342904 4342906 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat exon 4342283 4342918 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat exon 4350281 4350473 0.000000 - . gene_id "Rp1"; transcript_id "Rp1"; -chr1 mm9_refFlat stop_codon 4481797 4481799 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat CDS 4481800 4482749 0.000000 - 2 gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat exon 4481009 4482749 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat CDS 4483181 4483487 0.000000 - 0 gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat start_codon 4483485 4483487 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat exon 4483181 4483547 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat exon 4483853 4483944 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat exon 4485217 4486023 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat exon 4486372 4486494 0.000000 - . gene_id "Sox17"; transcript_id "Sox17"; -chr1 mm9_refFlat stop_codon 4766545 4766547 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat CDS 4766548 4766882 0.000000 - 2 gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat exon 4763279 4766882 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat CDS 4767606 4767729 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat exon 4767606 4767729 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat CDS 4772649 4772814 0.000000 - 1 gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat exon 4772649 4772814 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat CDS 4774032 4774186 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat exon 4774032 4774186 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat CDS 4775654 4775758 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat start_codon 4775756 4775758 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat exon 4775654 4775807 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15"; -chr1 mm9_refFlat stop_codon 4764533 4764535 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat CDS 4764536 4764597 0.000000 - 2 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat exon 4763279 4764597 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat CDS 4767606 4767729 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat exon 4767606 4767729 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat CDS 4772649 4772814 0.000000 - 1 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat exon 4772649 4772814 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat CDS 4774032 4774186 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat exon 4774032 4774186 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat CDS 4775654 4775758 0.000000 - 0 gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat start_codon 4775756 4775758 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat exon 4775654 4775807 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup1"; -chr1 mm9_refFlat exon 4763279 4764597 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; -chr1 mm9_refFlat exon 4767606 4767729 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; -chr1 mm9_refFlat exon 4772649 4772814 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; -chr1 mm9_refFlat exon 4775654 4775807 0.000000 - . gene_id "Mrpl15"; transcript_id "Mrpl15_dup2"; -chr1 mm9_refFlat start_codon 4797995 4797997 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4797995 4798063 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4797974 4798063 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4798536 4798567 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4798536 4798567 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4818665 4818730 0.000000 + 1 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4818665 4818730 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4820349 4820396 0.000000 + 1 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4820349 4820396 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4822392 4822462 0.000000 + 1 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4822392 4822462 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4827082 4827155 0.000000 + 2 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4827082 4827155 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4829468 4829569 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4829468 4829569 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4831037 4831213 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4831037 4831213 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat CDS 4835044 4835094 0.000000 + 0 gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat stop_codon 4835095 4835097 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat exon 4835044 4836816 0.000000 + . gene_id "Lypla1"; transcript_id "Lypla1"; -chr1 mm9_refFlat start_codon 4847995 4847997 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4847995 4848057 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4847775 4848057 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4857551 4857613 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4857551 4857613 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4868108 4868213 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4868108 4868213 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4876825 4876912 0.000000 + 2 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4876825 4876912 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4879538 4879683 0.000000 + 1 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4879538 4879683 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4880821 4880877 0.000000 + 2 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4880821 4880877 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4881996 4882150 0.000000 + 2 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4881996 4882150 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4883498 4883644 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4883498 4883644 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4885015 4885086 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4885015 4885086 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat CDS 4886437 4886442 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat stop_codon 4886443 4886445 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat exon 4886437 4887987 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1"; -chr1 mm9_refFlat start_codon 4847995 4847997 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; -chr1 mm9_refFlat CDS 4847995 4848057 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1_dup1"; -chr1 mm9_refFlat exon 4847775 4848057 0.000000 + . gene_id "Tcea1"; transcript_id "Tcea1_dup1"; -chr1 mm9_refFlat CDS 4857551 4857613 0.000000 + 0 gene_id "Tcea1"; transcript_id "Tcea1_dup1"; diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffcompare_out1.tmap --- a/test-data/cuffcompare_out1.tmap +++ /dev/null @@ -1,51 +0,0 @@ -ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id ref_match_len -- - u CUFF.1 CUFF.1.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.1.1 - -- - u CUFF.3 CUFF.3.1 100 27.255658 0.000000 65.800979 1.741935 31 CUFF.3.1 - -- - u CUFF.5 CUFF.5.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.5.1 - -- - u CUFF.7 CUFF.7.1 100 9.999117 0.000000 19.998234 0.639053 169 CUFF.7.1 - -- - u CUFF.9 CUFF.9.1 100 17.776896 9.153835 26.399957 1.136139 404 CUFF.9.1 - -- - u CUFF.11 CUFF.11.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.11.1 - -Xkr4 Xkr4 c CUFF.13 CUFF.13.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.13.1 3634 -Xkr4 Xkr4 i CUFF.15 CUFF.15.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.15.1 3634 -Xkr4 Xkr4 i CUFF.17 CUFF.17.1 100 8.710571 0.000000 21.029179 0.556701 97 CUFF.17.1 3634 -Xkr4 Xkr4 i CUFF.19 CUFF.19.1 100 29.337687 3.097262 55.578113 1.875000 72 CUFF.19.1 3634 -Xkr4 Xkr4 i CUFF.21 CUFF.21.1 100 13.851236 0.000000 33.439842 0.885246 61 CUFF.21.1 3634 -Xkr4 Xkr4 i CUFF.23 CUFF.23.1 100 23.470150 0.000000 50.571145 1.500000 54 CUFF.23.1 3634 -Xkr4 Xkr4 i CUFF.25 CUFF.25.1 100 14.567679 5.354270 23.781089 0.931034 290 CUFF.25.1 3634 -Xkr4 Xkr4 i CUFF.27 CUFF.27.1 100 34.253732 0.000000 73.806535 2.189189 37 CUFF.27.1 3634 -- - u CUFF.29 CUFF.29.1 100 107.103219 71.402146 142.804292 6.845070 142 CUFF.29.1 - -- - u CUFF.31 CUFF.31.1 100 122.650461 40.883487 204.417435 7.838710 31 CUFF.31.1 - -- - u CUFF.33 CUFF.33.1 100 109.527366 26.732460 192.322273 7.000000 27 CUFF.33.1 - -- - u CUFF.35 CUFF.35.1 100 96.747183 61.420107 132.074259 6.183206 131 CUFF.35.1 - -- - u CUFF.37 CUFF.37.1 100 104.085013 53.596365 154.573660 6.652174 69 CUFF.37.1 - -- - u CUFF.39 CUFF.39.1 100 23.912983 0.000000 51.525317 1.528302 53 CUFF.39.1 - -- - u CUFF.41 CUFF.41.1 100 10.695258 0.000000 25.820637 0.683544 79 CUFF.41.1 - -- - u CUFF.43 CUFF.43.1 100 10.561567 0.000000 25.497879 0.675000 80 CUFF.43.1 - -- - u CUFF.45 CUFF.45.1 100 20.708956 2.186303 39.231609 1.323529 102 CUFF.45.1 - -- - u CUFF.47 CUFF.47.1 100 20.607936 0.000000 49.751960 1.317073 41 CUFF.47.1 - -- - u CUFF.49 CUFF.49.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.49.1 - -- - u CUFF.51 CUFF.51.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.51.1 - -- - u CUFF.53 CUFF.53.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.53.1 - -- - u CUFF.55 CUFF.55.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.55.1 - -- - u CUFF.57 CUFF.57.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.57.1 - -- - u CUFF.59 CUFF.59.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.59.1 - -Xkr4 Xkr4 i CUFF.61 CUFF.61.1 100 45.263860 0.000000 97.530065 2.892857 28 CUFF.61.1 3634 -Xkr4 Xkr4 i CUFF.63 CUFF.63.1 100 15.646767 0.000000 46.940300 1.000000 27 CUFF.63.1 3634 -Xkr4 Xkr4 i CUFF.65 CUFF.65.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.65.1 3634 -Xkr4 Xkr4 i CUFF.67 CUFF.67.1 100 12.998852 0.000000 31.382005 0.830769 65 CUFF.67.1 3634 -Xkr4 Xkr4 i CUFF.69 CUFF.69.1 100 10.058636 0.000000 24.283695 0.642857 84 CUFF.69.1 3634 -Xkr4 Xkr4 i CUFF.71 CUFF.71.1 100 8.621688 0.000000 20.814595 0.551020 98 CUFF.71.1 3634 -Xkr4 Xkr4 i CUFF.73 CUFF.73.1 100 15.362280 0.000000 37.087825 0.981818 55 CUFF.73.1 3634 -Xkr4 Xkr4 i CUFF.75 CUFF.75.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.75.1 3634 -Xkr4 Xkr4 i CUFF.77 CUFF.77.1 100 16.248565 0.000000 39.227507 1.038462 52 CUFF.77.1 3634 -Xkr4 Xkr4 i CUFF.79 CUFF.79.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.79.1 3634 -Xkr4 Xkr4 i CUFF.81 CUFF.81.1 100 13.201959 0.000000 31.872349 0.843750 64 CUFF.81.1 3634 -Xkr4 Xkr4 i CUFF.83 CUFF.83.1 100 13.201959 0.000000 28.446269 0.843750 96 CUFF.83.1 3634 -Xkr4 Xkr4 i CUFF.85 CUFF.85.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.85.1 3634 -Xkr4 Xkr4 i CUFF.87 CUFF.87.1 100 17.243375 0.000000 41.629191 1.102041 49 CUFF.87.1 3634 -Xkr4 Xkr4 i CUFF.89 CUFF.89.1 100 16.567165 0.000000 39.996674 1.058824 51 CUFF.89.1 3634 -Xkr4 Xkr4 i CUFF.91 CUFF.91.1 100 31.293533 0.000000 75.549272 2.000000 27 CUFF.91.1 3634 -Xkr4 Xkr4 i CUFF.93 CUFF.93.1 100 21.664754 0.000000 52.303342 1.384615 39 CUFF.93.1 3634 -Xkr4 Xkr4 i CUFF.95 CUFF.95.1 100 46.940300 0.000000 101.142289 3.000000 27 CUFF.95.1 3634 -Xkr4 Xkr4 i CUFF.97 CUFF.97.1 100 21.481154 0.000000 46.285454 1.372881 59 CUFF.97.1 3634 -Xkr4 Xkr4 i CUFF.99 CUFF.99.1 100 14.567679 0.000000 35.169489 0.931034 58 CUFF.99.1 3634 diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffcompare_out2.refmap --- a/test-data/cuffcompare_out2.refmap +++ /dev/null @@ -1,2 +0,0 @@ -ref_gene_id ref_id class_code cuff_id_list -Xkr4 Xkr4 c CUFF.13|CUFF.13.1 diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffcompare_out3.tmap --- a/test-data/cuffcompare_out3.tmap +++ /dev/null @@ -1,51 +0,0 @@ -ref_gene_id ref_id class_code cuff_gene_id cuff_id FMI FPKM FPKM_conf_lo FPKM_conf_hi cov len major_iso_id ref_match_len -- - u CUFF.1 CUFF.1.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.1.1 - -- - u CUFF.3 CUFF.3.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.3.1 - -- - u CUFF.5 CUFF.5.1 100 21.226627 0.000000 59.889707 1.205672 27 CUFF.5.1 - -- - u CUFF.7 CUFF.7.1 100 29.709524 19.806349 39.612698 1.687500 576 CUFF.7.1 - -- - u CUFF.9 CUFF.9.1 100 34.072933 23.364686 44.781179 1.935341 565 CUFF.9.1 - -- - u CUFF.11 CUFF.11.1 100 32.531777 24.582998 40.480555 1.847804 979 CUFF.11.1 - -- - u CUFF.13 CUFF.13.1 100 16.582060 0.000000 35.729373 0.941860 86 CUFF.13.1 - -- - u CUFF.15 CUFF.15.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.15.1 - -- - u CUFF.17 CUFF.17.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.17.1 - -- - u CUFF.19 CUFF.19.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.19.1 - -- - u CUFF.21 CUFF.21.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.21.1 - -- - u CUFF.23 CUFF.23.1 100 16.205195 0.000000 34.917342 0.920455 88 CUFF.23.1 - -- - u CUFF.25 CUFF.25.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.25.1 - -- - u CUFF.26 CUFF.26.1 100 29.709524 0.000000 71.725135 1.687500 32 CUFF.26.1 - -- - u CUFF.29 CUFF.29.1 100 13.581496 0.000000 32.788633 0.771429 70 CUFF.29.1 - -- - u CUFF.31 CUFF.31.1 100 22.635827 0.000000 45.271655 1.285714 84 CUFF.31.1 - -Xkr4 Xkr4 i CUFF.33 CUFF.33.1 100 23.767619 0.000000 57.380108 1.350000 40 CUFF.33.1 3634 -Xkr4 Xkr4 i CUFF.35 CUFF.35.1 100 11.317914 0.000000 27.323861 0.642857 84 CUFF.35.1 3634 -Xkr4 Xkr4 i CUFF.37 CUFF.37.1 100 11.500461 0.000000 24.780049 0.653226 124 CUFF.37.1 3634 -Xkr4 Xkr4 i CUFF.39 CUFF.39.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.39.1 3634 -Xkr4 Xkr4 i CUFF.41 CUFF.41.1 100 43.213852 0.000000 93.112911 2.454545 33 CUFF.41.1 3634 -Xkr4 Xkr4 i CUFF.43 CUFF.43.1 100 23.474191 0.000000 46.948383 1.333333 81 CUFF.43.1 3634 -Xkr4 Xkr4 i CUFF.45 CUFF.45.1 100 20.667495 0.000000 49.895746 1.173913 46 CUFF.45.1 3634 -Xkr4 Xkr4 i CUFF.47 CUFF.47.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.47.1 3634 -Xkr4 Xkr4 i CUFF.49 CUFF.49.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.49.1 3634 -Xkr4 Xkr4 i CUFF.51 CUFF.51.1 100 14.948188 7.228977 22.667399 0.849057 477 CUFF.51.1 3634 -Xkr4 Xkr4 i CUFF.53 CUFF.53.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.53.1 3634 -Xkr4 Xkr4 i CUFF.55 CUFF.55.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.55.1 3634 -Xkr4 Xkr4 i CUFF.57 CUFF.57.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.57.1 3634 -Xkr4 Xkr4 i CUFF.59 CUFF.59.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.59.1 3634 -Xkr4 Xkr4 i CUFF.61 CUFF.61.1 100 13.204233 0.000000 31.877838 0.750000 72 CUFF.61.1 3634 -Xkr4 Xkr4 i CUFF.63 CUFF.63.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.63.1 3634 -Xkr4 Xkr4 i CUFF.65 CUFF.65.1 100 31.170648 0.000000 62.341295 1.770492 61 CUFF.65.1 3634 -Xkr4 Xkr4 i CUFF.67 CUFF.67.1 100 15.681351 3.378764 27.983938 0.890700 197 CUFF.67.1 3634 -Xkr4 Xkr4 i CUFF.69 CUFF.69.1 100 18.799247 8.750627 28.847866 1.067797 354 CUFF.69.1 3634 -Xkr4 Xkr4 i CUFF.71 CUFF.71.1 100 22.635827 0.000000 54.647722 1.285714 42 CUFF.71.1 3634 -Xkr4 Xkr4 i CUFF.73 CUFF.73.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.73.1 3634 -Xkr4 Xkr4 i CUFF.75 CUFF.75.1 100 52.816931 0.000000 113.804669 3.000000 27 CUFF.75.1 3634 -Xkr4 Xkr4 i CUFF.77 CUFF.77.1 100 17.605644 0.000000 52.816931 1.000000 27 CUFF.77.1 3634 -Xkr4 Xkr4 i CUFF.79 CUFF.79.1 100 13.390208 0.000000 32.326821 0.760563 71 CUFF.79.1 3634 -Xkr4 Xkr4 i CUFF.81 CUFF.81.1 100 11.211141 1.183592 21.238690 0.636792 212 CUFF.81.1 3634 -Xkr4 Xkr4 i CUFF.83 CUFF.83.1 100 21.126772 0.000000 51.004540 1.200000 45 CUFF.83.1 3634 -Xkr4 Xkr4 i CUFF.85 CUFF.85.1 100 19.014095 0.000000 38.028190 1.080000 100 CUFF.85.1 3634 -Xkr4 Xkr4 i CUFF.87 CUFF.87.1 100 24.170460 0.000000 52.080103 1.372881 59 CUFF.87.1 3634 -Xkr4 Xkr4 i CUFF.89 CUFF.89.1 100 29.709524 0.000000 64.015126 1.687500 48 CUFF.89.1 3634 -Xkr4 Xkr4 i CUFF.91 CUFF.91.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.91.1 3634 -Xkr4 Xkr4 i CUFF.93 CUFF.93.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.93.1 3634 -Xkr4 Xkr4 i CUFF.95 CUFF.95.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.95.1 3634 -Xkr4 Xkr4 i CUFF.97 CUFF.97.1 100 35.211287 0.000000 85.007567 2.000000 27 CUFF.97.1 3634 -Xkr4 Xkr4 i CUFF.99 CUFF.99.1 100 19.602160 0.000000 39.204320 1.113402 97 CUFF.99.1 3634 diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffcompare_out4.refmap --- a/test-data/cuffcompare_out4.refmap +++ /dev/null @@ -1,1 +0,0 @@ -ref_gene_id ref_id class_code cuff_id_list diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffcompare_out5.gtf --- a/test-data/cuffcompare_out5.gtf +++ /dev/null @@ -1,90 +0,0 @@ -chr1 Cufflinks exon 3204755 3204833 . - . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.13.1"; nearest_ref "Xkr4"; class_code "c"; tss_id "TSS1"; -chr1 Cufflinks exon 3111450 3111490 . . . gene_id "XLOC_000002"; transcript_id "TCONS_00000002"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS2"; -chr1 Cufflinks exon 3111546 3111576 . . . gene_id "XLOC_000003"; transcript_id "TCONS_00000003"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS3"; -chr1 Cufflinks exon 3174766 3174792 . . . gene_id "XLOC_000004"; transcript_id "TCONS_00000051"; exon_number "1"; oId "CUFF.1.1"; class_code "u"; tss_id "TSS4"; -chr1 Cufflinks exon 3187402 3187428 . . . gene_id "XLOC_000005"; transcript_id "TCONS_00000052"; exon_number "1"; oId "CUFF.3.1"; class_code "u"; tss_id "TSS5"; -chr1 Cufflinks exon 3188522 3188548 . . . gene_id "XLOC_000006"; transcript_id "TCONS_00000053"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS6"; -chr1 Cufflinks exon 3189811 3190789 . . . gene_id "XLOC_000007"; transcript_id "TCONS_00000054"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS7"; -chr1 Cufflinks exon 3190859 3191434 . . . gene_id "XLOC_000008"; transcript_id "TCONS_00000055"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS10"; -chr1 Cufflinks exon 3191513 3192077 . . . gene_id "XLOC_000009"; transcript_id "TCONS_00000056"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS11"; -chr1 Cufflinks exon 3192251 3192336 . . . gene_id "XLOC_000010"; transcript_id "TCONS_00000057"; exon_number "1"; oId "CUFF.13.1"; class_code "u"; tss_id "TSS13"; -chr1 Cufflinks exon 3192442 3192494 . . . gene_id "XLOC_000011"; transcript_id "TCONS_00000009"; exon_number "1"; oId "CUFF.39.1"; class_code "u"; tss_id "TSS14"; -chr1 Cufflinks exon 3192551 3192629 . . . gene_id "XLOC_000012"; transcript_id "TCONS_00000010"; exon_number "1"; oId "CUFF.41.1"; class_code "u"; tss_id "TSS15"; -chr1 Cufflinks exon 3192650 3192676 . . . gene_id "XLOC_000013"; transcript_id "TCONS_00000058"; exon_number "1"; oId "CUFF.15.1"; class_code "u"; tss_id "TSS16"; -chr1 Cufflinks exon 3192732 3192811 . . . gene_id "XLOC_000014"; transcript_id "TCONS_00000011"; exon_number "1"; oId "CUFF.43.1"; class_code "u"; tss_id "TSS17"; -chr1 Cufflinks exon 3192941 3193042 . . . gene_id "XLOC_000015"; transcript_id "TCONS_00000012"; exon_number "1"; oId "CUFF.45.1"; class_code "u"; tss_id "TSS18"; -chr1 Cufflinks exon 3194186 3194226 . . . gene_id "XLOC_000016"; transcript_id "TCONS_00000013"; exon_number "1"; oId "CUFF.47.1"; class_code "u"; tss_id "TSS19"; -chr1 Cufflinks exon 3194303 3194329 . . . gene_id "XLOC_000017"; transcript_id "TCONS_00000014"; exon_number "1"; oId "CUFF.49.1"; class_code "u"; tss_id "TSS20"; -chr1 Cufflinks exon 3194707 3194733 . . . gene_id "XLOC_000018"; transcript_id "TCONS_00000059"; exon_number "1"; oId "CUFF.17.1"; class_code "u"; tss_id "TSS21"; -chr1 Cufflinks exon 3195084 3195110 . . . gene_id "XLOC_000019"; transcript_id "TCONS_00000015"; exon_number "1"; oId "CUFF.51.1"; class_code "u"; tss_id "TSS22"; -chr1 Cufflinks exon 3195451 3195477 . . . gene_id "XLOC_000020"; transcript_id "TCONS_00000016"; exon_number "1"; oId "CUFF.53.1"; class_code "u"; tss_id "TSS23"; -chr1 Cufflinks exon 3197090 3197116 . . . gene_id "XLOC_000021"; transcript_id "TCONS_00000017"; exon_number "1"; oId "CUFF.55.1"; class_code "u"; tss_id "TSS24"; -chr1 Cufflinks exon 3197247 3197273 . . . gene_id "XLOC_000022"; transcript_id "TCONS_00000018"; exon_number "1"; oId "CUFF.57.1"; class_code "u"; tss_id "TSS25"; -chr1 Cufflinks exon 3197347 3197373 . . . gene_id "XLOC_000023"; transcript_id "TCONS_00000019"; exon_number "1"; oId "CUFF.59.1"; class_code "u"; tss_id "TSS26"; -chr1 Cufflinks exon 3197426 3197452 . . . gene_id "XLOC_000024"; transcript_id "TCONS_00000060"; exon_number "1"; oId "CUFF.19.1"; class_code "u"; tss_id "TSS27"; -chr1 Cufflinks exon 3200023 3200191 . . . gene_id "XLOC_000025"; transcript_id "TCONS_00000020"; exon_number "1"; oId "CUFF.7.1"; class_code "u"; tss_id "TSS28"; -chr1 Cufflinks exon 3200326 3200352 . . . gene_id "XLOC_000026"; transcript_id "TCONS_00000021"; exon_number "1"; oId "CUFF.5.1"; class_code "u"; tss_id "TSS29"; -chr1 Cufflinks exon 3200431 3200457 . . . gene_id "XLOC_000027"; transcript_id "TCONS_00000062"; exon_number "1"; oId "CUFF.21.1"; class_code "u"; tss_id "TSS30"; -chr1 Cufflinks exon 3201008 3201039 . . . gene_id "XLOC_000028"; transcript_id "TCONS_00000063"; exon_number "1"; oId "CUFF.26.1"; class_code "u"; tss_id "TSS31"; -chr1 Cufflinks exon 3201078 3201481 . . . gene_id "XLOC_000029"; transcript_id "TCONS_00000022"; exon_number "1"; oId "CUFF.9.1"; class_code "u"; tss_id "TSS32"; -chr1 Cufflinks exon 3201597 3201666 . . . gene_id "XLOC_000030"; transcript_id "TCONS_00000065"; exon_number "1"; oId "CUFF.29.1"; class_code "u"; tss_id "TSS33"; -chr1 Cufflinks exon 3201673 3201699 . . . gene_id "XLOC_000031"; transcript_id "TCONS_00000023"; exon_number "1"; oId "CUFF.11.1"; class_code "u"; tss_id "TSS34"; -chr1 Cufflinks exon 3201726 3201809 . . . gene_id "XLOC_000032"; transcript_id "TCONS_00000066"; exon_number "1"; oId "CUFF.31.1"; class_code "u"; tss_id "TSS35"; -chr1 Cufflinks exon 3211522 3211561 . . . gene_id "XLOC_000033"; transcript_id "TCONS_00000067"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.33.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS36"; -chr1 Cufflinks exon 3212214 3212292 . . . gene_id "XLOC_000034"; transcript_id "TCONS_00000024"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.15.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS37"; -chr1 Cufflinks exon 3212368 3212439 . . . gene_id "XLOC_000035"; transcript_id "TCONS_00000025"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.19.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS38"; -chr1 Cufflinks exon 3212718 3212801 . . . gene_id "XLOC_000036"; transcript_id "TCONS_00000068"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.35.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS39"; -chr1 Cufflinks exon 3213096 3213192 . . . gene_id "XLOC_000037"; transcript_id "TCONS_00000026"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.17.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS40"; -chr1 Cufflinks exon 3213119 3213242 . . . gene_id "XLOC_000037"; transcript_id "TCONS_00000069"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.37.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS40"; -chr1 Cufflinks exon 3240607 3240633 . . . gene_id "XLOC_000038"; transcript_id "TCONS_00000070"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.39.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS41"; -chr1 Cufflinks exon 3242480 3242512 . . . gene_id "XLOC_000039"; transcript_id "TCONS_00000071"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.41.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS42"; -chr1 Cufflinks exon 3242634 3242923 . . . gene_id "XLOC_000040"; transcript_id "TCONS_00000027"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.25.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS43"; -chr1 Cufflinks exon 3242925 3243005 . . . gene_id "XLOC_000041"; transcript_id "TCONS_00000072"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.43.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS44"; -chr1 Cufflinks exon 3243019 3243079 . . . gene_id "XLOC_000042"; transcript_id "TCONS_00000028"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.21.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS45"; -chr1 Cufflinks exon 3243109 3243154 . . . gene_id "XLOC_000043"; transcript_id "TCONS_00000073"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.45.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS46"; -chr1 Cufflinks exon 3243348 3243401 . . . gene_id "XLOC_000044"; transcript_id "TCONS_00000029"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.23.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS47"; -chr1 Cufflinks exon 3254080 3254106 . . . gene_id "XLOC_000045"; transcript_id "TCONS_00000074"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.47.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS48"; -chr1 Cufflinks exon 3256975 3257011 . . . gene_id "XLOC_000046"; transcript_id "TCONS_00000030"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.27.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS49"; -chr1 Cufflinks exon 3277156 3277182 . . . gene_id "XLOC_000047"; transcript_id "TCONS_00000075"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.49.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS50"; -chr1 Cufflinks exon 3277191 3277218 . . . gene_id "XLOC_000048"; transcript_id "TCONS_00000031"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.61.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS51"; -chr1 Cufflinks exon 3277914 3278390 . . . gene_id "XLOC_000049"; transcript_id "TCONS_00000076"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.51.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS52"; -chr1 Cufflinks exon 3280118 3280144 . . . gene_id "XLOC_000050"; transcript_id "TCONS_00000077"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.53.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS54"; -chr1 Cufflinks exon 3280499 3280525 . . . gene_id "XLOC_000051"; transcript_id "TCONS_00000078"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.55.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS55"; -chr1 Cufflinks exon 3280687 3280741 . . . gene_id "XLOC_000052"; transcript_id "TCONS_00000033"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.65.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS56"; -chr1 Cufflinks exon 3282505 3282531 . . . gene_id "XLOC_000053"; transcript_id "TCONS_00000079"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.57.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS57"; -chr1 Cufflinks exon 3282651 3282677 . . . gene_id "XLOC_000054"; transcript_id "TCONS_00000080"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.59.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS58"; -chr1 Cufflinks exon 3282761 3282832 . . . gene_id "XLOC_000055"; transcript_id "TCONS_00000081"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.61.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS59"; -chr1 Cufflinks exon 3284967 3284993 . . . gene_id "XLOC_000056"; transcript_id "TCONS_00000082"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.63.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS60"; -chr1 Cufflinks exon 3290489 3290553 . . . gene_id "XLOC_000057"; transcript_id "TCONS_00000034"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.67.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS61"; -chr1 Cufflinks exon 3290799 3290859 . . . gene_id "XLOC_000058"; transcript_id "TCONS_00000083"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.65.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS62"; -chr1 Cufflinks exon 3290920 3291273 . . . gene_id "XLOC_000059"; transcript_id "TCONS_00000084"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.69.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS63"; -chr1 Cufflinks exon 3299444 3299640 . . . gene_id "XLOC_000060"; transcript_id "TCONS_00000085"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.67.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS65"; -chr1 Cufflinks exon 3299610 3299664 . . . gene_id "XLOC_000060"; transcript_id "TCONS_00000037"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.73.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS66"; -chr1 Cufflinks exon 3299692 3299733 . . . gene_id "XLOC_000061"; transcript_id "TCONS_00000086"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.71.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS67"; -chr1 Cufflinks exon 3300052 3300078 . . . gene_id "XLOC_000062"; transcript_id "TCONS_00000038"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.75.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS68"; -chr1 Cufflinks exon 3307749 3307775 . . . gene_id "XLOC_000063"; transcript_id "TCONS_00000087"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.73.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS69"; -chr1 Cufflinks exon 3318621 3318647 . . . gene_id "XLOC_000064"; transcript_id "TCONS_00000088"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.75.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS70"; -chr1 Cufflinks exon 3319000 3319051 . . . gene_id "XLOC_000065"; transcript_id "TCONS_00000039"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.77.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS71"; -chr1 Cufflinks exon 3330528 3330554 . . . gene_id "XLOC_000066"; transcript_id "TCONS_00000089"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.77.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS72"; -chr1 Cufflinks exon 3351241 3351311 . . . gene_id "XLOC_000067"; transcript_id "TCONS_00000090"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.79.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS73"; -chr1 Cufflinks exon 3355888 3355914 . . . gene_id "XLOC_000068"; transcript_id "TCONS_00000040"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.79.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS74"; -chr1 Cufflinks exon 3355908 3356119 . . . gene_id "XLOC_000068"; transcript_id "TCONS_00000091"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS74"; -chr1 Cufflinks exon 3356181 3356225 . . . gene_id "XLOC_000069"; transcript_id "TCONS_00000092"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS75"; -chr1 Cufflinks exon 3363077 3363176 . . . gene_id "XLOC_000070"; transcript_id "TCONS_00000093"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS76"; -chr1 Cufflinks exon 3363215 3363278 . . . gene_id "XLOC_000071"; transcript_id "TCONS_00000041"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.81.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS77"; -chr1 Cufflinks exon 3363388 3363446 . . . gene_id "XLOC_000072"; transcript_id "TCONS_00000094"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS78"; -chr1 Cufflinks exon 3363754 3363849 . . . gene_id "XLOC_000073"; transcript_id "TCONS_00000042"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.83.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS79"; -chr1 Cufflinks exon 3364872 3364919 . . . gene_id "XLOC_000074"; transcript_id "TCONS_00000095"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS80"; -chr1 Cufflinks exon 3367136 3367162 . . . gene_id "XLOC_000075"; transcript_id "TCONS_00000043"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.85.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS81"; -chr1 Cufflinks exon 3367211 3367237 . . . gene_id "XLOC_000076"; transcript_id "TCONS_00000096"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS82"; -chr1 Cufflinks exon 3367334 3367382 . . . gene_id "XLOC_000077"; transcript_id "TCONS_00000044"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.87.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS83"; -chr1 Cufflinks exon 3369581 3369607 . . . gene_id "XLOC_000078"; transcript_id "TCONS_00000097"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS84"; -chr1 Cufflinks exon 3375002 3375028 . . . gene_id "XLOC_000079"; transcript_id "TCONS_00000098"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS85"; -chr1 Cufflinks exon 3377212 3377262 . . . gene_id "XLOC_000080"; transcript_id "TCONS_00000045"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.89.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS86"; -chr1 Cufflinks exon 3379889 3379915 . . . gene_id "XLOC_000081"; transcript_id "TCONS_00000099"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS87"; -chr1 Cufflinks exon 3386740 3386836 . . . gene_id "XLOC_000082"; transcript_id "TCONS_00000100"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS88"; -chr1 Cufflinks exon 3391326 3391352 . . . gene_id "XLOC_000083"; transcript_id "TCONS_00000046"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.91.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS89"; -chr1 Cufflinks exon 3435842 3435880 . . . gene_id "XLOC_000084"; transcript_id "TCONS_00000047"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.93.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS90"; -chr1 Cufflinks exon 3447762 3447788 . . . gene_id "XLOC_000085"; transcript_id "TCONS_00000048"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.95.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS91"; -chr1 Cufflinks exon 3450907 3450965 . . . gene_id "XLOC_000086"; transcript_id "TCONS_00000049"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.97.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS92"; -chr1 Cufflinks exon 3451052 3451109 . . . gene_id "XLOC_000087"; transcript_id "TCONS_00000050"; exon_number "1"; gene_name "Xkr4"; oId "CUFF.99.1"; nearest_ref "Xkr4"; class_code "i"; tss_id "TSS93"; diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffcompare_out6.tracking --- a/test-data/cuffcompare_out6.tracking +++ /dev/null @@ -1,100 +0,0 @@ -TCONS_00000001 XLOC_000001 Xkr4|Xkr4 c q1:CUFF.13|CUFF.13.1|100|10.695258|0.000000|25.820637|0.683544|- - -TCONS_00000002 XLOC_000002 - u q1:CUFF.1|CUFF.1.1|100|20.607936|0.000000|49.751960|1.317073|- - -TCONS_00000003 XLOC_000003 - u q1:CUFF.3|CUFF.3.1|100|27.255658|0.000000|65.800979|1.741935|- - -TCONS_00000004 XLOC_000007 - u q1:CUFF.29|CUFF.29.1|100|107.103219|71.402146|142.804292|6.845070|- - -TCONS_00000005 XLOC_000007 - u q1:CUFF.31|CUFF.31.1|100|122.650461|40.883487|204.417435|7.838710|- - -TCONS_00000006 XLOC_000007 - u q1:CUFF.33|CUFF.33.1|100|109.527366|26.732460|192.322273|7.000000|- - -TCONS_00000007 XLOC_000009 - u q1:CUFF.35|CUFF.35.1|100|96.747183|61.420107|132.074259|6.183206|- - -TCONS_00000008 XLOC_000009 - u q1:CUFF.37|CUFF.37.1|100|104.085013|53.596365|154.573660|6.652174|- - -TCONS_00000009 XLOC_000011 - u q1:CUFF.39|CUFF.39.1|100|23.912983|0.000000|51.525317|1.528302|- - -TCONS_00000010 XLOC_000012 - u q1:CUFF.41|CUFF.41.1|100|10.695258|0.000000|25.820637|0.683544|- - -TCONS_00000011 XLOC_000014 - u q1:CUFF.43|CUFF.43.1|100|10.561567|0.000000|25.497879|0.675000|- - -TCONS_00000012 XLOC_000015 - u q1:CUFF.45|CUFF.45.1|100|20.708956|2.186303|39.231609|1.323529|- - -TCONS_00000013 XLOC_000016 - u q1:CUFF.47|CUFF.47.1|100|20.607936|0.000000|49.751960|1.317073|- - -TCONS_00000014 XLOC_000017 - u q1:CUFF.49|CUFF.49.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000015 XLOC_000019 - u q1:CUFF.51|CUFF.51.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000016 XLOC_000020 - u q1:CUFF.53|CUFF.53.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000017 XLOC_000021 - u q1:CUFF.55|CUFF.55.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000018 XLOC_000022 - u q1:CUFF.57|CUFF.57.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000019 XLOC_000023 - u q1:CUFF.59|CUFF.59.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000020 XLOC_000025 - u q1:CUFF.7|CUFF.7.1|100|9.999117|0.000000|19.998234|0.639053|- - -TCONS_00000021 XLOC_000026 - u q1:CUFF.5|CUFF.5.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000022 XLOC_000029 - u q1:CUFF.9|CUFF.9.1|100|17.776896|9.153835|26.399957|1.136139|- - -TCONS_00000023 XLOC_000031 - u q1:CUFF.11|CUFF.11.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000024 XLOC_000034 Xkr4|Xkr4 i q1:CUFF.15|CUFF.15.1|100|10.695258|0.000000|25.820637|0.683544|- - -TCONS_00000025 XLOC_000035 Xkr4|Xkr4 i q1:CUFF.19|CUFF.19.1|100|29.337687|3.097262|55.578113|1.875000|- - -TCONS_00000026 XLOC_000037 Xkr4|Xkr4 i q1:CUFF.17|CUFF.17.1|100|8.710571|0.000000|21.029179|0.556701|- - -TCONS_00000027 XLOC_000040 Xkr4|Xkr4 i q1:CUFF.25|CUFF.25.1|100|14.567679|5.354270|23.781089|0.931034|- - -TCONS_00000028 XLOC_000042 Xkr4|Xkr4 i q1:CUFF.21|CUFF.21.1|100|13.851236|0.000000|33.439842|0.885246|- - -TCONS_00000029 XLOC_000044 Xkr4|Xkr4 i q1:CUFF.23|CUFF.23.1|100|23.470150|0.000000|50.571145|1.500000|- - -TCONS_00000030 XLOC_000046 Xkr4|Xkr4 i q1:CUFF.27|CUFF.27.1|100|34.253732|0.000000|73.806535|2.189189|- - -TCONS_00000031 XLOC_000048 Xkr4|Xkr4 i q1:CUFF.61|CUFF.61.1|100|45.263860|0.000000|97.530065|2.892857|- - -TCONS_00000032 XLOC_000049 Xkr4|Xkr4 i q1:CUFF.63|CUFF.63.1|100|15.646767|0.000000|46.940300|1.000000|- - -TCONS_00000033 XLOC_000052 Xkr4|Xkr4 i q1:CUFF.65|CUFF.65.1|100|15.362280|0.000000|37.087825|0.981818|- - -TCONS_00000034 XLOC_000057 Xkr4|Xkr4 i q1:CUFF.67|CUFF.67.1|100|12.998852|0.000000|31.382005|0.830769|- - -TCONS_00000035 XLOC_000059 Xkr4|Xkr4 i q1:CUFF.69|CUFF.69.1|100|10.058636|0.000000|24.283695|0.642857|- - -TCONS_00000036 XLOC_000059 Xkr4|Xkr4 i q1:CUFF.71|CUFF.71.1|100|8.621688|0.000000|20.814595|0.551020|- - -TCONS_00000037 XLOC_000060 Xkr4|Xkr4 i q1:CUFF.73|CUFF.73.1|100|15.362280|0.000000|37.087825|0.981818|- - -TCONS_00000038 XLOC_000062 Xkr4|Xkr4 i q1:CUFF.75|CUFF.75.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000039 XLOC_000065 Xkr4|Xkr4 i q1:CUFF.77|CUFF.77.1|100|16.248565|0.000000|39.227507|1.038462|- - -TCONS_00000040 XLOC_000068 Xkr4|Xkr4 i q1:CUFF.79|CUFF.79.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000041 XLOC_000071 Xkr4|Xkr4 i q1:CUFF.81|CUFF.81.1|100|13.201959|0.000000|31.872349|0.843750|- - -TCONS_00000042 XLOC_000073 Xkr4|Xkr4 i q1:CUFF.83|CUFF.83.1|100|13.201959|0.000000|28.446269|0.843750|- - -TCONS_00000043 XLOC_000075 Xkr4|Xkr4 i q1:CUFF.85|CUFF.85.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000044 XLOC_000077 Xkr4|Xkr4 i q1:CUFF.87|CUFF.87.1|100|17.243375|0.000000|41.629191|1.102041|- - -TCONS_00000045 XLOC_000080 Xkr4|Xkr4 i q1:CUFF.89|CUFF.89.1|100|16.567165|0.000000|39.996674|1.058824|- - -TCONS_00000046 XLOC_000083 Xkr4|Xkr4 i q1:CUFF.91|CUFF.91.1|100|31.293533|0.000000|75.549272|2.000000|- - -TCONS_00000047 XLOC_000084 Xkr4|Xkr4 i q1:CUFF.93|CUFF.93.1|100|21.664754|0.000000|52.303342|1.384615|- - -TCONS_00000048 XLOC_000085 Xkr4|Xkr4 i q1:CUFF.95|CUFF.95.1|100|46.940300|0.000000|101.142289|3.000000|- - -TCONS_00000049 XLOC_000086 Xkr4|Xkr4 i q1:CUFF.97|CUFF.97.1|100|21.481154|0.000000|46.285454|1.372881|- - -TCONS_00000050 XLOC_000087 Xkr4|Xkr4 i q1:CUFF.99|CUFF.99.1|100|14.567679|0.000000|35.169489|0.931034|- - -TCONS_00000051 XLOC_000004 - u - q2:CUFF.1|CUFF.1.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000052 XLOC_000005 - u - q2:CUFF.3|CUFF.3.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000053 XLOC_000006 - u - q2:CUFF.5|CUFF.5.1|100|21.226627|0.000000|59.889707|1.205672|- -TCONS_00000054 XLOC_000007 - u - q2:CUFF.11|CUFF.11.1|100|32.531777|24.582998|40.480555|1.847804|- -TCONS_00000055 XLOC_000008 - u - q2:CUFF.7|CUFF.7.1|100|29.709524|19.806349|39.612698|1.687500|- -TCONS_00000056 XLOC_000009 - u - q2:CUFF.9|CUFF.9.1|100|34.072933|23.364686|44.781179|1.935341|- -TCONS_00000057 XLOC_000010 - u - q2:CUFF.13|CUFF.13.1|100|16.582060|0.000000|35.729373|0.941860|- -TCONS_00000058 XLOC_000013 - u - q2:CUFF.15|CUFF.15.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000059 XLOC_000018 - u - q2:CUFF.17|CUFF.17.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000060 XLOC_000024 - u - q2:CUFF.19|CUFF.19.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000061 XLOC_000025 - u - q2:CUFF.23|CUFF.23.1|100|16.205195|0.000000|34.917342|0.920455|- -TCONS_00000062 XLOC_000027 - u - q2:CUFF.21|CUFF.21.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000063 XLOC_000028 - u - q2:CUFF.26|CUFF.26.1|100|29.709524|0.000000|71.725135|1.687500|- -TCONS_00000064 XLOC_000029 - u - q2:CUFF.25|CUFF.25.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000065 XLOC_000030 - u - q2:CUFF.29|CUFF.29.1|100|13.581496|0.000000|32.788633|0.771429|- -TCONS_00000066 XLOC_000032 - u - q2:CUFF.31|CUFF.31.1|100|22.635827|0.000000|45.271655|1.285714|- -TCONS_00000067 XLOC_000033 Xkr4|Xkr4 i - q2:CUFF.33|CUFF.33.1|100|23.767619|0.000000|57.380108|1.350000|- -TCONS_00000068 XLOC_000036 Xkr4|Xkr4 i - q2:CUFF.35|CUFF.35.1|100|11.317914|0.000000|27.323861|0.642857|- -TCONS_00000069 XLOC_000037 Xkr4|Xkr4 i - q2:CUFF.37|CUFF.37.1|100|11.500461|0.000000|24.780049|0.653226|- -TCONS_00000070 XLOC_000038 Xkr4|Xkr4 i - q2:CUFF.39|CUFF.39.1|100|52.816931|0.000000|113.804669|3.000000|- -TCONS_00000071 XLOC_000039 Xkr4|Xkr4 i - q2:CUFF.41|CUFF.41.1|100|43.213852|0.000000|93.112911|2.454545|- -TCONS_00000072 XLOC_000041 Xkr4|Xkr4 i - q2:CUFF.43|CUFF.43.1|100|23.474191|0.000000|46.948383|1.333333|- -TCONS_00000073 XLOC_000043 Xkr4|Xkr4 i - q2:CUFF.45|CUFF.45.1|100|20.667495|0.000000|49.895746|1.173913|- -TCONS_00000074 XLOC_000045 Xkr4|Xkr4 i - q2:CUFF.47|CUFF.47.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000075 XLOC_000047 Xkr4|Xkr4 i - q2:CUFF.49|CUFF.49.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000076 XLOC_000049 Xkr4|Xkr4 i - q2:CUFF.51|CUFF.51.1|100|14.948188|7.228977|22.667399|0.849057|- -TCONS_00000077 XLOC_000050 Xkr4|Xkr4 i - q2:CUFF.53|CUFF.53.1|100|52.816931|0.000000|113.804669|3.000000|- -TCONS_00000078 XLOC_000051 Xkr4|Xkr4 i - q2:CUFF.55|CUFF.55.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000079 XLOC_000053 Xkr4|Xkr4 i - q2:CUFF.57|CUFF.57.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000080 XLOC_000054 Xkr4|Xkr4 i - q2:CUFF.59|CUFF.59.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000081 XLOC_000055 Xkr4|Xkr4 i - q2:CUFF.61|CUFF.61.1|100|13.204233|0.000000|31.877838|0.750000|- -TCONS_00000082 XLOC_000056 Xkr4|Xkr4 i - q2:CUFF.63|CUFF.63.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000083 XLOC_000058 Xkr4|Xkr4 i - q2:CUFF.65|CUFF.65.1|100|31.170648|0.000000|62.341295|1.770492|- -TCONS_00000084 XLOC_000059 Xkr4|Xkr4 i - q2:CUFF.69|CUFF.69.1|100|18.799247|8.750627|28.847866|1.067797|- -TCONS_00000085 XLOC_000060 Xkr4|Xkr4 i - q2:CUFF.67|CUFF.67.1|100|15.681351|3.378764|27.983938|0.890700|- -TCONS_00000086 XLOC_000061 Xkr4|Xkr4 i - q2:CUFF.71|CUFF.71.1|100|22.635827|0.000000|54.647722|1.285714|- -TCONS_00000087 XLOC_000063 Xkr4|Xkr4 i - q2:CUFF.73|CUFF.73.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000088 XLOC_000064 Xkr4|Xkr4 i - q2:CUFF.75|CUFF.75.1|100|52.816931|0.000000|113.804669|3.000000|- -TCONS_00000089 XLOC_000066 Xkr4|Xkr4 i - q2:CUFF.77|CUFF.77.1|100|17.605644|0.000000|52.816931|1.000000|- -TCONS_00000090 XLOC_000067 Xkr4|Xkr4 i - q2:CUFF.79|CUFF.79.1|100|13.390208|0.000000|32.326821|0.760563|- -TCONS_00000091 XLOC_000068 Xkr4|Xkr4 i - q2:CUFF.81|CUFF.81.1|100|11.211141|1.183592|21.238690|0.636792|- -TCONS_00000092 XLOC_000069 Xkr4|Xkr4 i - q2:CUFF.83|CUFF.83.1|100|21.126772|0.000000|51.004540|1.200000|- -TCONS_00000093 XLOC_000070 Xkr4|Xkr4 i - q2:CUFF.85|CUFF.85.1|100|19.014095|0.000000|38.028190|1.080000|- -TCONS_00000094 XLOC_000072 Xkr4|Xkr4 i - q2:CUFF.87|CUFF.87.1|100|24.170460|0.000000|52.080103|1.372881|- -TCONS_00000095 XLOC_000074 Xkr4|Xkr4 i - q2:CUFF.89|CUFF.89.1|100|29.709524|0.000000|64.015126|1.687500|- -TCONS_00000096 XLOC_000076 Xkr4|Xkr4 i - q2:CUFF.91|CUFF.91.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000097 XLOC_000078 Xkr4|Xkr4 i - q2:CUFF.93|CUFF.93.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000098 XLOC_000079 Xkr4|Xkr4 i - q2:CUFF.95|CUFF.95.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000099 XLOC_000081 Xkr4|Xkr4 i - q2:CUFF.97|CUFF.97.1|100|35.211287|0.000000|85.007567|2.000000|- -TCONS_00000100 XLOC_000082 Xkr4|Xkr4 i - q2:CUFF.99|CUFF.99.1|100|19.602160|0.000000|39.204320|1.113402|- diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffcompare_out7.txt --- a/test-data/cuffcompare_out7.txt +++ /dev/null @@ -1,33 +0,0 @@ -# Cuffcompare v2.0.2 | Command line was: -#cuffcompare -o cc_output -r /Users/jeremy/projects/galaxy-central/database/files/002/dataset_2770.dat -R ./input1 ./input2 -# - -#= Summary for dataset: ./input1 : -# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) -# (0 multi-transcript loci, ~1.0 transcripts per locus) -# Reference mRNAs : 1 in 1 loci (1 multi-exon) -# Corresponding super-loci: 1 -#--------------------| Sn | Sp | fSn | fSp - Base level: 2.2 2.3 - - - Exon level: 0.0 0.0 0.0 0.0 - Intron level: 0.0 nan 0.0 nan -Intron chain level: 0.0 nan 0.0 nan - Transcript level: 0.0 0.0 0.0 0.0 - Locus level: 0.0 0.0 0.0 0.0 - -Matching intron chains: 0 - Matching loci: 0 - - Missed exons: 2/3 ( 66.7%) - Novel exons: 49/50 ( 98.0%) - Missed introns: 2/2 (100.0%) - Missed loci: 0/1 ( 0.0%) - Novel loci: 49/50 ( 98.0%) - -#= Summary for dataset: ./input2 : -# Query mRNAs : 50 in 50 loci (0 multi-exon transcripts) -# (0 multi-transcript loci, ~1.0 transcripts per locus) -# Reference mRNAs : 0 in 0 loci (0 multi-exon) - - Total union super-loci across all input datasets: 87 - (0 multi-transcript, ~1.1 transcripts per locus) diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffdiff_in1.sam --- a/test-data/cuffdiff_in1.sam +++ /dev/null @@ -1,400 +0,0 @@ -EAS38_8_212_338_985 0 chr1 3004981 0 35M * 0 0 CCAATGGGCCTCTATTTGCAGTGATGGGCGAGTAG hhhhhhhhhhhhhEhhhhYhhhhUhhh@Ih?BZ?e NM:i:2 -EAS38_8_8_215_414 0 chr1 3035356 0 35M * 0 0 TACCCCATAAAAGCCCCTGGCTTTCGCGCCTCGTG hhhhhhhhhhhhhhhhhhhhhhh`GI>PPIQPBOH NM:i:1 -EAS38_8_8_622_393 16 chr1 3065512 0 35M * 0 0 AAAAAAAAAAAAACAAAAAAAAAAAAAACAGCGAG hhHhhhhhhhhhhMhhhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_53_557_326 16 chr1 3075162 0 35M * 0 0 TAGAGAAATGGATACAGAAAGTGTGGTAATTTACA Ihehhhhh]hhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_259_911_538 0 chr1 3099409 0 35M * 0 0 TTTGGCTGGGAGACAATTAATGACTGCTTTTTTTT hhhhhhhhhhhh_hhhhhNhhP\hhaEhhHhNhhh NM:i:2 -EAS38_8_284_729_569 16 chr1 3113004 255 35M * 0 0 CTATCTGTTGCAAAGAGAACTTTCCTTGGTGTAAG EIIEKhRh@K_hahhhhhhh`ehhhhhhhhhhhhh NM:i:0 -EAS38_8_27_537_242 0 chr1 3118613 255 35M * 0 0 AGGACTCACATTCCCTTACTTTGTTTACAAAATGA hhh`hhhhhhhhhhhhhhhhhhhhhh]hhYXOhD` NM:i:0 -EAS38_8_38_947_12 0 chr1 3131368 0 35M * 0 0 TATTAGTCCCCTATCANATTTAGGATTGTTAATAA hhhhhhh_bchhhhUh;\hhhhh`EXcIVhNJZ]P NM:i:2 -EAS38_8_205_433_879 16 chr1 3136988 0 35M * 0 0 CATATCAATTGAACGGAACTAAAGTCTGTGACAGT hhhhchhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_155_191_162 16 chr1 3136999 0 35M * 0 0 AACGGAACTAAAGTCTGTGACAGTGGACATAGCTG hh_h\hhYhhhhhMhfhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_216_635_828 0 chr1 3137063 0 35M * 0 0 ATCTGGAATTATGTGATTATAATTTTCTTAGCATT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_317_949_784 0 chr1 3137063 0 35M * 0 0 ATCTGGAATTATGTGATTATAATTTTCTTAGCATT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhNchh NM:i:0 -EAS38_8_278_281_786 16 chr1 3137078 0 35M * 0 0 ATTATAATTTTCTTAGCATTTTCTTTGTAAAAAAA AhhhQhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_228_462_705 0 chr1 3137133 0 35M * 0 0 GTTGGTGTATAGTAAAAAGTAAAGAAATTCTGAGA hhhhhhhhhhhhhhhhhhh_hghhWhYh`LhhKbY NM:i:0 -EAS38_8_299_582_840 0 chr1 3137133 0 35M * 0 0 GTTGGTGTATAGTAAAAAGTAAAGAAATTCTGAGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhWhhhhh NM:i:0 -EAS38_8_125_742_683 16 chr1 3137135 0 35M * 0 0 TGGTGTATAGTAAAAAGTAAAGAAATTCTGAGAGG GJCZSShchhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_208_212_874 0 chr1 3137137 0 35M * 0 0 GTGTATAGTAAAAAGTAAAGAAATTCTGAGAGGAG hhhhhhhhhhhhhhhhhhhhhhhhh[hhhhhhh`h NM:i:0 -EAS38_8_241_424_62 16 chr1 3137137 0 35M * 0 0 GTGTATAGTAAAAAGTAAAGAAATTCTGAGAGGAG hhhhhhhhehhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_245_195_910 16 chr1 3137137 0 35M * 0 0 GTGTATAGTAAAAAGTAAAGAAATTCTGAGAGGAG Bhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_234_890_706 0 chr1 3137138 0 35M * 0 0 TGTATAGTAAAAAGTAAAGAAATTCTGAGAGGAGT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhUhh NM:i:0 -EAS38_8_317_909_810 16 chr1 3137175 0 35M * 0 0 TATTTTAGGATAATACATATATACATATGCAGTGT hhhhhhhaThhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_111_444_456 0 chr1 3137180 0 35M * 0 0 TAGGTTAATACATATATACATATGCAGTGTGTGTG hhhhhhhhhhhhhhhhhhhahhhhhhhhgehhhhH NM:i:1 -EAS38_8_134_193_731 0 chr1 3137180 0 35M * 0 0 TAGGATAATACATATATACATATGCAGTGTGTGTG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_138_869_374 0 chr1 3137180 0 35M * 0 0 TAGGATAATACATATATACATATGCAGTGTGTGTG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_36_257_907 0 chr1 3137192 0 35M * 0 0 TATATACATATGCAGTGTGTGTGCCAGTGGTGTTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhNJDhS NM:i:0 -EAS38_8_50_322_852 0 chr1 3137192 0 35M * 0 0 TATATACATATGCAGTGTGTGTGCCAGTGGTGTTA hhhhhhhhhhhhhhhhhhhhhhhRcZhhhhVhShY NM:i:0 -EAS38_8_207_430_640 16 chr1 3146524 0 35M * 0 0 AAAAAACATCGGCACAACAATCAAAAAAAAAAAAA VE_AhhhhFhhhhh]hhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_289_914_684 0 chr1 3154024 255 35M * 0 0 TCACAGAAGGCTCACTTCCTTTCTGTCTGTGTCAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhdhhMGT NM:i:0 -EAS38_8_35_737_747 16 chr1 3174758 255 35M * 0 0 TTTTGGGTGAGATGGAATCTCAGAGTAGTTATTTT [hghdhMhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_75_492_572 16 chr1 3174758 255 35M * 0 0 TTTTGGGTGAGATGGAATCTCAGAGTAGTTATTTT [Vhhh^hhhhhhhhhhhdhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_187_160_172 16 chr1 3175562 255 35M * 0 0 TAGTCTGGTCTGTGGCTTCAGCGGTAGGATGGCCT BT\JAGMQVRN[QhYZGchhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_56_600_894 0 chr1 3175828 255 35M * 0 0 GAGAAAGAGGTGGGAAGGGAAAGAGAGAGAGAAGA hhhhhhhhhhhhhhhhhhhhhhhhhhhShChDKhI NM:i:0 -EAS38_8_106_467_709 16 chr1 3181781 255 35M * 0 0 CTTTAGTACAGGTTACATTCCATACCTATAGCAAG hhhhhhhhhhh`hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_199_476_527 16 chr1 3181781 255 35M * 0 0 CTTTAGTACAGGTTACATTCCATACCTATAGCAAG E[dbhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_116_967_124 16 chr1 3187134 255 35M * 0 0 ATAGCTCTTCATCTAGGGGTGGGACTTTTGAGATT hghYhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_182_44_990 16 chr1 3187394 255 35M * 0 0 GAAATGCTCATTCTCATAGAGAAGAGATTGCCTAG EhhhaKhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_203_996_132 16 chr1 3187394 255 35M * 0 0 GAAATGATCATTCTCATAGAGAAGAGATTGCCTAG JXJ`_eFVVhhhhhchhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_318_612_118 0 chr1 3188522 255 35M * 0 0 GTATTCTTAATCTATTGTGTTTTGTTTGTTCTTTG hhhhhhhhhhhhhhhhhhShhhhIhhhWhh_hYhC NM:i:1 -EAS38_8_52_573_715 16 chr1 3188914 255 35M * 0 0 TTTGGAAGATAGTTTTCATTTCAGGACTGTCATTA hh]hDhh\hhhghhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_82_668_114 16 chr1 3189123 255 35M * 0 0 TAGATTCTGTTGAAAGCTGCTTGTGTAGGTGCTGG Jhfheh@_Nh`hhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_229_732_980 16 chr1 3189293 255 35M * 0 0 ATATGTAGAAAAAGAAAGCAATTAGATGTATCATA hhhhWhhOhhhhhghhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_49_685_15 0 chr1 3189811 255 35M * 0 0 CTTTTAAAATGACCACAGTGTACTTTATTTAATTA hhhhhhhhhhhhhhhhhhhhhhhhhh]hhhPahZQ NM:i:2 -EAS38_8_228_500_937 0 chr1 3189812 255 35M * 0 0 TTTTAAAATGACCACAGTGTACTTTATTTAATGAT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhLh NM:i:1 -EAS38_8_8_865_653 0 chr1 3189812 255 35M * 0 0 TTTTAAAATGACCACAGTGTACTTTATTTAATGAT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_284_550_449 0 chr1 3189815 255 35M * 0 0 TGAAATGACCACAGTGTACTTTATTTAATGATTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhPhhhh NM:i:1 -EAS38_8_44_493_707 0 chr1 3189839 255 35M * 0 0 TTAATGATTTTTGTACTTTGTGTTGCAATAAAATA hhhhhhhhhhhhhhhhhhhhhhhhRhhhhhhhhhh NM:i:0 -EAS38_8_173_339_743 0 chr1 3189847 255 35M * 0 0 TTTTGTACTTTGTGTTGCAATAAAATAAAAAAAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhZhhhf NM:i:0 -EAS38_8_69_320_425 16 chr1 3189862 255 35M * 0 0 TGAAATAAAAAAAAAAAAAAATCTACAAAATTCAA _OahhShhhhAhhhhhhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_253_215_784 0 chr1 3189882 255 35M * 0 0 ATCTACAAAATTCAAATATATAAAATTTCAAGTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_254_492_492 0 chr1 3189882 255 35M * 0 0 ATCTACAAAATTCAAATATATAAAATTTCAAGTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhchhhhh NM:i:0 -EAS38_8_164_969_744 0 chr1 3189884 255 35M * 0 0 CTACAAAATTCAAATATATAAAATTTCAAGTTTTC hhhhhhhhhhhhhhhhhhhhhVhhWhTNchDhhgA NM:i:0 -EAS38_8_76_118_672 0 chr1 3189938 255 35M * 0 0 AGAAAAAAAATCAGATAACCGAGGAAAATTATTCA hhhhhhhhhhhhhhhhhhhhhhhh]hhhhhThhR] NM:i:0 -EAS38_8_322_903_184 16 chr1 3189967 255 35M * 0 0 TATTCATTATGAAGTACTACTTTCCACTTCATTTC O[ENehNVh`ahh]hhhhhhWhhhhhhhhhhhhhh NM:i:0 -EAS38_8_122_863_114 16 chr1 3189975 255 35M * 0 0 ATGAAGTACTACTTTCCACTTCATTTCATCACAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_328_905_544 0 chr1 3189975 255 35M * 0 0 ATGAAGTACTACTTTCCACTTCATTTCATCACAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhXhO NM:i:0 -EAS38_8_49_611_982 16 chr1 3189991 255 35M * 0 0 CACTTCATTTCATCACAAATTGTAACTTACTTAAC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_149_471_590 0 chr1 3189993 255 35M * 0 0 CTTCATTTCATCACAAATTGTAACTTACTTAACTG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhc NM:i:0 -EAS38_8_176_471_461 0 chr1 3189993 255 35M * 0 0 CTTCATTTCATCACAAATTGTAACTTACTTAACTG hhhhhhhhhhhhhhhhhhhhhhchhh`hhh[hhhO NM:i:0 -EAS38_8_330_91_472 16 chr1 3189999 255 35M * 0 0 TTAATCACAAATTGTAACTTACTTAACTGACCAAA hhOhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_330_964_788 16 chr1 3189999 255 35M * 0 0 TTCATCACAAATTGTAACTTACTTAACTGACCAAA aIhhhh`hhhhhhhhhhhhhBhhhhhhhchhhhhh NM:i:0 -EAS38_8_281_200_582 16 chr1 3190038 255 35M * 0 0 CTATGGTACTGCAGTATAGAAAATACTCCACACAC ONK[MhhhdhhQhhhhhhhMhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_241_125_175 16 chr1 3190056 255 35M * 0 0 GAAAATAATCCACACACTGTGCTTTGAGCTAGAGC HhhhhShIhhShhhhhhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_274_895_968 0 chr1 3190074 255 35M * 0 0 GTGCTTTGAGCTAGAGCACTTGGAGTCACTGCACA hhhhhhhhhhhhhhhhPhOhhhhPhhMTMXhLBMC NM:i:1 -EAS38_8_274_589_297 16 chr1 3190081 255 35M * 0 0 GAGCTAGAGCACTGGGAGTCACTGCCCAGGGCAGC ]W_IHUh_hh^WZDhhhhKhhh[hhhhhhhhhhhh NM:i:1 -EAS38_8_11_418_433 0 chr1 3190094 255 35M * 0 0 TGGAGTCACTGCCCAGGGCAGCAGCCTCCAACCAA hhhhhhhhhhhhhhhhhhbCchhb`PUPhJWIOGA NM:i:0 -EAS38_8_324_436_604 16 chr1 3190136 255 35M * 0 0 ACACTTACAAGTTGAATTCTAAAGGAAGGTCTGGT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_131_262_425 16 chr1 3190137 255 35M * 0 0 CACGTACAAGTTGAATTCTAAAGGAAGGTCTGGTT dVKEhhhhhhhWhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_5_661_318 16 chr1 3190137 255 35M * 0 0 CACTTACAAGTTGAATTCTAAAGGAAGGTCTGGTT F^O_ZhhhhhAhhhhhMh`hhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_109_581_805 0 chr1 3190144 255 35M * 0 0 AAGTTGAATTCTAAAGGAAGGTCTGGTTATGTGGG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_279_908_963 0 chr1 3190154 255 35M * 0 0 CTAAAGGAAGGTCTGGTTATGTGGGGTTGGAATAT hhhhhhhhhhhhhhhhhhhhhhhhhhDhhhRDEhH NM:i:0 -EAS38_8_207_793_649 16 chr1 3190155 255 35M * 0 0 TAAAGGAAGGTCTGGTTATGTGGGGTTGGAATATG FThTO[ZcIHRhhShhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_249_136_550 0 chr1 3190167 255 35M * 0 0 TGGTTATGTGGGGTTGGAATATGTATATCTATATA hhhhhhhhhhhhhhhhhghhhhhhhhhhhhDhJhh NM:i:0 -EAS38_8_197_214_431 16 chr1 3190168 255 35M * 0 0 GGTTATGTGGGGTTGGAATATGTATATCTATATAT EUEU@QhJhhVgFUhhhhPhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_124_625_963 16 chr1 3190174 255 35M * 0 0 GTGGGGTTGGAATATGTATATCTATATATCTCTAT ]hdTChhhXhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_314_668_328 16 chr1 3190176 255 35M * 0 0 GGGGTTGGAATATGTATATCTATATATCTCTATAT hhhh]]hhhhOh_hhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_8_247_406 16 chr1 3190176 255 35M * 0 0 GGGGTTGGAATATGTATATCTATATATCTCTATAT fY]NUFQQhhVcRhhhhhhehhhhhhhhhhhhhhh NM:i:0 -EAS38_8_45_380_957 16 chr1 3190191 255 35M * 0 0 ATATCTATATATCTCTATATATATTTACATCAAAG hhhVhbhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_224_453_647 16 chr1 3190214 255 35M * 0 0 TTTACATCAAAGAATTTAATAACTCATTTAAATTT hKhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_120_914_892 0 chr1 3190236 255 35M * 0 0 CTCATTTAAATTTTTGTTTCAAATAAAATTCCAAA hhhhhhhhhhhhhhhhhhhhhhhhhhfhhhLWh]K NM:i:0 -EAS38_8_8_442_670 0 chr1 3190258 255 35M * 0 0 ATAAAATTCCAAATACATTTGTACAATGTTTACAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhRhhTe_\ NM:i:0 -EAS38_8_245_767_298 16 chr1 3190284 255 35M * 0 0 TGTTTACAAAGTAAGAGACAGGACTGGCAGGTTTG WOF`hhhhhhhbhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_94_374_121 16 chr1 3190284 255 35M * 0 0 TGTTTACAAAGTAAGAGACAGGACTGGCAGGTTTG Shh`hhRhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_256_414_787 0 chr1 3190333 255 35M * 0 0 CACCGTGATGTCCGGGTGATATATCTTCACGTTGC hhhhhhhhhhhhhhhhdhchhhhh`hhJRBhfhhJ NM:i:0 -EAS38_8_215_417_539 16 chr1 3190353 255 35M * 0 0 ATATCTTCACGTTGCCTGCACACACCTTATTTCTG VAHGh@XhBhhhRhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_167_839_349 0 chr1 3190379 255 35M * 0 0 TTATTTCTGAAATGGAGAGAGAAACTCAAGAATGT hhhhhhhhhhhhhhhhhhhhhdhhhhhPhhDhhCh NM:i:0 -EAS38_8_235_344_488 0 chr1 3190402 255 35M * 0 0 ACTCAAGAATGTCACCGACTATGCATCAGAATACT hhhhhhhhhhhhhhhhhLhhhhbfhGUILPJQQPL NM:i:0 -EAS38_8_287_803_220 0 chr1 3190402 255 35M * 0 0 ACTCAAGAATGTCACCGACTATGCATCAGAATACT hhhhhhhhhhhhhhhhhhhhhhhhdhgTMVEh\^N NM:i:0 -EAS38_8_23_488_181 16 chr1 3190434 255 35M * 0 0 ACTATGTACAGTTGAAGTTAGGGAGCTGAGAACCT hChhhhOhhhhgUhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_137_662_459 16 chr1 3190469 255 35M * 0 0 AGTGTTCTGTTCTCTTCTGGTTTGTCTTCATCTAC eOKeGUhIhVhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_228_762_237 16 chr1 3190469 255 35M * 0 0 AGTGGTCTGTTCTCTTCTGGTTTGTCTTCATCTAC ZhMhbWK\hgShShhhh^hhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_65_836_536 16 chr1 3190469 255 35M * 0 0 AGTGTTCTGTTCTCTTCTGGTTTGTCTTCATCTAC ahYhThhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_100_122_849 0 chr1 3190545 255 35M * 0 0 CAAACATTGGAAAGAGGAAGGAGAAAAACACAAAA hhhhhhhhhhhhhhhhhhhhhXhhhhhhCdM[TUh NM:i:1 -EAS38_8_172_157_846 16 chr1 3190553 255 35M * 0 0 GGAAAGAGGAAGGAGAAAAGTACAAAATATTTAAG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_166_123_980 16 chr1 3190565 255 35M * 0 0 GAGAAAAGCACAAAATATTTAAGGCAAATTAAGCA FhThhhhLhhhhhhhhhhhhhhhbhhhhhhhhhhh NM:i:0 -EAS38_8_202_25_949 16 chr1 3190601 255 35M * 0 0 ATATGTATAGTCTCTTTGTGCCAGGAGGATGTGAC OKTX@[hhdGVhVhhhhMhdhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_135_382_764 0 chr1 3190604 255 35M * 0 0 TGTACAGTCTCTTTGTGCCAGGAGGATGTGACTTT hhhhhhhhhhhhhhhhhhhhhhhhhOhhhhYHhhh NM:i:0 -EAS38_8_256_748_407 16 chr1 3190604 255 35M * 0 0 TGTACAGTCTCTTTGTGCCAGGAGGATGTGACTTT RWEhhhhZhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_328_369_595 0 chr1 3190604 255 35M * 0 0 TGTACAGTCTCTTTGTGCCAGGAGGATGTGACTTT hhhhhhhhhhhhhhhhhhhhhhhhhFahJORXhhh NM:i:0 -EAS38_8_13_985_934 16 chr1 3190609 255 35M * 0 0 AGTCTCTTTGTGCCAGGAGGATGTGACTTTCTTTT STZhQhhUhcdhhhhdSh^Zhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_13_657_254 0 chr1 3190659 255 35M * 0 0 GCTTTAAAAAATTCAAATAAAGCAAGTCTGGTGTG hhhhhhhhhhhhhhhhhhhhhhhhZhhhhhYh]h\ NM:i:0 -EAS38_8_97_368_634 0 chr1 3190659 255 35M * 0 0 GCTTTAAAAAATTCAAATAAAGCAAGTCTGGTGTG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_158_637_333 0 chr1 3190697 255 35M * 0 0 TGGGTTGCTTGTGTTGTTTTAATTTTTTTTGAAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh@ZMhQ NM:i:0 -EAS38_8_7_431_889 0 chr1 3190697 255 35M * 0 0 TGGGTTGCTTGTGTTGTTTTAATTTTTTTTGAAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_129_799_390 0 chr1 3190859 255 35M * 0 0 TAAAATAATGAGAGAATGGAGAACCAATGTAAGGA hhhhhhhhhhhhbhQMhhhXhJgFNJVKJLT>BI? NM:i:0 -EAS38_8_186_234_660 16 chr1 3190910 255 35M * 0 0 TCTGGAAGCAGGCTCACCAAGTATGATGGTTTCAT bb\hhhhhhhhdhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_99_392_34 16 chr1 3190940 255 35M * 0 0 TTCATACACAGAAAAACATTTGTTCTTTTGGATGC `dAhhhEUMhhhhhhhhhhThhhhhhhhhhhhhhh NM:i:1 -EAS38_8_141_299_800 0 chr1 3190964 255 35M * 0 0 CTTTTGGATGCCATTAGTTCAGCCAGTGTCAACAT hhhhhhhhhhhhhhhhhhhhhhhhahhhhhhhQh] NM:i:0 -EAS38_8_41_30_673 0 chr1 3190983 255 35M * 0 0 CAGCCAGTGTCAACATGACTAGTGGTTTCCCCAGC hhhhhhhhhhhhhhhhhhQhhhhhhJhh>SWHLEM NM:i:1 -EAS38_8_270_818_467 16 chr1 3191047 255 35M * 0 0 CTGCTTTCCAGGCTTCTCATCTATAGATAGAGAAG YADUL]DhhhhYhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_295_700_520 0 chr1 3191049 255 35M * 0 0 GCTTTCCAGGCTTCTCATCTATAGATAGAGAAGAC hhhhhhhhhhhhhhhhhhhhRhhhhhhah`IhRXG NM:i:0 -EAS38_8_326_937_869 0 chr1 3191049 255 35M * 0 0 GCTTTCCAGGCTTCTCATCTATAGATAGAGAAGAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhQMhFG? NM:i:1 -EAS38_8_156_546_203 0 chr1 3191080 255 35M * 0 0 AGACTTTTACAAGGTGTATGTATTGAATCCATTAT hhhhhhhhhhhhhhhhhhhfhhhhDhhVhhRhhPh NM:i:1 -EAS38_8_226_788_95 0 chr1 3191080 255 35M * 0 0 AGACTTTTACAAGGTGTATGTATTTAAGCCATTAT hhhhhhhhhhhhhhhhhhhhhhhhPhhSghchhhh NM:i:1 -EAS38_8_206_454_499 16 chr1 3191117 255 35M * 0 0 AAAATGACATTATTTATCATTATTAGAAATTCCAA hhhhZhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_126_432_418 0 chr1 3191141 255 35M * 0 0 AGAAATTCCAACCCTAGTTATGAAAGATTGAGGGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhYhchR NM:i:0 -EAS38_8_255_473_525 0 chr1 3191143 255 35M * 0 0 AAATTCCAACCCTAGTTATGAAAGATTGAGGGAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhWhhhafh NM:i:0 -EAS38_8_293_908_459 16 chr1 3191160 255 35M * 0 0 ATGAAAGATTGAGGGAAAGTGATAAAGAACAAAAG hhehhhhhhYhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_126_512_733 0 chr1 3191163 255 35M * 0 0 AAAGATTGAGGGAAAGTGATAAAGAACAAAAGGGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhN NM:i:0 -EAS38_8_132_357_350 0 chr1 3191163 255 35M * 0 0 AAAGATTGAGGGAAAGTGATAAAGAACAAAAGGGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh^hL NM:i:0 -EAS38_8_225_963_686 16 chr1 3191186 255 35M * 0 0 GAACAAAAGGGAGGGATATTATTCTCTCATTTTTA UchhhhfhhhahNhahhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_91_183_721 0 chr1 3191203 255 35M * 0 0 ATTATTCTCTCATTTTTAACAGCATATTTGTCTTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh[ NM:i:0 -EAS38_8_91_184_720 0 chr1 3191203 255 35M * 0 0 ATTATTCTCTCATTTTTAACAGCATATTTGTCTTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhX NM:i:0 -EAS38_8_37_742_366 16 chr1 3191253 255 35M * 0 0 TACTGTGTGGCTTCAAAGAAGATAGTCATCTCTGG h]hQhhB_hhRhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_164_833_223 16 chr1 3191267 255 35M * 0 0 AAAGAAGATAGTCATCTCTGGTTCTCTTACTGAGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_20_3_646 16 chr1 3191299 255 35M * 0 0 AGAATAGAAAGTCTCTCCTTACTGAGAATAGGAAG hVhh_hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_305_336_434 16 chr1 3191299 255 35M * 0 0 AGAATAGAAAGTCTCTCCTTACTGAGAATAGGAAG hhhhhhhhhhhUhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_133_876_487 16 chr1 3191301 255 35M * 0 0 AATAGAAAGTCTCTCCTTACTGAGAATAGGAAGCC hhGhThhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_58_243_264 16 chr1 3191305 255 35M * 0 0 GAAAGTCTCTAATTACTGAGAATAGGAAGCCATCT hhhhh?UQLOIAhhhWhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_158_87_484 16 chr1 3191325 255 35M * 0 0 AATAGGAAGCCATCTTCATACCTGTCCCTCTGCAT gh@hChhhh`LhFhhghhRhhhhhghhhhhhhhhh NM:i:0 -EAS38_8_49_289_587 16 chr1 3191360 255 35M * 0 0 TTATTCTTGAGGTTACTGAGCCATCTGGCTACAGA hhh^XhKUhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_226_316_409 0 chr1 3191368 255 35M * 0 0 GAGGTTACTGAGCCATCTGGCTACAGAGAAGAAAA hhhhhhhhhhhhhhhhhhahhhah_UOhDENhC[G NM:i:0 -EAS38_8_27_871_685 16 chr1 3191375 255 35M * 0 0 CAGAGCCATCTGGCTACAGAGAAGAAAAGCAAGAG gAhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_323_782_711 16 chr1 3191375 255 35M * 0 0 CTGAGCCATCTGGCTACAGAGAAGAAAAGCAAGAG hGdhZhghhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_138_990_817 16 chr1 3191399 255 35M * 0 0 AAAAGCAAGAGTTGTTTTTTTATTTTTATTTTATT hhhhKhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_185_443_369 16 chr1 3191399 255 35M * 0 0 AAAAGCAAGAGTTGTTTTTTTATTTTTATTTTATT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_16_393_343 16 chr1 3191400 255 35M * 0 0 AAAGCAAGAGTTGTTTTTTTATTTTTATTTTATTT hhhhVhhhhhI]hPJhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_50_691_313 16 chr1 3191400 255 35M * 0 0 AAAGCAAGAGTTGTTTTTTTATTTTTATTTTATTT hhhhhhhhhhhhhXhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_189_168_310 16 chr1 3191408 255 35M * 0 0 AGTTGTTTTTTTATTTTTATTTTATTTTTATTTTT hhWWhhh[hh_hhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_247_520_310 16 chr1 3191408 255 35M * 0 0 AGTTGTTTTTTTATTTTTATTTTATTTTTATTTTT hhTRhhh]hhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_8_620_387 0 chr1 3191411 3 35M * 0 0 TTTTTTTTTATTTTTATTTTATTTTTATTTTTTTA hhhhhhhhhhhhhhh`hhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_264_985_305 0 chr1 3191415 1 35M * 0 0 TTTTTATTTTTATTTTATTTTTATTTTTTTAATTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhOhh NM:i:1 -EAS38_8_290_750_320 16 chr1 3191505 255 35M * 0 0 CAGACAATGGCTTTAAGTGGGGCCTATATGAACTG BaFA>PbShGXfXhh_hJhh[hhhhhhhhhhhhhh NM:i:1 -EAS38_8_220_527_228 16 chr1 3191562 255 35M * 0 0 CGGTTTTGTGAAGGTAATATATCAGTAATATGGTT E[gYhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_181_540_123 0 chr1 3191572 255 35M * 0 0 AAGGTAATATATCAGTAATATGGTTGACATAAATA hhhhhhhhhhhhhhhhhhhhhhhhhOfhPhhEZDS NM:i:0 -EAS38_8_28_698_660 0 chr1 3191572 255 35M * 0 0 AAGGTAATATATCAGTAATATGGTTGACATAAATA hhhhhhhhhhhhhhhhhhhhhhhhhheRchhHhGh NM:i:0 -EAS38_8_304_298_316 0 chr1 3191572 255 35M * 0 0 AAGGTAATATATCAGTAATATGTTTGACATAAATA hhhhhhhhhhhhhhhhhhhhhhhhhhbchhhTchh NM:i:1 -EAS38_8_146_777_942 0 chr1 3191575 255 35M * 0 0 GTAATATATCAGTAATATGGTTGACATAAATAAGC hhhhhhhhhhhhhhhhhhhhhhhhahhhhhhhhhG NM:i:0 -EAS38_8_206_582_659 0 chr1 3191575 255 35M * 0 0 GTAATATATCAGTAATATGGTTGACATAAATAAAC hhhhhhhhhhhhhhhhhhhhhhhhhhhhgh[hh@T NM:i:1 -EAS38_8_113_379_524 0 chr1 3191576 255 35M * 0 0 TAATATATCAGTAATATGGTTGACATAAATAAGCT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhIh NM:i:0 -EAS38_8_197_772_581 16 chr1 3191611 255 35M * 0 0 GGGAAATAGTTCTTTTAGGAAGTAGAAGATTTTTC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_256_457_159 16 chr1 3191611 255 35M * 0 0 GGGAAATAGTTCTTTTAGGAAGTAGAAGATTTTTC hhhhhhUhhhgPhhghhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_315_836_955 0 chr1 3191675 255 35M * 0 0 TGAAAAGAATGTTAGTTGGCTGTAACCATAAAATT hhhhhhhhhhhhhhhhhhhLhhHhhhEMhghJhUW NM:i:0 -EAS38_8_255_763_380 16 chr1 3191702 255 35M * 0 0 ATAAAATGGGCAGTTGTATTTACAAATAATCACAT hhhhhhhBhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_279_818_155 0 chr1 3191716 255 35M * 0 0 TGTATTTACAAATAATCACATATATGATGCTTACA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhT^G NM:i:0 -EAS38_8_48_883_242 16 chr1 3191719 255 35M * 0 0 ATTTAAAAATAATCACATATATGATGCTTACAGAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_78_140_97 0 chr1 3191764 255 35M * 0 0 ATTTCTAAATAATCACATATGCTAAAAGCTAGTTT hhhhhhhhhhhhhhhhhhhhPhhh\ThGhhDILh] NM:i:1 -EAS38_8_322_980_805 16 chr1 3191782 255 35M * 0 0 ATGCTAAAAGCTAGGTTTTTCTAATACACTTTTAT hSYhhhhhh\hhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_319_99_291 16 chr1 3191786 255 35M * 0 0 TAAAAGCTAGGTTTTTCTAATACACTTTTACTTTC hhhhhhhdhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_64_224_620 0 chr1 3191811 255 35M * 0 0 TTTTATTTTCATGGAGGGCTCTAGAGGTTTCCACG hhhhhhhhhhhhhPhhhhhhhhhhZh]>hhCPJQJ NM:i:1 -EAS38_8_108_348_710 0 chr1 3191850 255 35M * 0 0 ATAGAAACCACTGAAAAGAGACTCAACTCTTTTTC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh\ NM:i:0 -EAS38_8_231_364_552 0 chr1 3191864 255 35M * 0 0 AAAGAGACTCAACTCTTTTTCCCCCCAGCAATATT hhhhhhhhhhhhhhhhhhhhhhhhhhfhhhRhEhh NM:i:0 -EAS38_8_116_293_619 0 chr1 3191865 255 35M * 0 0 AAGAGACTCAACTCTTTTTCCCCCCAGCAATATTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhchhhhX NM:i:0 -EAS38_8_145_345_869 0 chr1 3191865 255 35M * 0 0 AAGAGACTCAACTCTTTTTCCCCCCAGCAATATTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhchhXhhh NM:i:0 -EAS38_8_275_299_203 0 chr1 3191865 255 35M * 0 0 AAGAGACTCAACTCTTTTTCCCCCCAGCAATATTA hhhhhhhhhhhhhhhhhhhhhhhhhHBhhBhXh^\ NM:i:0 -EAS38_8_14_653_187 16 chr1 3191901 255 35M * 0 0 GTTGCTCTGGGCTGCTCTATGCATATGGCATGTTG NQKhhRTYh@hNdhhWMhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_123_560_667 16 chr1 3191909 255 35M * 0 0 GTGCTGCTCTATGCATATGGCATGTTGTTGGTACC eThh]hhfhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_158_848_347 16 chr1 3191913 255 35M * 0 0 GGCTCTATGCATATGGCATGTTGTTGGTACCTGTA @U\EWWhRbhhhhbhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_259_577_716 0 chr1 3191933 255 35M * 0 0 TTGTTGGTACCTGTACCATTCTCTTCCATTGAGAA hhhhhhhhhhhhhhhRhhhhhhhhh]hhhhhKhhh NM:i:0 -EAS38_8_37_266_444 16 chr1 3191981 255 35M * 0 0 GGTGGAGGAGCTGTTCAGCTCTCTCTAACCTATTT EfQhWOhh`hhWhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_298_155_843 16 chr1 3191988 255 35M * 0 0 GAGCTGTTCAGCTCTCTCTAACCTATTTAGATTTT Lhh`hhh[hhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_171_911_326 16 chr1 3192010 255 35M * 0 0 CTATTTAGATTTTATCTTTCACTTTGTGATAGAAT [hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_213_546_978 16 chr1 3192010 255 35M * 0 0 CTATTTAGATTTTATCTTTCACTTTGTGATAGAAT afhhhhh\hhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_165_431_451 0 chr1 3192012 255 35M * 0 0 ATTTAGATTTTATCTTTCACTTTGTGATAGAATCT hhhhhhhhhhhhhhhhhhhhhhhhhhhhh]Chhhh NM:i:0 -EAS38_8_130_352_184 16 chr1 3192020 255 35M * 0 0 TTTATCTTTCACTTTGTGATAGAATCTCTCTATAG hfdhhYhhhghJhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_303_420_658 16 chr1 3192025 255 35M * 0 0 CTTTCACTTTGTGATAGAATCTCTCTATAGAATGT hKhhhUhhhhhhhhhhhhh]hhhhhhhhhhhhhhh NM:i:0 -EAS38_8_11_860_892 16 chr1 3192043 255 35M * 0 0 ATCTCTCTATAGAATGTTCTCTCCACCACCTCCTG LLhXhchhhh^@hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_166_250_850 16 chr1 3192043 255 35M * 0 0 ACCTCTCTATAGAATGTTCTCTCCACCACCTCCTG M@X?CGhhhhhLhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_41_436_855 0 chr1 3192251 255 35M * 0 0 TACCTTTTACCCACTTACTGTTCTTACATGACCTG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhbAhhh NM:i:0 -EAS38_8_1_614_740 0 chr1 3192310 255 35M * 0 0 GCACTGTAGATATTTTTGAGGAGTCACATAATTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_1_615_739 0 chr1 3192310 255 35M * 0 0 GCACTGTAGATATTTTTGAGGAGTCACATAATTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_11_667_100 0 chr1 3192520 255 35M * 0 0 CTCCTCAAGGGAAAATTTGGAAAGTATTTCATATT hhhhhhhhhhhhhhhhhhh\hhhHhhhhhhhhhhh NM:i:0 -EAS38_8_142_397_982 16 chr1 3192642 255 35M * 0 0 CTGTTAGCACAGTTCAATGATACATTCTTATTTTA hVShThOhhhhGhhhhhhhAhFhhhhhhhhhhhhh NM:i:2 -EAS38_8_201_45_850 16 chr1 3192642 255 35M * 0 0 CTGTTAGCACAGTTCAATGGTGCATTCTTATTTTA hfMfYhhhVhh[hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_198_171_959 0 chr1 3192730 255 35M * 0 0 TAGTCATTTAGGCAAGGAAATAGACATTGTTTTGA hhhhhhhhhhhhhhhhhhhhhhhfZhhhhhhhhTR NM:i:0 -EAS38_8_300_863_946 16 chr1 3193601 255 35M * 0 0 ATTCCTTTCTTCTTTGTTGCTATCATTGAACCACA BGbhah[IhhhhhhfOhh^hhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_311_818_593 0 chr1 3193885 255 35M * 0 0 CACAGATGCACAGATTGATGATCTCTAGGAAAAAG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhZ]hh NM:i:0 -EAS38_8_126_604_962 0 chr1 3194707 255 35M * 0 0 TGGATCAAACAATTTAAACAACTTTAGCTTTACAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhKWh NM:i:1 -EAS38_8_95_901_210 0 chr1 3194707 255 35M * 0 0 TGGATCAAACAATTTAAACAACTTTAGCTTTACAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_145_407_869 16 chr1 3195051 255 35M * 0 0 TAGGTTGCAGTTGCTCTATGTGATGTATTTCTCTT ShP?MhHhhZhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_111_861_260 16 chr1 3196449 255 35M * 0 0 TTTTTTCCTGGAGTGCATAATGGATACATTTGATG \OhfhMhhShhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_167_257_42 16 chr1 3197418 255 35M * 0 0 AATTAAGGCATCAGTGTTCTGAACTGTGTGATAGC hhhAhhhhUhVhhhbhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_233_573_175 16 chr1 3197418 255 35M * 0 0 AATTAAGGCATAAGTGTTCTGAACTGTGTGATAGC hhDIhhhh[h_BhhVhhhdhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_305_871_204 16 chr1 3199438 255 35M * 0 0 AGTTGCTCACTTTCATGAGTAGCTTTGACTAATTA hXGMDTVdhhYhZhhPhhhhhhhhchhhhhhhhhh NM:i:0 -EAS38_8_231_724_560 0 chr1 3200057 255 35M * 0 0 TACAGCAATAACACATGGCAAATTCTTAATAATGA hhhhhhhhhhhhhhhhhhhhQhhhhhgJhShQeAA NM:i:0 -EAS38_8_203_543_728 0 chr1 3200118 255 35M * 0 0 CCACAAGGAAATCTATAGGCAAACAAAATAACCAA hhhhhhhhhhhhhhhhhhhhhhh^Xhhh_hh\@Ch NM:i:0 -EAS38_8_229_849_498 0 chr1 3200118 255 35M * 0 0 CCACAAGGAAATCTATAGGCAAACAAAATAACTAA hhhhhhhhhhhhhhhhhhhbhfhhY`hQcaK?hBV NM:i:1 -EAS38_8_119_995_590 0 chr1 3200431 255 35M * 0 0 CTTATTTCTGTGGGCACATGGCTGGTTGCCACTTC hhhhhhhhhhhhhhhhhhhhhhhhDVhEEJICIh@ NM:i:1 -EAS38_8_253_690_533 0 chr1 3200431 255 35M * 0 0 CTTATTTCTGTGGGCACATGGCTGCTTGCCCCTTC hhhhhhhhhhhhhhhhhhhhhhhhIhRHM@GQMR? NM:i:1 -EAS38_8_2_361_608 16 chr1 3200848 255 35M * 0 0 CAAATGTTGGGTAGCAGATTGGTGTCATAAGTCAA G^h^PNLLKh@hhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_19_443_443 16 chr1 3201005 255 35M * 0 0 GGTCCACCTTGGTCCTGCTGTGCTGTCAGCTTCTG N\MhhAVhQYhh]hhShhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_240_860_321 0 chr1 3201008 255 35M * 0 0 CCACCTTGGTCCTGCTGTGCTGTCAGCTTTTGTCT hhhhhhhhhhhhhhhhhhehhhhSGhHhP@YI`CL NM:i:1 -EAS38_8_159_889_369 16 chr1 3201153 255 35M * 0 0 TATATAGAAATAGTCGTGGCTAATGGCAAAGATAT Nh`hPhhhhhhhhNhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_6_649_343 16 chr1 3201153 255 35M * 0 0 TATATAGAAATAGTCGTGGCTAATGGCAAAGATAT hhhhhhhhhhhhhhhhhhhZhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_159_13_859 16 chr1 3201231 255 35M * 0 0 CATTAGAAAAAATTCACAGGATTCTTGTCTAAACA hhghhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_206_389_817 0 chr1 3201597 255 35M * 0 0 CATGCATTTCTAAGTTTATCTCTGTGTAGATGCAT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhZhahhh NM:i:0 -EAS38_8_8_834_910 16 chr1 3201632 255 35M * 0 0 GTAAGAGAGTCAGTCTTTCTGTCTGTCTGTTTCTG KTEPRY\hhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_193_381_989 0 chr1 3201726 255 35M * 0 0 GGCAAATCTGTAGAAATTGATATCTCTTTATGTTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_218_286_583 16 chr1 3201770 255 35M * 0 0 CAGGGATCAAATTCAGGTCAAGTTTGCATCTTTTT hh[a\h\hhhh^hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_231_842_613 16 chr1 3201775 255 35M * 0 0 ATCAAGTTCAGGTCAAGTTTGCATCTTTTTTCAGT hahhhOhbhhhKhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_69_697_617 16 chr1 3201775 255 35M * 0 0 ATCAAATTCAGGTCAAGTTTGCATCTTTTTTCAGT heghhhOhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_315_783_294 16 chr1 3205321 255 35M * 0 0 CTAAAAGTAAAAACAAATCCTGAAATATGTAGAAA ERhhhhhXhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_208_943_432 16 chr1 3206163 255 35M * 0 0 CCTTGGAGGAGATGGGGAACATTCAAAAGCTAAAA bVQHbOhahhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_17_380_277 0 chr1 3209126 255 35M * 0 0 TTGGTGTGCTTATCCGACACTGTAGGTAGAAACCA hhhhhhhhhhhhhhhh]hPh\NhhJQhEKCEOJhG NM:i:1 -EAS38_8_156_409_184 16 chr1 3211514 255 35M * 0 0 CAAGAAAGATTGATGAGACACAGTTGATAGAGGGA HKhThhhhhhOhhghhhhLhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_189_963_938 0 chr1 3211535 255 35M * 0 0 AGTTGATAGAGGGATGATAAATAATCCTTTCCTTT hhhhhhhhhhhhhhhhahhh^hhdSGTTZ`>D[XR NM:i:0 -EAS38_8_194_593_290 0 chr1 3212718 255 35M * 0 0 GCTTAAGACACTTTGCATCCCTCTTTTGTAACATT hhhhhhhhhhhhhhhhhhhhhhhhhhhWhRK^Jhb NM:i:0 -EAS38_8_54_951_1001 0 chr1 3212775 255 35M * 0 0 ACTTTCCTTTTCAGGAAAAAAAATGTATATAATAT hhhhhhhhhhhhhhhhhhh[hhhhhIHhhdbaSOJ NM:i:0 -EAS38_8_55_222_593 16 chr1 3213111 255 35M * 0 0 CTCACTGCCTCCCTCTTAGGACTCTTACACTGAAA h>hPhf`ZhYhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_192_865_198 16 chr1 3213157 255 35M * 0 0 AGTCAATGCAAGAAAGCAGATGCTTCCATCTTGCT _JHhOhFhBhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_257_284_263 16 chr1 3213208 255 35M * 0 0 AAAAAAAACAAAACAAATCTCCACTTTTTGTAAAT hXhMhhhhOhhhhIhhhfhPhQhhhhhhhhhhhhh NM:i:2 -EAS38_8_14_341_452 0 chr1 3234830 255 35M * 0 0 CCTTGATGTCTTGATGGTTGAAATAGGTTACATTT hhhhhhhhhhhhhhhhhhhh`hhh^IhhhN`Lhhh NM:i:0 -EAS38_8_171_140_943 0 chr1 3239649 255 35M * 0 0 TCCCTGTTAGATTCAAATGTTACTTTATAGTTAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh^h NM:i:0 -EAS38_8_98_123_525 16 chr1 3240599 255 35M * 0 0 ACATCCCTCCCTAAATAAACCACAATCCACCCCCA hdhLDhEMhhfhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_178_873_141 16 chr1 3242478 255 35M * 0 0 TTTTTTTTTTTTTTTAAACAAGATTTTTAGTTTTT OVhhRhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_215_180_235 16 chr1 3242478 255 35M * 0 0 TGTTTTTTTTTTTTTAAACAAGATTTTTAGTTTTT hThhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_7_814_774 16 chr1 3242478 255 35M * 0 0 TTTTTTTTTTTTTTTAAACAAGATTTTTAGTTTTT Jhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_315_926_983 16 chr1 3242791 255 35M * 0 0 ACCTCCTCCTATAGCTTCTAGAGACAACAGACCTT @<BEAZIMRhHhIdhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_163_191_986 16 chr1 3242917 255 35M * 0 0 AATCATATTTTGACCTCAATTAGCCTTGGGGTTGA hhTRhSaeh\UAThhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_173_800_35 16 chr1 3242917 255 35M * 0 0 AATAATATTTTGACCTCAATTAGCCTTGGGGTTGA hh=FhRhVhOhShGhcZhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_25_295_514 0 chr1 3242979 255 35M * 0 0 GCTCTTCTGTCAAGAGTACCTGAAATTTATCTGTG hhhhhhhhhhhhhhhhhhhhhhhehhhhhhZhhhc NM:i:0 -EAS38_8_260_745_595 0 chr1 3242979 255 35M * 0 0 GCTCTTCTGTCAAGAGTACCTGAAATTTATCTGTG hhhhhhhhhhhhhhhhhhhhhhLhhhhhhhhhhfM NM:i:0 -EAS38_8_162_854_426 16 chr1 3243101 255 35M * 0 0 GAAAAAACCTGTCTTGGTCTGAGGTCTGGGCCACT >hhhhhPhhU_XhXZhhhhehhhhhhhhhhhhhhh NM:i:0 -EAS38_8_120_168_509 16 chr1 3243120 255 35M * 0 0 TGAGGTCTGGGCCACTGTTATTCAGAGTGAACAAC AZc^hCcMhhhWhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_219_315_931 16 chr1 3243676 255 35M * 0 0 TTTGTTGAAGGAGAACACAATGAGAGGTGCATATT ]OhYhhchhahhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_180_247_88 16 chr1 3244868 255 35M * 0 0 GCATACTTAAAATTAGGCTGCAATCAGTCTTCCTT _@hhhCJhhhhhhIhhhhShhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_144_513_481 0 chr1 3252847 255 35M * 0 0 AATGGCATTCAGTTAGCTTTAGTGACTGATCCCAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhBC NM:i:0 -EAS38_8_125_631_236 0 chr1 3253217 255 35M * 0 0 TGAGGCATGACCTCCTTTCACTGAATCTTAGTCTT hhhhhhhhhhhhhhhhhhhhhhhhehhhhhLChhh NM:i:1 -EAS38_8_312_169_822 16 chr1 3253312 255 35M * 0 0 AAGGCTAAAATTGCTGTTACCAGCTGCTATGCTTG [JNDIONDhWhhhhhhIhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_10_227_417 0 chr1 3253759 255 35M * 0 0 CAAATTTTAGCTCCTTTCCCAGTTTCCCTCTGGAA hYhhhhhhhhhhhhhhhh`hG_heh\V^hXhUBH? NM:i:0 -EAS38_8_144_231_566 0 chr1 3253759 255 35M * 0 0 CAAATTTTAGCTCCTTTCCCAGTTTCCCTCTGGAA hhhhhhhhhhhhhhhhhhXhghhhhROZWKbU\MM NM:i:0 -EAS38_8_208_276_857 16 chr1 3254072 255 35M * 0 0 TCAACTTCACAAGGAATTTGGAGTGACTGGCCTCC VdMOhLchXhhhh^hhhZhhhhhhh_hhhhhhhhh NM:i:0 -EAS38_8_6_640_930 16 chr1 3254072 255 35M * 0 0 TCAACTTCACAAGGAATTTGGAGTGACTGGCCTCC IHhOhJThchhhhWhhh_hhYhhhhhhhhehhhhh NM:i:0 -EAS38_8_261_856_180 0 chr1 3254263 255 35M * 0 0 GTTCCGCAACACCTGCCCTCACATTCCACTGAACT hhhhhhhhhhhhhhhhhhhhMhThh[NCKQD?DJK NM:i:1 -EAS38_8_97_169_815 0 chr1 3254597 3 35M * 0 0 ATCAGGCTACTTTCAGCAAGCACTTCTTGTCATCT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhAh^hUh NM:i:1 -EAS38_8_250_270_899 0 chr1 3259536 255 35M * 0 0 CTAGATTAGCAGGTAATTTCTAAATCACACATTTA hhhhhhhhhhhhhhhhhhhhhhhhhahUJOhhYhb NM:i:0 -EAS38_8_267_436_563 0 chr1 3273793 255 35M * 0 0 TTTTTTTGTTTGTTTGTTTGTTTTTATACAACAGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhchhh NM:i:1 -EAS38_8_244_916_490 16 chr1 3274218 255 35M * 0 0 GAGCCTAAACCAACCAACCAATGAATATACATAGG ThCYE@AhhhOhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_111_703_424 16 chr1 3274366 255 35M * 0 0 ACAGGGCACATGTTCTTCTAGCTGAGCTGCCTTGT L[gE[hhhhhghhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_224_315_306 16 chr1 3274921 255 35M * 0 0 GGAACTGTGCAAATTGTGTAACTGGAGAAAATAAT hhhh^hh_hhhhhhhhhhhhh`hhhhhhhhhhhhh NM:i:0 -EAS38_8_256_842_769 0 chr1 3277156 255 35M * 0 0 AATGATATTGGTTTGAAGTTCTTTAGCCCCATATT hhhhhhhhhhhhhhhhhhhhhhhhhhhh\hhh]hh NM:i:0 -EAS38_8_292_619_933 0 chr1 3277156 255 35M * 0 0 AATGATATTGGTTTGAAGTTCTTTAGCCTCATATT hhhhhhhhhhhhhhhhhhhhhhhhhhbOLhMhhhh NM:i:1 -EAS38_8_212_928_881 0 chr1 3277700 0 35M * 0 0 TCCTTTTCCTTTCCTTCCTTCCTTCCATCCTTCCT hhhhhhhdZghhaehhTVhhZhhhNT?h^MX]OBQ NM:i:2 -EAS38_8_223_507_484 0 chr1 3277914 255 35M * 0 0 TTCTGAAACTTGAGTACAGTGTTATTACCAATATT hhhhhhhhhhhhhhhhhhhLhhhhhhhKhLbheha NM:i:0 -EAS38_8_264_464_724 0 chr1 3277925 255 35M * 0 0 GAGTACAGTGTTATTACCAATATTCCCCCATTTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhghhhhh NM:i:0 -EAS38_8_97_398_795 0 chr1 3277927 255 35M * 0 0 GTACAGTGTTATTACCAATATTCCCCCATTTTTCC hhhhhhhhhhhhhhhhhhhhhhhLhhhVhhhhh^h NM:i:0 -EAS38_8_271_224_790 16 chr1 3277983 255 35M * 0 0 AGTGATGTCCTAACATGCTTGCTCTCTCATAACCA FhhQ`hhhhhhhhhhhhhhhhhghhhhhhhhhhhh NM:i:0 -EAS38_8_249_919_47 16 chr1 3277988 255 35M * 0 0 TGTCCTAACATGCTTGCTCTCTCATAACCAGACTT K=DFHUhLXhaJSbfLPfhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_264_398_810 16 chr1 3278029 255 35M * 0 0 AGTTTTGTTAGGTTTGCTGGTCTTTTAAAAGGTCT ZghhHhhhhTh[hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_202_252_118 16 chr1 3278057 255 35M * 0 0 AAGGTCTAGATTTTTGTTTCATTATTTTTTTTCTG hhhTDhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_195_472_45 0 chr1 3278134 255 35M * 0 0 CTTTTATTATATTCTTCCTCTTCGTTATTTTGAAT hhhhhhhhhhhhhhhhhhhhhhhPhhh]hhhWENh NM:i:1 -EAS38_8_200_268_981 0 chr1 3278134 255 35M * 0 0 CTTTTATTATATTCTTCCTCTTCGTTAGTTTGAAT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheh NM:i:0 -EAS38_8_87_755_875 16 chr1 3278180 255 35M * 0 0 TTCTCTTAAGTATATGTTCTTATTAACTATTTTTT hhhUhhhhhThhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_184_481_627 16 chr1 3278254 255 35M * 0 0 GAGGCATTTTAGTGTTATGAACTCCCCTTGGCACT NH?=BNI[BT^YdUZ[hKJhhhPhhhhhhhhhhhh NM:i:0 -EAS38_8_241_955_483 16 chr1 3278295 255 35M * 0 0 GACACAGATAGGTTTTTATGTGCTATACTTACATT DbHYMhVhhhVhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_24_420_629 0 chr1 3278309 255 35M * 0 0 TTTATGTGCTATACTTACATTCAGTTCAATGTAAT hhhhhhhhhhhhhhhhhhhhhhhhhhhhfhhhhhh NM:i:0 -EAS38_8_307_620_12 16 chr1 3278356 255 35M * 0 0 TTAGACTTCATTTTCTTCTTCTTTTTGGTTGTGAG IOhKhhJdLhhhJhIeTVZhhhhhhhfWhhhhhhh NM:i:0 -EAS38_8_55_835_895 0 chr1 3278373 255 35M * 0 0 CTTCTTTTTGGTTGTGAGCCTAGCCTTCAACGGTT hhhhhhhhhhhhhhhhhhWWhhhMTIhPTHIhc>D NM:i:1 -EAS38_8_230_275_815 16 chr1 3278376 0 35M * 0 0 TTTTTTGTTTGTGAGCCTAGCCTTCAACGGCTGAG \_NF]RQGZhWPOXPhhhahhhhhhhMhhXhhhhh NM:i:2 -EAS38_8_24_167_957 16 chr1 3278397 255 35M * 0 0 CTTCAACGTCTGAGCCATCTCTCCAGCCCTCTTCT VFA`N?hQ@hhLhehhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_253_546_769 0 chr1 3278576 255 35M * 0 0 TTCCCACTCTCTGGGGCCTCAAGTCTCTCAAATTA hhhhhhhhhhhhhhhhhhhhKRZhhhhh`KMhRTM NM:i:2 -EAS38_8_283_280_992 0 chr1 3278576 255 35M * 0 0 TTCCCACTCTCTGGGGCCTCAAGTCTCTCAAATGT hhhhhhhhhhhhhhhhhhhYhhhFHcBQJHUNK?C NM:i:0 -EAS38_8_4_499_790 0 chr1 3278607 255 35M * 0 0 ATGTTAGGCACATCTCCCACTGATTCCAGACCAGG hhhhhhhhhhhhhhhhe[hhhhUhcVOP`I?LTXH NM:i:0 -EAS38_8_166_353_693 0 chr1 3278725 255 35M * 0 0 GGTTAGTTGAGATTGCTGGTCTTTCTATGGGTTGC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhKhhhFS NM:i:0 -EAS38_8_227_305_410 16 chr1 3278920 255 35M * 0 0 TCAGACCTCTGCTGATCACCTGCATAGTTGGAGAT KJhH@NRIA_B`hhhhhhhhThhhhhhhhhhhhhh NM:i:1 -EAS38_8_151_783_299 16 chr1 3279317 255 35M * 0 0 CTTTTTTGTTCTATAGATATCAATTATTTACCCAC BTS^WdIUehQhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_130_64_600 0 chr1 3280118 255 35M * 0 0 GGTTTCGAGAAAATGTTTTGAAGTGTTTATGCGCT hhhhhhhhhhhhhhhhhhhhhhhhhhhhchKOhSh NM:i:0 -EAS38_8_204_14_612 0 chr1 3280118 255 35M * 0 0 GGTTTCGAGAAAATGTTTTGAAGTGTTTATTCGCT hhhhhhhhhhhhhhhhhhhhfhhhhhhhhhBQhL\ NM:i:1 -EAS38_8_242_889_996 0 chr1 3280118 255 35M * 0 0 GGTTTCGAGAAAATGTTTTGAAGTGTTTATGCGCT hhhhhhhhhhhhhhhhhhhhh^hVhaahgeh@Z?N NM:i:0 -EAS38_8_82_262_363 0 chr1 3280320 255 35M * 0 0 AACATATTTTAAATTCCTCTCAGATTAAGAGAATT hhhhhhhhhhhhehhhhhhhh^hWhKhShWD@hhB NM:i:2 -EAS38_8_111_150_178 0 chr1 3282505 255 35M * 0 0 AGATACATAGAAAAGCTACTTGACTTTAGGTCAAC hhhhhhhhhhhhhhhhhhhhhUfhhhhhQOhh\Sh NM:i:0 -EAS38_8_260_477_698 0 chr1 3282505 255 35M * 0 0 AGATACATAGAAAAGCTACTTGACTTTAGGTCAAC hhhhhhhhhhhhhhhhhhhhhhhhhhhXhhhh`hM NM:i:0 -EAS38_8_187_894_354 16 chr1 3282753 255 35M * 0 0 CTGCACTTGTTTAGAGAAGTGCTGTCTACATGAAG dhNhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_219_350_890 0 chr1 3282806 255 35M * 0 0 TTTTGGAACTTAGGCAAGAATGTTCTTTGGCTCCT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhPVh NM:i:0 -EAS38_8_185_258_316 16 chr1 3282902 255 35M * 0 0 TGAGAGCTAAATGTAAAGCTCAGTAATGCCAGCTC IJhhhhh^hhhhMhhhhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_5_912_317 16 chr1 3284777 255 35M * 0 0 CTCTCGCTCTCTCTCTCTCTCCCCTCACTCCTTTC BPWFbChNSRhFhShehOh_hhhhhhhhhhhhhhh NM:i:1 -EAS38_8_119_362_614 0 chr1 3284967 255 35M * 0 0 TGTACCCTGAGATCAAGTACTTATTGCTTTCACTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_276_838_443 0 chr1 3284967 255 35M * 0 0 TGTACCCTGAGATCAAGTACTTATTGCTTTCACTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhahhhh NM:i:0 -EAS38_8_74_720_526 0 chr1 3286259 255 35M * 0 0 CAAATTGTAGAAAATTTGCATGTGTACTGAACACA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhL NM:i:0 -EAS38_8_273_582_300 16 chr1 3289456 255 35M * 0 0 TCTTCAGTTCTTTGTTAAATATATCATCTGGGTCT HhYchhhQhRhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_232_852_815 0 chr1 3290417 255 35M * 0 0 TTTTTTTTTTTAACTTTCATATGTAGTAGTTATTT hhhhhhhhhhhhh^hhhKhhhhhhhGV^hh[MHhh NM:i:2 -EAS38_8_121_748_181 0 chr1 3290799 255 35M * 0 0 ACCACACCCTGCTGCTCCATATTTCTTATCTTTTT hhhhhhhhhhhhhhhhhhhhhhhhhhh\Bhhhhhh NM:i:1 -EAS38_8_36_138_632 0 chr1 3290826 255 35M * 0 0 AGCTTTTTTTTTTTAACAGCTACTGGGTGGTTTGC hhhhhhhhhhhhhhhhhhhhhOhhbhCXHZLI\BF NM:i:1 -EAS38_8_141_369_534 0 chr1 3290833 255 35M * 0 0 TTTTTTTAACAGCTACTGGGTGGTCTGCATAGCTT hhhhhhhhhhhhhhhhhhhhhhhhhhhfPRLdhhS NM:i:0 -EAS38_8_84_402_647 0 chr1 3290833 255 35M * 0 0 TTTTTTTAACAGCTACTGGGTGGTCTGCCTAGCTT hhhhhhhhhhhhhhhhhhhhhhhhhhVhBhThahe NM:i:1 -EAS38_8_169_576_313 16 chr1 3290912 255 35M * 0 0 ATGCTTCTTTCCACAGTTGAGTGGAATTGTAGGGG hPhRWPJhVLhhhhhh[hhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_279_571_717 16 chr1 3290912 255 35M * 0 0 ATGCTTCTTTCCACAGTTGAGTGGAATTGTAGGGG he\hhYhaOYhhThhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_234_793_825 16 chr1 3290951 255 35M * 0 0 AAAAGACATTTCTGAGTTCTAGCACTCTCAGGTCT hhhhRhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_217_210_636 16 chr1 3290952 255 35M * 0 0 AANGACATTTCTGAGTTCTAGCACTCTCAGGTCTG hh;PYhhWXhh^hhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_168_998_377 0 chr1 3290961 255 35M * 0 0 TCTGAGTTCTAGCACTCTCAGGTCTGGCTTTGACA hhhhhhWhhhhhhhhhhhhTe\YThhOIWJaC@A? NM:i:0 -EAS38_8_179_44_982 16 chr1 3290986 255 35M * 0 0 GCCTTTGACATTAGCTTCCTGACAGGCTGGCAGGT ?@[_GhH[hhhhhEhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_210_147_536 0 chr1 3291026 255 35M * 0 0 TCCTGAAGGTCAGGACTGTGCAAAACTGTCAGGCA hhhhhhhhhhhhhhhhhhhhhhQg`hh^hbGYYPH NM:i:0 -EAS38_8_228_906_499 0 chr1 3291047 255 35M * 0 0 AAAACTGTCAGGCAGCTATTTCAGGAGTGCCTTTT hhhhhhhhhhhhhThhh_hhhhUThYZPVED[@C@ NM:i:2 -EAS38_8_223_934_468 16 chr1 3291092 255 35M * 0 0 GCCCTGGATGATTTTTGAATGGGAATAATCCCTAT RXhf\Phh`hhhhhVhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_27_794_86 16 chr1 3291130 255 35M * 0 0 TCCATATAGGCTCATATATTTAAACACCTAGTCAT X@FSSZhhhADhShhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_205_713_101 16 chr1 3291163 255 35M * 0 0 ATTGTTGGTGGCACTGTCTGTAAGGATCACGAACC CEJLUB`WcgZ]hLhheHahhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_269_175_878 16 chr1 3291192 255 35M * 0 0 CAAACCCATTAGAAGGTAACAACATGCTAAAAAAA eChhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_127_466_820 0 chr1 3291247 255 35M * 0 0 GTGAGGGCTTGTGTTCTCTCTGCTTCCTCTGTGTG hhhhhhhhhhhhhhhhhhhhhhhhhV_hTeSWhhh NM:i:0 -EAS38_8_29_659_107 0 chr1 3291649 255 35M * 0 0 TCCTGAGTTGGGAGGACAGATGAGAAGGGCTTTTT hhhhhhhhhhhhhhhXhhhShhh`PFVhALNChJd NM:i:2 -EAS38_8_210_520_140 16 chr1 3299511 255 35M * 0 0 GAAATAAAGAAAATTCTAATCTACAGGCTGACCAT VhhLDhhhhhhhhVLHShhPhfhhhhhhhhhhhhh NM:i:2 -EAS38_8_45_100_198 0 chr1 3299523 255 35M * 0 0 ATTCTAATCTACAGGCTGACCATACTGTATTTCAC hhhhhhhhhhhhhhhhhhhhhhhZhhIh^hhhhHh NM:i:0 -EAS38_8_145_894_137 0 chr1 3299538 255 35M * 0 0 CTGACCATACTGTATTTCACTAATATAATGGTGTC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhRChhhU NM:i:0 -EAS38_8_231_634_172 16 chr1 3299568 255 35M * 0 0 GTGACAGTGATGCCAGAGAGCTCTAGCTGTGGCTG MHS?]hVChhPhHVhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_68_279_670 16 chr1 3299606 255 35M * 0 0 TGAATACTGGGTAGAAAATAAAAAAATTTACGGAC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_157_544_34 16 chr1 3299684 255 35M * 0 0 TCATAAGATCGGGTAGTTAGTAAACCCTGCCTAGA ?MhFhhHMRZGSdhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_317_518_457 0 chr1 3299798 255 35M * 0 0 GATTTCTGTCTACTAGATCAAAACCTGATAACATA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhMhh NM:i:0 -EAS38_8_87_383_194 16 chr1 3300173 255 35M * 0 0 AAACTACAAAATTGTGGATGTTTGGCTGTTCTTTT hhhSZhhhhhhKhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_220_990_452 16 chr1 3300259 255 35M * 0 0 TGCACCATCTTAGGAGTGAGGGAGGCAGCTGAGTG NHPUJ]hhSPa`ChhhYhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_168_713_356 0 chr1 3307749 255 35M * 0 0 GGTTAACCCGAAGCCAAACTTTTCTTTGTAATTTC hhhhhhhhhhhhhhhhhRhhhhhhhHhRhhIhhhJ NM:i:1 -EAS38_8_222_724_349 0 chr1 3307749 255 35M * 0 0 GGTTAACCCGAAGCCAAACTTTTCTGTGTAATTTC hhhhhhhhhhahhhh`eGhhhhhhhJhPhNKhhhQ NM:i:0 -EAS38_8_223_971_288 16 chr1 3310176 255 35M * 0 0 AATAATCATCACCTGAATGTCATGATCTAAAGGCT hhChhAhh\Ghhh[hhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_288_770_517 0 chr1 3310786 255 35M * 0 0 AGGTTTTGAGTTTTTGATCCAGAGGCTATGTTTAT hhhhhhhhhhhhhhhhgh\h]hQgQH\FS`HRJEW NM:i:0 -EAS38_8_310_958_947 16 chr1 3311201 255 35M * 0 0 CAATTTTTGATCATTCATCTTGTTTTCTTAACAAT hP\hJhh_Hhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_140_291_179 16 chr1 3313701 255 35M * 0 0 ACCGCTGCCTTCCTTTCTTCTCTCCTTCCTTTCTT PW`@dP@hYhKhhhhchh]hZhahhhhhhhhhhhh NM:i:2 -EAS38_8_113_205_724 16 chr1 3318613 255 35M * 0 0 ACCTGGAAGAATTTCATAAAAATTCCCTTCCCAGC HhedLQhhbhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_236_727_634 16 chr1 3318613 255 35M * 0 0 ACCTGGAAGAATTTCATAAAAATTCCCTTCCCAGC Sd]QXehhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_21_827_590 0 chr1 3319045 255 35M * 0 0 TACAAACCAAGAGAAAAATCTGAAAATGAAAAATT hhhhhhhhhhhhhhhhhhhhhh_hhhhhhghhhhh NM:i:0 -EAS38_8_204_62_686 0 chr1 3321977 255 35M * 0 0 AAGCTGGCAATGTTTGGGATATAAACAAGCAAACA hhhhhhhhhhhhhhhhhhhhhhhhhhhahhhh[Yh NM:i:0 -EAS38_8_86_854_652 16 chr1 3324385 255 35M * 0 0 GCAGTGGCTGAGTGATATAACACAGGGATGCAGGT hhhhhhh[hhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_192_343_954 0 chr1 3329232 255 35M * 0 0 CTGCCCTTTTTCTCCCTGCCTATTCATTATAGTTC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhU NM:i:0 -EAS38_8_6_774_928 0 chr1 3330010 255 35M * 0 0 GCACTGTAGCCAGGAGTGACACACAGCAAGGATGC hhhhhhhhhhhhhhhhhhhhhhhN`hUhhhhT`h? NM:i:0 -EAS38_8_256_461_804 16 chr1 3330063 1 23M11637N12M * 0 0 TTTGTTTGTTTGTTTGTTTGTTTGTTTTGACAGGG dhh@ZhhRhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:2 XS:A:+ NS:i:2 -EAS38_8_288_334_735 0 chr1 3330212 0 35M * 0 0 TTATAGCTATAAAAAGTAACATTCTTTGATTGGTC hhQhhhhhKhhQ`hhNKaXAXUaGQQVLOWKRFC> NM:i:1 -EAS38_8_11_615_231 0 chr1 3330440 255 35M * 0 0 ATTGGTTACAAAAAAGTTAGCTTTAACTTTGTAAC hhhhhhhhhhhhhhhhhhhhhhhhIhhhhTLhehR NM:i:1 -EAS38_8_284_883_215 0 chr1 3330528 255 35M * 0 0 ACTAGGCCTCTAGAGTACTTCTAAATTGAGATATT hhhhhhhhhhhhhhhhhhhhhhYhhhhIWEKh`hh NM:i:0 -EAS38_8_30_530_423 16 chr1 3330584 255 35M * 0 0 AGTAGACTTATAGAGATAAGCATTAAAATTTGTAC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_202_722_286 16 chr1 3330653 255 35M * 0 0 ACTTTGTAACGTTAAAGTGATGTTTCTGGTATTGA NB[KZhhcYhhhdhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_214_253_466 16 chr1 3330653 255 35M * 0 0 ACTTGGTAACGTTAAAGTGATGTTTCTGGTATTGA hSN[DRShhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_4_564_326 16 chr1 3330653 255 35M * 0 0 ACTTTGTAACGTTAAAGTGATGTTTCTGGTATTGA ZXSVTYQhehh\hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_142_357_440 16 chr1 3330660 255 35M * 0 0 AACGTTAAAGTGATGTTTCTGGTATTGATCTTTAA hhhhhdhhhhhhhhhhh_hhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_317_782_44 16 chr1 3330660 255 35M * 0 0 AACGTTAAAGTGATGTTTCTGGTATTGATCTTTAA hhFHbhhhhhhbhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_137_536_758 16 chr1 3330697 255 35M * 0 0 TAATAAATTGTTTAAAATTGGGTTTTGCTAACCAA `hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_129_924_268 16 chr1 3330838 255 35M * 0 0 CAATTCACCTATATATTGTAATTAGGATAATTACA BhhhDhhCZhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_48_834_938 0 chr1 3331062 255 35M * 0 0 GTTGTTCTAAATAAAGATTAAATTCAGAATTTATA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_154_283_922 0 chr1 3331674 255 35M * 0 0 TTAACTAGTAAAGAACAAAAGGCTTTGCAGAAAGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh_hhX NM:i:0 -EAS38_8_215_43_278 0 chr1 3331674 255 35M * 0 0 TTAACTAGTAAAGAACAAAAGGCTTTGCAGAAATA hhhhhhhhhhhhhhhhhhh\hhhhhhKhhVONhB@ NM:i:1 -EAS38_8_227_874_535 16 chr1 3341199 255 35M * 0 0 AGACCAAGATGATGGGAACATCTTCTCCACCCCAT =>?NBTPFLEDVHOaEhhhh\hghhYhhhhhhhhh NM:i:2 -EAS38_8_255_514_861 0 chr1 3341232 255 35M * 0 0 ATCAGAATTCCCAAGTCCCTGGGTCTTCAAGTCTC hhhhhhhhhhhhhhhhhhhhhhhhhhhhY^h_RhH NM:i:0 -EAS38_8_135_67_741 16 chr1 3341341 255 35M * 0 0 AACTCAGCTGTTGTATGCTGCCTGGTTGGTGACTC @FHPQGOXhYO[Whhhhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_230_743_701 16 chr1 3341490 255 35M * 0 0 GCTTCTGTCCATTTGTTGGGTATGAGTATCTGCAT NhLahhUKhhhhhcWhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_212_374_788 0 chr1 3341507 255 35M * 0 0 GGGTATGAGTATCTGCATCTTACTCTTTCAGCTGC hhhhhhhhhhhhhhhhghhhhhhhhhhhh\hHhh[ NM:i:0 -EAS38_8_250_863_818 0 chr1 3341507 255 35M * 0 0 GGGTATGAGTATCTGCATCTTACTCTTTCAGGTGC hhhhhhhhhhhhfhh[Ph]hh]\^N`XhLQE>LGD NM:i:1 -EAS38_8_48_225_977 0 chr1 3341551 255 35M * 0 0 TTCTCAGAAGGTAGTTATGCTAGGCTCCTGTCTGC hhhhhhhhhhhhhhhhhhhhhhhhOhSYh\MF]hI NM:i:0 -EAS38_8_83_343_929 16 chr1 3341762 255 35M * 0 0 TCCCCTATTTCTCTACTGAAGGAGGACTCTACCAC TRhhhhhhhbhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_96_862_886 16 chr1 3341818 255 35M * 0 0 CCCCATGATTGTTTTCTTCTCCCTCCCATGTTGAA hhhh^hJhhhhhhhhhbhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_134_781_817 0 chr1 3342105 255 35M * 0 0 ACTCTTTAATAGAGTCTCCTGAAGAGGTAAAAATT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_155_230_356 16 chr1 3342124 255 35M * 0 0 TGAAGAGGTAAAAATTTTAATTTTGACAGTCCAAT ]hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_179_463_472 16 chr1 3347662 255 35M * 0 0 TACCCTTGCGTCAAGGTGTGTTTTCTTACTCAAAT OG?[DIQhbAhdhLhhhhRhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_4_219_976 16 chr1 3347662 255 35M * 0 0 TATCCTTGCCTCAAGGTGTGTTTTCTTACTCAAAT hhhhhhhchhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_79_243_815 16 chr1 3349048 0 35M * 0 0 AAAAAGAGAAACCCTGTCTCAGAAAGAAAAAAAAA ]WhAhHh_hhhhhhehhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_8_133_197_589 0 chr1 3349165 255 35M * 0 0 CACCAGTTCTCCTGTGCATCCTCAGGAGAAATCAT hhhhhhhhhhhhhhhhhhhhhhhhhhUhKSPhUJh NM:i:0 -EAS38_8_188_649_421 0 chr1 3351241 255 35M * 0 0 GTAGATGGACAAACATCTCCCTCACGCATTCTCAG hhhhhhhhhhhhhhhhhhhhhhhhhhhhahhhbP> NM:i:0 -EAS38_8_268_213_808 0 chr1 3355908 255 35M * 0 0 ATCTAACTAAGTAAACTATGTTATAGGAAAGAAAT hhhhhhhhhhhhhhhhhhhh^hhhhhhhhhhZhhZ NM:i:0 -EAS38_8_11_161_707 0 chr1 3355956 255 35M * 0 0 TTTGTCACATGATCAGCATAGTAGATGATGTGTCT hhhhhhhhhhhhhhhhhhhhhhhhhhhPhhhhhHh NM:i:0 -EAS38_8_291_670_580 16 chr1 3356011 255 35M * 0 0 GAAGCAGTTAAAATTGTGTGTGTGTGGTTCTGGAT hV_OXh[VIhXNhP^hhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_44_851_834 16 chr1 3356011 255 35M * 0 0 GAAGCAGTTAAAATTGTGTGTGTGTGTTTCTGGAT ECD@MDGhJXDSAChdhPh]hUhbhhEhhhhhHhh NM:i:1 -EAS38_8_105_754_762 0 chr1 3356093 255 35M * 0 0 TATAGATGTAGTTTATCTCCTAATCCCACCCTTCC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_219_312_881 16 chr1 3356191 255 35M * 0 0 TTTAATTACTTTCCCATCAAAGGCCCATTGAGCAG XZNhNLhHhhZhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_299_450_385 0 chr1 3356483 255 35M * 0 0 ATTCTGGTGGGCTTTCGAGTGTTTCAGTTTCATCT hhhhhhhhhhhhhhhhhVhhhhhhhhhhhhhhhAh NM:i:1 -EAS38_8_52_623_649 0 chr1 3356578 255 35M * 0 0 GGAGCATATGTGAGTAAGCAAATGATGTTCTTGGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhh]hEUNE NM:i:1 -EAS38_8_117_306_426 16 chr1 3359531 255 35M * 0 0 TCAGAGTGTCCACCTCATTCCTCTGGGTCAGTCTT @EN_DgWhhhh_hhhhhhdhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_120_120_744 16 chr1 3361583 255 35M * 0 0 CAAAGACAAGTAGGATAATGCTGAAAGCCCAAGCA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_307_422_12 0 chr1 3362018 255 35M * 0 0 CTGAAAAATTACAGTGTTCTTGTACTGGACACTAC hhhhhhhhhhhhhhhdhSahhKDYGhECFJF@TI? NM:i:2 -EAS38_8_101_691_200 0 chr1 3363077 255 35M * 0 0 CTTTTTTCCATTTTAATGTTTGCATGCAAATCTTA hhhhhhhhhhhhhhhhhXhNhh`hhhhhMhhChhI NM:i:2 -EAS38_8_205_648_802 0 chr1 3363077 255 35M * 0 0 CTTTTTTCCATTTTAATGTGTGCATGCAAATGTTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhZ NM:i:0 -EAS38_8_265_441_688 0 chr1 3363150 255 35M * 0 0 CAGGAATCAATCTCAACCACTTTTCATCTTACTCA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhOhhch NM:i:0 -EAS38_8_53_996_162 0 chr1 3363150 255 35M * 0 0 CAGGAATCAATCTCAACCACTTTTCATCTTACTCA hhhhUhh_hYhUhc^LEHALV^]]MIVE_MMB[MO NM:i:0 -EAS38_8_28_805_359 0 chr1 3363388 255 35M * 0 0 CCAACACCTTATTATCACTTATTTTTGTCATTCTA hhhhhhhhhhhhhhhhhhhhhhhhhhIhhhh@hhZ NM:i:1 -EAS38_8_229_300_432 16 chr1 3363412 255 35M * 0 0 TTGTGATGCTATATATGTGTGCATTAACCACTGCC RObh>QWGShUahhhhBUhNhPhhhhhhhhhhhhh NM:i:2 -EAS38_8_247_121_676 16 chr1 3363412 255 35M * 0 0 TTGTCATGCTATATATTTGTGCATTAACCACTGCC QQMhgLRNfhh[hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_180_822_42 16 chr1 3363658 255 35M * 0 0 GAGTAACTGCTGCATGTTAATCTATGTCATCCCTA MXE@dhhIP__Xhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_83_317_544 0 chr1 3364348 255 35M * 0 0 GCATTTCTGAGCCTGGGTGATCTTACTTTATATTC hhhhhhhhhhhhhhhhhhhhhhhhchhhhhhhhhb NM:i:0 -EAS38_8_194_299_688 16 chr1 3364585 255 35M * 0 0 AAGGATGTTATAATTGAATCATATGGAAGTTCTTT ^hh_h_hhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_42_578_279 0 chr1 3364694 255 35M * 0 0 AAGATGTATTTTTATTTGTTTACTGTATAATTTCC hhhhhhhhhhhhhhhhhhhhhhhhChhhh_hhCP\ NM:i:2 -EAS38_8_309_762_904 16 chr1 3364864 255 35M * 0 0 AAAAGGACATCTGAATTACCTACTTGTTTTTATCA hhhhhFhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_236_498_116 16 chr1 3364885 255 35M * 0 0 ACTTGTTTTTATCAGGTTGGTCTGTAAGCATATCT LI_hhQhhMahh\hhbhFhhh\hhhhhhhhhhhhh NM:i:0 -EAS38_8_184_968_83 0 chr1 3365051 255 35M * 0 0 TAATTGCCAGGAGTTCATTGTTTTCCATATTGTCT hhhhhhhhhhhhhhhhfhhhhhhhh]EhVhhHhUh NM:i:0 -EAS38_8_194_34_599 16 chr1 3367203 255 35M * 0 0 ATTGTGGATATAAGTGGAGAAAGAGCAAGAAAAAA hhHhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_73_896_111 16 chr1 3367203 255 35M * 0 0 ATTGTGGATATAAGTGGAGAAAGAGCAAGAAAAAA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_115_579_578 16 chr1 3369573 255 35M * 0 0 TCAGAGCATTTGGATTTTGGTCTTTAGATTAAGGT ^hhhhhhhhXhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_260_546_322 16 chr1 3369573 255 35M * 0 0 TCAGAGCATTGGGATTTTGGTCTTTAGATTAAGGT >>NELH=IJ@@@QIMBDDKOS\KJfhhh[Phhhhh NM:i:1 -EAS38_8_168_10_541 16 chr1 3375680 255 35M * 0 0 CCGTGCAGACATTCTGATGTTGGGTAATATCAAAT LT>IKNhhhWhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_8_316_251_752 0 chr1 3377312 255 35M * 0 0 TCACAATATTGTCTATACTTCTAAACATCCTCAGA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhchhh NM:i:0 -EAS38_8_127_130_231 0 chr1 3379889 255 35M * 0 0 AATAAATTTCTCTTGTTTGCAAGCTATCTACTCTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhbhhhhe NM:i:1 -EAS38_8_262_614_438 0 chr1 3379889 255 35M * 0 0 AATAAATTTCTCTTGTTTGCAAGCTATCTACTCTA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhA NM:i:1 -EAS38_8_152_675_620 0 chr1 3379983 255 35M * 0 0 ATCACACTTCAATTTTCATTTTCCAGCAAAAGCTT hhhhhhhhhhhhhhhhhhhhhhhhhhhghZhhhhh NM:i:2 -EAS38_8_315_641_621 16 chr1 3380977 255 35M * 0 0 CATTTATTCTATGTCAATTTATCTTTTGAGTATAA hhhhhhahhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_223_839_518 16 chr1 3381656 255 35M * 0 0 GTCCTTTTTCTAGTGTCGTGTTTAAGCTCCCGTGA PVLMUG`YLSVhaNhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_189_893_589 16 chr1 3382043 255 35M * 0 0 GCAGAGCCTCTGTGTCATTGCCTGGCAGGTAGGAG =L`KeShhhhdhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_8_228_882_739 0 chr1 3383793 255 35M * 0 0 TGGTGAGTATTGGAACGACTAAATCAGTGTATTAA hhhhhhhhhhhhhhh]hhfhhhh]^]hehbghNHO NM:i:0 -EAS38_8_290_281_824 16 chr1 3386732 255 35M * 0 0 GTAGAAAACTGGATTTTTTTTTTTTGGTGATATAG `GUEhEhhhd\hhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffdiff_in2.sam --- a/test-data/cuffdiff_in2.sam +++ /dev/null @@ -1,400 +0,0 @@ -EAS38_1_126_860_867 16 chr1 3009675 0 35M * 0 0 ATAGTCCCTTACTGCTTTTAGTATTCTATCTTTAT WFGAeC\gVShhhLh`hhPbPhhhhhhhhhhhhhh NM:i:2 -EAS38_1_125_842_97 0 chr1 3023056 0 35M * 0 0 ATCTTCTTCAATTTGTTTCTTCAGAGACTTTAATT hhhhhhhhhhhhhhhhhhhhhhhJhhNhhh_KINh NM:i:2 -EAS38_1_261_52_728 16 chr1 3035247 0 35M * 0 0 AATCCCCCACCCCACAGGAACAAAGTCCTGATGCA @???GIH@C?HXINLQJ=VVhhgTFHfhYhhJLhb NM:i:2 -EAS38_1_71_500_217 16 chr1 3081731 0 35M * 0 0 AGGAGATAAATAACTAATAAAAAATGAAAAAAAAA h?DhLhFhfhKhRFhhhShhhhhhThhhhhhhhhh NM:i:2 -EAS38_1_2_666_566 0 chr1 3111450 255 35M * 0 0 CCACTCACAAGACAAGACCAGGATCCTGGAGAGAT hhhhhhhhhhhhhhNh^Yh]d]GRNVYURK^JU>I NM:i:0 -EAS38_1_220_990_991 0 chr1 3111546 255 35M * 0 0 AAAAGCTGAGAGTCAGCATGAATCAAGAGATAGAA hhchhMabNhP_>BKXQSNKDRD?@@TBJJ=GL@G NM:i:1 -EAS38_1_133_518_728 0 chr1 3111550 255 35M * 0 0 GCTGAGAGTCAGCATGAATCCAGAGATAGAAAAAG hhhhhhhhhhhhhhhhhhhOhQhhhNL^ZT[PLNN NM:i:0 -EAS38_1_219_471_934 0 chr1 3117684 255 35M * 0 0 TGTCCTTTGGCTTACAGAAGTTTTATAATTTTATG hhhhhhhhhhhhhhhhhhhhhhhhRhhehhhh]hH NM:i:0 -EAS38_1_180_265_430 16 chr1 3131249 0 35M * 0 0 TGATCAGCCCTTTGGCATTCCTCAGTTGAGAATTC GICHVhhCY`\TYhhhh[fdhhhhhhhhhhhhhhh NM:i:2 -EAS38_1_155_516_677 0 chr1 3137065 0 35M * 0 0 CTGGAATTATGTGATTATAATTTTCTTATCATTTT hhhhhhhhhhhhhhhhhhhhhhhhhhh`Dhhhhhh NM:i:1 -EAS38_1_156_788_924 0 chr1 3137065 0 35M * 0 0 CTGGAATTATGTGATTATAATTTTCTTAGCATTTT hhhhhhhhhhhhhhhhhhhhhhhhbhhhh]Shhhh NM:i:0 -EAS38_1_219_907_956 0 chr1 3137065 0 35M * 0 0 CTGGAATTATGTGATTATAATTTTCTTAGCATTTT hhhhhhhhhhh\hhhhhhhhRhhh^hhg`h\hhhh NM:i:0 -EAS38_1_224_924_816 0 chr1 3137074 0 35M * 0 0 TGTGATTATAATTTTNTTAGCATTTTCTTCGTAAA hhhhhhhhhhhhhhh;hhhhh`hhhhhhhXhhhg] NM:i:2 -EAS38_1_128_932_926 16 chr1 3137133 0 35M * 0 0 GTTGGTGTATAGTAAAAAGTAAAGAAATTCTGAGA XYV[Lhfhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_146_271_903 16 chr1 3137133 0 35M * 0 0 TTTGGTGTATAGTAAAAAGTAAAGAAATTCTGAGA HVhT[`hhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_127_823_362 0 chr1 3137183 0 35M * 0 0 GATAATACATATATACATATGCAGTGTGTGTGCCA hhhhhhhhhhhhhhhhhhhhhhhXhhhhhhhNU[H NM:i:0 -EAS38_1_282_34_255 16 chr1 3137183 0 35M * 0 0 GATAATACATATATAAATATGCAGTGTGTGTGCCA KhNhhLhQh\h`hJhCh`h^hLhhdhhhhhhhheh NM:i:1 -EAS38_1_215_971_567 0 chr1 3137204 0 35M * 0 0 CAGTGTGTGTGCCAGTGGTGTTAACAATACTAATA hhhhh[hhhhhhhhh\hSQeLYcVFKGAKH]XD^H NM:i:1 -EAS38_1_143_6_639 16 chr1 3137450 0 35M * 0 0 ATGTTCCCACACGGTCTATCTCCCTGACAAATCCC RH?>EJUcHhhILIhFhhYShb`hhhhhhhhchhh NM:i:2 -EAS38_1_132_603_749 0 chr1 3154107 255 35M * 0 0 TATATTTGGAAAAAAAAAGAAAGGAGTGTAGAGTC hhhhhhhhhhhhhhhhhhhhhhhhhhehhhhPhSS NM:i:0 -EAS38_1_238_595_598 0 chr1 3178632 0 35M * 0 0 GCTTTTTGCTTTTTGCTTTTTGCTTTTTGCTTTTT hhhhhhhhhhhhhhdhhhhhhOhhhhhhLXhhhhh NM:i:0 -EAS38_1_238_595_598 0 chr1 3178639 0 35M * 0 0 GCTTTTTGCTTTTTGCTTTTTGCTTTTTGCTTTTT hhhhhhhhhhhhhhdhhhhhhOhhhhhhLXhhhhh NM:i:0 -EAS38_1_238_595_598 0 chr1 3178646 0 35M * 0 0 GCTTTTTGCTTTTTGCTTTTTGCTTTTTGCTTTTT hhhhhhhhhhhhhhdhhhhhhOhhhhhhLXhhhhh NM:i:0 -EAS38_1_238_595_598 0 chr1 3178653 0 35M * 0 0 GCTTTTTGCTTTTTGCTTTTTGCTTTTTGCTTTTT hhhhhhhhhhhhhhdhhhhhhOhhhhhhLXhhhhh NM:i:0 -EAS38_1_118_1000_212 0 chr1 3179061 0 35M * 0 0 ATGTGATTTTAAATCATAGTCTTGCTTTTCCATTG hhhhhhhhhhhhghhhEMDPKhhLNh[hhMPNETJ NM:i:2 -EAS38_1_311_90_296 16 chr1 3179539 255 35M * 0 0 ACATAGGAAATGGAAGAGTACTTTATTATTATTAT bEhIhhhhTCNhhhhhhhVhRQhhhhhhhhhhhhh NM:i:1 -EAS38_1_221_489_194 16 chr1 3183282 3 35M * 0 0 ACTGACAGAAAAGAGACAGAGGTAGGACTTCTAGG >>FL[@RL@^WSRYUP@`UZeSLhhRQbOGWThhh NM:i:2 -EAS38_1_221_489_194 16 chr1 3183945 3 35M * 0 0 ACTGACAGAAAAGAGACAGAGGTAGGACTTCTAGG >>FL[@RL@^WSRYUP@`UZeSLhhRQbOGWThhh NM:i:2 -EAS38_1_205_642_159 16 chr1 3186543 255 35M * 0 0 CACATGCCTTTTTCATTTTTTCCAAGTGCCATCTG KhUhSHT]VS]_hFhhMhDbheHhhhhhhhhhhhh NM:i:0 -EAS38_1_26_282_635 16 chr1 3188051 255 35M * 0 0 TTCTGATCCTCAGGATCTGGAGTTACAGATGGTTG ECaSghKhh]ZhhhhdhVhhhh]hhhhhhhhhhhh NM:i:0 -EAS38_1_221_487_440 16 chr1 3188179 255 35M * 0 0 TTACTAAATTTTGTAATACTACTTAGTCTGGAAAA Oge[WhhhTKRShhhhbhhYhhchhh]hhhhhhhh NM:i:0 -EAS38_1_7_602_714 16 chr1 3188938 255 35M * 0 0 GACTGTCATTACATTATTTTAGTAGTTGTATTTTC A\h^SLhhChQhhhhhhhhUhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_239_803_441 16 chr1 3189316 255 35M * 0 0 AGATGTATCATAGCTCAGAAAGTACATTTGTAAGA hhhVhWhRJhYhh^Wbhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_318_649_84 16 chr1 3189316 255 35M * 0 0 AGATGTATCATAGCTCAGAAAGTACATTTGTAAGA hhh\hhhhKhhhhKMhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_178_556_269 0 chr1 3189808 255 35M * 0 0 CTTTTTTTAAAATGACCACAGTGTACTTTATTTAA hhhhhhhhhhhhhhhhhhhhLhhhXhhhhZhhhhX NM:i:2 -EAS38_1_184_810_767 16 chr1 3189830 255 35M * 0 0 GTACTTTATTTAATGATTTTTGTACTTTGTGTTGC dhah]hhhhhhhhhchh_hhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_307_56_994 16 chr1 3189841 255 35M * 0 0 AATGATTTTTGTACTTTGTGTTGCAATAAAATAAA hh[Shhhhhh`hhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_1_924_497 16 chr1 3189853 255 35M * 0 0 ACTTTGTGTTGAAATAAAATAAAAAAAAAATCTAC SNT[Za]ahh]Lhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_95_808_182 0 chr1 3189880 255 35M * 0 0 AAATCTACAAAATTCAAATATATAAAATTTCAAGT hhhhhhhhhhhhhhhehhhhhhhhhMhhhhh\h^h NM:i:0 -EAS38_1_43_924_188 0 chr1 3189887 255 35M * 0 0 CAAAATTCAAATATATAAAATTTCAAGTTTTCTTT hhhhhhhhh^Xhhhh?hh[RhhhhOMDhhhhhhhh NM:i:0 -EAS38_1_11_826_352 16 chr1 3189890 255 35M * 0 0 AATTCAAATATATAAAATTTCACGTTTTCTTTGTT hhIQAhhhShchchhhhUNU[hChhehhhhbhAhh NM:i:2 -EAS38_1_131_730_378 16 chr1 3189892 255 35M * 0 0 TTCAAATATATAAAATTTCAAGTTTTCTTTCTTTT HIhhhhhhhhhhhhhhhZhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_317_700_555 16 chr1 3189893 255 35M * 0 0 ACAAATATATAAAAGTTCAAGTTTTCTTTCTTTTA ?hhhhhh[hThhhhHhYhEhhhhhhhhhhhhhhhh NM:i:2 -EAS38_1_46_519_952 0 chr1 3189903 255 35M * 0 0 AAAATTTCAAGTTTTNTTTCTTTTAAAGTTTTACA hhhhhhhhhhhhhhh;hhhhhhhhhhhhhhhhhPf NM:i:1 -EAS38_1_26_849_836 0 chr1 3189906 255 35M * 0 0 ATTTCAAGTTTTCTTTCTTTTAAAGTTTTACAAGA hhhhhhhhhhhhhhhhhhhhhdhhhhhhhhhhNXU NM:i:0 -EAS38_1_271_964_726 0 chr1 3189906 255 35M * 0 0 ATTTCAAGTTTTCTTACTTTTAAAGTTTTACAAGA hhhhhhhhhhhhhhhCXhhhhhhhHhhhhhhVhhh NM:i:1 -EAS38_1_305_225_753 16 chr1 3189909 255 35M * 0 0 TCAAGTTTTCTTTCTTTTAAAGTTTTACAAGAAAA Zhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_210_231_735 16 chr1 3189912 255 35M * 0 0 AGTTTTCTTTCTTTTAAAGTTTTACAAGAAAAAAA hhVhhhhhh_hhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_210_55_110 0 chr1 3189915 255 35M * 0 0 TTTCTTTCTTTTAAATTTTTACAATAAAAAAAATC hhhhhhhhhhhhUPh\hhhhdhLRcCLTRW@FMhh NM:i:2 -EAS38_1_230_130_609 16 chr1 3189915 255 35M * 0 0 TTTCTTTCTTTTAAAGTTTTACAAGAAAAAAAATC TDMO]K^FLYWWhhhh[S^Rhhhh^hhhhhhhhhh NM:i:0 -EAS38_1_203_262_383 16 chr1 3189917 255 35M * 0 0 TCTTTCTTTTAAAGTTTTACAAGAAAAAAAATCAG ]hJh[ahhhPhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_23_872_103 0 chr1 3189918 255 35M * 0 0 CTTTCTTTTAAATTTTTACAATAAAAAAAATCAGA hhhhhhhhhb_[Dhhhhhh[XAT[hUfKFhhVTM> NM:i:2 -EAS38_1_74_546_492 0 chr1 3189937 255 35M * 0 0 AAGAAAAAAAATCAGATAACCGAGGAAAATTCTTC hhhhhhhhhhhhhhh`h]hhhhThaRPOOhhBhhX NM:i:1 -EAS38_1_177_466_463 0 chr1 3189943 255 35M * 0 0 AAAAATCAGATAACCGAGGAAAATTATTCATTATG hhhhhhhhhhhhhhhhOhMSIIhhhdhh\hhhfhB NM:i:0 -EAS38_1_326_846_82 0 chr1 3189943 255 35M * 0 0 AAAAATCAGATAACCGAGGAAAATTATTCATTATT hhhhhhhhhhhhhhhh]hJdRdhhhZhhhYhbhhG NM:i:1 -EAS38_1_235_891_810 0 chr1 3189957 255 35M * 0 0 CGAGGAAAATTATTCATTATGAAGTACTACTTTCC hhhhhhhhhhhhhhhhhhhhhhhhh_HhOJhhPWI NM:i:0 -EAS38_1_73_865_289 16 chr1 3189961 255 35M * 0 0 GAAAATTATTCATTATGAAGTACTACTTTCCACTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_201_984_898 0 chr1 3189963 255 35M * 0 0 AAATTATTCATTATGAAGTACTACTTTCCACTTCA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_37_723_474 16 chr1 3189968 255 35M * 0 0 ATTCATTATGAAGTACTACTTTCCACTTCATTTCA hHEJhFThZhhhhXhUShhhhhhhhhXhhhhhhhh NM:i:0 -EAS38_1_183_791_724 0 chr1 3189973 255 35M * 0 0 TTATGAAGTACTACTTTCCACTTCAGTTCATCACA hhhhhhhhhhhhhhhhhafhhhhdWBhhPYhHPh[ NM:i:1 -EAS38_1_69_87_770 16 chr1 3189978 255 35M * 0 0 AAGTACTACTTTCCACTTCATTTCATCACAAATTG hhJhghhhhhhghhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_54_211_781 16 chr1 3189984 255 35M * 0 0 TACTTTCCACTTCATTTCATCACAAATTGTAACTT hghhhLhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_203_766_573 16 chr1 3189985 255 35M * 0 0 ACTTTCCACTTCATTTCATCACAAATTGTAACTTA SQPbUhhZhhhhhhhWhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_195_866_158 0 chr1 3189991 255 35M * 0 0 CACTTCATTTCAACACAAATTGTAACTTACTTAAC hhhhhhRhhhhh@hchHOThhRh[F`hhPShbNSI NM:i:1 -EAS38_1_122_739_820 16 chr1 3190001 255 35M * 0 0 CATCACAAATTGTAACATACTTAACTGACCAAAAA hhXhfYhhhhSORhhhAghhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_144_950_152 16 chr1 3190008 255 35M * 0 0 AATTGTAACTTACTTAACTGAACAAAAAAACTATG hhIIc_hhI[\hHghhhYhhhHhhhhhhhhhhhhh NM:i:1 -EAS38_1_168_613_587 0 chr1 3190008 255 35M * 0 0 AATTGTAACTTACTTAACTGACCAAAAAAACTATG hhhhhhhhhhhhhhhhhhhhgh`SNhfhhRahZf\ NM:i:0 -EAS38_1_134_699_616 16 chr1 3190013 255 35M * 0 0 TAACTTACTTAACTGACCAAAAAAACTATGGTACT hhhQhMhhehhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_210_777_789 0 chr1 3190014 255 35M * 0 0 AACTTACTTAACTGACCAAAAAAACTATGGTACTG hhhhhhhhhhhhhhhWfh\`hHhhShgYhXGZIQU NM:i:0 -EAS38_1_66_446_787 0 chr1 3190014 255 35M * 0 0 AACTTACTTAACTGACCAAAAAAACTATGGTACTG hhhhhhhhhhhhhhhhhhhhhhh]dhhhhdghShh NM:i:0 -EAS38_1_179_978_676 16 chr1 3190032 255 35M * 0 0 AAAAAACTATGGTACTGCAGTATAGCAAATACTCC hhhhhghWhZhFhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_308_776_503 16 chr1 3190032 255 35M * 0 0 AAAAAACTATGGTACTGCAGTATAGCAAATACTCC hhhhhh^?hRhThhhghbhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_172_693_734 16 chr1 3190040 255 35M * 0 0 ATGGTACTGCAGTATAGCANATACTCCACACACTG hLD?UFaLLhaJhhhh[hh;hhhhhhhhhhhhhhh NM:i:1 -EAS38_1_239_423_396 16 chr1 3190040 255 35M * 0 0 AGGGTACTGAAGTATAGCAAATACTCCACACACTG _AH?>LADTCZh^h]hhDhhhZhhehhhhhhhhhh NM:i:2 -EAS38_1_284_912_582 16 chr1 3190042 255 35M * 0 0 GGTACTGCAGTATAGCAAATACTCCACACACTGTG LhhhhhhhhhhhhhhWhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_209_687_576 0 chr1 3190073 255 35M * 0 0 TGTGCTTTGAGCTAGAGCACTTGGAGTCACTGCCC hhhhhhhhhhhhhhhdhhZdhhYhPMhRPIeMWGP NM:i:0 -EAS38_1_185_490_551 16 chr1 3190085 255 35M * 0 0 TAGAGCACTTGGAGTCACTGCCCAGGGCAGCAGCC FJDFJGJJODb\`hJQ_hNghhhhhhhh`hhhhhh NM:i:0 -EAS38_1_65_838_419 0 chr1 3190102 255 35M * 0 0 CTGCCCAGGGCAGCAGCCTCCAACCAAGAAAGACA hhhhhhhhhhh]_hKhhchceBdGaOCG@?BGIIP NM:i:0 -EAS38_1_323_255_975 0 chr1 3190107 255 35M * 0 0 CAGGGCAGCAGCCTCCAACCAAGAAAGACACACTT hhhhhhhh\hhUShNYh]@Uh\hMXMaJ?YRRBFH NM:i:0 -EAS38_1_296_538_461 0 chr1 3190126 255 35M * 0 0 CAAGAAATACACACTTACAAGTTGAATTCTAAAGG hhhhhhhhhhhhhhhhhh]hhhhh\hhhhhMhbhh NM:i:1 -EAS38_1_132_195_514 16 chr1 3190129 255 35M * 0 0 GAAAGACACACTTACAAGTTGAATTCTAAAGGAAG chbhhhShFhhYhhghhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_155_895_725 16 chr1 3190140 255 35M * 0 0 TTTCAAGTTGAATTCTAAAGGAAGGTCTGGTTATG VhO[ghWSchhh_hZhhhhhhhhhXhhhhhhhhhh NM:i:1 -EAS38_1_193_609_633 16 chr1 3190140 255 35M * 0 0 TTACAAGTTGAATTCTAAAGGAAGGTCTGGTTATG Q`hbhhh[hhhhShhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_135_816_228 16 chr1 3190142 255 35M * 0 0 AAAAGTTGAATTCTAAAGGAAGGTCTGGTTATGTG fC_]SH_VhhIABLhhhhfhhhWfZhhhhhhhhhh NM:i:1 -EAS38_1_145_593_539 0 chr1 3190150 255 35M * 0 0 AATTCTAAAGGAAGGTCTGGTTATGTGGGGTTGTA hhhhhhhhhhhhhhhhhhhhhhhhQh`ShhhhhAH NM:i:1 -EAS38_1_121_577_810 16 chr1 3190177 255 35M * 0 0 GGGTTGGAGTATGTATATCTATATATCTCTATATA KJM]OSdhbXhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_194_207_828 0 chr1 3190207 255 35M * 0 0 ATATATATTTACATCAAAGAATTTAATAACTCATT hhhhhhhhhhhhhhhhhhhhhhhhchhTh_h_`hh NM:i:0 -EAS38_1_113_803_974 0 chr1 3190221 255 35M * 0 0 CAAAGAATTTAATAACTCATTTAAATTTTTGTTTC hhhhhhhhhhhhhhhchQhhhhhgOhh_hhh_hhL NM:i:0 -EAS38_1_160_812_510 16 chr1 3190244 255 35M * 0 0 AATTTTTGTTTCAAATAAAATTCCAAATACACTTG hhWOhG]h^hhQhhhhhhhhh_\hhhhhhhhBhhh NM:i:1 -EAS38_1_40_88_508 16 chr1 3190249 255 35M * 0 0 TTGTTTCAAATAAAATTCCAAATACATTTGTACAA QhhgVhdhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_84_935_631 16 chr1 3190249 255 35M * 0 0 TTGTTTCAAATAAAATTCCAAATACATTTGTACAA ^]hJhZWhhhhhhhhhUhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_36_762_603 0 chr1 3190263 255 35M * 0 0 ATTCCAAATACATTTGTACAATGTTTACAAAGTAA hhhhhhhhhhhhhhhhhhhhhh^hhhhahX\]_hb NM:i:0 -EAS38_1_16_788_728 16 chr1 3190265 255 35M * 0 0 TCCAAATACATTTGTACAATGTTTACAAAGTAAGA @hEhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_172_782_398 16 chr1 3190269 255 35M * 0 0 AATACATTTGTACAATGTTNACAAAGTAAGAGACA hhZhhhaZhhWhhhhhheh;hThhhhehhhhhhhh NM:i:1 -EAS38_1_319_78_862 16 chr1 3190274 255 35M * 0 0 ATTTGTACAATGTTTACAAAGTAAGAGACAGGACT dLhZM_ehdhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_27_817_428 16 chr1 3190276 255 35M * 0 0 TTGTAAAATGTTTACAAAGTAAGAGACAGGACTGG VPhchChh_ghfhhEhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_188_256_713 0 chr1 3190325 255 35M * 0 0 AGGCCAGGCACCGTGATGTCCGGGTGATATATCTT hhhhhhhhhhhhhhhKhhaMhUhhNgA_E[GhM[G NM:i:0 -EAS38_1_315_859_502 16 chr1 3190329 255 35M * 0 0 CAGGAACCGTGATGTCCGGGTGATATATCTTCACG BNSIKHNI\SK]VdXZR`Uhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_152_381_800 16 chr1 3190355 255 35M * 0 0 ATCTTCACGTTGCCTGCACACACCTTATTTCTGAA ZVhQIhhhhhhXhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_282_558_872 0 chr1 3190364 255 35M * 0 0 TTGTCTGCACACACCTTATTTCTGAAATGGAGAGA hhh=hhhhhhhhh_hhhhhhhYhh`hhhhhQhhhC NM:i:1 -EAS38_1_215_759_830 0 chr1 3190407 255 35M * 0 0 AGAATGTCACCGACTATGCATCAGAATACTATGTA hhhhhhhhhhhhhhhhhhh_hh[hUWhhbh^hhXc NM:i:0 -EAS38_1_277_471_798 16 chr1 3190412 255 35M * 0 0 GTCACCGACTATGCATCAGAATACTATGTACAGTT KJYK\eYhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_279_405_802 16 chr1 3190418 255 35M * 0 0 GACTATGCATCAGAATACTATGTACAGTTGAAGTT Chhhhhhhhhhhhhhhhhhhhhhhhh`hhhhhhhh NM:i:0 -EAS38_1_75_573_457 16 chr1 3190428 255 35M * 0 0 CAGAATACTATGTACAGTTGAAGTTAGGGAGCTGA Zhdhh_dhYhRh\hhhhUKhhhhhUhhhhhhhhhh NM:i:0 -EAS38_1_238_427_419 16 chr1 3190444 255 35M * 0 0 GTTGAAGTTAGGGAGCTGAGAACCTAGTGGTCTGT XKEQdhhNKZhhhhhhdhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_24_788_817 0 chr1 3190444 255 35M * 0 0 GTTGAAGTTAGGGAGCTGAGAACCTAGTGGGCTGT hhhhhhhhhhhhhQhHhhUeK_AGXKhNfe>=ITO NM:i:1 -EAS38_1_307_22_417 16 chr1 3190449 255 35M * 0 0 AGTTAGGGAGCTGAGAACCTAGTGGTCTGTTCTCT KU@DX`XWbV@JhghhTETVhh^hTWh_hh[hhhh NM:i:0 -EAS38_1_104_731_910 0 chr1 3190455 255 35M * 0 0 GGAGCTGAGAACCTAGTGGTCTGTTCTCTTCTGGT hhhhhhhhhhhJYhhhhhhZOhhhhBhF\hFhhaO NM:i:0 -EAS38_1_189_367_978 16 chr1 3190466 255 35M * 0 0 CCTAGTGTTCTGTTCTCTTCTGGTTTGTCTTCATC HhCMIbQEShcKTYhhh\hhhYPhhhhhhhhhhhh NM:i:1 -EAS38_1_288_697_269 0 chr1 3190470 255 35M * 0 0 GTGGTCTGTTCTCTTCTTGTTTGTCTTCATCTACC hhhhhhhhhhhhhhhhhBChhhDhhhhhQhhhI?c NM:i:1 -EAS38_1_239_232_371 16 chr1 3190490 255 35M * 0 0 GTGTCTTAATCTACCAGCTATTACTCCTCTTTTGC DKK?ADHAhKCIhVhhhB_hchhhbhhZhhhhhhh NM:i:2 -EAS38_1_17_329_620 16 chr1 3190509 255 35M * 0 0 ATTACTCCTCTTTTGCTCAGAGATAAATTTAAAAT h^E_hMhchhhThVhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_145_66_863 0 chr1 3190520 255 35M * 0 0 TTTGCTCAGAGATAAATTTAAAATACAAACATTGG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhc NM:i:0 -EAS38_1_318_476_736 0 chr1 3190562 255 35M * 0 0 AAGGAGAAAAGCACAAAATATTTAAGGCAAATTAA hhhhhhhhhhhhhhhhhhhhhhhhfhh^hF\hhhH NM:i:0 -EAS38_1_91_887_139 16 chr1 3190577 255 35M * 0 0 AAATATTTAAGGCAAATTAAGCAAATATGTACAGT hhhhhK^ThhZhThhh\hhhhZhhhhhhhhhhhhh NM:i:0 -EAS38_1_42_628_869 16 chr1 3190582 255 35M * 0 0 TTTAAGGCAAATTAAGCAAATATGTACAGTCTCTT EYEhhBDYhhh^hhhLhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_266_296_122 16 chr1 3190587 255 35M * 0 0 GGAAAATTAAGAAAATATGTACAGTCTCTTTGTGC hUJhhh@ehhhFhhhShIhehhhh`h\hhbhhhhh NM:i:2 -EAS38_1_296_47_651 0 chr1 3190588 255 35M * 0 0 GCAAATTAAGCAAATATGTACAGTCTCTTTTTTCC hhhhhhhhhhhhhhhhhhhhh[hhhhhhhhDhIRE NM:i:2 -EAS38_1_298_622_554 16 chr1 3190612 255 35M * 0 0 CTCTGTGTGCCAGGAGGATGTGACTTTCTTTTTAA QXfIBXhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_55_346_335 16 chr1 3190613 255 35M * 0 0 TCGGTGTGCCAGGAGGATGTGACTTTCTTTTTAAA KABCGhGh@hhhhhhhhhh^hhhhhhhhhhhhhhh NM:i:2 -EAS38_1_144_104_681 16 chr1 3190646 255 35M * 0 0 AATCCCAAACCATGCTTTAAAAAATTCAAATAAAG hhVhJThhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_307_505_905 0 chr1 3190650 255 35M * 0 0 CCAAACCATGCTTTAAAAAATTCAAATAAAGCAAG hhhhhhhhhhhhhhhhhhhhhhhhShhhh_h\`hh NM:i:0 -EAS38_1_4_468_915 0 chr1 3190667 255 35M * 0 0 AAATTCAAATAAAGCAAGTCTGGTGTGAGTTGGGT hhhhhhhhhhhhhhhhhhhhhhhahfhJhhhhhha NM:i:0 -EAS38_1_177_100_872 0 chr1 3190682 255 35M * 0 0 AAGTCTGGTGTGAGTTGGGTTGCTTGTGTTGTTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhThhhhh NM:i:0 -EAS38_1_201_448_983 0 chr1 3190733 255 35M * 0 0 TGTTTTGCACAAAATAACCATTTGGAATTTGCAGT hhhhhhhahhhhhhhhhZMhhhhhhNhhhhXGXhH NM:i:0 -EAS38_1_205_905_511 16 chr1 3190740 255 35M * 0 0 AACAAAATAACCATTTGGAATTTGCAGTGGAATAA hhFhhhhahhhhhhahhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_22_834_621 0 chr1 3190741 255 35M * 0 0 ACAAAATAACCATTTGGAATTTGCAGTGGAATAAT hhhhhhhhhhhhhhhhhYhhhhhh]h]h[NVhI`h NM:i:0 -EAS38_1_297_847_594 16 chr1 3190753 255 35M * 0 0 TTTGGAATTTGCAGTGGAATAATTTGTTAATTGTG `KYZ\hX^dhYhhhhbhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_105_929_305 16 chr1 3190768 255 35M * 0 0 GGAATAATTTGTTAATTGAGAAGTGTATGGTTTTG hhhhhhhQ]hhhhhh_hhEhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_323_29_609 0 chr1 3190771 255 35M * 0 0 ATAATTTGTTAATTGTGAAGTGTATGGTTTTGTAT hhhhhhhhhhhhhhhhhhhOhhhhhhhhhhh@hGh NM:i:0 -EAS38_1_174_674_495 0 chr1 3190781 255 35M * 0 0 AATTGTGAAGTGTATGGTTTTGTATTTTTAAACCA hhhhhhhhhhhhhhhhhhhhhFhhhhhhLUPaeSG NM:i:1 -EAS38_1_156_965_73 16 chr1 3190814 255 35M * 0 0 CAAAAAACAGTAGCTGAGGTAGTTAAATGTGAAAC DhhhCghNhhhhhRhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_264_136_776 0 chr1 3190842 255 35M * 0 0 GTGAAACTTACACAACTTAAAATAATGAGAGAATG hhhhhhhhhh`hbhhYhhbh_eh_hhbM\O]IVYR NM:i:0 -EAS38_1_269_103_855 16 chr1 3190853 255 35M * 0 0 ACAACTTAAAATAATGAGAGAATGGAGAACCAATG ShhhhhXhhhhchhLhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_133_823_893 0 chr1 3190856 255 35M * 0 0 GCTTAAAATAATGAGAGAATGGAGAAACAATGTAA hhhhhhhhhhhhhhhbhhVhhhahQZ@KZhSUKgH NM:i:2 -EAS38_1_316_626_26 0 chr1 3190872 255 35M * 0 0 GAATGGAGAACCAATGTAAGGAGCCCAGACTCTTG hhhhhhhhhh]hhhhh^hXNhhXLcGGFEMVIL\A NM:i:0 -EAS38_1_14_936_623 0 chr1 3190882 255 35M * 0 0 CCAATGTAAGGAGCCCAGACTCTTGCCATCTGGGA hhhhhhhhdhhhhYTbFhTWehhNJdKDJVREM?E NM:i:1 -EAS38_1_112_85_814 16 chr1 3190885 255 35M * 0 0 ATGTAAGGAACCCAGACTCTTGCCATCTGGAAGCA dBCDhhRNh?RhWhWhhWhZh[hhhhhhhhhhhhh NM:i:1 -EAS38_1_153_136_402 16 chr1 3190885 255 35M * 0 0 ATGTAAGGAGCCCAGACTCTTGCCATCTGGAAGCA QUhWhhh[hTahhhhQhhUhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_267_293_629 16 chr1 3190891 255 35M * 0 0 GGAGCCCAGACTCTTGCCATCTGGAAGCAGGCTCA Zg]YhEhhhhfd`hZhJhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_60_948_719 16 chr1 3190944 255 35M * 0 0 TACCCAGAAAAACATTTGTTCTTTTGGATGCCATT BAHQQhFehhhRhUPKJVf\hh^bWh_hhhhhhhh NM:i:0 -EAS38_1_279_273_497 0 chr1 3190975 255 35M * 0 0 CATTAGTTCAGCCAGTGTCAACATGACTAGTGGTT hhhhhhhhhhhhhhhZYhhhhahhh`Uh`ELGVVg NM:i:0 -EAS38_1_35_405_941 16 chr1 3190979 255 35M * 0 0 AGTTCAGCCAGTGTCAACATGACTAGTGGTTTCCC E??>bfB^hhOIT_hhhhhhUWhhhhh^hhhhhhh NM:i:0 -EAS38_1_307_828_462 16 chr1 3190995 255 35M * 0 0 ACATGACTAGTGGTTTCCCAAGCACTTGCTTGGAA hRhhhhh^hhhhhhhhGfhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_118_418_323 16 chr1 3191023 255 35M * 0 0 CGTGGAAGCAAAGATAAAGAAAGTCTGCTTTCCAG IS@dWhh]NhhhHhbhhhhhhhhZhchhhhghhhh NM:i:2 -EAS38_1_144_10_603 0 chr1 3191023 255 35M * 0 0 CTTGGAAGCAAATATAAAGAAAGTCTGCTTTCCAG hhhhhhhhhhZhhhhhhdhWhhhhhhh^hhhDhKU NM:i:0 -EAS38_1_219_965_773 16 chr1 3191038 255 35M * 0 0 AAAGAAAGTCTGCTTTCCACGCTTCTCATCTATAG hhhIhhh[ehXQhhhahhhJhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_56_375_762 16 chr1 3191134 255 35M * 0 0 CATTATTAGAAATTCCAACCCTAGTTATGAAAGAT hh_VhKZhMhhhSXbhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_148_601_688 16 chr1 3191142 255 35M * 0 0 GAAATTCCAACCCTAGTTATGAAAGATTGAGGGGA hhhhhTdhhhhhhhhhhhhhhhhhhhhhhhhhh>h NM:i:1 -EAS38_1_236_489_757 0 chr1 3191149 255 35M * 0 0 CAACCCTAGTTATGAAAGATTGAGGGAAAGTGATA hhhhhhhhhhhhhhhhhhThhhbhhhSKhhXhTh_ NM:i:0 -EAS38_1_144_552_470 0 chr1 3191153 255 35M * 0 0 CCTAGTTATGAAAGATTGAGGGAAAGTGATAAAGA hhhhhhhhhhhhhhehhhh`h\IPThhhThGKUML NM:i:0 -EAS38_1_288_225_365 16 chr1 3191173 255 35M * 0 0 GGAAAGTGATAAAGAACAAAAGGGAGGGATATTAT hhhhhh\hh`hhhhhhMhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_33_904_669 0 chr1 3191192 255 35M * 0 0 AAGGGAGGGATATTATTCTCTCATTTTTAACAGCA hhhhhhhhhhhhhhhhhhhhhhghhhhhhhhYKJH NM:i:0 -EAS38_1_123_430_125 16 chr1 3191220 255 35M * 0 0 AACAGCATATTTGTCTTAGCTTTAAATCCAGAGTA hhDh`Ch`h[UTh[RhehhcThhhhhhhhhhhhhh NM:i:0 -EAS38_1_179_676_404 16 chr1 3191241 255 35M * 0 0 TTAAATCCAGAGTACTGTTTGGCTTCAAAGAAGAT QhhhhLZUhhhhfhhbhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_120_22_725 0 chr1 3191250 255 35M * 0 0 GAGTACTGTTTGGCTTCAAAGAAGATAGTCATCTC hhhhhhhhhhhhhhhhfhhhhahhhhdhhhZhNhX NM:i:0 -EAS38_1_223_373_449 0 chr1 3191268 255 35M * 0 0 AAGAAGATAGTCATCACTGGTTCTCTTACTGAGAA hhhhhhhhhhhhhhhDhhhhZhhhhhh^hh[NFCQ NM:i:1 -EAS38_1_112_183_986 0 chr1 3191269 255 35M * 0 0 AGAAGATAGTCATCTCTGGTTCTCTTACTGAGAAT hhhhhhhhhhhhhhhfhhhehhhfhhX\hhVhbKg NM:i:0 -EAS38_1_172_99_819 16 chr1 3191287 255 35M * 0 0 GTTCTCTTACTGAGAATAGNAAGTCTCTCCTTACT U\VhOhhhhhhhhhhhhhh;hhhhhhhhhhhhhhh NM:i:1 -EAS38_1_210_930_591 16 chr1 3191287 255 35M * 0 0 GTTCTCTTACTGAGAATAGAAAGTCTCTCCTTACT LWK^Khh^ShNhhhhhhhhhhhhXhhhhhhhhhhh NM:i:0 -EAS38_1_100_778_539 16 chr1 3191290 255 35M * 0 0 CTCTTACTGAGAATAGAAAGTCTCTCCTTACTGAG hhfhhhThhhhhhhhhhhhh^hhhhhhhhhhhhhh NM:i:0 -EAS38_1_25_830_623 16 chr1 3191298 255 35M * 0 0 GAGAATAGAAAGTCTCTCCTTACTGAGAATAGGAA YhRhhLhhhhhh`h\hhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_304_473_442 0 chr1 3191304 255 35M * 0 0 AGAAAGTCTCTCCTTACTGAGAATAGGAAGCCATC `hhhThehhhhh\hhXYhgJ`ILQLDNBIAAM=HD NM:i:0 -EAS38_1_205_508_718 16 chr1 3191307 255 35M * 0 0 AAGTCTCTCCTTACTGAGAATAGGAAGCCATCTTC hhRBOThbhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_293_376_615 16 chr1 3191307 255 35M * 0 0 AAGTCTCTCCTTACTGAGAATAGGAAGCCATCTTC hhh@hFhOhhghhh[hh`hhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_182_907_727 16 chr1 3191326 255 35M * 0 0 ATAGGAAGCNATCTTCATACCTGTCCCTCTGCATT hM^FJg`Mh;hhhhfhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_222_741_776 0 chr1 3191358 255 35M * 0 0 ATTTATTCTTGAGGTTACTGAGCCATCTGGCTACA hhhhhhhhhhhhhhChhYhTehDVghIhh][ZF?K NM:i:0 -EAS38_1_88_323_543 16 chr1 3191374 255 35M * 0 0 ACTGAGCCATCTGGCTACAGAGAAGAAAAGCAAGA X\Ghhe^JhNaXhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_66_197_743 16 chr1 3191383 255 35M * 0 0 TCTGGCTACAGAGAAGAAAAGCAAGAGTTGTTTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_173_864_740 16 chr1 3191391 255 35M * 0 0 CAGAGAAGAAAAGCAAGAGTTGTTTTTTTATTTTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_124_858_171 16 chr1 3191398 255 35M * 0 0 GAAAAGCAAGAGTTGTTTTTTTATTTTTATTTTAT chhhhU\hhhhcOchhObh]hhhhhhhhhhhhhhh NM:i:0 -EAS38_1_126_138_418 16 chr1 3191410 255 35M * 0 0 TTGTGTTTTTATTTTTATTTTATTTTTATTTTTTT U`hhBfhZZhhh`Yhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_221_397_462 0 chr1 3191429 255 35M * 0 0 TTTTTTTTATTTTTTTAAGTAGAAGCAAGATTCTC hhhhhhhhZhhhhhhhhVFhbKMSWhRG]?hhQh[ NM:i:1 -EAS38_1_216_901_971 0 chr1 3191444 255 35M * 0 0 TAAGTAGAAGCAAGATTCTCATTAAGGCTAACTAT hhhhhhhhhhhhhhhhhahZZhbhabfQ[MKFWGU NM:i:0 -EAS38_1_282_128_662 0 chr1 3191445 255 35M * 0 0 AAGTAGAAGCAAGATTCTCATTAAGGCTAACTATG hhhhhhhchhhhh]hhhhhVhhZhhhZhZ@MbMaL NM:i:0 -EAS38_1_77_686_871 0 chr1 3191446 255 35M * 0 0 AGTAGAAGCAAGATTCTCATTAAGGCTAATTATGT hhhhhhhhhhhhhhhdhhhhhhhhh^hh]@hhh`B NM:i:2 -EAS38_1_95_356_853 0 chr1 3191446 255 35M * 0 0 AGTAGAAGCAAGATTCTCATTAAGGCTAACTATGC hhhhhhhhhhhhhhhhhhhhhhPhhfh\HJGUhLN NM:i:0 -EAS38_1_315_80_525 0 chr1 3191449 255 35M * 0 0 AGATGCAAGATTCTCATTAAGGCTAACTATGCTAT hhhhhhhhhhhhhhhehhhR\Khh]]gh[hZ_hJh NM:i:1 -EAS38_1_211_797_532 0 chr1 3191471 255 35M * 0 0 CTAACTATGCTATTCTCCACTGCGCCCCATTGATC hhhhhhhhhhhhhhhhhhhhhfcIhLh[HhgUUhK NM:i:0 -EAS38_1_326_311_799 0 chr1 3191471 255 35M * 0 0 CTAACTATGCTATTCTCCACTGCGCCCCATTGATC hhhhhhhhhhhhhhhhhhhhhhhhghhhhhhhVhG NM:i:0 -EAS38_1_107_806_891 16 chr1 3191478 255 35M * 0 0 TCCTATTCTCCACTGCGCCCCATTGATCAGACAAT LBfP^MWhAhh_hh^hZhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_121_349_512 0 chr1 3191489 255 35M * 0 0 ACTGCGCCCCATTGATCAGACAATGGCTTTAAGTG hhhhhhhhhhhhhhhhhhhhhBhhhhhhhhOOJeT NM:i:0 -EAS38_1_219_430_836 16 chr1 3191498 255 35M * 0 0 CATTGATCAGACAATGGCTTTAAGTGGGGCCTAAA c_WRRdUhhN[hhhdaWhOhhhghhhhhhhhhhhh NM:i:0 -EAS38_1_98_807_431 16 chr1 3191517 255 35M * 0 0 TTAAGTGGGGCCTAAATGAACTGTTGGACATCAGG PQg^SGhO[eOKhhhh`hhhYahhXhhhhhhhhhh NM:i:0 -EAS38_1_155_241_829 16 chr1 3191535 255 35M * 0 0 AACTGTTGGACATCAGGTTCATGAAAACGGTTTTG ]QbLHKRRThhhWhhh[hdghhhhhhhhhhhhhhh NM:i:0 -EAS38_1_223_732_501 0 chr1 3191535 255 35M * 0 0 AACTGTTGGACATCAGGTTCATGAAAACGGTTTTG hhhhhhhhhYhahh\EQghh\hPMJd_hSX[XhgE NM:i:0 -EAS38_1_320_444_109 16 chr1 3191535 255 35M * 0 0 AACTGTTGGACATCAGGTTCATGAAAACGGTTTTG hbHUhhGhhhRhhhhhWZhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_103_761_542 0 chr1 3191537 255 35M * 0 0 CTGTTGGACATCAGGTTCATGAAAACGGTTTTGTG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_245_218_950 0 chr1 3191539 255 35M * 0 0 GTTGGACATCAGGTTCATGAAAACGGTTTTGTGCA hhhhhhhhhchhhhhhhhhhhhhKhhhhhh_\R>f NM:i:1 -EAS38_1_54_654_789 0 chr1 3191548 255 35M * 0 0 CAGGTTCATGAAAACGGTTTTGTGAAGGTAATATA hhhhhhhhhhhhhhhhhhhhhhhhhhhhLhChhh^ NM:i:0 -EAS38_1_242_532_556 0 chr1 3191553 255 35M * 0 0 TCATGAAAACGGTTTTGTGAAGGTAATATATCAGT hhhhhh]hhhhhhhhhZhTfchhO[LhUhXTCJJP NM:i:0 -EAS38_1_37_578_493 16 chr1 3191563 255 35M * 0 0 GGTTTGGTGAAGGTAATATATCAGTAATATGGTTG THOCeDUEhhZQgchhhhhhJhhhhhhhhhhhhhh NM:i:1 -EAS38_1_151_713_632 0 chr1 3191572 255 35M * 0 0 AAGGTAATATATCAGTAATATGGTTGACATAAATA hhhhhhhhhhhhhhhhhhhhhhhhhhh`hhhSThh NM:i:0 -EAS38_1_152_680_718 0 chr1 3191572 255 35M * 0 0 AAGGTAATATATCAGTAATATGGTTGACATAAATA hhhhhhhhhhhhhhhhhhhhhhhhh^g\hhbhhh^ NM:i:0 -EAS38_1_152_24_706 0 chr1 3191573 255 35M * 0 0 AGGTAATATATCAGTAATATGGTTGACATAAATAA hhhhhhhhhhhhhhhhhhhhhhhhhOehhhWhhhW NM:i:0 -EAS38_1_330_686_422 16 chr1 3191575 255 35M * 0 0 GTAATATATCAGTAATATGGTTGACATAAATAAGC GLhhdhbhGJhh_hhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_275_44_659 0 chr1 3191579 255 35M * 0 0 TATATCAGTAATATGGTTGACATAAATAAGCTGGG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhTcg NM:i:0 -EAS38_1_324_589_894 0 chr1 3191579 255 35M * 0 0 TATATCAGTAATATGGTTGACATAAATAAGATGGG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhXhhhh NM:i:1 -EAS38_1_121_763_313 0 chr1 3191589 255 35M * 0 0 ATATGGTTGACATAAATAAGCTGGGAAATAGTTCT hhhhhhhhhhhhhhhhhhhhhhchhWFhhTChhfh NM:i:0 -EAS38_1_130_668_987 16 chr1 3191610 255 35M * 0 0 TGGGAAATAGTTCTTTTAGGAAGTAGAAGATTTTT UT>Khbhbhhh[hhhhZhhfhhhhhhhhhhhhhBh NM:i:0 -EAS38_1_80_262_758 16 chr1 3191611 255 35M * 0 0 GGGAAATAGTTCTTTTAGGAAGTAGAAGATTTTTC PYdhhhMhh\HhhVhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_272_104_967 0 chr1 3191614 255 35M * 0 0 AAATAGTTCTTTTAGAAAGTAGAAGATTTTTCTCT hhhhhhhhhhhhhhhGhhhhhhhehXhhhhhZhZh NM:i:1 -EAS38_1_142_144_587 16 chr1 3191617 255 35M * 0 0 TAGTTCTTTTAGGAAGTAGAAGATTTTTCTCTTTG bhhhHPhNhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_282_509_344 16 chr1 3191618 255 35M * 0 0 AGTTCTTTTAGGAAGTAGAAGATTTTTCTCTTTGT hh^YdVSKWhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_3_797_743 0 chr1 3191619 255 35M * 0 0 GTTCTTTTAGGAAGCAGAAGATTTTTCTCTTTTTG hhhhhhhhhhhhhhAhhhhhXhhhhhhhfhhhHhb NM:i:2 -EAS38_1_311_266_241 16 chr1 3191633 255 35M * 0 0 TAGAAGATTTTTCTCTTTGTGTCTGTGTCTTTCAT LhhhhhhXGFHH_HhhhThhhdhhhhhhhhhhhhh NM:i:0 -EAS38_1_282_320_153 16 chr1 3191635 255 35M * 0 0 GAAGATTTTTCTCTTTGTGTCTGTGTCTTTCATTT OQ\\PEA[JHNGRQJhhhhXNhhWhVhhUfhhhhh NM:i:0 -EAS38_1_74_839_687 16 chr1 3191635 255 35M * 0 0 GAAGATTTTTCTCTTTGTGTCTGTGTCTTTCATTT MhhWhS[hhGhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_119_931_54 16 chr1 3191636 255 35M * 0 0 AAGATTTTTCTCTTTGTGTCTGTGTCTTTCATTTG QJ?JRKXIZaOhYYdbhhhhbhhhfhhhhhhhhhh NM:i:0 -EAS38_1_171_559_793 16 chr1 3191638 255 35M * 0 0 GATTTTTCTCTTTGTGTCTGTGTCTTTCATTTGCC U_NhR[ZhhhRhWhhhhhh>hhhhhhhhhhhhhhh NM:i:0 -EAS38_1_9_831_797 0 chr1 3191643 255 35M * 0 0 TTCTCTTTGTGTCTGTGTCTTTCATTTGCCTTTGT hhhhhhhhhhhhhhhhhhGhhhGChhhH>Kd?hEA NM:i:2 -EAS38_1_112_463_853 0 chr1 3191663 255 35M * 0 0 TTCATTTGCCTATGAAAAGAATGTTAGTTGGCTGT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhah^h NM:i:0 -EAS38_1_200_507_523 16 chr1 3191673 255 35M * 0 0 TATGAAAAGAATGTTAGTTGGCTGTAACCATAAAA @hW^hhhhehhKgXh\hh^hhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_307_105_716 0 chr1 3191676 255 35M * 0 0 GAAAAGAATGTTAGTTGGCTGTAACCATAAAATTG hhhhhhhhhhhhhhhhhhhhhhUh[_Hh]aQdhhZ NM:i:0 -EAS38_1_81_670_875 16 chr1 3191698 255 35M * 0 0 AACCATAAAATTGGCAGTTGTATTTACAAATAATC hehhhhhhhhhhhZhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_285_30_406 0 chr1 3191712 255 35M * 0 0 CAGTTGTATTTACAAATAATCACATATATTATGCT h_hhhhh_hhh]hQQShILhhYhQhIhHhCIh@U_ NM:i:1 -EAS38_1_45_791_522 16 chr1 3191716 255 35M * 0 0 TGTATTTACAAATAATCACATATATGATGCTTACA hh`hhXhhhhhhhhhfhhhHhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_43_819_567 16 chr1 3191719 255 35M * 0 0 ATTTACAAATAATCACATATATGATGCTTACAGAA hhQhhChhhhhhhhhhhhh@hhhhhhhhhhhhhhh NM:i:0 -EAS38_1_26_772_717 0 chr1 3191761 255 35M * 0 0 CTCATTTCTAAATAATCACATATGCTAAAAGCTAG hhhhhhhhhhhhhhhhhhhhhZhhYhWfahSIhHS NM:i:0 -EAS38_1_130_865_419 0 chr1 3191766 255 35M * 0 0 TTCTAAATAATCACATATGCTAAAAGCTAGGTTTT hhhhhhhhhhhhhhhhhhhhh\`hhOhhELh_hhh NM:i:0 -EAS38_1_327_933_866 0 chr1 3191766 255 35M * 0 0 TTCTAAATAATCACATATGCTAAAAGCTAGGTTTT hhhhhhhhhhhhhhhhhhhhhhh]chYhPhLYhhh NM:i:0 -EAS38_1_126_547_811 16 chr1 3191773 255 35M * 0 0 TAATCACATATGCTAAAAGCTAGGTTTTTCTAATA hhhThhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_277_668_994 16 chr1 3191773 255 35M * 0 0 TAATCACATATGCTAAAAGCTAGGTTTTTCTAATA _hhJhhhhhhh]hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_181_734_387 16 chr1 3191780 255 35M * 0 0 ATATGCTAAAAGCTAGGTTTTTCTAATACACTTTT hNhNTARh`hhhIOhhhXeRMhLahhhhhhhhhhh NM:i:0 -EAS38_1_174_224_835 16 chr1 3191785 255 35M * 0 0 CTAAAAGCTAGGTTTTTCTAATACACTTTTACTTT hhhhhhhhhhdghhhhhhhhhhhhhhhhhhh>hhh NM:i:1 -EAS38_1_192_253_159 16 chr1 3191794 255 35M * 0 0 AGGTTTTTATAATACACTTTTATTTTCATGGAGGG hhc\PLNGAfhhhhhh[hZ[_hh[ahhhYhhhhhh NM:i:1 -EAS38_1_184_325_530 16 chr1 3191800 255 35M * 0 0 TTCTAATACACTTTTATTTTCATGGAGGGCTCTAG hGV[hhWhhhhhXh^hghhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_250_311_830 16 chr1 3191810 255 35M * 0 0 CTTTTATTTTCATGGAGGGCTCTAGAGGATTCCAC YLGJTUPJNNXgKQR_VKThhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_275_852_575 16 chr1 3191813 255 35M * 0 0 TTATTTTCATGGAGGGCTCTAGAGGATTCCACGTG JVeYM[E`hJSLV]SQVRChhhhhhhhhhhShhhh NM:i:0 -EAS38_1_77_390_526 0 chr1 3191818 255 35M * 0 0 TTCATGGAGGGCTCTAGAGGATTCCCCGTGGCATA hhhhhhhhhhhhhhhThNhhOhhOQA_^TEV=^EG NM:i:2 -EAS38_1_299_893_564 16 chr1 3191846 255 35M * 0 0 TGGAATAGAAACCACTGAAAAGAGACTCAACTCTT @aVhhKhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_294_440_933 16 chr1 3191865 255 35M * 0 0 TAGAGACTCAACTCTTTTTCCCCCCAGCAATATTA O^EV?MhDhhUh\hYKVTKhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_278_780_674 16 chr1 3191873 255 35M * 0 0 CAACTCTTTTTCCCCCCAGCAATATTATGTTGCTC hhVWchcZHXMhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_86_970_279 0 chr1 3191876 255 35M * 0 0 CTCTTTTTCCCCCCAGCAATATTATGTTGCTCTGT hhhhhhhhhhhhhhPhheHhfhhehOhhEOhUhAF NM:i:0 -EAS38_1_148_146_536 0 chr1 3191881 255 35M * 0 0 TCTCCCCCCAGCAATATTATGTTGCTCTGTGCTGC hDhhhhhhh]hhhdhhhhhhhhhEhhhh\hEhhHG NM:i:1 -EAS38_1_224_888_484 16 chr1 3191884 255 35M * 0 0 CACCCCAGCAATATTATGTTGCTCTGTGCTGCTCT P?KJEARLNW`TdVWhF^OThhMgQ\hhhhfhhhh NM:i:1 -EAS38_1_223_648_752 0 chr1 3191887 255 35M * 0 0 CCCAGCAATATTATGCTGCTCTGTGCTGCTCTATG h_hhhhhhhhhhhhh=hhhhYhhOVghhB\AhWhM NM:i:1 -EAS38_1_300_220_617 0 chr1 3191891 255 35M * 0 0 GCAATATTATGTTGCTCTGTGCTGCTCTATGCATA hhdhhhhhhhhhhhhhhhhhh\hhhhZhhhhPKhL NM:i:0 -EAS38_1_63_467_696 16 chr1 3191897 255 35M * 0 0 TTATGTTGCTCTGTGCTGCTCTATGCATATGGCAT FHh^h]Fhe?hfhhchhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_24_141_869 0 chr1 3191905 255 35M * 0 0 CTCTGTGCTGCTCTATGCATATGGCATGTTGTTGG hhhhhhh^hhUhUhhhhYhhfhh_BPcfh`RXOLS NM:i:0 -EAS38_1_184_494_683 16 chr1 3191911 255 35M * 0 0 GCTGCTCTATGCATATGGCATGTTGTTGGTACCTG =Qab\ahVhchahhh]hhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_263_460_363 16 chr1 3191919 255 35M * 0 0 ATGCATATGGCATGTTGTTGGTACCTGTACCATTC h?UIhJhWhhOhghhKhDhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_80_670_426 16 chr1 3191919 255 35M * 0 0 ATGCATATGGCATGTTGTTGGTACCTGTACCATTC cPgPhNh\hhhh[hhhhUahhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_118_725_870 0 chr1 3191927 255 35M * 0 0 GGCATGTTGTTGGTACCTGTACCATTCTCTTCCAT hhhhhhhhhhhhhhhcghhhhRSQhhUhHhhGKLh NM:i:0 -EAS38_1_88_806_693 16 chr1 3191952 255 35M * 0 0 TCTCTTCCATTGAGAATTCTAAGCCATTATGTGGA fhhhhahhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_160_191_877 16 chr1 3191955 255 35M * 0 0 CTTCCATTGAGAATTCTAAGCCATTATGTGGAGGA hhXhhh\hhhhhhehhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_300_179_943 16 chr1 3191975 255 35M * 0 0 CCATTATGTGGAGGAGCTGTTCAGCTCTCTCTAAC h^IRPXZNMBIMZL[Ehh[hdhhQhchhhhhhhhh NM:i:0 -EAS38_1_208_195_556 0 chr1 3191986 255 35M * 0 0 AGGAGCTGTTCAGCTCTCTCTAACCTATTTAGATT hhhhhhhhhhhdhhhhhhhhhPhehhMhhhTH?bh NM:i:0 -EAS38_1_16_568_852 0 chr1 3191993 255 35M * 0 0 GTTCAGCTCTCTCTAACCTATTTAGATTTTATCTT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhLhMhh NM:i:0 -EAS38_1_290_6_992 16 chr1 3192030 255 35M * 0 0 ACTTTGTGATAGAATCTCTCTATAGAATGTTCTCT F_UhhHhLhbeKhhhh^hhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_300_29_772 16 chr1 3192030 255 35M * 0 0 TCTTTGTGATAGAATCTCTCTATAGAATGTTCTCT Ahh`Vhh[hhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_109_466_314 0 chr1 3192031 255 35M * 0 0 CTTTGTGATAGAATCTCTCTATAGAATGTTCTCTC hhhhhhhhhhhfhhhhhhhhKhhGLXhRhhPhLhS NM:i:0 -EAS38_1_112_657_773 0 chr1 3192037 255 35M * 0 0 GATAGAATCTCTCTATAGAATGTTCTCTCCACCCA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh]BG NM:i:2 -EAS38_1_137_971_213 16 chr1 3192048 255 35M * 0 0 TATATAGAATGTTCTCTCAACCACCTCCTGCTAGT C@BHTcZhaFFRSB\hVT@Oehhhhhhhhhhhhhh NM:i:2 -EAS38_1_185_636_515 16 chr1 3192048 255 35M * 0 0 TCTATAGAATGATCTCTCAACCACCTCCTGCTAGT F@J\Jd]Q\ABBAcA[Mhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_1_44_970_650 0 chr1 3192058 255 35M * 0 0 GTTCTCTCCACCACCCCCTGCTAGTCATACCAAAC hhhhhhhhhhhhhhThMhhhac\h[e_WRGfUIMH NM:i:1 -EAS38_1_92_965_745 0 chr1 3192064 255 35M * 0 0 TCCACCACCTCCTGCTAGTCATACCAAACCCACCC hhhhhhhhhhhhhhhhhhhhhhhJh_hhPIV_X?G NM:i:0 -EAS38_1_261_922_44 0 chr1 3192119 255 35M * 0 0 ACTTCAGTTTTTCTTTATAAAACTTAATCAAAACC hhhh_hhfhhhhhhEh_hTTY]hh@aJhOFMTOLM NM:i:2 -EAS38_1_123_430_987 16 chr1 3192133 255 35M * 0 0 GTATAAAACTGAATCAAAACCGATGTTTATTTTTA GZhdhhh]hhdhhdhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_234_381_448 0 chr1 3192142 255 35M * 0 0 TGAATCAAAACCGATGTTTATTTTTATGATAAAAA hhBhhh]hhhhhhhhhhhhFhhhhhThB_hQ]O@Y NM:i:0 -EAS38_1_46_449_600 0 chr1 3192148 255 35M * 0 0 AAAACCGATGTTTATNTTTATGATAAAAAGGATAT hhhhhhhahhhhhhh;hhhhhhfhThNh^OGWh]h NM:i:1 -EAS38_1_239_737_373 0 chr1 3192153 255 35M * 0 0 CGATGTTTATTTTTATTATAAAAAGGATATACTTT hhhhhhhhhhhhhhdhK[hhhRW\JMPhbhNhhhh NM:i:1 -EAS38_1_24_496_314 0 chr1 3192169 255 35M * 0 0 GATAAAAAGGATATACTTTTGTATTTTGTTGTAGA hhhhhhhhhhhhhhhhhhhhDhLhhhhHM[O]EA? NM:i:2 -EAS38_1_150_229_75 16 chr1 3192202 255 35M * 0 0 GAAAAAATATTGGTTTAAGAAGGAGATAAAAAGTC hhhhhhhJhA]hhSPARhhhhhhhhhbhhhhhhhh NM:i:1 -EAS38_1_170_110_874 16 chr1 3192248 255 35M * 0 0 AATTACCTTTTACCCACTTACTGTTCTTACATGAC hhhhXhh]hQhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_142_857_213 0 chr1 3192280 255 35M * 0 0 GACCTGACTATCCTAACAAACTCTATTCTAGCACT hhhhhhhhhhhhhhh\hQh_hhhhYhhhhRB]Wbh NM:i:0 -EAS38_1_7_223_584 0 chr1 3192314 255 35M * 0 0 TGTAGATATTTTTGAGGAGTCACATACTTTTCTAT hhhhhhhhhhhhhghhK^YhhhhJhhDhhhhhhMh NM:i:1 -EAS38_1_95_195_644 16 chr1 3192330 255 35M * 0 0 GAGTCACATAATTTTCTATGCTACAGTCATGCTTC hhhbPhZhhhhOhh`hhhYhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_219_903_777 0 chr1 3192346 255 35M * 0 0 TATGCTACAGTCATGATTCAGAAAGTCTAATGTCG hhhhhhhhhhhhhhhBhhhhhhhhhghh\hhhhJ[ NM:i:1 -EAS38_1_108_439_554 16 chr1 3192349 255 35M * 0 0 GCTACAGTCATGCTTCAGAAAGTCTAATGTCGTGA aThhhhhehhdhhXhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_239_516_540 0 chr1 3192442 255 35M * 0 0 TAATTTTAGAGAATCAGAGGAGATTATATTGTGTG hhhhhhhhhhhhhhhhhhhhNhLhhThhhheOfhW NM:i:1 -EAS38_1_196_124_875 16 chr1 3192460 255 35M * 0 0 GGAGATTATATTGGGTGTCAATACTGTAAGTATTC ?N[Mhh_hWhXh[LVhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_222_834_314 16 chr1 3192460 255 35M * 0 0 GGAGATTAGATTGGGTGTCGATACTGTAAGTATTC WDXGRJOR?hCMfKhR]OAIhPXZRh^hhhhhhSh NM:i:2 -EAS38_1_230_638_588 0 chr1 3192551 255 35M * 0 0 TATTTGAAGAGTATGGAATTTATTTTGTAAATGAA hhhhhhhhhhhhhhhhhhhhhWhhhhhh\`hhhG` NM:i:0 -EAS38_1_264_255_706 0 chr1 3192603 255 35M * 0 0 AGTACTGAATGGAGCCACATCATTCACATATTTCC hhhhhhhhhhhhhhhhhhhhhghhbhhdhfhhhdP NM:i:0 -EAS38_1_105_766_448 16 chr1 3192724 255 35M * 0 0 TTAGTTTAGTCATTTAGGCAAGGAAATAGACATTG Ghhhhhhhhhhhghhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_281_8_752 0 chr1 3192785 255 35M * 0 0 GCTCAGGTTGTTTTTCCTACCATCTCTCCACATTT hhhEhhhhhhhhhhhN\hh@MOhHU>WDGHW?WTd NM:i:1 -EAS38_1_273_517_672 16 chr1 3192933 255 35M * 0 0 ATAATATGGAGATGAATCAGCTCAAGAGTTCTGAG hhhhghCfdhhhhhhhhhhhhahhhhhhhhhhhhh NM:i:0 -EAS38_1_194_915_453 16 chr1 3192959 255 35M * 0 0 AGTCCTGAGCAGAAACACCATTCCACATTCTTCTG hbIGI_hhhOhhhhhfV\hhhdhhhhhhQhhhhhh NM:i:1 -EAS38_1_270_767_516 16 chr1 3193008 255 35M * 0 0 TGTTAGAAATGGTATAAAATCCCAGTTAAACCATT ThUchhhhhfhJhhhhhhhDOhchhhhhhhhhhhh NM:i:1 -EAS38_1_311_398_506 16 chr1 3193008 255 35M * 0 0 TGTTAGAAATGGTATAAAAACCCAGTTAAACCATT OWRbhhhhhUhZhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_77_151_681 16 chr1 3193008 255 35M * 0 0 TGTTAGAAATGGTATAAAAACCCAGTTAAACCATT WCP`hhhhhRhO\hhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_210_41_603 16 chr1 3193471 255 35M * 0 0 CACATTCCTTATAACACACTGTGAGGTAGGTGAAG ^bZV`R]hh_hOhhh`hhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_124_634_862 16 chr1 3193821 255 35M * 0 0 TTTCTGGGTATGATTGCTGTTAGCCTTTCTGTTTT h^HhhhDBhhhhhhhdhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_101_162_624 0 chr1 3194186 255 35M * 0 0 TTGCACTGTGTTTAGAAATCCCTCAAAAGGTTTGC hhhhhhhhhhhhhhhhhhhhhhhhW[hPfeUhhVY NM:i:0 -EAS38_1_235_609_726 0 chr1 3194200 255 35M * 0 0 GACATCCCTCAAAAGGTTTGCATAGCCAAATGCCT QJH]I]TaV[_X^\QIERLJHEG?H>JFFD@BCC? NM:i:1 -EAS38_1_162_13_894 16 chr1 3194295 255 35M * 0 0 GGGAATTGTTCACACAATTTGTGTGTTTTTCTGTC ?HCMeVTN?Sh[hRhhhhZhbhhhhhhhhhhhhhh NM:i:2 -EAS38_1_201_123_722 0 chr1 3194814 255 35M * 0 0 AACCATTATGTAAAGTATACTTTATAAATGTTTAA hhhhhhhhhhhhhhhhhhhhhhhhh]hhhhhhh\M NM:i:0 -EAS38_1_251_938_580 16 chr1 3195076 255 35M * 0 0 TATTTATCTTTGTACAACAAAGAGACTCTTAGCAG dYGWNFSQhWVPhhGhh`hhhehhhhhhhhhhhhh NM:i:1 -EAS38_1_8_777_292 16 chr1 3195076 255 35M * 0 0 TATTTATCTTTGTACAAAAAAGAGACTCTTAGCAG JQFAH@BLJGRNEhQhhDhhhfhhhh]]hhhhhhh NM:i:2 -EAS38_1_212_466_584 0 chr1 3195258 255 35M * 0 0 GCTATCCCAAAACCATATGTGCTGCTTGTATGAAC hhhhhhhhhghhhhfhhhh]hZhhhhhbhfhOD>M NM:i:1 -EAS38_1_137_805_954 0 chr1 3195451 255 35M * 0 0 GGAAAAGTCAGAACTTTGGGGTGATCAAACGTCTA hhhhhhhhhhhhhhhhhhhhhghhhCPhPIhMJYD NM:i:1 -EAS38_1_63_741_75 0 chr1 3195451 255 35M * 0 0 GGAAAAGTCAGAACTTTTGTGTGATCAACCGTCTA hhhhhhhhhhhVhhhhhFEJFhOHhSVRG@N_D_Q NM:i:2 -EAS38_1_146_999_561 16 chr1 3197082 255 35M * 0 0 GGAATCCATTGGCTGATCTTTTAAGAAGTAGTTCT SahhhRhhhXh\hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_295_1_556 16 chr1 3197082 255 35M * 0 0 GGAATCCATTGGCTGATCTTTTAAGAAGTAGTTCT bdhhMFhhgehhhhhhbIhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_133_696_323 16 chr1 3197239 255 35M * 0 0 CCTGCAATGAACCAACTGCTCCTTTCCCATTAATT ??FCJ??@DSCECKJ]JbhLXbXh\hUhhh^hhhf NM:i:2 -EAS38_1_184_992_275 0 chr1 3197347 255 35M * 0 0 GATTAATTAACTGCAATTCATCTCCAGTAAAATTT hhhhhhhhhhhhhhhShhhhhhhhh^`WILU_hhh NM:i:0 -EAS38_1_261_311_801 16 chr1 3197969 255 35M * 0 0 ATAAAAATTGAACAAAAAAAAGAAATGGGTTTCTT hchhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_199_494_378 16 chr1 3198110 255 35M * 0 0 GCCATGCCAGAATGCTAGGACAATAGTTAAATTAA ?Dhh\hKPhhhhUhZhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_186_296_431 16 chr1 3199201 255 35M * 0 0 GTTAGCACTTTGTCACATATTCCACTGCTTTTAAA S>MhSKKDFJVhGHhPh]hdWhhhhhhhhhhhhhh NM:i:0 -EAS38_1_32_939_527 0 chr1 3199927 255 35M * 0 0 TTTCCCTAGTTTAGCTGTGATGCCTTTGACAAGCT hhhhhhhhhhhhhhhhhhhhhhghhhhVFYNVGYh NM:i:0 -EAS38_1_174_562_297 0 chr1 3200023 255 35M * 0 0 AAGGGAGATAGATCCCAGAGGTAAGGATCTTCAAG hbhRL^hCXHWNdNTMIH?IJG?DDE?C>KFH@B? NM:i:2 -EAS38_1_80_292_639 0 chr1 3200090 255 35M * 0 0 GATACTCTTAACTGATATGGGAATCAAGCCACACG hhhhhhhhhhhhhhhhhhhYcEhhh^d^TOhh]K? NM:i:1 -EAS38_1_146_971_305 16 chr1 3200157 255 35M * 0 0 ACGTTCAGCTTAGATTGTTTCTGAGTTTGTGTCCT RMOUAJ[YRHYh\hZhhhW[hhhhhhhhhhhhhhh NM:i:0 -EAS38_1_103_633_813 16 chr1 3200318 255 35M * 0 0 TATAATATAATAAGGATCTAACATGTTGCTTTCTC YghhhNhUhh^hhThh]hhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_268_250_819 16 chr1 3200318 255 35M * 0 0 TATAATATAATAAGGATCTAACATGTTGCTTTCTC hhhhhVhhhhhhhgVhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_195_376_807 16 chr1 3200796 255 35M * 0 0 TCAGGGAGGGGGACTAAAGTGAGGTCACCTATTCC Ihe[Ihh]XahhhhhhhhhhhhFhhhhhhhhhhhh NM:i:1 -EAS38_1_92_137_414 0 chr1 3200902 0 35M * 0 0 TTTTTTTTTTTTTTTTTTTTTTTTCTCTATTTTCC hhhhhhhhhhhhhhhhhhhhhhdhCA@hJ@IK@AE NM:i:2 -EAS38_1_142_636_259 0 chr1 3200903 0 35M * 0 0 TTTTTTTTTTTTTTTTTTTTTTTTCCTATTTTCTA hhhhhhhhhhhhhhhhhhhhhhM?EM@>FLICF@@ NM:i:2 -EAS38_1_72_206_749 0 chr1 3200905 0 35M * 0 0 TTTTTTTTTTTTTTTTTTTTTTGATACTTTCCAAA hhhhhhhhhhhhhhhhhhhhhhBAN@UOE@YEE=@ NM:i:2 -EAS38_1_111_883_143 16 chr1 3201070 255 35M * 0 0 AAAGACAGTTGGAACTATTTTTAAAAGGCGCTTTA hhhhhQhhH`hchhfhhh\ghhhhhhhhhhhhhhh NM:i:0 -EAS38_1_255_841_137 0 chr1 3201133 255 35M * 0 0 CAGGCATCTCATCCAAGCTTTATATATAAATAGTC hhhhh\hhhhdhahDPDhhhhKhSh`LFPEePCYI NM:i:1 -EAS38_1_25_534_590 0 chr1 3201133 255 35M * 0 0 CAGGCATCTCATCCAAGCTTTATATAGAAATAGTC hhhhhUhhhhhh`hVYhYhchMgO^LWKGJHFDNE NM:i:0 -EAS38_1_11_826_739 0 chr1 3201151 255 35M * 0 0 CTAATATAGAAATAGTCGTGGCTAATGGCAAAGAT hhBhhhhhhhhhhhhhhhLhhR]`]TY^@DNPQ@D NM:i:2 -EAS38_1_200_667_750 0 chr1 3201166 255 35M * 0 0 TCGTGGCTAATGGCAAAGATATGTGATGAATGCAA hhhhhhhhhhhhhLRhIhbQ]fZYULURBNRG?EP NM:i:0 -EAS38_1_148_510_997 0 chr1 3201180 255 35M * 0 0 AAAGATATGTGATGAATGCAAGGGAGCATATATTT hhhhhhhhhhhehhhhhhZhMhhZD`FOXSV_SPZ NM:i:0 -EAS38_1_221_65_299 16 chr1 3201185 255 35M * 0 0 TATGTGATGAATGAAAGGGAGAATATATTTAGTCT BhG[Egh]hhhLhAhhhhhhhPhbhUhTWMhhSVh NM:i:2 -EAS38_1_149_164_972 0 chr1 3201186 255 35M * 0 0 ATGTGATGAATGCAAGGGAGGATATATTTAGTGTA hhhhhhhhhhhhNhhhhhdhCWh_MhhWOVhVBhU NM:i:2 -EAS38_1_269_935_919 16 chr1 3201203 255 35M * 0 0 AAACATATATTTAGTCTAGAAAGTAGTTCATTAGA FWQhh[hbhhbhhQXhhhhhhhhhhhhhhhhhhhh NM:i:2 -EAS38_1_289_238_636 0 chr1 3201226 255 35M * 0 0 TAGTTCATTAGAAAAAATTCACAGGATTCTTGTCT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_125_517_695 16 chr1 3201271 255 35M * 0 0 TCAGAATTTGTTTCCACTCAGTAGCATCCAATGCA hJhHhhhWPehh\hhhhhchhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_22_489_754 16 chr1 3201281 255 35M * 0 0 TTTCCACTCGGTAGCATCCAATGCATTTGAAAGTG VNChUNhM\fDhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_122_450_662 16 chr1 3201346 255 35M * 0 0 TACACGTTTTCCTTGACTTAAGCCACGTGTTCAAT \PhJh`h[hKhhhhh`hhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_157_676_368 16 chr1 3201388 255 35M * 0 0 GAAGTAACATAAACTATTCAATTAGGCCACTTACA ghhYehhhhThhhhhh[Yhhh]hhhhhhhhhhhhh NM:i:0 -EAS38_1_4_358_468 16 chr1 3201390 255 35M * 0 0 AGTAAAAGAAACTATTCAATTAGGCCACTTACAAG hNDhhAhBhhhhWhMKdhhKbhhhhhhhhhhhhhh NM:i:2 -EAS38_1_15_825_658 16 chr1 3201447 255 35M * 0 0 AGTTCAGTCAAATCATGGAGCAAGGAATTCCATGT ]BZOJhZ`hhhhhhhhhhhhhhh]hhhhhhhhhhh NM:i:0 -EAS38_1_222_809_300 0 chr1 3201569 255 35M * 0 0 CAAAAAGTCATGGAAGTTTAAATTATCCCATGCAT hhhhh]hhhhhhS\c>hhhYhPhhhhhhhUhPhWh NM:i:1 -EAS38_1_116_429_381 16 chr1 3201665 255 35M * 0 0 TGTGTGTTTATTGAGAGTATGTGAGAAGATACCTG PhhhLhhchhh`hhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_156_372_572 16 chr1 3201665 255 35M * 0 0 TGTGTGTTTATTGAGAGTATGTGAGAAGATACCTG hhhhhhhEhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_79_182_652 16 chr1 3201849 255 35M * 0 0 TACAAAAAGCTATCATATAACAATCCATCTATCAT IAYhhhhhbhXhhhhhhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_186_626_713 16 chr1 3202147 255 35M * 0 0 CATTTATCAATCAATCTAATCTAACTTATCTATCT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_16_258_505 16 chr1 3203603 255 35M * 0 0 TTCCAGCTGGGAGGGTGAGTCTTCAGAGTTCATCA ?AIDSAPEhhhhhhhhhhhhhhfhhhhhhhhhhhh NM:i:1 -EAS38_1_197_118_218 16 chr1 3204368 255 35M * 0 0 GGTGAGGTAGGCTGATGGATTTGTAGACTGGATTC VPGgUMhAXhh@GchGdhhOXLhfhhfhhhhhhhh NM:i:1 -EAS38_1_141_404_857 0 chr1 3204755 255 35M * 0 0 TTTTTAATGGCATACACATTGCATCTGTATGCTCT hhhhhhhhhhhhhhhhhhhhhhhh_hdhhhhIhEh NM:i:0 -EAS38_1_125_490_276 16 chr1 3204799 255 35M * 0 0 AATTGTGACCCAAAGTCTCTAGTAGACACATCATT h\]@VFQ@QPAhhhhGhhI_hhhhhhhhhhhhhhh NM:i:1 -EAS38_1_171_771_691 16 chr1 3205563 255 35M * 0 0 TATGGGTATTTTGCCTGCATATATGTCTATGCACC ]hOhKfhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_284_911_331 0 chr1 3210849 255 35M * 0 0 CTCTGTATTCTCTTCTTCTATTCACATCTCTACAA hhhhhhhhhhhhhhhhhhhbhhhhhbhhhhhFhhG NM:i:0 -EAS38_1_101_808_273 0 chr1 3212214 255 35M * 0 0 AGATGGTTGGTTGTAGTTTGACCCTTGAAGTTTAT hhhhhhhhhhhhhh^XhhhhJ]hhhhHLHR\hhKh NM:i:0 -EAS38_1_161_452_506 16 chr1 3212258 255 35M * 0 0 CCGGAGTTCCCGGTGTGTTGCTACTGGCATGGTGG HJ>@_ZEEc]R[hWhfhhThhhhh]hhhhhhhhhh NM:i:2 -EAS38_1_246_740_824 0 chr1 3212368 255 35M * 0 0 TGTGTTGTTCTCTTCCACCAGAATGAACTATTGTG hhhhhhhhhhhhhh]hh[OhhhhhhOZZhMh_`Lh NM:i:0 -EAS38_1_328_863_236 0 chr1 3212368 255 35M * 0 0 TGTGTTGTTCTCTTCCACCAGAATGAACTATTGTG hhhhhhhhhhhfhhhh[hhRIhahh`ghh[hhhhW NM:i:0 -EAS38_1_71_507_507 0 chr1 3212368 255 35M * 0 0 TGTGTTGTTCTCTTCCACCAGAATGAACTATTGTT hhhhhhhhhhhhhhhhhhhg]LQhhhOhhShhHc? NM:i:1 -EAS38_1_156_360_657 0 chr1 3212393 255 35M * 0 0 AACTATTGTGAGTCTAGAGCTTCTCCAAATGCCTC hhhhhhhhhhhhhhhhhhhhhhXhVhChhhhhdbh NM:i:0 -EAS38_1_327_554_773 0 chr1 3212413 255 35M * 0 0 TTCTCCAAATGCCTCTTGTTACAAACATGCATATA hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_316_581_646 0 chr1 3213096 255 35M * 0 0 TTTTAATCTTATCTCCTCACTGCCTCCCTCTTAGG hhhhhhhhhhhhhhhhhgdhh_dRhhG^hfhYKJF NM:i:0 -EAS38_1_90_952_487 16 chr1 3214147 255 35M * 0 0 TCCCTGGATGAAGGAGGTTCAATTGGATTGAATTA DCQNQXOaeUhhUThcNhh`hhhhhhhhhhhhhhh NM:i:0 -EAS38_1_191_680_14 0 chr1 3225128 255 35M * 0 0 ATATTTTCCAACAGGTAAGAAGTATGCAAGCTCCA hhMhhhhhhchhhJJUIhEOPPDHhE[T@@IDD?A NM:i:1 -EAS38_1_138_982_940 0 chr1 3233636 0 35M * 0 0 TACCTCTCGCCATCTGTCAATCTCTGGAGTCAGTT hJhhhhh^hahYhhhhJBhhhLhJhhVaXJAB_BL NM:i:2 -EAS38_1_158_9_677 16 chr1 3242626 255 35M * 0 0 AAAATAAATAAGAGAGAGGAGCCTTACTGTGCTTG hhhhPhhh^hhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_253_923_934 16 chr1 3242672 255 35M * 0 0 AACATTGTCTTTCTGCCAGGTTTCTGTGGAGCATA CIOHFhHOhO@LhTLhhhhKhh[hhhhhchXhhhh NM:i:1 -EAS38_1_5_178_743 16 chr1 3242672 255 35M * 0 0 AACATTTTCTGTCTGCCAGGTTTCTGTGGAGCATA QEDJM@C?]OOKhKRh^fUOR^Nhchehhhhhhhh NM:i:1 -EAS38_1_198_267_632 0 chr1 3242722 255 35M * 0 0 CGACACACCCCTTCTGCATACTGGCCTGTCACTGA hhhhhhhhhhhhhhhhhhhhhhhhhQhJT?ISHLA NM:i:2 -EAS38_1_19_755_678 0 chr1 3242782 255 35M * 0 0 GAGAACAGCAACTCCTCCTATAGCTTCTAGAGACA hhhhhhhhhhVRhUZghFgEhYhLQROfI?OCIGE NM:i:0 -EAS38_1_243_907_786 0 chr1 3242782 255 35M * 0 0 GAGAACAGCAACTCCTCCTATAGCTTCTAGAGACC hhhhhVhhNhhhhUahhWhJWhZOKhO\MPTGN?> NM:i:1 -EAS38_1_278_440_897 0 chr1 3242782 255 35M * 0 0 GAGAACAGCAACTCCTCCTATAGCTTCTAGAGACA hhhhhhhhhhhhhehh_YhhhhhDhhDhNMEXANO NM:i:0 -EAS38_1_173_938_288 0 chr1 3242827 255 35M * 0 0 GCACTGGGCCTTTCTTCTGTGTCTGAGCTATTTCA hhhhhhhhhhhhhhhhhhhhhINhg?e\hVhhHhC NM:i:1 -EAS38_1_157_930_237 16 chr1 3242836 255 35M * 0 0 CTTTCTTCTGTGTCTGAGCTATTGCATTATATCTT PMUNNFZYHhFaVhUhhh^Shhhhhhhhhhhhhhh NM:i:0 -EAS38_1_266_172_602 16 chr1 3242889 255 35M * 0 0 TTCTAATCACTGATGCATTAATTAAAAGAATCATA XJLLBhchhNehhhhYhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_149_88_885 0 chr1 3243019 255 35M * 0 0 TTCTCTATATTCCTAGAGTTGTGTGGAAACTAATA hhhhhhhhhhhhhhhhhhhhhhhhhadLhObALgf NM:i:1 -EAS38_1_62_896_441 16 chr1 3243045 255 35M * 0 0 AAAATCATATGATACCATTTATGCTTGCCAGAACG hh_CZJh[hhhhhhhhhhXhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_12_294_576 16 chr1 3243367 255 35M * 0 0 AGAATAATAAATTATCCTATAAGCTGGGCTTGATG _hhhQhhahhhNNhDh[\hNhhhhWhhhhdhh>hh NM:i:1 -EAS38_1_2_533_514 16 chr1 3243367 255 35M * 0 0 AGAATAATAAATGATCCTATAAGCGGGGCTTGGTG hahhPh\ChZhhXhPhBNRZKhhh\hhhhhhhhhh NM:i:2 -EAS38_1_305_285_786 16 chr1 3243648 255 35M * 0 0 CAAAATATTGTTAGATTTGTTTGAGAGATTTGTTG hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_67_916_874 0 chr1 3243986 255 35M * 0 0 GATTATAATACCCTCGTTGAGATTTGTTTGTTATT hhhhhhhhhhhhhhhhhhh\hZhhhhhhhh^hfhh NM:i:0 -EAS38_1_123_564_954 16 chr1 3254091 255 35M * 0 0 GGAGTGACTGGCCTCCCCTCTTCTTTATAAAGCGT CDM?P<Mh@=FhhThhhhhhhdhhhhhhhhhhhhh NM:i:0 -EAS38_1_55_599_652 16 chr1 3254559 3 35M * 0 0 GTGTCAAGCTCTTGCAGAGCCTCTCAGGAGACAGC @AC=EhKFhAZMGW^Zhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_143_932_612 16 chr1 3256967 255 35M * 0 0 CCTAGAGACAAGGGCTGAAGCAGGCCAGTTATTTT JEEKSVIQNMSdN_h[dhhhhhehhhhhhhhhhhh NM:i:0 -EAS38_1_212_69_386 16 chr1 3256977 255 35M * 0 0 AGGGCTGAAGCAGGCCAGTTATTTTAGGAGAGCAG ROJUGJhhhhCUh]RJhhhhhh[hhhhhhhhhhhh NM:i:0 -EAS38_1_256_785_413 16 chr1 3256977 255 35M * 0 0 AGGGATGAAGCAGGCCAGTTATTTTAGGAGAGCAG U`MUAAebhaM[WbHHhhNhhfhh`hhhhhhhhhh NM:i:1 -EAS38_1_105_481_788 16 chr1 3268974 255 35M * 0 0 GCCCGAAAAAATCTGCTTTATATTGGCCACATACG DhGaahhhhhhhhhchhhhhhhhhhhhhhhhhhhh NM:i:1 -EAS38_1_16_282_422 16 chr1 3273908 255 35M * 0 0 CAAATGGGACACCATTGTCTACATTTATGGTAAGT AOBNCFVEVCWFM_PCdOFGhRhXLahhhhehhhh NM:i:2 -EAS38_1_283_187_798 0 chr1 3274213 255 35M * 0 0 TTAGTGAGCCTGAACCAACCAACCAATGAATATAC hhhhhhhhhhhhhhVhhhPhhhLhhXhhZOhhhhY NM:i:0 -EAS38_1_329_178_196 0 chr1 3274786 255 35M * 0 0 GGAAGGCAGATCAGTATAGGTTACCAATAAAATTG hhhhhhhdhhhhhhhchh_@ERhhhEhhCgUWhha NM:i:1 -EAS38_1_300_318_77 16 chr1 3276576 255 35M * 0 0 GAAGAAGAAATATAAGCAGTCCAAGCAGGTTTCAG hhhhMhhhhhhhZKhhghhhARhhhhhhhhhhhhh NM:i:2 -EAS38_1_118_479_935 0 chr1 3276843 255 35M * 0 0 TTTTATCCTCTAGCATGTCAGTCAGGTACAGGGAT hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh?O NM:i:0 -EAS38_1_41_971_61 0 chr1 3277038 255 35M * 0 0 TGATAAAACAAAAATGTAGACCTTTTAACAGACCC hhhhh\`Z^NhV[]hO[ODJJHW`TbIE?GDBDE> NM:i:2 -EAS38_1_183_306_813 16 chr1 3277183 255 35M * 0 0 CCCATATTATCTTGGAGGTAGGATGATAGTGGTTT ehhhhhdhVNhZhhhhh[hhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_288_251_841 16 chr1 3277184 255 35M * 0 0 CCATATTATCTTGGAGGTAGGATGATAGTGGTTTC U[h^hNhh]hehhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_40_672_870 16 chr1 3277184 255 35M * 0 0 CCATATTATCTTGGAGGTAGGATGATAGTGGTTTC Uhh]hMhhNhhgQ[h_Nhh_fhhhhhhhhhhhhhh NM:i:0 -EAS38_1_325_652_299 0 chr1 3278086 255 35M * 0 0 TTTCTGTTTTAAATTAATTACCTTTATTCCATGTC hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhPhh NM:i:0 -EAS38_1_188_971_708 16 chr1 3278146 255 35M * 0 0 TCTTCCTCTTCGTTAGTTTGAATTTATTTCGTTCT P_QOhhWhhhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_295_186_302 16 chr1 3278229 255 35M * 0 0 CTTGTTGAGTGTTCTGCATGGAATAGAGGCATTTT CDG@ENd`[KQF@J?TEOBXYXaR\`V`hRhLhPh NM:i:1 -EAS38_1_314_975_553 16 chr1 3279235 255 35M * 0 0 ATTTGATAGGGACAGAATAAAAAGTGATAATTCTG hNJaVhahQDLhhhhhhRhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_220_655_831 16 chr1 3279355 255 35M * 0 0 AGAAAATACTTGCTTATTGCTGGAACACGTGACAT hShchXMRhK]Rhahhhhhhh^QhhhShhhhhhhh NM:i:0 -EAS38_1_267_333_743 16 chr1 3280494 255 35M * 0 0 CGTGATGCATCACCAGGGTATCCATGTATAGACTA FQNFhGVHhPfehVehKhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_165_158_507 16 chr1 3280679 255 35M * 0 0 GGGAACGTTATTTGGTGTCTATTGTGATTATTTCC hhbU`ZhhhhdX`hhYhhNhhhghhhhhhhhhchh NM:i:0 -EAS38_1_218_851_888 16 chr1 3280707 255 35M * 0 0 TATTTCCTAAATGCCCCTCNGTTTTTGTATGTTCT MPDILT_PI[`OLhc]hCh;hhh\VhKhhhdhhhh NM:i:1 -EAS38_1_144_853_896 16 chr1 3282690 255 35M * 0 0 GTATCACAAAGGCTCTTTTAACTCAAGAGTTTCTG MhhhhhhhhhXhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_232_504_623 0 chr1 3290489 255 35M * 0 0 TCCCTACATCTCTCCATGTTACTGTAAATGATAGT hhhhhhhhhhhhhhhhhhhhhhhh\Oee_PK`OV@ NM:i:1 -EAS38_1_238_304_582 0 chr1 3290527 255 35M * 0 0 TCATTCTTATTTAGCACTGAAATAATAACCGCCTA hhhhhhhhhhhhhMhhhhhhK]hRehha\DCGWhK NM:i:0 -EAS38_1_125_161_809 0 chr1 3290844 255 35M * 0 0 GCTACTGGGTGGTCTGCATAGCTTAGTGATACACT hh`bhhhhSYhhTE[QH@RFT>RJEVDCFLMCCBI NM:i:0 -EAS38_1_155_358_888 16 chr1 3290932 255 35M * 0 0 GTGGAATTGTAGGGGTGAAAAAAGACATTTCTGAG ghhRhhhhfhhhhhhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_157_904_203 0 chr1 3291089 255 35M * 0 0 ACAGCCCTGGATGATTTTTGAATGGGAATAATCCC hhhhhhhhhhLhh]hhhhhM^hhNI_@hhQ^hUMW NM:i:0 -EAS38_1_180_814_759 16 chr1 3291152 255 35M * 0 0 AACACCTAGTCATTGTTGGTGGCACTGTCTGTAAG NNWAgXVhhVh_RYhhSeYJh_hhhhhhhhhhhhh NM:i:0 -EAS38_1_170_391_724 16 chr1 3291373 255 35M * 0 0 AAGTAAACCCTTTCTCCTGTAAGTTTCCTTTGGTC _hhWhgQhhhUbchhhhhhhhhhhhhhhhhhhXhh NM:i:0 -EAS38_1_315_950_278 16 chr1 3291611 255 35M * 0 0 TCCATGCCCAGTTTCAGGTGGGAAAACAACTAAGT QAchLb^ChhhhhYhhhhhhhhhhhhhhhhhhhhh NM:i:0 -EAS38_1_330_167_763 16 chr1 3299360 255 35M * 0 0 AAAAATCTTTTTTCTTCTTCTTTCTTTCTTTCTAT hhhhhhhhLh__hhhhhhhhhhhhhhhhhhhhh=h NM:i:1 -EAS38_1_7_984_851 16 chr1 3299360 255 35M * 0 0 AAAAATCTTTTTTCTTCTTNTTTCTTTCTTTCTTT NLPMNN`LEdULNhVhhhh;Phhhhhhhhhhhhhh NM:i:1 -EAS38_1_133_814_850 0 chr1 3299443 1 35M * 0 0 TTTGAGACAGGGTTTCTTTATATAGCCATGGTTGG hhhhhhhhhhhhEhhChhhhhhhhhOTUhhf?SSG NM:i:2 -EAS38_1_303_411_338 16 chr1 3299602 255 35M * 0 0 GAGATGAATACTGGGTAGAAAATAAAAAAATTTAC ThYhFHhhI_JXh_XhhhhhhhYhhhhhhhhhhhh NM:i:0 diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffdiff_out1.txt --- a/test-data/cuffdiff_out1.txt +++ /dev/null @@ -1,91 +0,0 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant -TCONS_00000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TCONS_00000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000009 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 5.68095e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000010 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.15515e+06 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TCONS_00000011 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000012 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.02976e+06 1.79769e+308 1.79769e+308 0.0512352 0.150149 no -TCONS_00000013 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TCONS_00000014 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000015 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000016 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000017 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000018 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000019 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000020 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 959058 705514 -0.442943 0.376027 0.706897 1 no -TCONS_00000021 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000022 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 77513.9 285108 1.87898 -1.76152 0.0781506 1 no -TCONS_00000023 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000024 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000025 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.4671e+07 1.79769e+308 1.79769e+308 0.0512352 0.150149 no -TCONS_00000026 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 3.99739e+06 1.82908e+06 -1.12794 0.781831 0.434314 1 no -TCONS_00000027 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 56312.4 372827 2.72698 -1.67622 0.0936947 1 no -TCONS_00000028 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 2.66226e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000029 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.0951e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000030 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.06814e+09 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TCONS_00000031 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000033 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.29576e+07 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TCONS_00000034 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 9.79535e+06 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TCONS_00000037 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000038 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000039 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000040 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000041 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000042 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000043 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000044 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000045 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000046 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000047 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000048 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000049 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000050 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000051 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000052 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000053 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000054 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 368900 429265 0.21864 -0.483034 0.629072 1 no -TCONS_00000055 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 404373 338500 -0.25653 0.342922 0.731657 1 no -TCONS_00000056 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 402276 686974 0.772069 -1.24554 0.212932 1 no -TCONS_00000057 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 3.994e+06 2.93812e+06 -0.442943 0.217099 0.828131 1 no -TCONS_00000058 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000059 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000060 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000062 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000063 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000065 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.89853e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.150149 no -TCONS_00000066 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.31744e+07 0 -1.79769e+308 -1.79769e+308 0.0416323 0.150149 no -TCONS_00000067 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000068 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 4.39147e+06 0 -1.79769e+308 -1.79769e+308 0.158655 1 no -TCONS_00000069 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 1.36901e+06 0 0 0 1 1 no -TCONS_00000070 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000071 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000072 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000073 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 9.99919e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TCONS_00000074 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000075 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000076 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 265614 41870.3 -2.66534 2.48499 0.0129556 1 no -TCONS_00000077 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000078 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000079 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000080 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000081 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000082 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000083 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.8095e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TCONS_00000084 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 342218 75524 -2.17991 1.96162 0.049807 1 no -TCONS_00000085 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 937403 137917 -2.76487 1.66807 0.0953024 1 no -TCONS_00000086 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000087 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000088 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000089 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000090 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 8.91489e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TCONS_00000091 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 585828 0 -1.79769e+308 -1.79769e+308 0.0512352 1 no -TCONS_00000092 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.19208e+08 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TCONS_00000093 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 4.42166e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 1 no -TCONS_00000094 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 4.28358e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.150149 no -TCONS_00000095 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 7.29939e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TCONS_00000096 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000097 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000098 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000099 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no -TCONS_00000100 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffdiff_out10.txt --- a/test-data/cuffdiff_out10.txt +++ /dev/null @@ -1,88 +0,0 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant -XLOC_000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000004 XLOC_000004 - chr1:3174765-3174792 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000005 XLOC_000005 - chr1:3187401-3187428 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000006 XLOC_000006 - chr1:3188521-3188548 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000007 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000008 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000009 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000010 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000011 XLOC_000011 - chr1:3192441-3192494 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000012 XLOC_000012 - chr1:3192550-3192629 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000013 XLOC_000013 - chr1:3192649-3192676 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000014 XLOC_000014 - chr1:3192731-3192811 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000015 XLOC_000015 - chr1:3192940-3193042 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000016 XLOC_000016 - chr1:3194185-3194226 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000017 XLOC_000017 - chr1:3194302-3194329 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000018 XLOC_000018 - chr1:3194706-3194733 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000019 XLOC_000019 - chr1:3195083-3195110 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000020 XLOC_000020 - chr1:3195450-3195477 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000021 XLOC_000021 - chr1:3197089-3197116 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000022 XLOC_000022 - chr1:3197246-3197273 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000023 XLOC_000023 - chr1:3197346-3197373 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000024 XLOC_000024 - chr1:3197425-3197452 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000025 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000026 XLOC_000026 - chr1:3200325-3200352 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000027 XLOC_000027 - chr1:3200430-3200457 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000028 XLOC_000028 - chr1:3201007-3201039 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000029 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000030 XLOC_000030 - chr1:3201596-3201666 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000031 XLOC_000031 - chr1:3201672-3201699 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000032 XLOC_000032 - chr1:3201725-3201809 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000033 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000034 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000035 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000036 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000037 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000038 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000039 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000040 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000041 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000042 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000043 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000044 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000045 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000046 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000047 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000048 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000049 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000050 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000051 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000052 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000053 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000054 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000055 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000056 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000057 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000058 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000059 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000060 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000061 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000062 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000063 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000064 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000065 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000066 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000067 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000068 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000069 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000070 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000071 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000072 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000073 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000074 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000075 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000076 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000077 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000078 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000079 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000080 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000081 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000082 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000083 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000084 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000085 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000086 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 LOWDATA 0 0 0 0 0 1 no -XLOC_000087 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 LOWDATA 0 0 0 0 0 1 no diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffdiff_out11.txt --- a/test-data/cuffdiff_out11.txt +++ /dev/null @@ -1,1 +0,0 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffdiff_out2.txt --- a/test-data/cuffdiff_out2.txt +++ /dev/null @@ -1,88 +0,0 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant -XLOC_000001 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.157299 no -XLOC_000002 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.16621 no -XLOC_000003 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000004 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000005 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000006 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000007 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 368900 429265 0.21864 -0.483034 0.629072 1 no -XLOC_000008 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 404373 338500 -0.25653 0.342922 0.731657 1 no -XLOC_000009 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 402276 686974 0.772069 -1.24554 0.212932 1 no -XLOC_000010 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 3.994e+06 2.93812e+06 -0.442943 0.217099 0.828131 1 no -XLOC_000011 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 5.68095e+07 1.79769e+308 1.79769e+308 0.0786496 0.157299 no -XLOC_000012 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.15515e+06 1.79769e+308 1.79769e+308 0.158655 0.16621 no -XLOC_000013 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000014 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000015 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.02976e+06 1.79769e+308 1.79769e+308 0.0512352 0.157299 no -XLOC_000016 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.16621 no -XLOC_000017 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000018 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000019 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000020 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000021 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000022 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000023 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000024 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000025 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 959058 705514 -0.442943 0.376027 0.706897 1 no -XLOC_000026 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000027 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000028 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000029 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 77513.9 285108 1.87898 -1.76152 0.0781506 1 no -XLOC_000030 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.89853e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.157299 no -XLOC_000031 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000032 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.31744e+07 0 -1.79769e+308 -1.79769e+308 0.0416323 0.157299 no -XLOC_000033 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000034 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.157299 no -XLOC_000035 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.4671e+07 1.79769e+308 1.79769e+308 0.0512352 0.157299 no -XLOC_000036 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 4.39147e+06 0 -1.79769e+308 -1.79769e+308 0.158655 1 no -XLOC_000037 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 5.3664e+06 1.82908e+06 -1.55284 0.839459 0.401212 0.401212 no -XLOC_000038 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000039 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000040 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 56312.4 372827 2.72698 -1.67622 0.0936947 1 no -XLOC_000041 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000042 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 2.66226e+07 1.79769e+308 1.79769e+308 0.0786496 0.157299 no -XLOC_000043 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 9.99919e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.16621 no -XLOC_000044 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.0951e+07 1.79769e+308 1.79769e+308 0.0786496 0.157299 no -XLOC_000045 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000046 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.06814e+09 1.79769e+308 1.79769e+308 0.0786496 0.157299 no -XLOC_000047 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000048 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000049 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 265614 41870.3 -2.66534 2.48499 0.0129556 1 no -XLOC_000050 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000051 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000052 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.29576e+07 1.79769e+308 1.79769e+308 0.158655 0.16621 no -XLOC_000053 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000054 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000055 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000056 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000057 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 9.79535e+06 1.79769e+308 1.79769e+308 0.158655 0.16621 no -XLOC_000058 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.8095e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.16621 no -XLOC_000059 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 342218 75524 -2.17991 1.96162 0.049807 1 no -XLOC_000060 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 937403 137917 -2.76487 1.66807 0.0953024 1 no -XLOC_000061 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000062 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000063 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000064 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000065 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000066 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000067 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 8.91489e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.16621 no -XLOC_000068 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 585828 0 -1.79769e+308 -1.79769e+308 0.0512352 1 no -XLOC_000069 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.19208e+08 0 -1.79769e+308 -1.79769e+308 0.158655 0.16621 no -XLOC_000070 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 4.42166e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 1 no -XLOC_000071 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000072 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 4.28358e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.157299 no -XLOC_000073 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000074 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 7.29939e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.16621 no -XLOC_000075 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000076 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000077 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000078 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000079 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000080 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000081 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000082 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000083 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000084 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000085 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000086 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no -XLOC_000087 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffdiff_out3.txt --- a/test-data/cuffdiff_out3.txt +++ /dev/null @@ -1,91 +0,0 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant -TSS1 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TSS11 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 404373 338500 -0.25653 0.342922 0.731657 1 no -TSS12 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 402276 686974 0.772069 -1.24554 0.212932 1 no -TSS15 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 3.994e+06 2.93812e+06 -0.442943 0.217099 0.828131 1 no -TSS16 XLOC_000011 - chr1:3192441-3192494 q1 q2 OK 0 5.68095e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TSS17 XLOC_000012 - chr1:3192550-3192629 q1 q2 OK 0 4.15515e+06 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TSS18 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS19 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS2 XLOC_000002 - chr1:3111449-3111490 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TSS20 XLOC_000015 - chr1:3192940-3193042 q1 q2 OK 0 6.02976e+06 1.79769e+308 1.79769e+308 0.0512352 0.150149 no -TSS21 XLOC_000016 - chr1:3194185-3194226 q1 q2 OK 0 2.1403e+08 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TSS22 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS23 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS24 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS25 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS26 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS27 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS28 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS29 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS3 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS30 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 959058 705514 -0.442943 0.376027 0.706897 1 no -TSS32 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS33 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS34 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS35 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 77513.9 285108 1.87898 -1.76152 0.0781506 1 no -TSS37 XLOC_000030 - chr1:3201596-3201666 q1 q2 OK 1.89853e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.150149 no -TSS38 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS39 XLOC_000032 - chr1:3201725-3201809 q1 q2 OK 1.31744e+07 0 -1.79769e+308 -1.79769e+308 0.0416323 0.150149 no -TSS4 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS40 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS41 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 OK 0 8.3103e+06 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TSS42 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 OK 0 2.4671e+07 1.79769e+308 1.79769e+308 0.0512352 0.150149 no -TSS43 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 4.39147e+06 0 -1.79769e+308 -1.79769e+308 0.158655 1 no -TSS44 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 3.99739e+06 1.82908e+06 -1.12794 0.489836 0.62425 1 no -TSS45 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 1.36901e+06 0 0 0 1 1 no -TSS46 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS47 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS48 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 56312.4 372827 2.72698 -1.67622 0.0936947 1 no -TSS49 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS5 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS50 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 OK 0 2.66226e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TSS51 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 OK 9.99919e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TSS52 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 OK 0 5.0951e+07 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TSS53 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS54 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 OK 0 2.06814e+09 1.79769e+308 1.79769e+308 0.0786496 0.150149 no -TSS55 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS56 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS57 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 265614 41870.3 -2.66534 2.48499 0.0129556 1 no -TSS59 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS6 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS60 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS61 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 OK 0 2.29576e+07 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TSS62 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS63 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS64 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS65 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS66 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 OK 0 9.79535e+06 1.79769e+308 1.79769e+308 0.158655 0.158655 no -TSS67 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 OK 1.8095e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TSS68 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 342218 75524 -2.17991 1.96162 0.049807 1 no -TSS7 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 368900 429265 0.21864 -0.483034 0.629072 1 no -TSS70 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 937403 137917 -2.76487 1.66807 0.0953024 1 no -TSS71 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS72 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS73 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS74 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS75 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS76 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS77 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS78 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 OK 8.91489e+06 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TSS79 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS80 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 585828 0 -1.79769e+308 -1.79769e+308 0.0512352 1 no -TSS81 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 OK 1.19208e+08 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TSS82 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 4.42166e+06 0 -1.79769e+308 -1.79769e+308 0.0786496 1 no -TSS83 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS84 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 OK 4.28358e+07 0 -1.79769e+308 -1.79769e+308 0.0786496 0.150149 no -TSS85 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS86 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 OK 7.29939e+07 0 -1.79769e+308 -1.79769e+308 0.158655 0.158655 no -TSS87 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS88 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS89 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS90 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS91 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS92 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS93 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS94 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS95 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS96 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS97 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS98 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS99 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 1 1 no diff -r 56e6257ba73d599a86be2e7731134b398bc79ad7 -r 5019491835c7d196c5545a60aaf2061f629d8f07 test-data/cuffdiff_out4.txt --- a/test-data/cuffdiff_out4.txt +++ /dev/null @@ -1,1 +0,0 @@ -test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/da46b521540d/ Changeset: da46b521540d User: Dave Bouvier Date: 2013-10-01 19:55:16 Summary: Remove migrated tools from tool_conf.xml.main. Affected #: 1 file diff -r 5019491835c7d196c5545a60aaf2061f629d8f07 -r da46b521540df29f936aa51cd03e75068eff1204 tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -289,10 +289,6 @@ <label id="rna_seq" text="RNA-seq" /><tool file="ngs_rna/tophat_wrapper.xml" /><tool file="ngs_rna/tophat2_wrapper.xml" /> - <tool file="ngs_rna/cufflinks_wrapper.xml" /> - <tool file="ngs_rna/cuffcompare_wrapper.xml" /> - <tool file="ngs_rna/cuffmerge_wrapper.xml" /> - <tool file="ngs_rna/cuffdiff_wrapper.xml" /><tool file="ngs_rna/express_wrapper.xml" /><label id="filtering" text="Filtering" /><tool file="ngs_rna/filter_transcripts_via_tracking.xml" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Extend the make_directory action to create the specified directory under the current working directory if it is not prefixed with $INSTALL_DIR.
by commits-noreply＠bitbucket.org 01 Oct '13

01 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/56e6257ba73d/ Changeset: 56e6257ba73d User: Dave Bouvier Date: 2013-10-01 17:51:58 Summary: Extend the make_directory action to create the specified directory under the current working directory if it is not prefixed with $INSTALL_DIR. Affected #: 1 file diff -r 1d1084581b6219ee8ae7968c8109c8132e32a915 -r 56e6257ba73d599a86be2e7731134b398bc79ad7 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -272,7 +272,11 @@ with lcd( current_dir ): action_type, action_dict = action_tup if action_type == 'make_directory': - td_common_util.make_directory( full_path=action_dict[ 'full_path' ] ) + if os.path.isabs( action_dict[ 'full_path' ] ): + full_path = action_dict[ 'full_path' ] + else: + full_path = os.path.join( current_dir, action_dict[ 'full_path' ] ) + td_common_util.make_directory( full_path=full_path ) elif action_type == 'move_directory_files': td_common_util.move_directory_files( current_dir=current_dir, source_dir=os.path.join( action_dict[ 'source_directory' ] ), Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: When installing repositories containing tools that have been migrated from the distribution to the tool shed, handle cases where the repository may have been successfully cloned, but is still in a New state.
by commits-noreply＠bitbucket.org 01 Oct '13

01 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1d1084581b62/ Changeset: 1d1084581b62 User: Dave Bouvier Date: 2013-10-01 16:59:42 Summary: When installing repositories containing tools that have been migrated from the distribution to the tool shed, handle cases where the repository may have been successfully cloned, but is still in a New state. Affected #: 1 file diff -r 7978a2884aa79c87650eb5aca1f934969f276fc0 -r 1d1084581b6219ee8ae7968c8109c8132e32a915 lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -133,7 +133,7 @@ # Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<installed changeset revision> relative_clone_dir = os.path.join( self.tool_shed, 'repos', owner, name, changeset_revision ) clone_dir = os.path.join( self.tool_path, relative_clone_dir ) - if not self.__isinstalled( clone_dir ): + if not self.__iscloned( clone_dir ): repository_clone_url = os.path.join( self.tool_shed_url, 'repos', owner, name ) relative_install_dir = os.path.join( relative_clone_dir, name ) install_dir = os.path.join( clone_dir, name ) @@ -478,7 +478,15 @@ tool_shed_repository.name, tool_shed_repository.installed_changeset_revision ) clone_dir = os.path.join( self.tool_path, relative_clone_dir ) - if self.__isinstalled( clone_dir ): + cloned_ok = self.__iscloned( clone_dir ) + is_installed = False + # Any of the following states should count as installed in this context. + if tool_shed_repository.status in [ self.app.model.ToolShedRepository.installation_status.INSTALLED, + self.app.model.ToolShedRepository.installation_status.ERROR, + self.app.model.ToolShedRepository.installation_status.UNINSTALLED, + self.app.model.ToolShedRepository.installation_status.DEACTIVATED ]: + is_installed = True + if cloned_ok and is_installed: print "Skipping automatic install of repository '", tool_shed_repository.name, "' because it has already been installed in location ", clone_dir else: repository_clone_url = os.path.join( self.tool_shed_url, 'repos', tool_shed_repository.owner, tool_shed_repository.name ) @@ -489,9 +497,10 @@ tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) - suc.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.CLONING ) - cloned_ok, error_message = suc.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev ) - if cloned_ok: + if not cloned_ok: + suc.update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.CLONING ) + cloned_ok, error_message = suc.clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev ) + if cloned_ok and not is_installed: self.handle_repository_contents( tool_shed_repository=tool_shed_repository, repository_clone_url=repository_clone_url, relative_install_dir=relative_install_dir, @@ -592,7 +601,7 @@ return True return False - def __isinstalled( self, clone_dir ): + def __iscloned( self, clone_dir ): full_path = os.path.abspath( clone_dir ) if os.path.exists( full_path ): for root, dirs, files in os.walk( full_path ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: Dave Bouvier: Fill form by name rather than number when uploading files for tool functional tests.
by commits-noreply＠bitbucket.org 01 Oct '13

01 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7978a2884aa7/ Changeset: 7978a2884aa7 User: Dave Bouvier Date: 2013-10-01 16:23:59 Summary: Fill form by name rather than number when uploading files for tool functional tests. Affected #: 1 file diff -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 -r 7978a2884aa79c87650eb5aca1f934969f276fc0 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -191,20 +191,20 @@ self.visit_url( "%s/tool_runner?tool_id=upload1" % self.url ) try: self.refresh_form( "file_type", ftype ) #Refresh, to support composite files - tc.fv("1","dbkey", dbkey) + tc.fv( "tool_form", "dbkey", dbkey ) if metadata: for elem in metadata: - tc.fv( "1", "files_metadata|%s" % elem.get( 'name' ), elem.get( 'value' ) ) + tc.fv( "tool_form", "files_metadata|%s" % elem.get( 'name' ), elem.get( 'value' ) ) if composite_data: for i, composite_file in enumerate( composite_data ): filename = self.get_filename( composite_file.get( 'value' ), shed_tool_id=shed_tool_id ) - tc.formfile( "1", "files_%i|file_data" % i, filename ) - tc.fv( "1", "files_%i|space_to_tab" % i, composite_file.get( 'space_to_tab', False ) ) + tc.formfile( "tool_form", "files_%i|file_data" % i, filename ) + tc.fv( "tool_form", "files_%i|space_to_tab" % i, composite_file.get( 'space_to_tab', False ) ) else: filename = self.get_filename( filename, shed_tool_id=shed_tool_id ) - tc.formfile( "1", "file_data", filename ) - tc.fv( "1", "space_to_tab", space_to_tab ) - tc.submit("runtool_btn") + tc.formfile( "tool_form", "file_data", filename ) + tc.fv( "tool_form", "space_to_tab", space_to_tab ) + tc.submit( "runtool_btn" ) self.home() except AssertionError, err: errmsg = "Uploading file resulted in the following exception. Make sure the file (%s) exists. " % filename Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 01 Oct '13

01 Oct '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8f0476edc6a2/ Changeset: 8f0476edc6a2 User: jgoecks Date: 2013-10-01 02:24:00 Summary: Trackster: improvements for viewing a VCF dataset without samples. Affected #: 3 files diff -r e599b3d6a83347bf1f7a6f5cfadfe541c2c1e035 -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -690,33 +690,38 @@ allele_counts = [ 0 for i in range ( alt.count( ',' ) + 1 ) ] sample_gts = [] - # Process and pack samples' genotype and count alleles across samples. - alleles_seen = {} - has_alleles = False + if samples_data: + # Process and pack samples' genotype and count alleles across samples. + alleles_seen = {} + has_alleles = False - for i, sample in enumerate( samples_data ): - # Parse and count alleles. - genotype = sample.split( ':' )[ 0 ] - has_alleles = False - alleles_seen.clear() - for allele in genotype_re.split( genotype ): - try: - # This may throw a ValueError if allele is missing. - allele = int( allele ) + for i, sample in enumerate( samples_data ): + # Parse and count alleles. + genotype = sample.split( ':' )[ 0 ] + has_alleles = False + alleles_seen.clear() + for allele in genotype_re.split( genotype ): + try: + # This may throw a ValueError if allele is missing. + allele = int( allele ) - # Only count allele if it hasn't been seen yet. - if allele != 0 and allele not in alleles_seen: - allele_counts[ allele - 1 ] += 1 - alleles_seen[ allele ] = True - has_alleles = True - except ValueError: - pass + # Only count allele if it hasn't been seen yet. + if allele != 0 and allele not in alleles_seen: + allele_counts[ allele - 1 ] += 1 + alleles_seen[ allele ] = True + has_alleles = True + except ValueError: + pass - # If no alleles, use empty string as proxy. - if not has_alleles: - genotype = '' + # If no alleles, use empty string as proxy. + if not has_alleles: + genotype = '' - sample_gts.append( genotype ) + sample_gts.append( genotype ) + else: + # No samples, so set allele count and sample genotype manually. + allele_counts = [ 1 ] + sample_gts = [ '1/1' ] # Add locus data. locus_data = [ diff -r e599b3d6a83347bf1f7a6f5cfadfe541c2c1e035 -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -408,7 +408,6 @@ * Abstract function for drawing an individual feature. */ draw_element: function(ctx, mode, feature, slot, tile_low, tile_high, w_scale, y_scale, width ) { - console.log("WARNING: Unimplemented function."); return [0, 0]; } }); @@ -1542,8 +1541,12 @@ * Returns required height to draw a particular number of samples in a given mode. */ get_required_height: function(num_samples) { + // FIXME: for single-sample data, height should be summary_height when zoomed out and + // row_height when zoomed in. var height = this.prefs.summary_height; - if (this.prefs.show_sample_data) { + + // If showing sample data, height is summary + divider + samples. + if (num_samples > 1 && this.prefs.show_sample_data) { height += this.divider_height + num_samples * this.get_row_height(); } return height; @@ -1573,6 +1576,8 @@ genotype, // Always draw variants at least 1 pixel wide. base_px = Math.max(1, Math.floor(w_scale)), + // Determine number of samples. + num_samples = (this.data.length ? this.data[0][7].split(',').length : 0), row_height = (this.mode === 'Squish' ? SQUISH_TRACK_HEIGHT : PACK_TRACK_HEIGHT), // If zoomed out, fill the whole row with feature to make it easier to read; // when zoomed in, use feature height so that there are gaps in sample rows. @@ -1580,10 +1585,19 @@ row_height : (this.mode === 'Squish' ? SQUISH_FEATURE_HEIGHT : PACK_FEATURE_HEIGHT) ), + draw_summary = true, j; + // If there's a single sample, update drawing variables. + if (num_samples === 1) { + row_height = feature_height = + (w_scale < ctx.canvas.manager.char_width_px ? this.prefs.summary_height : row_height); + // No summary when there's a single sample. + draw_summary = false; + } + // Draw divider between summary and samples. - if (this.prefs.show_sample_data) { + if (this.prefs.show_sample_data && draw_summary) { ctx.fillStyle = '#F3F3F3'; ctx.globalAlpha = 1; ctx.fillRect(0, this.prefs.summary_height - this.divider_height, width, this.divider_height); @@ -1608,26 +1622,28 @@ draw_x_start = Math.floor( Math.max(-0.5 * w_scale, (pos - this.view_start - 0.5) * w_scale) ); char_x_start = Math.floor( Math.max(0, (pos - this.view_start) * w_scale) ); - // Draw summary. - ctx.fillStyle = '#999999'; - ctx.globalAlpha = 1; - // Draw background for summary. - ctx.fillRect(draw_x_start, 0, base_px, this.prefs.summary_height); - draw_y_start = this.prefs.summary_height; - // Draw allele fractions onto summary. - for (j = 0; j < alt.length; j++) { - ctx.fillStyle = this.base_color_fn(alt[j]); - allele_frac = allele_counts / sample_gts.length; - draw_height = Math.ceil(this.prefs.summary_height * allele_frac); - ctx.fillRect(draw_x_start, draw_y_start - draw_height, base_px, draw_height); - draw_y_start -= draw_height; + // Draw summary. + if (draw_summary) { + ctx.fillStyle = '#999999'; + ctx.globalAlpha = 1; + // Draw background for summary. + ctx.fillRect(draw_x_start, 0, base_px, this.prefs.summary_height); + draw_y_start = this.prefs.summary_height; + // Draw allele fractions onto summary. + for (j = 0; j < alt.length; j++) { + ctx.fillStyle = this.base_color_fn(alt[j]); + allele_frac = allele_counts / sample_gts.length; + draw_height = Math.ceil(this.prefs.summary_height * allele_frac); + ctx.fillRect(draw_x_start, draw_y_start - draw_height, base_px, draw_height); + draw_y_start -= draw_height; + } } // Done drawing if not showing samples data. if (!this.prefs.show_sample_data) { continue; } - // Draw sample genotypes. - draw_y_start = this.prefs.summary_height + this.divider_height; + // Draw sample genotype(s). + draw_y_start = (draw_summary ? this.prefs.summary_height + this.divider_height : 0); for (j = 0; j < sample_gts.length; j++, draw_y_start += row_height) { genotype = (sample_gts[j] ? sample_gts[j].split(/\/|\|/) : ['0', '0']); diff -r e599b3d6a83347bf1f7a6f5cfadfe541c2c1e035 -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -4278,7 +4278,6 @@ return this.summary_draw_height; } else { - var dummy_painter = new (this.painter)(null, null, null, this.prefs, mode); // HACK: sample_names is not be defined when dataset definition is fetched before // dataset is complete (as is done when running tools). In that case, fall back on // # of samples in data. This can be fixed by re-requesting dataset definition @@ -4295,6 +4294,7 @@ } } + var dummy_painter = new (this.painter)(null, null, null, this.prefs, mode); return dummy_painter.get_required_height(num_samples); } }, @@ -4304,6 +4304,8 @@ */ predraw_init: function() { var deferreds = [ Track.prototype.predraw_init.call(this) ]; + // FIXME: updating dataset metadata is only needed for visual analysis. Can + // this be moved somewhere else? if (!this.dataset.get_metadata('sample_names')) { deferreds.push(this.dataset.fetch()); } @@ -4322,7 +4324,8 @@ }); // Add summary/sample labels if needed and not already included. - if ( line_track_tiles.length === 0 && this.prefs.show_labels) { + var sample_names = this.dataset.get_metadata('sample_names'); + if (line_track_tiles.length === 0 && this.prefs.show_labels && sample_names) { var font_size; // Add and/or style labels. @@ -4340,7 +4343,7 @@ // Show sample labels. if (this.prefs.show_sample_data) { - var samples_div_html = this.dataset.get('metadata').get('sample_names').join('<br/>'); + var samples_div_html = sample_names.join('<br/>'); this.tiles_div.prepend( $("<div/>").html(samples_div_html).addClass('yaxislabel variant top sample').css({ https://bitbucket.org/galaxy/galaxy-central/commits/47f3bec46ced/ Changeset: 47f3bec46ced User: jgoecks Date: 2013-10-01 06:28:30 Summary: Automated merge. Affected #: 40 files diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 lib/galaxy/model/custom_types.py --- a/lib/galaxy/model/custom_types.py +++ b/lib/galaxy/model/custom_types.py @@ -29,6 +29,8 @@ try: if value[0] == 'x': return binascii.unhexlify(value[1:]) + elif value.startswith( '\\x' ): + return binascii.unhexlify( value[2:] ) else: return value except Exception, ex: diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 lib/galaxy/webapps/galaxy/api/folders.py --- a/lib/galaxy/webapps/galaxy/api/folders.py +++ b/lib/galaxy/webapps/galaxy/api/folders.py @@ -52,7 +52,7 @@ o payload's relevant params: - folder_id: This is the parent folder's id (required) """ - log.debug( "FoldersController.create: enter" ) +# log.debug( "FoldersController.create: enter" ) # TODO: Create a single point of exit if possible. For now we only # exit at the end and on exceptions. if 'folder_id' not in payload: @@ -90,7 +90,7 @@ name = v.name, url = url_for( 'folder', id=encoded_id ) ) ) else: - log.debug( "Error creating folder; setting output and status" ) +# log.debug( "Error creating folder; setting output and status" ) trans.response.status = status rval = output return rval diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -28,7 +28,7 @@ :returns: list of dictionaries containing library information .. seealso:: :attr:`galaxy.model.Library.dict_collection_visible_keys` """ - log.debug( "LibrariesController.index: enter" ) +# log.debug( "LibrariesController.index: enter" ) query = trans.sa_session.query( trans.app.model.Library ) deleted = util.string_as_bool( deleted ) if deleted: @@ -73,7 +73,7 @@ :returns: detailed library information .. seealso:: :attr:`galaxy.model.Library.dict_element_visible_keys` """ - log.debug( "LibraryContentsController.show: enter" ) +# log.debug( "LibraryContentsController.show: enter" ) library_id = id deleted = util.string_as_bool( deleted ) try: diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 lib/galaxy/webapps/galaxy/api/library_contents.py --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -53,8 +53,8 @@ can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ld.library_dataset_dataset_association.dataset ) if (admin or can_access) and not ld.deleted: - log.debug( "type(folder): %s" % type( folder ) ) - log.debug( "type(api_path): %s; folder.api_path: %s" % ( type(folder.api_path), folder.api_path ) ) + #log.debug( "type(folder): %s" % type( folder ) ) + #log.debug( "type(api_path): %s; folder.api_path: %s" % ( type(folder.api_path), folder.api_path ) ) #log.debug( "attributes of folder: %s" % str(dir(folder)) ) ld.api_path = folder.api_path + '/' + ld.name ld.api_type = 'file' @@ -72,13 +72,13 @@ if not library or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library( current_user_roles, library ) ): trans.response.status = 400 return "Invalid library id ( %s ) specified." % str( library_id ) - log.debug( "Root folder type: %s" % type( library.root_folder ) ) + #log.debug( "Root folder type: %s" % type( library.root_folder ) ) encoded_id = 'F' + trans.security.encode_id( library.root_folder.id ) rval.append( dict( id = encoded_id, type = 'folder', name = '/', url = url_for( 'library_content', library_id=library_id, id=encoded_id ) ) ) - log.debug( "Root folder attributes: %s" % str(dir(library.root_folder)) ) + #log.debug( "Root folder attributes: %s" % str(dir(library.root_folder)) ) library.root_folder.api_path = '' for content in traverse( library.root_folder ): encoded_id = trans.security.encode_id( content.id ) diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -771,7 +771,7 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) shed_tool_conf = kwd.get( 'shed_tool_conf', None ) - tool_shed_url = kwd[ 'tool_shed_url' ] + tool_shed_url = kwd.get( 'tool_shed_url', None ) # Handle repository dependencies, which do not include those that are required only for compiling a dependent repository's tool dependencies. has_repository_dependencies = util.string_as_bool( kwd.get( 'has_repository_dependencies', False ) ) install_repository_dependencies = kwd.get( 'install_repository_dependencies', '' ) @@ -785,7 +785,9 @@ includes_tools_for_display_in_tool_panel = util.string_as_bool( kwd.get( 'includes_tools_for_display_in_tool_panel', False ) ) includes_tool_dependencies = util.string_as_bool( kwd.get( 'includes_tool_dependencies', False ) ) install_tool_dependencies = kwd.get( 'install_tool_dependencies', '' ) - encoded_repo_info_dicts = util.listify( kwd.get( 'encoded_repo_info_dicts', None ) ) + encoded_repo_info_dicts = kwd.get( 'encoded_repo_info_dicts', '' ) + if encoded_repo_info_dicts: + encoded_repo_info_dicts = encoded_repo_info_dicts.split( encoding_util.encoding_sep ) if not encoded_repo_info_dicts: # The request originated in the tool shed via a tool search. repository_ids = kwd.get( 'repository_ids', None ) @@ -941,6 +943,8 @@ install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=install_tool_dependencies_check_box_checked ) # Handle repository dependencies check box. install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True ) + encoded_repo_info_dicts = encoding_util.encoding_sep.join( encoded_repo_info_dicts ) + tool_shed_url = kwd[ 'tool_shed_url' ] if includes_tools_for_display_in_tool_panel: return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako', encoded_repo_info_dicts=encoded_repo_info_dicts, @@ -955,7 +959,7 @@ shed_tool_conf=shed_tool_conf, shed_tool_conf_select_field=shed_tool_conf_select_field, tool_panel_section_select_field=tool_panel_section_select_field, - tool_shed_url=kwd[ 'tool_shed_url' ], + tool_shed_url=tool_shed_url, message=message, status=status ) else: @@ -974,7 +978,7 @@ shed_tool_conf=shed_tool_conf, shed_tool_conf_select_field=shed_tool_conf_select_field, tool_panel_section_select_field=tool_panel_section_select_field, - tool_shed_url=kwd[ 'tool_shed_url' ], + tool_shed_url=tool_shed_url, message=message, status=status ) diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 lib/galaxy/webapps/tool_shed/model/__init__.py --- a/lib/galaxy/webapps/tool_shed/model/__init__.py +++ b/lib/galaxy/webapps/tool_shed/model/__init__.py @@ -378,6 +378,23 @@ self.user_value = None +class PostJobAction( object ): + + def __init__( self, action_type, workflow_step, output_name = None, action_arguments = None): + self.action_type = action_type + self.output_name = output_name + self.action_arguments = action_arguments + self.workflow_step = workflow_step + + +class StoredWorkflowAnnotationAssociation( object ): + pass + + +class WorkflowStepAnnotationAssociation( object ): + pass + + class Workflow( object ): def __init__( self ): diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py --- a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py +++ b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py @@ -10,35 +10,35 @@ def generate_deprecated_repository_img_str( include_mouse_over=False ): if include_mouse_over: - deprecated_tip_str = 'class="icon-button tooltip" title="This repository is deprecated in the Tool Shed"' + deprecated_tip_str = 'class="icon-button" title="This repository is deprecated in the Tool Shed"' else: deprecated_tip_str = '' return '<img src="/static/images/icon_error_sml.gif" %s/>' % deprecated_tip_str def generate_latest_revision_img_str( include_mouse_over=False ): if include_mouse_over: - latest_revision_tip_str = 'class="icon-button tooltip" title="This is the latest installable revision of this repository"' + latest_revision_tip_str = 'class="icon-button" title="This is the latest installable revision of this repository"' else: latest_revision_tip_str = '' return '<img src="/static/june_2007_style/blue/ok_small.png" %s/>' % latest_revision_tip_str def generate_revision_updates_img_str( include_mouse_over=False ): if include_mouse_over: - revision_updates_tip_str = 'class="icon-button tooltip" title="Updates are available in the Tool Shed for this revision"' + revision_updates_tip_str = 'class="icon-button" title="Updates are available in the Tool Shed for this revision"' else: revision_updates_tip_str = '' return '<img src="/static/images/icon_warning_sml.gif" %s/>' % revision_updates_tip_str def generate_revision_upgrades_img_str( include_mouse_over=False ): if include_mouse_over: - revision_upgrades_tip_str = 'class="icon-button tooltip" title="A newer installable revision is available for this repository"' + revision_upgrades_tip_str = 'class="icon-button" title="A newer installable revision is available for this repository"' else: revision_upgrades_tip_str = '' return '<img src="/static/images/up.gif" %s/>' % revision_upgrades_tip_str def generate_unknown_img_str( include_mouse_over=False ): if include_mouse_over: - unknown_tip_str = 'class="icon-button tooltip" title="Unable to get information from the Tool Shed"' + unknown_tip_str = 'class="icon-button" title="Unable to get information from the Tool Shed"' else: unknown_tip_str = '' return '<img src="/static/june_2007_style/blue/question-octagon-frame.png" %s/>' % unknown_tip_str diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 lib/tool_shed/util/workflow_util.py --- a/lib/tool_shed/util/workflow_util.py +++ b/lib/tool_shed/util/workflow_util.py @@ -389,13 +389,14 @@ workflow.has_errors = True # Stick this in the step temporarily. step.temp_input_connections = step_dict[ 'input_connections' ] - annotation = step_dict.get( 'annotation', '') - if annotation: - annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) - new_step_annotation = trans.model.WorkflowStepAnnotationAssociation() - new_step_annotation.annotation = annotation - new_step_annotation.user = trans.user - step.annotations.append(new_step_annotation) + if trans.webapp.name == 'galaxy': + annotation = step_dict.get( 'annotation', '') + if annotation: + annotation = sanitize_html( annotation, 'utf-8', 'text/html' ) + new_step_annotation = trans.model.WorkflowStepAnnotationAssociation() + new_step_annotation.annotation = annotation + new_step_annotation.user = trans.user + step.annotations.append( new_step_annotation ) # Unpack and add post-job actions. post_job_actions = step_dict.get( 'post_job_actions', {} ) for name, pja_dict in post_job_actions.items(): diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/scripts/galaxy.frame.js --- a/static/scripts/galaxy.frame.js +++ b/static/scripts/galaxy.frame.js @@ -1062,7 +1062,7 @@ '<span class="f-icon f-pin fa-icon-pushpin"></span>' + '<span class="f-icon f-close fa-icon-trash"></span>' + '</div>' + - '<div class="f-content corner">' + content + + '<div class="f-content">' + content + '<div class="f-cover"></div>' + '</div>' + '<span class="f-resize f-icon corner fa-icon-resize-full"></span>' + diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -1,5 +1,5 @@ /* - galaxy modal v1.0 + galaxy modal */ // dependencies @@ -9,91 +9,105 @@ var GalaxyModal = Backbone.View.extend( { // base element - el_main: '#everything', + elMain: '#everything', // defaults inputs - options: - { + optionsDefaults: { title : "galaxy-modal", body : "No content available." }, // initialize - initialize : function(options) - { + initialize : function(options) { // create if (options) - { this.create(options); - - // hide - $(this.el).hide(); - } }, // adds and displays a new frame/window - show: function(options) - { + show: function(options) { // create - if (options) - this.create(options); - - // fade out - this.$el.fadeIn('fast'); + this.initialize(options); + + // fix height + var body = (this.$el).find('.modal-body'); + body.css('max-height', $(document).height() / 2); + + // show + if (this.visible) + this.$el.show(); + else + this.$el.fadeIn('fast'); + + // set visibility flag + this.visible = true; }, // hide modal - hide: function() - { + hide: function(){ // fade out this.$el.fadeOut('fast'); + + // set visibility flag + this.visible = false; }, - // destroy modal - create: function (options) - { - // remove element - this.$el.remove(); + // create + create: function(options) { + // configure options + options = _.defaults(options, this.optionsDefault); + + // check for progress bar request + if (options.body == 'progress') + options.body = '<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>'; + + // remove former element + if (this.$el) + this.$el.remove(); - // read in defaults - if (!options) - options = this.options; - else - options = _.defaults(options, this.options); - - // create element - this.setElement(this.template(options.title, options.body)); - - // append template - $(this.el_main).append($(this.el)); + // create new element + this.setElement(this.template(options.title)); // link elements - var footer = (this.$el).find('.buttons'); - + var body = (this.$el).find('.modal-body'); + var footer = (this.$el).find('.modal-footer'); + var buttons = (this.$el).find('.buttons'); + + // append body + body.append($(options.body)); + + // fix height if available + if (options.height) + body.css('height', options.height); + // append buttons - var self = this; - if (options.buttons) - { + if (options.buttons) { // link functions - $.each(options.buttons, function(name, value) - { - footer.append($('<button id="' + String(name).toLowerCase() + '"></button>').text(name).click(value)).append(" "); + $.each(options.buttons, function(name, value) { + buttons.append($('<button id="' + String(name).toLowerCase() + '"></button>').text(name).click(value)).append(" "); }); } else - // default close button - footer.append($('<button></button>').text('Close').click(function() { self.hide() })).append(" "); + // hide footer + footer.hide(); + + // append to main element + $(this.elMain).append($(this.el)); }, // enable buttons - enable: function(name) - { + enable: function(name) { $(this.el).find('#' + String(name).toLowerCase()).prop('disabled', false); }, // disable buttons - disable: function(name) + disable: function(name) { + $(this.el).find('#' + String(name).toLowerCase()).prop('disabled', true); + }, + + // returns scroll top for body element + scrollTop: function() { - $(this.el).find('#' + String(name).toLowerCase()).prop('disabled', true); + return $(this.el).find('.modal-body').scrollTop(); }, /* @@ -101,8 +115,7 @@ */ // fill regular modal template - template: function(title, body) - { + template: function(title) { return '<div class="modal in">' + '<div class="modal-backdrop in" style="z-index: -1;"></div>' + '<div class="modal-dialog">' + @@ -110,7 +123,7 @@ '<div class="modal-header">' + '<span><h3 class="title">' + title + '</h3></span>' + '</div>' + - '<div class="modal-body style="min-width: 540px; max-height: 445px;">' + body + '</div>' + + '<div class="modal-body"></div>' + '<div class="modal-footer">' + '<div class="buttons" style="float: right;"></div>' + '</div>' + diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/scripts/galaxy.panels.js --- a/static/scripts/galaxy.panels.js +++ b/static/scripts/galaxy.panels.js @@ -125,15 +125,22 @@ this.$body = this.$dialog.find( ".modal-body" ); this.$footer = this.$dialog.find( ".modal-footer" ); this.$backdrop = options.backdrop; + // Close button + this.$header.find( ".close" ).on( "click", $.proxy( this.hide, this ) ); } $.extend( Modal.prototype, { setContent: function( options ) { + this.$header.hide(); // Title if ( options.title ) { this.$header.find( ".title" ).html( options.title ); this.$header.show(); + } + if ( options.closeButton ) { + this.$header.find( ".close" ).show(); + this.$header.show(); } else { - this.$header.hide(); + this.$header.find( ".close" ).hide(); } // Buttons this.$footer.hide(); @@ -223,8 +230,8 @@ hide_modal(); $("#overlay-background").unbind( "click.overlay" ); }); - show_modal( null, $( "<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='" + galaxy_config.root + "static/images/closebox.png'><iframe style='margin: 0; padding: 0;' src='" + options.url + "' width='" + width + "' height='" + height + "' scrolling='" + scroll + "' frameborder='0'></iframe></div>" ) ); - $("#close_button").bind( "click", function() { hide_modal(); } ); + modal.setContent( { closeButton: true, title: " ", body: $( "<div style='margin: -5px;'><iframe style='margin: 0; padding: 0;' src='" + options.url + "' width='" + width + "' height='" + height + "' scrolling='" + scroll + "' frameborder='0'></iframe></div>" ) } ); + modal.show( { backdrop: true } ); } function user_changed( user_email, is_admin ) { diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/scripts/galaxy.upload.js --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -9,7 +9,7 @@ var GalaxyUpload = Backbone.View.extend( { // own modal - modal : null, + modal : null, // button button_show : null, @@ -346,7 +346,8 @@ 'Upload' : function() {self.event_upload()}, 'Reset' : function() {self.event_reset()}, 'Close' : function() {self.modal.hide()} - } + }, + height : '250px' }); // set element @@ -369,7 +370,7 @@ // setup info this.update_screen(); } - + // show modal this.modal.show(); }, @@ -411,7 +412,7 @@ message = 'Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.' } else { if (this.counter.running == 0) - message = 'You added ' + this.counter.announce + ' file(s) to the queue. Add more files or click "Upload" to proceed.'; + message = 'You added ' + this.counter.announce + ' file(s) to the queue. Add more files or click \'Upload\' to proceed.'; else message = 'Please wait...' + this.counter.announce + ' out of ' + this.counter.running + ' remaining.'; } diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/scripts/packed/galaxy.frame.js --- a/static/scripts/packed/galaxy.frame.js +++ b/static/scripts/packed/galaxy.frame.js @@ -1,1 +1,1 @@ -define(["galaxy.master","libs/backbone/backbone-relational"],function(b){var a=Backbone.View.extend({el_main:"#everything",options:{frame:{cols:6,rows:3},rows:1000,cell:130,margin:5,scroll:5,top_min:40,frame_max:9},cols:0,top:0,top_max:0,frame_z:0,frame_counter:0,frame_counter_id:0,frame_list:[],frame_shadow:null,visible:false,active:false,button_active:null,button_load:null,initialize:function(d){var c=this;this.button_active=new b.GalaxyMasterIcon({icon:"fa-icon-th",tooltip:"Enable/Disable Scratchbook",on_click:function(f){c.event_panel_active(f)}});Galaxy.master.append(this.button_active);this.button_load=new b.GalaxyMasterIcon({icon:"fa-icon-eye-open",tooltip:"Show/Hide Scratchbook",on_click:function(f){c.event_panel_load(f)},with_number:true});Galaxy.master.append(this.button_load);if(d){this.options=_.defaults(d,this.options)}this.top=this.top_max=this.options.top_min;this.setElement(this.template());$(this.el).append(this.template_background());$(this.el).append(this.template_menu());$(this.el_main).append($(this.el));var e="#frame-shadow";$(this.el).append(this.template_shadow(e.substring(1)));this.frame_shadow={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};this.frame_resize(this.frame_shadow,{width:0,height:0});this.frame_list[e]=this.frame_shadow;this.panel_refresh();var c=this;$(window).resize(function(){if(c.visible){c.panel_refresh()}});window.onbeforeunload=function(){if(c.frame_counter>0){return"You opened "+c.frame_counter+" frame(s) which will be lost."}}},event:{type:null,target:null,xy:null},events:{mousemove:"event_frame_mouse_move",mouseup:"event_frame_mouse_up",mouseleave:"event_frame_mouse_up",mousewheel:"event_panel_scroll",DOMMouseScroll:"event_panel_scroll","mousedown .frame":"event_frame_mouse_down","mousedown .frame-background":"event_panel_load","mousedown .frame-scroll-up":"event_panel_scroll_up","mousedown .frame-scroll-down":"event_panel_scroll_down","mousedown .f-close":"event_frame_close","mousedown .f-pin":"event_frame_lock"},event_frame_mouse_down:function(c){if(this.event.type!==null){return}if($(c.target).hasClass("f-header")||$(c.target).hasClass("f-title")){this.event.type="drag"}if($(c.target).hasClass("f-resize")){this.event.type="resize"}if(this.event.type===null){return}c.preventDefault();this.event.target=this.event_get_frame(c.target);if(this.event.target.grid_lock){this.event.type=null;return}this.event.xy={x:c.originalEvent.pageX,y:c.originalEvent.pageY};this.frame_drag_start(this.event.target)},event_frame_mouse_move:function(i){if(this.event.type!="drag"&&this.event.type!="resize"){return}var g={x:i.originalEvent.pageX,y:i.originalEvent.pageY};var d={x:g.x-this.event.xy.x,y:g.y-this.event.xy.y};this.event.xy=g;var h=this.frame_screen(this.event.target);if(this.event.type=="resize"){h.width+=d.x;h.height+=d.y;var f=this.options.cell-this.options.margin-1;h.width=Math.max(h.width,f);h.height=Math.max(h.height,f);this.frame_resize(this.event.target,h);h.width=this.to_grid_coord("width",h.width)+1;h.height=this.to_grid_coord("height",h.height)+1;h.width=this.to_pixel_coord("width",h.width);h.height=this.to_pixel_coord("height",h.height);this.frame_resize(this.frame_shadow,h);this.frame_insert(this.frame_shadow,{top:this.to_grid_coord("top",h.top),left:this.to_grid_coord("left",h.left)})}if(this.event.type=="drag"){h.left+=d.x;h.top+=d.y;this.frame_offset(this.event.target,h);var c={top:this.to_grid_coord("top",h.top),left:this.to_grid_coord("left",h.left)};if(c.left!==0){c.left++}this.frame_insert(this.frame_shadow,c)}},event_frame_mouse_up:function(c){if(this.event.type!="drag"&&this.event.type!="resize"){return}this.frame_drag_stop(this.event.target);this.event.type=null},event_frame_close:function(d){if(this.event.type!==null){return}d.preventDefault();var f=this.event_get_frame(d.target);var c=this;$(f.id).fadeOut("fast",function(){$(f.id).remove();delete c.frame_list[f.id];c.frame_counter--;c.panel_refresh(true);c.panel_animation_complete();if(c.visible&&c.frame_counter==0){c.panel_show_hide()}})},event_frame_lock:function(c){if(this.event.type!==null){return}c.preventDefault();var d=this.event_get_frame(c.target);if(d.grid_lock){d.grid_lock=false;$(d.id).find(".f-pin").removeClass("toggle");$(d.id).find(".f-header").removeClass("f-not-allowed");$(d.id).find(".f-title").removeClass("f-not-allowed");$(d.id).find(".f-resize").show();$(d.id).find(".f-close").show()}else{d.grid_lock=true;$(d.id).find(".f-pin").addClass("toggle");$(d.id).find(".f-header").addClass("f-not-allowed");$(d.id).find(".f-title").addClass("f-not-allowed");$(d.id).find(".f-resize").hide();$(d.id).find(".f-close").hide()}},event_panel_load:function(c){if(this.event.type!==null){return}this.panel_show_hide()},event_panel_active:function(c){if(this.event.type!==null){return}this.panel_active_disable()},event_panel_scroll:function(c){if(this.event.type!==null||!this.visible){return}c.preventDefault();var d=c.originalEvent.detail?c.originalEvent.detail:c.originalEvent.wheelDelta/-3;this.panel_scroll(d)},event_panel_scroll_up:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_scroll(-this.options.scroll)},event_panel_scroll_down:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_scroll(this.options.scroll)},event_get_frame:function(c){return this.frame_list["#"+$(c).closest(".frame").attr("id")]},frame_drag_start:function(d){this.frame_focus(d,true);var c=this.frame_screen(d);this.frame_resize(this.frame_shadow,c);this.frame_grid(this.frame_shadow,d.grid_location);d.grid_location=null;$(this.frame_shadow.id).show();$(".f-cover").show()},frame_drag_stop:function(d){this.frame_focus(d,false);var c=this.frame_screen(this.frame_shadow);this.frame_resize(d,c);this.frame_grid(d,this.frame_shadow.grid_location,true);this.frame_shadow.grid_location=null;$(this.frame_shadow.id).hide();$(".f-cover").hide();this.panel_animation_complete()},to_grid_coord:function(e,d){var c=(e=="width"||e=="height")?1:-1;if(e=="top"){d-=this.top}return parseInt((d+c*this.options.margin)/this.options.cell,10)},to_pixel_coord:function(e,f){var c=(e=="width"||e=="height")?1:-1;var d=(f*this.options.cell)-c*this.options.margin;if(e=="top"){d+=this.top}return d},to_grid:function(c){return{top:this.to_grid_coord("top",c.top),left:this.to_grid_coord("left",c.left),width:this.to_grid_coord("width",c.width),height:this.to_grid_coord("height",c.height)}},to_pixel:function(c){return{top:this.to_pixel_coord("top",c.top),left:this.to_pixel_coord("left",c.left),width:this.to_pixel_coord("width",c.width),height:this.to_pixel_coord("height",c.height)}},is_collision:function(e){function c(h,g){return !(h.left>g.left+g.width-1||h.left+h.width-1<g.left||h.top>g.top+g.height-1||h.top+h.height-1<g.top)}for(var d in this.frame_list){var f=this.frame_list[d];if(f.grid_location===null){continue}if(c(e,f.grid_location)){return true}}return false},location_rank:function(c){return(c.top*this.cols)+c.left},menu_refresh:function(){this.button_load.number(this.frame_counter);if(this.frame_counter==0){this.button_load.hide()}else{this.button_load.show()}if(this.top==this.options.top_min){$(".frame-scroll-up").hide()}else{$(".frame-scroll-up").show()}if(this.top==this.top_max){$(".frame-scroll-down").hide()}else{$(".frame-scroll-down").show()}},panel_animation_complete:function(){var c=this;$(".frame").promise().done(function(){c.panel_scroll(0,true)})},panel_refresh:function(c){this.cols=parseInt($(window).width()/this.options.cell,10)+1;this.frame_insert(null,null,c)},panel_scroll:function(h,c){var e=this.top-this.options.scroll*h;e=Math.max(e,this.top_max);e=Math.min(e,this.options.top_min);if(this.top!=e){for(var d in this.frame_list){var g=this.frame_list[d];if(g.grid_location!==null){var f={top:g.screen_location.top-(this.top-e),left:g.screen_location.left};this.frame_offset(g,f,c)}}this.top=e}this.menu_refresh()},panel_show_hide:function(){if(this.visible){this.visible=false;$(".frame").fadeOut("fast");this.button_load.icon("fa-icon-eye-close");this.button_load.untoggle();$(".frame-background").hide();$(".frame-menu").hide()}else{this.visible=true;$(".frame").fadeIn("fast");this.button_load.icon("fa-icon-eye-open");this.button_load.toggle();$(this.frame_shadow.id).hide();$(".frame-background").show();this.panel_refresh()}},panel_active_disable:function(){if(this.active){this.active=false;this.button_active.untoggle();if(this.visible){this.panel_show_hide()}}else{this.active=true;this.button_active.toggle()}},frame_new:function(d){if(!this.active){if(d.location=="center"){var c=$(window.parent.document).find("iframe#galaxy_main");c.attr("src",d.content)}else{window.location=d.content}return}if(this.frame_counter>=this.options.frame_max){alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").");return}var e="#frame-"+(this.frame_counter_id++);if($(e).length!==0){alert("This frame already exists. This page might contain multiple frame managers.");return}this.top=this.options.top_min;$(this.el).append(this.template_frame(e.substring(1),d.title,d.type,d.content));var f={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};d.width=this.to_pixel_coord("width",this.options.frame.cols);d.height=this.to_pixel_coord("height",this.options.frame.rows);this.frame_z=parseInt($(f.id).css("z-index"));this.frame_list[e]=f;this.frame_counter++;this.frame_resize(f,{width:d.width,height:d.height});this.frame_insert(f,{top:0,left:0},true);if(!this.visible){this.panel_show_hide()}},frame_insert:function(j,c,e){var d=[];if(j){j.grid_location=null;d.push([j,this.location_rank(c)])}var g=null;for(g in this.frame_list){var h=this.frame_list[g];if(h.grid_location!==null&&!h.grid_lock){h.grid_location=null;d.push([h,h.grid_rank])}}d.sort(function(k,f){var m=k[1];var l=f[1];return m<l?-1:(m>l?1:0)});for(g=0;g<d.length;g++){this.frame_place(d[g][0],e)}this.top_max=0;for(var g in this.frame_list){var j=this.frame_list[g];if(j.grid_location!==null){this.top_max=Math.max(this.top_max,j.grid_location.top+j.grid_location.height)}}this.top_max=$(window).height()-this.top_max*this.options.cell-2*this.options.margin;this.top_max=Math.min(this.top_max,this.options.top_min);this.menu_refresh()},frame_place:function(k,d){k.grid_location=null;var h=this.to_grid(this.frame_screen(k));var c=false;for(var f=0;f<this.options.rows;f++){for(var e=0;e<Math.max(1,this.cols-h.width);e++){h.top=f;h.left=e;if(!this.is_collision(h)){c=true;break}}if(c){break}}if(c){this.frame_grid(k,h,d)}else{console.log("Grid dimensions exceeded.")}},frame_focus:function(e,c){var d=this.frame_z+(c?1:0);$(e.id).css("z-index",d)},frame_offset:function(f,e,d){f.screen_location.left=e.left;f.screen_location.top=e.top;if(d){this.frame_focus(f,true);var c=this;$(f.id).animate({top:e.top,left:e.left},"fast",function(){c.frame_focus(f,false)})}else{$(f.id).css({top:e.top,left:e.left})}},frame_resize:function(d,c){$(d.id).css({width:c.width,height:c.height});d.screen_location.width=c.width;d.screen_location.height=c.height},frame_grid:function(e,c,d){e.grid_location=c;this.frame_offset(e,this.to_pixel(c),d);e.grid_rank=this.location_rank(c)},frame_screen:function(d){var c=d.screen_location;return{top:c.top,left:c.left,width:c.width,height:c.height}},template:function(){return'<div class="galaxy-frame"></div>'},template_frame:function(f,e,c,d){if(!e){e=""}if(c=="url"){d='<iframe scrolling="auto" class="f-iframe" src="'+d+'"></iframe>'}return'<div id="'+f+'" class="frame corner"><div class="f-header corner"><span class="f-title">'+e+'</span><span class="f-icon f-pin fa-icon-pushpin"></span><span class="f-icon f-close fa-icon-trash"></span></div><div class="f-content corner">'+d+'<div class="f-cover"></div></div><span class="f-resize f-icon corner fa-icon-resize-full"></span></div>'},template_shadow:function(c){return'<div id="'+c+'" class="frame-shadow corner"></div>'},template_background:function(){return'<div class="frame-background"></div>'},template_menu:function(){return'<div class="frame-scroll-up frame-menu fa-icon-chevron-up fa-icon-2x"></div><div class="frame-scroll-down frame-menu fa-icon-chevron-down fa-icon-2x"></div>'}});return{GalaxyFrameManager:a}}); \ No newline at end of file +define(["galaxy.master","libs/backbone/backbone-relational"],function(b){var a=Backbone.View.extend({el_main:"#everything",options:{frame:{cols:6,rows:3},rows:1000,cell:130,margin:5,scroll:5,top_min:40,frame_max:9},cols:0,top:0,top_max:0,frame_z:0,frame_counter:0,frame_counter_id:0,frame_list:[],frame_shadow:null,visible:false,active:false,button_active:null,button_load:null,initialize:function(d){var c=this;this.button_active=new b.GalaxyMasterIcon({icon:"fa-icon-th",tooltip:"Enable/Disable Scratchbook",on_click:function(f){c.event_panel_active(f)}});Galaxy.master.append(this.button_active);this.button_load=new b.GalaxyMasterIcon({icon:"fa-icon-eye-open",tooltip:"Show/Hide Scratchbook",on_click:function(f){c.event_panel_load(f)},with_number:true});Galaxy.master.append(this.button_load);if(d){this.options=_.defaults(d,this.options)}this.top=this.top_max=this.options.top_min;this.setElement(this.template());$(this.el).append(this.template_background());$(this.el).append(this.template_menu());$(this.el_main).append($(this.el));var e="#frame-shadow";$(this.el).append(this.template_shadow(e.substring(1)));this.frame_shadow={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};this.frame_resize(this.frame_shadow,{width:0,height:0});this.frame_list[e]=this.frame_shadow;this.panel_refresh();var c=this;$(window).resize(function(){if(c.visible){c.panel_refresh()}});window.onbeforeunload=function(){if(c.frame_counter>0){return"You opened "+c.frame_counter+" frame(s) which will be lost."}}},event:{type:null,target:null,xy:null},events:{mousemove:"event_frame_mouse_move",mouseup:"event_frame_mouse_up",mouseleave:"event_frame_mouse_up",mousewheel:"event_panel_scroll",DOMMouseScroll:"event_panel_scroll","mousedown .frame":"event_frame_mouse_down","mousedown .frame-background":"event_panel_load","mousedown .frame-scroll-up":"event_panel_scroll_up","mousedown .frame-scroll-down":"event_panel_scroll_down","mousedown .f-close":"event_frame_close","mousedown .f-pin":"event_frame_lock"},event_frame_mouse_down:function(c){if(this.event.type!==null){return}if($(c.target).hasClass("f-header")||$(c.target).hasClass("f-title")){this.event.type="drag"}if($(c.target).hasClass("f-resize")){this.event.type="resize"}if(this.event.type===null){return}c.preventDefault();this.event.target=this.event_get_frame(c.target);if(this.event.target.grid_lock){this.event.type=null;return}this.event.xy={x:c.originalEvent.pageX,y:c.originalEvent.pageY};this.frame_drag_start(this.event.target)},event_frame_mouse_move:function(i){if(this.event.type!="drag"&&this.event.type!="resize"){return}var g={x:i.originalEvent.pageX,y:i.originalEvent.pageY};var d={x:g.x-this.event.xy.x,y:g.y-this.event.xy.y};this.event.xy=g;var h=this.frame_screen(this.event.target);if(this.event.type=="resize"){h.width+=d.x;h.height+=d.y;var f=this.options.cell-this.options.margin-1;h.width=Math.max(h.width,f);h.height=Math.max(h.height,f);this.frame_resize(this.event.target,h);h.width=this.to_grid_coord("width",h.width)+1;h.height=this.to_grid_coord("height",h.height)+1;h.width=this.to_pixel_coord("width",h.width);h.height=this.to_pixel_coord("height",h.height);this.frame_resize(this.frame_shadow,h);this.frame_insert(this.frame_shadow,{top:this.to_grid_coord("top",h.top),left:this.to_grid_coord("left",h.left)})}if(this.event.type=="drag"){h.left+=d.x;h.top+=d.y;this.frame_offset(this.event.target,h);var c={top:this.to_grid_coord("top",h.top),left:this.to_grid_coord("left",h.left)};if(c.left!==0){c.left++}this.frame_insert(this.frame_shadow,c)}},event_frame_mouse_up:function(c){if(this.event.type!="drag"&&this.event.type!="resize"){return}this.frame_drag_stop(this.event.target);this.event.type=null},event_frame_close:function(d){if(this.event.type!==null){return}d.preventDefault();var f=this.event_get_frame(d.target);var c=this;$(f.id).fadeOut("fast",function(){$(f.id).remove();delete c.frame_list[f.id];c.frame_counter--;c.panel_refresh(true);c.panel_animation_complete();if(c.visible&&c.frame_counter==0){c.panel_show_hide()}})},event_frame_lock:function(c){if(this.event.type!==null){return}c.preventDefault();var d=this.event_get_frame(c.target);if(d.grid_lock){d.grid_lock=false;$(d.id).find(".f-pin").removeClass("toggle");$(d.id).find(".f-header").removeClass("f-not-allowed");$(d.id).find(".f-title").removeClass("f-not-allowed");$(d.id).find(".f-resize").show();$(d.id).find(".f-close").show()}else{d.grid_lock=true;$(d.id).find(".f-pin").addClass("toggle");$(d.id).find(".f-header").addClass("f-not-allowed");$(d.id).find(".f-title").addClass("f-not-allowed");$(d.id).find(".f-resize").hide();$(d.id).find(".f-close").hide()}},event_panel_load:function(c){if(this.event.type!==null){return}this.panel_show_hide()},event_panel_active:function(c){if(this.event.type!==null){return}this.panel_active_disable()},event_panel_scroll:function(c){if(this.event.type!==null||!this.visible){return}c.preventDefault();var d=c.originalEvent.detail?c.originalEvent.detail:c.originalEvent.wheelDelta/-3;this.panel_scroll(d)},event_panel_scroll_up:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_scroll(-this.options.scroll)},event_panel_scroll_down:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_scroll(this.options.scroll)},event_get_frame:function(c){return this.frame_list["#"+$(c).closest(".frame").attr("id")]},frame_drag_start:function(d){this.frame_focus(d,true);var c=this.frame_screen(d);this.frame_resize(this.frame_shadow,c);this.frame_grid(this.frame_shadow,d.grid_location);d.grid_location=null;$(this.frame_shadow.id).show();$(".f-cover").show()},frame_drag_stop:function(d){this.frame_focus(d,false);var c=this.frame_screen(this.frame_shadow);this.frame_resize(d,c);this.frame_grid(d,this.frame_shadow.grid_location,true);this.frame_shadow.grid_location=null;$(this.frame_shadow.id).hide();$(".f-cover").hide();this.panel_animation_complete()},to_grid_coord:function(e,d){var c=(e=="width"||e=="height")?1:-1;if(e=="top"){d-=this.top}return parseInt((d+c*this.options.margin)/this.options.cell,10)},to_pixel_coord:function(e,f){var c=(e=="width"||e=="height")?1:-1;var d=(f*this.options.cell)-c*this.options.margin;if(e=="top"){d+=this.top}return d},to_grid:function(c){return{top:this.to_grid_coord("top",c.top),left:this.to_grid_coord("left",c.left),width:this.to_grid_coord("width",c.width),height:this.to_grid_coord("height",c.height)}},to_pixel:function(c){return{top:this.to_pixel_coord("top",c.top),left:this.to_pixel_coord("left",c.left),width:this.to_pixel_coord("width",c.width),height:this.to_pixel_coord("height",c.height)}},is_collision:function(e){function c(h,g){return !(h.left>g.left+g.width-1||h.left+h.width-1<g.left||h.top>g.top+g.height-1||h.top+h.height-1<g.top)}for(var d in this.frame_list){var f=this.frame_list[d];if(f.grid_location===null){continue}if(c(e,f.grid_location)){return true}}return false},location_rank:function(c){return(c.top*this.cols)+c.left},menu_refresh:function(){this.button_load.number(this.frame_counter);if(this.frame_counter==0){this.button_load.hide()}else{this.button_load.show()}if(this.top==this.options.top_min){$(".frame-scroll-up").hide()}else{$(".frame-scroll-up").show()}if(this.top==this.top_max){$(".frame-scroll-down").hide()}else{$(".frame-scroll-down").show()}},panel_animation_complete:function(){var c=this;$(".frame").promise().done(function(){c.panel_scroll(0,true)})},panel_refresh:function(c){this.cols=parseInt($(window).width()/this.options.cell,10)+1;this.frame_insert(null,null,c)},panel_scroll:function(h,c){var e=this.top-this.options.scroll*h;e=Math.max(e,this.top_max);e=Math.min(e,this.options.top_min);if(this.top!=e){for(var d in this.frame_list){var g=this.frame_list[d];if(g.grid_location!==null){var f={top:g.screen_location.top-(this.top-e),left:g.screen_location.left};this.frame_offset(g,f,c)}}this.top=e}this.menu_refresh()},panel_show_hide:function(){if(this.visible){this.visible=false;$(".frame").fadeOut("fast");this.button_load.icon("fa-icon-eye-close");this.button_load.untoggle();$(".frame-background").hide();$(".frame-menu").hide()}else{this.visible=true;$(".frame").fadeIn("fast");this.button_load.icon("fa-icon-eye-open");this.button_load.toggle();$(this.frame_shadow.id).hide();$(".frame-background").show();this.panel_refresh()}},panel_active_disable:function(){if(this.active){this.active=false;this.button_active.untoggle();if(this.visible){this.panel_show_hide()}}else{this.active=true;this.button_active.toggle()}},frame_new:function(d){if(!this.active){if(d.location=="center"){var c=$(window.parent.document).find("iframe#galaxy_main");c.attr("src",d.content)}else{window.location=d.content}return}if(this.frame_counter>=this.options.frame_max){alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").");return}var e="#frame-"+(this.frame_counter_id++);if($(e).length!==0){alert("This frame already exists. This page might contain multiple frame managers.");return}this.top=this.options.top_min;$(this.el).append(this.template_frame(e.substring(1),d.title,d.type,d.content));var f={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};d.width=this.to_pixel_coord("width",this.options.frame.cols);d.height=this.to_pixel_coord("height",this.options.frame.rows);this.frame_z=parseInt($(f.id).css("z-index"));this.frame_list[e]=f;this.frame_counter++;this.frame_resize(f,{width:d.width,height:d.height});this.frame_insert(f,{top:0,left:0},true);if(!this.visible){this.panel_show_hide()}},frame_insert:function(j,c,e){var d=[];if(j){j.grid_location=null;d.push([j,this.location_rank(c)])}var g=null;for(g in this.frame_list){var h=this.frame_list[g];if(h.grid_location!==null&&!h.grid_lock){h.grid_location=null;d.push([h,h.grid_rank])}}d.sort(function(k,f){var m=k[1];var l=f[1];return m<l?-1:(m>l?1:0)});for(g=0;g<d.length;g++){this.frame_place(d[g][0],e)}this.top_max=0;for(var g in this.frame_list){var j=this.frame_list[g];if(j.grid_location!==null){this.top_max=Math.max(this.top_max,j.grid_location.top+j.grid_location.height)}}this.top_max=$(window).height()-this.top_max*this.options.cell-2*this.options.margin;this.top_max=Math.min(this.top_max,this.options.top_min);this.menu_refresh()},frame_place:function(k,d){k.grid_location=null;var h=this.to_grid(this.frame_screen(k));var c=false;for(var f=0;f<this.options.rows;f++){for(var e=0;e<Math.max(1,this.cols-h.width);e++){h.top=f;h.left=e;if(!this.is_collision(h)){c=true;break}}if(c){break}}if(c){this.frame_grid(k,h,d)}else{console.log("Grid dimensions exceeded.")}},frame_focus:function(e,c){var d=this.frame_z+(c?1:0);$(e.id).css("z-index",d)},frame_offset:function(f,e,d){f.screen_location.left=e.left;f.screen_location.top=e.top;if(d){this.frame_focus(f,true);var c=this;$(f.id).animate({top:e.top,left:e.left},"fast",function(){c.frame_focus(f,false)})}else{$(f.id).css({top:e.top,left:e.left})}},frame_resize:function(d,c){$(d.id).css({width:c.width,height:c.height});d.screen_location.width=c.width;d.screen_location.height=c.height},frame_grid:function(e,c,d){e.grid_location=c;this.frame_offset(e,this.to_pixel(c),d);e.grid_rank=this.location_rank(c)},frame_screen:function(d){var c=d.screen_location;return{top:c.top,left:c.left,width:c.width,height:c.height}},template:function(){return'<div class="galaxy-frame"></div>'},template_frame:function(f,e,c,d){if(!e){e=""}if(c=="url"){d='<iframe scrolling="auto" class="f-iframe" src="'+d+'"></iframe>'}return'<div id="'+f+'" class="frame corner"><div class="f-header corner"><span class="f-title">'+e+'</span><span class="f-icon f-pin fa-icon-pushpin"></span><span class="f-icon f-close fa-icon-trash"></span></div><div class="f-content">'+d+'<div class="f-cover"></div></div><span class="f-resize f-icon corner fa-icon-resize-full"></span></div>'},template_shadow:function(c){return'<div id="'+c+'" class="frame-shadow corner"></div>'},template_background:function(){return'<div class="frame-background"></div>'},template_menu:function(){return'<div class="frame-scroll-up frame-menu fa-icon-chevron-up fa-icon-2x"></div><div class="frame-scroll-down frame-menu fa-icon-chevron-down fa-icon-2x"></div>'}});return{GalaxyFrameManager:a}}); \ No newline at end of file diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/scripts/packed/galaxy.modal.js --- a/static/scripts/packed/galaxy.modal.js +++ b/static/scripts/packed/galaxy.modal.js @@ -1,1 +1,1 @@ -define(["libs/backbone/backbone-relational"],function(){var a=Backbone.View.extend({el_main:"#everything",options:{title:"galaxy-modal",body:"No content available."},initialize:function(b){if(b){this.create(b);$(this.el).hide()}},show:function(b){if(b){this.create(b)}this.$el.fadeIn("fast")},hide:function(){this.$el.fadeOut("fast")},create:function(c){this.$el.remove();if(!c){c=this.options}else{c=_.defaults(c,this.options)}this.setElement(this.template(c.title,c.body));$(this.el_main).append($(this.el));var d=(this.$el).find(".buttons");var b=this;if(c.buttons){$.each(c.buttons,function(e,f){d.append($('<button id="'+String(e).toLowerCase()+'"></button>').text(e).click(f)).append(" ")})}else{d.append($("<button></button>").text("Close").click(function(){b.hide()})).append(" ")}},enable:function(b){$(this.el).find("#"+String(b).toLowerCase()).prop("disabled",false)},disable:function(b){$(this.el).find("#"+String(b).toLowerCase()).prop("disabled",true)},template:function(c,b){return'<div class="modal in"><div class="modal-backdrop in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><span><h3 class="title">'+c+'</h3></span></div><div class="modal-body style="min-width: 540px; max-height: 445px;">'+b+'</div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file +define(["libs/backbone/backbone-relational"],function(){var a=Backbone.View.extend({el_main:"#everything",defaults:{title:"galaxy-modal",body:"No content available."},initialize:function(b){if(b){this.create(b)}},show:function(c){if(c){this.create(c)}var b=(this.$el).find(".modal-body");b.css("max-height",$(document).height()/2);if(this.visible){this.$el.show()}else{this.$el.fadeIn("fast")}this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false},create:function(c){c=_.defaults(c,this.defaults);if(c.body=="progress"){c.body='<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>'}if(this.$el){this.$el.remove()}this.setElement(this.template(c.title));var b=(this.$el).find(".modal-body");var e=(this.$el).find(".modal-footer");var d=(this.$el).find(".buttons");b.append($(c.body));if(c.height){b.css("height",c.height)}if(c.buttons){$.each(c.buttons,function(f,g){d.append($('<button id="'+String(f).toLowerCase()+'"></button>').text(f).click(g)).append(" ")})}else{e.hide()}$(this.el_main).append($(this.el))},enable:function(b){$(this.el).find("#"+String(b).toLowerCase()).prop("disabled",false)},disable:function(b){$(this.el).find("#"+String(b).toLowerCase()).prop("disabled",true)},template:function(b){return'<div class="modal in"><div class="modal-backdrop in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><span><h3 class="title">'+b+'</h3></span></div><div class="modal-body"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/scripts/packed/galaxy.panels.js --- a/static/scripts/packed/galaxy.panels.js +++ b/static/scripts/packed/galaxy.panels.js @@ -1,1 +1,1 @@ -!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").appendTo("body").hide()}};var b=150,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var n=this;this.$toggle.remove().appendTo("body");this.$drag.on("dragstart",function(o,p){d("#DD-helper").show();p.width=n.$panel.width()}).on("dragend",function(){d("#DD-helper").hide()}).on("drag",function(p,q){var o;if(n.left){o=q.width+q.deltaX}else{o=q.width-q.deltaX}o=Math.min(h,Math.max(b,o));n.resize(o)});n.$toggle.on("click",function(){n.do_toggle()})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop};d.extend(f.prototype,{setContent:function(p){if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}else{this.$header.hide()}this.$footer.hide();var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$overlay.addClass("in");this.$body.css("min-width",this.$body.width());this.$body.css("max-height",d(window).height()-this.$footer.outerHeight()-this.$header.outerHeight()-parseInt(this.$dialog.css("padding-top"),10)-parseInt(this.$dialog.css("padding-bottom"),10))}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#top-modal"),dialog:d("#top-modal-dialog"),backdrop:d("#top-modal-backdrop")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});l(null,d("<div style='margin: -5px;'><img id='close_button' style='position:absolute;right:-17px;top:-15px;src='"+galaxy_config.root+"static/images/closebox.png'><iframe style='margin: 0; padding: 0;' src='"+p.url+"' width='"+q+"' height='"+o+"' scrolling='"+n+"' frameborder='0'></iframe></div>"));d("#close_button").bind("click",function(){a()})}function i(n,o){if(n){d(".loggedin-only").show();d(".loggedout-only").hide();d("#user-email").text(n);if(o){d(".admin-only").show()}}else{d(".loggedin-only").hide();d(".loggedout-only").show();d(".admin-only").hide()}}d(function(){var n=d("#masthead ul.nav > li.dropdown > .dropdown-menu");d("body").on("click.nav_popups",function(p){n.hide();d("#DD-helper").hide();if(d(p.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){return}var o=d(p.target).closest("#masthead ul.nav > li.dropdown");if(o.length){d("#DD-helper").show();o.children(".dropdown-menu").show();p.preventDefault()}})});c.ensure_dd_helper=e;c.Panel=k;c.Modal=f;c.hide_modal=a;c.show_modal=l;c.show_message=g;c.show_in_overlay=j;c.user_changed=i}(window,window.jQuery); \ No newline at end of file +!function(c,d){var e=function(){if(d("#DD-helper").length==0){d("<div id='DD-helper'/>").appendTo("body").hide()}};var b=150,h=800;var k=function(n){this.$panel=n.panel;this.$center=n.center;this.$drag=n.drag;this.$toggle=n.toggle;this.left=!n.right;this.hidden=false;this.hidden_by_tool=false;this.saved_size=null;this.init()};d.extend(k.prototype,{resize:function(n){this.$panel.css("width",n);if(this.left){this.$center.css("left",n)}else{this.$center.css("right",n)}if(document.recalc){document.recalc()}},do_toggle:function(){var n=this;if(this.hidden){this.$toggle.removeClass("hidden");if(this.left){this.$panel.css("left",-this.saved_size).show().animate({left:0},"fast",function(){n.resize(n.saved_size)})}else{this.$panel.css("right",-this.saved_size).show().animate({right:0},"fast",function(){n.resize(n.saved_size)})}n.hidden=false}else{n.saved_size=this.$panel.width();if(document.recalc){document.recalc()}if(this.left){this.$panel.animate({left:-this.saved_size},"fast")}else{this.$panel.animate({right:-this.saved_size},"fast")}if(this.left){this.$center.css("left",0)}else{this.$center.css("right",0)}n.hidden=true;n.$toggle.addClass("hidden")}this.hidden_by_tool=false},handle_minwidth_hint:function(n){var o=this.$center.width()-(this.hidden?this.saved_size:0);if(o<n){if(!this.hidden){this.do_toggle();this.hidden_by_tool=true}}else{if(this.hidden_by_tool){this.do_toggle();this.hidden_by_tool=false}}},force_panel:function(n){if((this.hidden&&n=="show")||(!this.hidden&&n=="hide")){this.do_toggle()}},init:function(){var n=this;this.$toggle.remove().appendTo("body");this.$drag.on("dragstart",function(o,p){d("#DD-helper").show();p.width=n.$panel.width()}).on("dragend",function(){d("#DD-helper").hide()}).on("drag",function(p,q){var o;if(n.left){o=q.width+q.deltaX}else{o=q.width-q.deltaX}o=Math.min(h,Math.max(b,o));n.resize(o)});n.$toggle.on("click",function(){n.do_toggle()})}});var f=function(n){this.$overlay=n.overlay;this.$dialog=n.dialog;this.$header=this.$dialog.find(".modal-header");this.$body=this.$dialog.find(".modal-body");this.$footer=this.$dialog.find(".modal-footer");this.$backdrop=n.backdrop;this.$header.find(".close").on("click",d.proxy(this.hide,this))};d.extend(f.prototype,{setContent:function(p){this.$header.hide();if(p.title){this.$header.find(".title").html(p.title);this.$header.show()}if(p.closeButton){this.$header.find(".close").show();this.$header.show()}else{this.$header.find(".close").hide()}this.$footer.hide();var o=this.$footer.find(".buttons").html("");if(p.buttons){d.each(p.buttons,function(r,s){o.append(d("<button></button> ").text(r).click(s)).append(" ")});this.$footer.show()}var q=this.$footer.find(".extra_buttons").html("");if(p.extra_buttons){d.each(p.extra_buttons,function(r,s){q.append(d("<button></button>").text(r).click(s)).append(" ")});this.$footer.show()}var n=p.body;if(n=="progress"){n=d("<div class='progress progress-striped active'><div class='progress-bar' style='width: 100%'></div></div>")}this.$body.html(n)},show:function(n,o){if(!this.$dialog.is(":visible")){if(n.backdrop){this.$backdrop.addClass("in")}else{this.$backdrop.removeClass("in")}this.$overlay.show();this.$dialog.show();this.$overlay.addClass("in");this.$body.css("min-width",this.$body.width());this.$body.css("max-height",d(window).height()-this.$footer.outerHeight()-this.$header.outerHeight()-parseInt(this.$dialog.css("padding-top"),10)-parseInt(this.$dialog.css("padding-bottom"),10))}if(o){o()}},hide:function(){var n=this;n.$dialog.fadeOut(function(){n.$overlay.hide();n.$backdrop.removeClass("in");n.$body.children().remove();n.$body.css("min-width",undefined)})}});var m;d(function(){m=new f({overlay:d("#top-modal"),dialog:d("#top-modal-dialog"),backdrop:d("#top-modal-backdrop")})});function a(){m.hide()}function l(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:true},q)}function g(r,n,p,o,q){m.setContent({title:r,body:n,buttons:p,extra_buttons:o});m.show({backdrop:false},q)}function j(p){var q=p.width||"600";var o=p.height||"400";var n=p.scroll||"auto";d("#overlay-background").bind("click.overlay",function(){a();d("#overlay-background").unbind("click.overlay")});m.setContent({closeButton:true,title:" ",body:d("<div style='margin: -5px;'><iframe style='margin: 0; padding: 0;' src='"+p.url+"' width='"+q+"' height='"+o+"' scrolling='"+n+"' frameborder='0'></iframe></div>")});m.show({backdrop:true})}function i(n,o){if(n){d(".loggedin-only").show();d(".loggedout-only").hide();d("#user-email").text(n);if(o){d(".admin-only").show()}}else{d(".loggedin-only").hide();d(".loggedout-only").show();d(".admin-only").hide()}}d(function(){var n=d("#masthead ul.nav > li.dropdown > .dropdown-menu");d("body").on("click.nav_popups",function(p){n.hide();d("#DD-helper").hide();if(d(p.target).closest("#masthead ul.nav > li.dropdown > .dropdown-menu").length){return}var o=d(p.target).closest("#masthead ul.nav > li.dropdown");if(o.length){d("#DD-helper").show();o.children(".dropdown-menu").show();p.preventDefault()}})});c.ensure_dd_helper=e;c.Panel=k;c.Modal=f;c.hide_modal=a;c.show_modal=l;c.show_message=g;c.show_in_overlay=j;c.user_changed=i}(window,window.jQuery); \ No newline at end of file diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/scripts/packed/galaxy.upload.js --- a/static/scripts/packed/galaxy.upload.js +++ b/static/scripts/packed/galaxy.upload.js @@ -1,1 +1,1 @@ -define(["galaxy.modal","galaxy.master","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(b,c){var a=Backbone.View.extend({modal:null,button_show:null,uploadbox:null,select_extension:{"":"Auto-detect",bed:"bed",ab1:"ab1"},state:{init:"fa-icon-trash",done:"fa-icon-caret-down"},counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(){if(!Galaxy.currHistoryPanel){var d=this;window.setTimeout(function(){d.initialize()},500);return}var d=this;this.button_show=new c.GalaxyMasterIcon({icon:"fa-icon-upload",tooltip:"Upload Files",on_click:function(f){d.event_show(f)},with_number:true});Galaxy.master.prepend(this.button_show)},events:{mouseover:"event_mouseover",mouseleave:"event_mouseleave"},event_mouseover:function(d){},event_mouseleave:function(d){},event_announce:function(e,f,h){var i="#upload-"+e;$(this.el).append(this.template_file(i,this.select_extension));var g=this.get_upload_item(e);g.fadeIn();g.find(".title").html(f.name);var d=this;g.find(".symbol").on("click",function(){d.event_remove(e)});this.event_progress(e,f,0);this.counter.announce++;this.update_screen()},event_initialize:function(d,e,g){this.button_show.number(this.counter.announce);var f=this.get_upload_item(d);var h={source:"upload",space_to_tabs:f.find("#space_to_tabs").is(":checked"),extension:f.find("#extension").val()};return h},event_progress:function(e,f,h){var g=this.get_upload_item(e);var d=parseInt(h);g.find(".progress-bar").css({width:d+"%"});g.find(".info").html(d+"% of "+this.size_to_string(f.size))},event_success:function(d,e,g){Galaxy.currHistoryPanel.refresh();this.event_progress(d,e,100);this.button_show.number("");this.counter.announce--;this.counter.success++;this.update_screen();var f=this.get_upload_item(d);f.addClass("panel-success");f.removeClass("panel-default");var h=f.find(".symbol");h.removeClass("fa-icon-spin");h.removeClass("fa-icon-spinner");h.addClass(this.state.done)},event_error:function(d,e,g){this.event_progress(d,e,0);this.button_show.number("");this.counter.announce--;this.counter.error++;this.update_screen();var f=this.get_upload_item(d);f.addClass("panel-danger");f.removeClass("panel-default");f.find(".progress").remove();f.find(".error").html("<strong>Failed:</strong> "+g);var h=f.find(".symbol");h.removeClass("fa-icon-spin");h.removeClass("fa-icon-spinner");h.addClass(this.state.done)},event_upload:function(){if(this.counter.announce==0||this.counter.running>0){return}var e=this;$(this.el).find(".symbol").each(function(){if($(this).hasClass(e.state.init)){$(this).removeClass(e.state.init);$(this).addClass("fa-icon-spinner");$(this).addClass("fa-icon-spin")}});$(this.el).find(".panel-body").hide();this.counter.running=this.counter.announce;this.update_screen();var d=Galaxy.currHistoryPanel.model.get("id");this.uploadbox.configure({url:galaxy_config.root+"api/histories/"+d+"/contents"});this.uploadbox.upload()},event_complete:function(){this.counter.running=0;this.update_screen()},event_reset:function(){if(this.counter.running==0){var d=$(this.el).find(".panel");d.fadeOut({complete:function(){d.remove()}});this.counter.reset();this.update_screen();this.uploadbox.reset()}},event_remove:function(d){var e=this.get_upload_item(d);var f=e.find(".symbol");if(f.hasClass(this.state.init)||f.hasClass(this.state.done)){if(e.hasClass("panel-default")){this.counter.announce--}else{if(e.hasClass("panel-success")){this.counter.success--}else{if(e.hasClass("panel-danger")){this.counter.error--}}}this.update_screen();this.uploadbox.remove(d);e.remove()}},event_show:function(f){f.preventDefault();if(!this.modal){var d=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template("upload-box"),buttons:{Select:function(){d.uploadbox.select()},Upload:function(){d.event_upload()},Reset:function(){d.event_reset()},Close:function(){d.modal.hide()}}});this.setElement("#upload-box");var d=this;this.uploadbox=this.$el.uploadbox({dragover:d.event_mouseover,dragleave:d.event_mouseleave,announce:function(e,g,h){d.event_announce(e,g,h)},initialize:function(e,g,h){return d.event_initialize(e,g,h)},success:function(e,g,h){d.event_success(e,g,h)},progress:function(e,g,h){d.event_progress(e,g,h)},error:function(e,g,h){d.event_error(e,g,h)},complete:function(){d.event_complete()},});this.update_screen()}this.modal.show()},get_upload_item:function(d){return $(this.el).find("#upload-"+d)},size_to_string:function(d){var e="";if(d>=100000000000){d=d/100000000000;e="TB"}else{if(d>=100000000){d=d/100000000;e="GB"}else{if(d>=100000){d=d/100000;e="MB"}else{if(d>=100){d=d/100;e="KB"}else{d=d*10;e="b"}}}}return"<strong>"+(Math.round(d)/10)+"</strong> "+e},update_screen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+' file(s) to the queue. Add more files or click "Upload" to proceed.'}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enable("Reset")}else{this.modal.disable("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enable("Upload")}else{this.modal.disable("Upload")}if(this.counter.running==0){this.modal.enable("Select")}else{this.modal.disable("Select")}},template:function(d){return'<div id="'+d+'" class="upload-box"></div><h6 id="upload-info" class="upload-info"></h6>'},template_file:function(f,e){var d='<div id="'+f.substr(1)+'" class="panel panel-default"><div class="panel-heading"><h5 class="title"></h5><h5 class="info"></h5><div class="symbol '+this.state.init+'"></div></div><div class="panel-body"><div class="menu">Select file type: <select id="extension">';for(key in e){d+='<option value="'+key+'">'+e[key]+"</option>"}d+='</select>, <span>Convert space to tabs: <input id="space_to_tabs" type="checkbox"></input></span></div></div><div class="panel-footer"><div class="progress"><div class="progress-bar progress-bar-success"></div></div><h6 class="error"></h6></div></div>';return d}});return{GalaxyUpload:a}}); \ No newline at end of file +define(["galaxy.modal","galaxy.master","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(b,c){var a=Backbone.View.extend({modal:null,button_show:null,uploadbox:null,select_extension:{"":"Auto-detect",bed:"bed",ab1:"ab1"},state:{init:"fa-icon-trash",done:"fa-icon-caret-down"},counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(){if(!Galaxy.currHistoryPanel){var d=this;window.setTimeout(function(){d.initialize()},500);return}var d=this;this.button_show=new c.GalaxyMasterIcon({icon:"fa-icon-upload",tooltip:"Upload Files",on_click:function(f){d.event_show(f)},with_number:true});Galaxy.master.prepend(this.button_show)},events:{mouseover:"event_mouseover",mouseleave:"event_mouseleave"},event_mouseover:function(d){},event_mouseleave:function(d){},event_announce:function(e,f,h){var i="#upload-"+e;$(this.el).append(this.template_file(i,this.select_extension));var g=this.get_upload_item(e);g.fadeIn();g.find(".title").html(f.name);var d=this;g.find(".symbol").on("click",function(){d.event_remove(e)});this.event_progress(e,f,0);this.counter.announce++;this.update_screen()},event_initialize:function(d,e,g){this.button_show.number(this.counter.announce);var f=this.get_upload_item(d);var h={source:"upload",space_to_tabs:f.find("#space_to_tabs").is(":checked"),extension:f.find("#extension").val()};return h},event_progress:function(e,f,h){var g=this.get_upload_item(e);var d=parseInt(h);g.find(".progress-bar").css({width:d+"%"});g.find(".info").html(d+"% of "+this.size_to_string(f.size))},event_success:function(d,e,g){Galaxy.currHistoryPanel.refresh();this.event_progress(d,e,100);this.button_show.number("");this.counter.announce--;this.counter.success++;this.update_screen();var f=this.get_upload_item(d);f.addClass("panel-success");f.removeClass("panel-default");var h=f.find(".symbol");h.removeClass("fa-icon-spin");h.removeClass("fa-icon-spinner");h.addClass(this.state.done)},event_error:function(d,e,g){this.event_progress(d,e,0);this.button_show.number("");this.counter.announce--;this.counter.error++;this.update_screen();var f=this.get_upload_item(d);f.addClass("panel-danger");f.removeClass("panel-default");f.find(".progress").remove();f.find(".error").html("<strong>Failed:</strong> "+g);var h=f.find(".symbol");h.removeClass("fa-icon-spin");h.removeClass("fa-icon-spinner");h.addClass(this.state.done)},event_upload:function(){if(this.counter.announce==0||this.counter.running>0){return}var e=this;$(this.el).find(".symbol").each(function(){if($(this).hasClass(e.state.init)){$(this).removeClass(e.state.init);$(this).addClass("fa-icon-spinner");$(this).addClass("fa-icon-spin")}});$(this.el).find(".panel-body").hide();this.counter.running=this.counter.announce;this.update_screen();var d=Galaxy.currHistoryPanel.model.get("id");this.uploadbox.configure({url:galaxy_config.root+"api/histories/"+d+"/contents"});this.uploadbox.upload()},event_complete:function(){this.counter.running=0;this.update_screen()},event_reset:function(){if(this.counter.running==0){var d=$(this.el).find(".panel");d.fadeOut({complete:function(){d.remove()}});this.counter.reset();this.update_screen();this.uploadbox.reset()}},event_remove:function(d){var e=this.get_upload_item(d);var f=e.find(".symbol");if(f.hasClass(this.state.init)||f.hasClass(this.state.done)){if(e.hasClass("panel-default")){this.counter.announce--}else{if(e.hasClass("panel-success")){this.counter.success--}else{if(e.hasClass("panel-danger")){this.counter.error--}}}this.update_screen();this.uploadbox.remove(d);e.remove()}},event_show:function(f){f.preventDefault();if(!this.modal){var d=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template("upload-box"),buttons:{Select:function(){d.uploadbox.select()},Upload:function(){d.event_upload()},Reset:function(){d.event_reset()},Close:function(){d.modal.hide()}},height:"250px"});this.setElement("#upload-box");var d=this;this.uploadbox=this.$el.uploadbox({dragover:d.event_mouseover,dragleave:d.event_mouseleave,announce:function(e,g,h){d.event_announce(e,g,h)},initialize:function(e,g,h){return d.event_initialize(e,g,h)},success:function(e,g,h){d.event_success(e,g,h)},progress:function(e,g,h){d.event_progress(e,g,h)},error:function(e,g,h){d.event_error(e,g,h)},complete:function(){d.event_complete()},});this.update_screen()}this.modal.show()},get_upload_item:function(d){return $(this.el).find("#upload-"+d)},size_to_string:function(d){var e="";if(d>=100000000000){d=d/100000000000;e="TB"}else{if(d>=100000000){d=d/100000000;e="GB"}else{if(d>=100000){d=d/100000;e="MB"}else{if(d>=100){d=d/100;e="KB"}else{d=d*10;e="b"}}}}return"<strong>"+(Math.round(d)/10)+"</strong> "+e},update_screen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.<br>Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enable("Reset")}else{this.modal.disable("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enable("Upload")}else{this.modal.disable("Upload")}if(this.counter.running==0){this.modal.enable("Select")}else{this.modal.disable("Select")}},template:function(d){return'<div id="'+d+'" class="upload-box"></div><h6 id="upload-info" class="upload-info"></h6>'},template_file:function(f,e){var d='<div id="'+f.substr(1)+'" class="panel panel-default"><div class="panel-heading"><h5 class="title"></h5><h5 class="info"></h5><div class="symbol '+this.state.init+'"></div></div><div class="panel-body"><div class="menu">Select file type: <select id="extension">';for(key in e){d+='<option value="'+key+'">'+e[key]+"</option>"}d+='</select>, <span>Convert space to tabs: <input id="space_to_tabs" type="checkbox"></input></span></div></div><div class="panel-footer"><div class="progress"><div class="progress-bar progress-bar-success"></div></div><h6 class="error"></h6></div></div>';return d}});return{GalaxyUpload:a}}); \ No newline at end of file diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/scripts/packed/viz/circster.js --- a/static/scripts/packed/viz/circster.js +++ b/static/scripts/packed/viz/circster.js @@ -1,1 +1,1 @@ -define(["libs/underscore","libs/d3","viz/visualization"],function(g,l,i){var m=Backbone.Model.extend({is_visible:function(q,n){var o=q.getBoundingClientRect(),p=$("svg")[0].getBoundingClientRect();if(o.right<0||o.left>p.right||o.bottom<0||o.top>p.bottom){return false}return true}});var h={drawTicks:function(r,q,v,p,n){var u=r.append("g").selectAll("g").data(q).enter().append("g").selectAll("g").data(v).enter().append("g").attr("class","tick").attr("transform",function(w){return"rotate("+(w.angle*180/Math.PI-90)+")translate("+w.radius+",0)"});var t=[],s=[],o=function(w){return w.angle>Math.PI?"end":null};if(n){t=[0,0,0,-4];s=[4,0,"",".35em"];o=null}else{t=[1,0,4,0];s=[0,4,".35em",""]}u.append("line").attr("x1",t[0]).attr("y1",t[1]).attr("x2",t[2]).attr("y1",t[3]).style("stroke","#000");u.append("text").attr("x",s[0]).attr("y",s[1]).attr("dx",s[2]).attr("dy",s[3]).attr("text-anchor",o).attr("transform",p).text(function(w){return w.label})},formatNum:function(o,n){if(n===undefined){n=2}if(o===null){return null}var q=null;if(o<1){q=o.toPrecision(n)}else{var p=Math.round(o.toPrecision(n));if(o<1000){q=p}else{if(o<1000000){q=Math.round((p/1000).toPrecision(3)).toFixed(0)+"K"}else{if(o<1000000000){q=Math.round((p/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return q}};var c=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(n){this.total_gap=n.total_gap;this.genome=n.genome;this.dataset_arc_height=n.dataset_arc_height;this.track_gap=10;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("tracks").on("add",this.add_track,this);this.model.get("tracks").on("remove",this.remove_track,this);this.get_circular_tracks()},get_circular_tracks:function(){return this.model.get("tracks").filter(function(n){return n.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("tracks").filter(function(n){return n.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var o=this.get_circular_tracks();dataset_arc_height=this.dataset_arc_height,min_dimension=Math.min(this.$el.width(),this.$el.height()),radius_start=min_dimension/2-o.length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),tracks_start_radii=l.range(radius_start,min_dimension/2,this.dataset_arc_height+this.track_gap);var n=this;return g.map(tracks_start_radii,function(p){return[p,p+n.dataset_arc_height]})},render:function(){var w=this,q=this.dataset_arc_height,n=w.$el.width(),v=w.$el.height(),s=this.get_circular_tracks(),p=this.get_chord_tracks(),r=this.get_tracks_bounds(),o=l.select(w.$el[0]).append("svg").attr("width",n).attr("height",v).attr("pointer-events","all").append("svg:g").call(l.behavior.zoom().on("zoom",function(){var x=l.event.scale;o.attr("transform","translate("+l.event.translate+") scale("+x+")");if(w.scale!==x){if(w.zoom_drag_timeout){clearTimeout(w.zoom_drag_timeout)}w.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+n/2+","+v/2+")").append("svg:g").attr("class","tracks");this.circular_views=s.map(function(y,z){var x=new d({el:o.append("g")[0],track:y,radius_bounds:r[z],genome:w.genome,total_gap:w.total_gap});x.render();return x});this.chords_views=p.map(function(y){var x=new j({el:o.append("g")[0],track:y,radius_bounds:r[0],genome:w.genome,total_gap:w.total_gap});x.render();return x});var u=this.circular_views[this.circular_views.length-1].radius_bounds[1],t=[u,u+this.label_arc_height];this.label_track_view=new b({el:o.append("g")[0],track:new c(),radius_bounds:t,genome:w.genome,total_gap:w.total_gap});this.label_track_view.render()},add_track:function(t){if(t.get("track_type")==="DiagonalHeatmapTrack"){var p=this.circular_views[0].radius_bounds,s=new j({el:l.select("g.tracks").append("g")[0],track:t,radius_bounds:p,genome:this.genome,total_gap:this.total_gap});s.render();this.chords_views.push(s)}else{var r=this.get_tracks_bounds();g.each(this.circular_views,function(u,v){u.update_radius_bounds(r[v])});g.each(this.chords_views,function(u){u.update_radius_bounds(r[0])});var q=this.circular_views.length,n=new d({el:l.select("g.tracks").append("g")[0],track:t,radius_bounds:r[q],genome:this.genome,total_gap:this.total_gap});n.render();this.circular_views.push(n);var o=r[r.length-1];o[1]=o[0];this.label_track_view.update_radius_bounds(o)}},remove_track:function(o,q,p){var n=this.circular_views[p.index];this.circular_views.splice(p.index,1);n.$el.remove();var r=this.get_tracks_bounds();g.each(this.circular_views,function(s,t){s.update_radius_bounds(r[t])})}});var k=Backbone.View.extend({tagName:"g",initialize:function(n){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=n.total_gap;this.track=n.track;this.radius_bounds=n.radius_bounds;this.genome=n.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=l.select(this.$el[0])},get_fill_color:function(){var n=this.track.get("config").get_value("block_color");if(!n){n=this.track.get("config").get_value("color")}return n},render:function(){var r=this.parent_elt;if(!r){console.log("no parent elt")}var q=this.chroms_layout,t=l.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),n=r.selectAll("g").data(q).enter().append("svg:g"),p=n.append("path").attr("d",t).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);p.append("title").text(function(v){return v.data.chrom});var o=this,s=o.track.get("data_manager"),u=(s?s.data_is_ready():true);$.when(u).then(function(){$.when(o._render_data(r)).then(function(){p.style("fill",o.bg_fill);o.render_labels()})})},render_labels:function(){},update_radius_bounds:function(o){this.radius_bounds=o;var n=l.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",n);this._transition_chrom_data();this._transition_labels()},update_scale:function(q){var p=this.scale;this.scale=q;if(q<=p){return}var o=this,n=new m();this.parent_elt.selectAll("path.chrom-data").filter(function(s,r){return n.is_visible(this)}).each(function(x,t){var w=l.select(this),s=w.attr("chrom"),v=o.genome.get_chrom_region(s),u=o.track.get("data_manager"),r;if(!u.can_get_more_detailed_data(v)){return}r=o.track.get("data_manager").get_more_detailed_data(v,"Coverage",0,q);$.when(r).then(function(A){w.remove();o._update_data_bounds();var z=g.find(o.chroms_layout,function(B){return B.data.chrom===s});var y=o.get_fill_color();o._render_chrom_data(o.parent_elt,z,A).style("stroke",y).style("fill",y)})});return o},_transition_chrom_data:function(){var o=this.track,q=this.chroms_layout,n=this.parent_elt.selectAll("g>path.chrom-data"),r=n[0].length;if(r>0){var p=this;$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(t){var s=g.reject(g.map(t,function(u,v){var w=null,x=p._get_path_function(q[v],u);if(x){w=x(u.data)}return w}),function(u){return u===null});n.each(function(v,u){l.select(this).transition().duration(1000).attr("d",s[u])})})}},_transition_labels:function(){},_update_data_bounds:function(){var n=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<n[0]||this.data_bounds[1]>n[1]){this._transition_chrom_data()}},_render_data:function(q){var p=this,o=this.chroms_layout,n=this.track,r=$.Deferred();$.when(n.get("data_manager").get_genome_wide_data(this.genome)).then(function(t){p.data_bounds=p.get_data_bounds(t);layout_and_data=g.zip(o,t),chroms_data_layout=g.map(layout_and_data,function(u){var v=u[0],w=u[1];return p._render_chrom_data(q,v,w)});var s=p.get_fill_color();p.parent_elt.selectAll("path.chrom-data").style("stroke",s).style("fill",s);r.resolve(q)});return r},_render_chrom_data:function(n,o,p){},_get_path_function:function(o,n){},_chroms_layout:function(){var o=this.genome.get_chroms_info(),q=l.layout.pie().value(function(s){return s.len}).sort(null),r=q(o),n=this.total_gap/o.length,p=g.map(r,function(u,t){var s=u.endAngle-n;u.endAngle=(s>u.startAngle?s:u.startAngle);return u});return p}});var b=k.extend({initialize:function(n){k.prototype.initialize.call(this,n);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.08},_render_data:function(p){var o=this,n=p.selectAll("g");n.selectAll("path").attr("id",function(t){return"label-"+t.data.chrom});n.append("svg:text").filter(function(t){return t.endAngle-t.startAngle>o.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("xlink:href",function(t){return"#label-"+t.data.chrom}).attr("startOffset","25%").attr("font-weight","bold").text(function(t){return t.data.chrom});var q=function(v){var t=(v.endAngle-v.startAngle)/v.value,u=l.range(0,v.value,25000000).map(function(w,x){return{radius:o.innerRadius,angle:w*t+v.startAngle,label:x===0?0:(x%3?null:o.formatNum(w))}});if(u.length<4){u[u.length-1].label=o.formatNum(Math.round((u[u.length-1].angle-v.startAngle)/t))}return u};var s=function(t){return t.angle>Math.PI?"rotate(180)translate(-16)":null};var r=g.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>o.min_arc_len});this.drawTicks(this.parent_elt,r,q,s)}});g.extend(b.prototype,h);var f=k.extend({_quantile:function(o,n){o.sort(l.ascending);return l.quantile(o,n)},_render_chrom_data:function(n,q,o){var r=this._get_path_function(q,o);if(!r){return null}var p=n.datum(o.data),s=p.append("path").attr("class","chrom-data").attr("chrom",q.data.chrom).attr("d",r);return s},_get_path_function:function(q,p){if(typeof p==="string"||!p.data||p.data.length===0){return null}var n=l.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var r=l.scale.linear().domain([0,p.data.length]).range([q.startAngle,q.endAngle]);var o=l.svg.line.radial().interpolate("linear").radius(function(s){return n(s[1])}).angle(function(t,s){return r(s)});return l.svg.area.radial().interpolate(o.interpolate()).innerRadius(n(0)).outerRadius(o.radius()).angle(o.angle())},render_labels:function(){var n=this,q=function(){return"rotate(90)"};var p=g.filter(this.chroms_layout,function(r){return r.endAngle-r.startAngle>0.08}),o=g.filter(p,function(s,r){return r%3===0});this.drawTicks(this.parent_elt,o,this._data_bounds_ticks_fn(),q,true)},_transition_labels:function(){if(this.data_bounds.length===0){return}var o=this,q=g.filter(this.chroms_layout,function(r){return r.endAngle-r.startAngle>0.08}),p=g.filter(q,function(s,r){return r%3===0}),n=g.flatten(g.map(p,function(r){return o._data_bounds_ticks_fn()(r)}));this.parent_elt.selectAll("g.tick").data(n).transition().attr("transform",function(r){return"rotate("+(r.angle*180/Math.PI-90)+")translate("+r.radius+",0)"})},_data_bounds_ticks_fn:function(){var n=this;visibleChroms=0;return function(o){return[{radius:n.radius_bounds[0],angle:o.startAngle,label:n.formatNum(n.data_bounds[0])},{radius:n.radius_bounds[1],angle:o.startAngle,label:n.formatNum(n.data_bounds[1])}]}},get_data_bounds:function(n){}});g.extend(f.prototype,h);var d=f.extend({get_data_bounds:function(o){var n=g.flatten(g.map(o,function(p){if(p){return g.map(p.data,function(q){return q[1]})}else{return 0}}));return[g.min(n),this._quantile(n,0.98)]}});var j=k.extend({render:function(){var n=this;$.when(n.track.get("data_manager").data_is_ready()).then(function(){$.when(n.track.get("data_manager").get_genome_wide_data(n.genome)).then(function(q){var p=[],o=n.genome.get_chroms_info();g.each(q,function(u,t){var r=o[t].chrom;var s=g.map(u.data,function(w){var v=n._get_region_angle(r,w[1]),x=n._get_region_angle(w[3],w[4]);return{source:{startAngle:v,endAngle:v+0.01},target:{startAngle:x,endAngle:x+0.01}}});p=p.concat(s)});n.parent_elt.append("g").attr("class","chord").selectAll("path").data(p).enter().append("path").style("fill",n.get_fill_color()).attr("d",l.svg.chord().radius(n.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(n){this.radius_bounds=n;this.parent_elt.selectAll("path").transition().attr("d",l.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(p,n){var o=g.find(this.chroms_layout,function(q){return q.data.chrom===p});return o.endAngle-((o.endAngle-o.startAngle)*(o.data.len-n)/o.data.len)}});var e=Backbone.View.extend({initialize:function(){var n=new i.Genome(galaxy_config.app.genome),o=new i.GenomeVisualization(galaxy_config.app.viz_config),q=new a({el:$("#center .unified-panel-body"),total_gap:2*Math.PI*0.1,genome:n,model:o,dataset_arc_height:25});q.render();$("#center .unified-panel-header-inner").append(galaxy_config.app.viz_config.title+" "+galaxy_config.app.viz_config.dbkey);var p=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){i.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",o.get("dbkey"),function(r){o.add_tracks(r)})}},{icon_class:"disk--arrow",title:"Save",on_click:function(){show_modal("Saving...","progress");var r=galaxy_config.app.viz_config;$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:r.vis_id,title:r.title,dbkey:r.dbkey,type:"trackster",vis_json:JSON.stringify(r)}}).success(function(s){hide_modal();r.vis_id=s.vis_id;r.has_changes=false;window.history.pushState({},"",s.url+window.location.hash)}).error(function(){show_modal("Could Not Save","Could not save visualization. Please try again later.",{Close:hide_modal})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});p.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(p.$el);$(".menu-button").tooltip({placement:"bottom"})}});return{GalaxyApp:e}}); \ No newline at end of file +define(["libs/underscore","libs/d3","viz/visualization"],function(g,l,i){var m=Backbone.Model.extend({is_visible:function(q,n){var o=q.getBoundingClientRect(),p=$("svg")[0].getBoundingClientRect();if(o.right<0||o.left>p.right||o.bottom<0||o.top>p.bottom){return false}return true}});var h={drawTicks:function(r,q,v,p,n){var u=r.append("g").selectAll("g").data(q).enter().append("g").selectAll("g").data(v).enter().append("g").attr("class","tick").attr("transform",function(w){return"rotate("+(w.angle*180/Math.PI-90)+")translate("+w.radius+",0)"});var t=[],s=[],o=function(w){return w.angle>Math.PI?"end":null};if(n){t=[0,0,0,-4];s=[4,0,"",".35em"];o=null}else{t=[1,0,4,0];s=[0,4,".35em",""]}u.append("line").attr("x1",t[0]).attr("y1",t[1]).attr("x2",t[2]).attr("y1",t[3]).style("stroke","#000");u.append("text").attr("x",s[0]).attr("y",s[1]).attr("dx",s[2]).attr("dy",s[3]).attr("text-anchor",o).attr("transform",p).text(function(w){return w.label})},formatNum:function(o,n){if(n===undefined){n=2}if(o===null){return null}var q=null;if(o<1){q=o.toPrecision(n)}else{var p=Math.round(o.toPrecision(n));if(o<1000){q=p}else{if(o<1000000){q=Math.round((p/1000).toPrecision(3)).toFixed(0)+"K"}else{if(o<1000000000){q=Math.round((p/1000000).toPrecision(3)).toFixed(0)+"M"}}}}return q}};var c=Backbone.Model.extend({});var a=Backbone.View.extend({className:"circster",initialize:function(n){this.total_gap=n.total_gap;this.genome=n.genome;this.dataset_arc_height=n.dataset_arc_height;this.track_gap=10;this.label_arc_height=50;this.scale=1;this.circular_views=null;this.chords_views=null;this.model.get("tracks").on("add",this.add_track,this);this.model.get("tracks").on("remove",this.remove_track,this);this.get_circular_tracks()},get_circular_tracks:function(){return this.model.get("tracks").filter(function(n){return n.get("track_type")!=="DiagonalHeatmapTrack"})},get_chord_tracks:function(){return this.model.get("tracks").filter(function(n){return n.get("track_type")==="DiagonalHeatmapTrack"})},get_tracks_bounds:function(){var o=this.get_circular_tracks();dataset_arc_height=this.dataset_arc_height,min_dimension=Math.min(this.$el.width(),this.$el.height()),radius_start=min_dimension/2-o.length*(this.dataset_arc_height+this.track_gap)-(this.label_arc_height+this.track_gap),tracks_start_radii=l.range(radius_start,min_dimension/2,this.dataset_arc_height+this.track_gap);var n=this;return g.map(tracks_start_radii,function(p){return[p,p+n.dataset_arc_height]})},render:function(){var w=this,q=this.dataset_arc_height,n=w.$el.width(),v=w.$el.height(),s=this.get_circular_tracks(),p=this.get_chord_tracks(),r=this.get_tracks_bounds(),o=l.select(w.$el[0]).append("svg").attr("width",n).attr("height",v).attr("pointer-events","all").append("svg:g").call(l.behavior.zoom().on("zoom",function(){var x=l.event.scale;o.attr("transform","translate("+l.event.translate+") scale("+x+")");if(w.scale!==x){if(w.zoom_drag_timeout){clearTimeout(w.zoom_drag_timeout)}w.zoom_drag_timeout=setTimeout(function(){},400)}})).attr("transform","translate("+n/2+","+v/2+")").append("svg:g").attr("class","tracks");this.circular_views=s.map(function(y,z){var x=new d({el:o.append("g")[0],track:y,radius_bounds:r[z],genome:w.genome,total_gap:w.total_gap});x.render();return x});this.chords_views=p.map(function(y){var x=new j({el:o.append("g")[0],track:y,radius_bounds:r[0],genome:w.genome,total_gap:w.total_gap});x.render();return x});var u=this.circular_views[this.circular_views.length-1].radius_bounds[1],t=[u,u+this.label_arc_height];this.label_track_view=new b({el:o.append("g")[0],track:new c(),radius_bounds:t,genome:w.genome,total_gap:w.total_gap});this.label_track_view.render()},add_track:function(t){if(t.get("track_type")==="DiagonalHeatmapTrack"){var p=this.circular_views[0].radius_bounds,s=new j({el:l.select("g.tracks").append("g")[0],track:t,radius_bounds:p,genome:this.genome,total_gap:this.total_gap});s.render();this.chords_views.push(s)}else{var r=this.get_tracks_bounds();g.each(this.circular_views,function(u,v){u.update_radius_bounds(r[v])});g.each(this.chords_views,function(u){u.update_radius_bounds(r[0])});var q=this.circular_views.length,n=new d({el:l.select("g.tracks").append("g")[0],track:t,radius_bounds:r[q],genome:this.genome,total_gap:this.total_gap});n.render();this.circular_views.push(n);var o=r[r.length-1];o[1]=o[0];this.label_track_view.update_radius_bounds(o)}},remove_track:function(o,q,p){var n=this.circular_views[p.index];this.circular_views.splice(p.index,1);n.$el.remove();var r=this.get_tracks_bounds();g.each(this.circular_views,function(s,t){s.update_radius_bounds(r[t])})}});var k=Backbone.View.extend({tagName:"g",initialize:function(n){this.bg_stroke="ccc";this.loading_bg_fill="000";this.bg_fill="ccc";this.total_gap=n.total_gap;this.track=n.track;this.radius_bounds=n.radius_bounds;this.genome=n.genome;this.chroms_layout=this._chroms_layout();this.data_bounds=[];this.scale=1;this.parent_elt=l.select(this.$el[0])},get_fill_color:function(){var n=this.track.get("config").get_value("block_color");if(!n){n=this.track.get("config").get_value("color")}return n},render:function(){var r=this.parent_elt;if(!r){console.log("no parent elt")}var q=this.chroms_layout,t=l.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]),n=r.selectAll("g").data(q).enter().append("svg:g"),p=n.append("path").attr("d",t).attr("class","chrom-background").style("stroke",this.bg_stroke).style("fill",this.loading_bg_fill);p.append("title").text(function(v){return v.data.chrom});var o=this,s=o.track.get("data_manager"),u=(s?s.data_is_ready():true);$.when(u).then(function(){$.when(o._render_data(r)).then(function(){p.style("fill",o.bg_fill);o.render_labels()})})},render_labels:function(){},update_radius_bounds:function(o){this.radius_bounds=o;var n=l.svg.arc().innerRadius(this.radius_bounds[0]).outerRadius(this.radius_bounds[1]);this.parent_elt.selectAll("g>path.chrom-background").transition().duration(1000).attr("d",n);this._transition_chrom_data();this._transition_labels()},update_scale:function(q){var p=this.scale;this.scale=q;if(q<=p){return}var o=this,n=new m();this.parent_elt.selectAll("path.chrom-data").filter(function(s,r){return n.is_visible(this)}).each(function(x,t){var w=l.select(this),s=w.attr("chrom"),v=o.genome.get_chrom_region(s),u=o.track.get("data_manager"),r;if(!u.can_get_more_detailed_data(v)){return}r=o.track.get("data_manager").get_more_detailed_data(v,"Coverage",0,q);$.when(r).then(function(A){w.remove();o._update_data_bounds();var z=g.find(o.chroms_layout,function(B){return B.data.chrom===s});var y=o.get_fill_color();o._render_chrom_data(o.parent_elt,z,A).style("stroke",y).style("fill",y)})});return o},_transition_chrom_data:function(){var o=this.track,q=this.chroms_layout,n=this.parent_elt.selectAll("g>path.chrom-data"),r=n[0].length;if(r>0){var p=this;$.when(o.get("data_manager").get_genome_wide_data(this.genome)).then(function(t){var s=g.reject(g.map(t,function(u,v){var w=null,x=p._get_path_function(q[v],u);if(x){w=x(u.data)}return w}),function(u){return u===null});n.each(function(v,u){l.select(this).transition().duration(1000).attr("d",s[u])})})}},_transition_labels:function(){},_update_data_bounds:function(){var n=this.data_bounds;this.data_bounds=this.get_data_bounds(this.track.get("data_manager").get_genome_wide_data(this.genome));if(this.data_bounds[0]<n[0]||this.data_bounds[1]>n[1]){this._transition_chrom_data()}},_render_data:function(q){var p=this,o=this.chroms_layout,n=this.track,r=$.Deferred();$.when(n.get("data_manager").get_genome_wide_data(this.genome)).then(function(t){p.data_bounds=p.get_data_bounds(t);layout_and_data=g.zip(o,t),chroms_data_layout=g.map(layout_and_data,function(u){var v=u[0],w=u[1];return p._render_chrom_data(q,v,w)});var s=p.get_fill_color();p.parent_elt.selectAll("path.chrom-data").style("stroke",s).style("fill",s);r.resolve(q)});return r},_render_chrom_data:function(n,o,p){},_get_path_function:function(o,n){},_chroms_layout:function(){var o=this.genome.get_chroms_info(),q=l.layout.pie().value(function(s){return s.len}).sort(null),r=q(o),n=this.total_gap/o.length,p=g.map(r,function(u,t){var s=u.endAngle-n;u.endAngle=(s>u.startAngle?s:u.startAngle);return u});return p}});var b=k.extend({initialize:function(n){k.prototype.initialize.call(this,n);this.innerRadius=this.radius_bounds[0];this.radius_bounds[0]=this.radius_bounds[1];this.bg_stroke="fff";this.bg_fill="fff";this.min_arc_len=0.08},_render_data:function(p){var o=this,n=p.selectAll("g");n.selectAll("path").attr("id",function(t){return"label-"+t.data.chrom});n.append("svg:text").filter(function(t){return t.endAngle-t.startAngle>o.min_arc_len}).attr("text-anchor","middle").append("svg:textPath").attr("xlink:href",function(t){return"#label-"+t.data.chrom}).attr("startOffset","25%").attr("font-weight","bold").text(function(t){return t.data.chrom});var q=function(v){var t=(v.endAngle-v.startAngle)/v.value,u=l.range(0,v.value,25000000).map(function(w,x){return{radius:o.innerRadius,angle:w*t+v.startAngle,label:x===0?0:(x%3?null:o.formatNum(w))}});if(u.length<4){u[u.length-1].label=o.formatNum(Math.round((u[u.length-1].angle-v.startAngle)/t))}return u};var s=function(t){return t.angle>Math.PI?"rotate(180)translate(-16)":null};var r=g.filter(this.chroms_layout,function(t){return t.endAngle-t.startAngle>o.min_arc_len});this.drawTicks(this.parent_elt,r,q,s)}});g.extend(b.prototype,h);var f=k.extend({_quantile:function(o,n){o.sort(l.ascending);return l.quantile(o,n)},_render_chrom_data:function(n,q,o){var r=this._get_path_function(q,o);if(!r){return null}var p=n.datum(o.data),s=p.append("path").attr("class","chrom-data").attr("chrom",q.data.chrom).attr("d",r);return s},_get_path_function:function(q,p){if(typeof p==="string"||!p.data||p.data.length===0){return null}var n=l.scale.linear().domain(this.data_bounds).range(this.radius_bounds).clamp(true);var r=l.scale.linear().domain([0,p.data.length]).range([q.startAngle,q.endAngle]);var o=l.svg.line.radial().interpolate("linear").radius(function(s){return n(s[1])}).angle(function(t,s){return r(s)});return l.svg.area.radial().interpolate(o.interpolate()).innerRadius(n(0)).outerRadius(o.radius()).angle(o.angle())},render_labels:function(){var n=this,q=function(){return"rotate(90)"};var p=g.filter(this.chroms_layout,function(r){return r.endAngle-r.startAngle>0.08}),o=g.filter(p,function(s,r){return r%3===0});this.drawTicks(this.parent_elt,o,this._data_bounds_ticks_fn(),q,true)},_transition_labels:function(){if(this.data_bounds.length===0){return}var o=this,q=g.filter(this.chroms_layout,function(r){return r.endAngle-r.startAngle>0.08}),p=g.filter(q,function(s,r){return r%3===0}),n=g.flatten(g.map(p,function(r){return o._data_bounds_ticks_fn()(r)}));this.parent_elt.selectAll("g.tick").data(n).transition().attr("transform",function(r){return"rotate("+(r.angle*180/Math.PI-90)+")translate("+r.radius+",0)"})},_data_bounds_ticks_fn:function(){var n=this;visibleChroms=0;return function(o){return[{radius:n.radius_bounds[0],angle:o.startAngle,label:n.formatNum(n.data_bounds[0])},{radius:n.radius_bounds[1],angle:o.startAngle,label:n.formatNum(n.data_bounds[1])}]}},get_data_bounds:function(n){}});g.extend(f.prototype,h);var d=f.extend({get_data_bounds:function(o){var n=g.flatten(g.map(o,function(p){if(p){return g.map(p.data,function(q){return q[1]})}else{return 0}}));return[g.min(n),this._quantile(n,0.98)]}});var j=k.extend({render:function(){var n=this;$.when(n.track.get("data_manager").data_is_ready()).then(function(){$.when(n.track.get("data_manager").get_genome_wide_data(n.genome)).then(function(q){var p=[],o=n.genome.get_chroms_info();g.each(q,function(u,t){var r=o[t].chrom;var s=g.map(u.data,function(w){var v=n._get_region_angle(r,w[1]),x=n._get_region_angle(w[3],w[4]);return{source:{startAngle:v,endAngle:v+0.01},target:{startAngle:x,endAngle:x+0.01}}});p=p.concat(s)});n.parent_elt.append("g").attr("class","chord").selectAll("path").data(p).enter().append("path").style("fill",n.get_fill_color()).attr("d",l.svg.chord().radius(n.radius_bounds[0])).style("opacity",1)})})},update_radius_bounds:function(n){this.radius_bounds=n;this.parent_elt.selectAll("path").transition().attr("d",l.svg.chord().radius(this.radius_bounds[0]))},_get_region_angle:function(p,n){var o=g.find(this.chroms_layout,function(q){return q.data.chrom===p});return o.endAngle-((o.endAngle-o.startAngle)*(o.data.len-n)/o.data.len)}});var e=Backbone.View.extend({initialize:function(){var n=new i.Genome(galaxy_config.app.genome),o=new i.GenomeVisualization(galaxy_config.app.viz_config),q=new a({el:$("#center .unified-panel-body"),total_gap:2*Math.PI*0.1,genome:n,model:o,dataset_arc_height:25});q.render();$("#center .unified-panel-header-inner").append(galaxy_config.app.viz_config.title+" "+galaxy_config.app.viz_config.dbkey);var p=create_icon_buttons_menu([{icon_class:"plus-button",title:"Add tracks",on_click:function(){i.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",o.get("dbkey"),function(r){o.add_tracks(r)})}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var r=galaxy_config.app.viz_config;$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:r.vis_id,title:r.title,dbkey:r.dbkey,type:"trackster",vis_json:JSON.stringify(r)}}).success(function(s){Galaxy.modal.hide();r.vis_id=s.vis_id;r.has_changes=false;window.history.pushState({},"",s.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization/list"}}],{tooltip_config:{placement:"bottom"}});p.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(p.$el);$(".menu-button").tooltip({placement:"bottom"})}});return{GalaxyApp:e}}); \ No newline at end of file diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/scripts/packed/viz/trackster.js --- a/static/scripts/packed/viz/trackster.js +++ b/static/scripts/packed/viz/trackster.js @@ -1,1 +1,1 @@ -var ui=null;var view=null;var browser_router=null;require(["utils/galaxy.css","libs/jquery/jstorage","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/select2","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating","mvc/ui"],function(a){a.load_file("static/style/jquery.rating.css");a.load_file("static/style/autocomplete_tagging.css");a.load_file("static/style/jquery-ui/smoothness/jquery-ui.css");a.load_file("static/style/library.css");a.load_file("static/style/trackster.css")});define(["libs/backbone/backbone-relational","viz/visualization","viz/trackster_ui"],function(c,a,b){var d=Backbone.View.extend({initialize:function(){ui=new b.TracksterUI(galaxy_config.root);ui.createButtonMenu();ui.buttonMenu.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);$("#right .unified-panel-title").append("Bookmarks");$("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(galaxy_config.app.id){this.view_existing()}else{this.view_new()}},set_up_router:function(e){browser_router=new a.TrackBrowserRouter(e);Backbone.history.start()},view_existing:function(){var e=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:e.title,vis_id:e.vis_id,dbkey:e.dbkey},e.viewport,e.tracks,e.bookmarks,true);this.init_editor()},view_new:function(){var e=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(f){show_modal("New Visualization",e.template_view_new(f),{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){e.create_browser($("#new-title").val(),$("#new-dbkey").val())}});if(galaxy_config.app.default_dbkey){$("#new-dbkey option[value='"+galaxy_config.app.default_dbkey+"']").attr("selected",true)}$("#new-title").focus();$("select[name='dbkey']").select2();$("#overlay").css("overflow","auto")}})},template_view_new:function(e){var g='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">';for(var f in e){g+='<option value="'+e[f][1]+'">'+e[f][0]+"</option>"}g+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+galaxy_config.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>';return g},create_browser:function(f,e){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:f,dbkey:e},galaxy_config.app.gene_region);this.init_editor();view.editor=true;hide_modal()},init_editor:function(){$("#center .unified-panel-title").text(view.name+" ("+view.dbkey+")");if(galaxy_config.app.add_dataset){$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){view.add_drawable(b.object_from_template(e,view,view))}})}$("#add-bookmark-button").click(function(){var f=view.chrom+":"+view.low+"-"+view.high,e="Bookmark description";return ui.add_bookmark(f,e,true)});ui.init_keyboard_nav(view);this.set_up_router({view:view})}});return{GalaxyApp:d}}); \ No newline at end of file +var ui=null;var view=null;var browser_router=null;require(["utils/galaxy.css","libs/jquery/jstorage","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/select2","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating","mvc/ui"],function(a){a.load_file("static/style/jquery.rating.css");a.load_file("static/style/autocomplete_tagging.css");a.load_file("static/style/jquery-ui/smoothness/jquery-ui.css");a.load_file("static/style/library.css");a.load_file("static/style/trackster.css")});define(["libs/backbone/backbone-relational","viz/visualization","viz/trackster_ui"],function(c,a,b){var d=Backbone.View.extend({initialize:function(){ui=new b.TracksterUI(galaxy_config.root);ui.createButtonMenu();ui.buttonMenu.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);$("#right .unified-panel-title").append("Bookmarks");$("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(galaxy_config.app.id){this.view_existing()}else{this.view_new()}},set_up_router:function(e){browser_router=new a.TrackBrowserRouter(e);Backbone.history.start()},view_existing:function(){var e=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:e.title,vis_id:e.vis_id,dbkey:e.dbkey},e.viewport,e.tracks,e.bookmarks,true);this.init_editor()},view_new:function(){var e=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(f){Galaxy.modal.show({title:"New Visualization",body:e.template_view_new(f),buttons:{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){e.create_browser($("#new-title").val(),$("#new-dbkey").val());Galaxy.modal.hide()}}});if(galaxy_config.app.default_dbkey){$("#new-dbkey option[value='"+galaxy_config.app.default_dbkey+"']").attr("selected",true)}$("#new-title").focus();$("select[name='dbkey']").select2();$("#overlay").css("overflow","auto")}})},template_view_new:function(e){var g='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">';for(var f in e){g+='<option value="'+e[f][1]+'">'+e[f][0]+"</option>"}g+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+galaxy_config.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>';return g},create_browser:function(f,e){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:f,dbkey:e},galaxy_config.app.gene_region);this.init_editor();view.editor=true},init_editor:function(){$("#center .unified-panel-title").text(view.name+" ("+view.dbkey+")");if(galaxy_config.app.add_dataset){$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){view.add_drawable(b.object_from_template(e,view,view))}})}$("#add-bookmark-button").click(function(){var f=view.chrom+":"+view.low+"-"+view.high,e="Bookmark description";return ui.add_bookmark(f,e,true)});ui.init_keyboard_nav(view);this.set_up_router({view:view})}});return{GalaxyApp:d}}); \ No newline at end of file diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ac,w,j,s,L,h,X,R){var o=ac.extend;var l={};var i=function(ad,ae){l[ad.attr("id")]=ae};var k=function(ad,af,ah,ag){ah=".group";var ae={};l[ad.attr("id")]=ag;ad.bind("drag",{handle:"."+af,relative:true},function(ap,aq){var ao=$(this),au=$(this).parent(),al=au.children(),an=l[$(this).attr("id")],ak,aj,ar,ai,am;aj=$(this).parents(ah);if(aj.length!==0){ar=aj.position().top;ai=ar+aj.outerHeight();if(aq.offsetY<ar){$(this).insertBefore(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable_before(an,at);return}else{if(aq.offsetY>ai){$(this).insertAfter(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable(an);return}}}aj=null;for(am=0;am<al.length;am++){ak=$(al.get(am));ar=ak.position().top;ai=ar+ak.outerHeight();if(ak.is(ah)&&this!==ak.get(0)&&aq.offsetY>=ar&&aq.offsetY<=ai){if(aq.offsetY-ar<ai-aq.offsetY){ak.find(".content-div").prepend(this)}else{ak.find(".content-div").append(this)}if(an.container){an.container.remove_drawable(an)}l[ak.attr("id")].add_drawable(an);return}}for(am=0;am<al.length;am++){ak=$(al.get(am));if(aq.offsetY<ak.position().top&&!(ak.hasClass("reference-track")||ak.hasClass("intro"))){break}}if(am===al.length){if(this!==al.get(am-1)){au.append(this);l[au.attr("id")].move_drawable(an,am)}}else{if(this!==al.get(am)){$(this).insertBefore(al.get(am));l[au.attr("id")].move_drawable(an,(aq.deltaY>0?am-1:am))}}}).bind("dragstart",function(){ae["border-top"]=ad.css("border-top");ae["border-bottom"]=ad.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ae)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,m="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ae,ad){if(!ad){ad=0}var af=Math.pow(10,ad);return Math.round(ae*af)/af}var p=function(ae,ad,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ag.name;this.view=ae;this.container=ad;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ah){ah.stopPropagation()});var af=this;this.container_div.hover(function(){af.icons_div.show()},function(){af.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ad){if(ad.content_visible){ad.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ad.hide_contents();ad.content_visible=false}else{ad.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ad.content_visible=true;ad.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ae){var ag=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){ae.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ad()}}};$(window).bind("keypress.check_enter_esc",af);show_modal("Configure",ae.config.build_form(),{Cancel:ag,OK:ad})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ad){$(".tooltip").remove();ad.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(ad){},to_dict:function(){},set_name:function(ad){this.old_name=this.name;this.name=ad;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ad=this.view;this.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ae,aj,ai,ah,ad,ag){var af=this;this.action_icons[ae]=$("<a/>").attr("href","javascript:void(0);").attr("title",aj).addClass("icon-button").addClass(ai).tooltip().click(function(){ah(af)}).appendTo(this.icons_div);if(ag){this.action_icons[ae].hide()}},build_action_icons:function(ad){var af;for(var ae=0;ae<ad.length;ae++){af=ad[ae];this.add_action_icon(af.name,af.title,af.css_class,af.on_click_fn,af.prepend,af.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ae,ad,af){p.call(this,ae,ad,af);this.obj_type=af.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(af){this.drawables=[];var ae;for(var ad=0;ad<af.length;ad++){ae=n(af[ad],this.view,this);this.add_drawable(ae)}},init:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].init()}},_draw:function(ad){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw(ad)}},to_dict:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ae}},add_drawable:function(ad){this.drawables.push(ad);ad.container=this;this.changed()},add_drawable_before:function(af,ad){this.changed();var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables.splice(ae,0,af);return true}return false},replace_drawable:function(af,ad,ae){var ag=this.drawables.indexOf(af);if(ag!==-1){this.drawables[ag]=ad;if(ae){af.container_div.replaceWith(ad.container_div)}this.changed()}return ag},remove_drawable:function(ae){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);ae.container=null;this.changed();return true}return false},move_drawable:function(ae,af){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);this.drawables.splice(af,0,ae);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ag){var ad=this.drawables.slice(0),ae=[],af;while(ad.length!==0){af=ad.shift();if(af instanceof ag){ae.push(af)}else{if(af.drawables){ad=ad.concat(af.drawables)}}}return ae}});var P=function(ae,ad,ag){o(ag,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ae,ad,ag);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ag){this.unpack_drawables(ag.drawables)}if("filters" in ag){var af=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ag.filters);af.parent_div.replaceWith(this.filters_manager.parent_div);if(ag.filters.visible){this.setup_multitrack_filtering()}}};o(P.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ad){$(".tooltip").remove();ad.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters();ad._restore_filter_managers()}else{ad.setup_multitrack_filtering();ad.request_draw({clear_tile_cache:true})}ad.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ad=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ad)}return ad},build_header_div:function(){var ad=$("<div/>").addClass("track-header");ad.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ad);return ad},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var af=this.drawables.length;if(af===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(af===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var am,al,aj,ap=true,ah=this.drawables[0].get_type(),ad=0;for(am=0;am<af;am++){aj=this.drawables[am];if(aj.get_type()!==ah){can_composite=false;break}if(aj instanceof c){ad++}}if(ap||ad===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ad>1&&ad===this.drawables.length){var aq={},ae;aj=this.drawables[0];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];aq[ae.name]=[ae]}for(am=1;am<this.drawables.length;am++){aj=this.drawables[am];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];if(ae.name in aq){aq[ae.name].push(ae)}}}this.filters_manager.remove_all();var ag,ai,ak,an;for(var ao in aq){ag=aq[ao];if(ag.length===ad){ai=new h.NumberFilter({name:ag[0].name,index:ag[0].index});this.filters_manager.add_filter(ai)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].filters_manager=this.saved_filters_managers[ad]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ad=0;ad<this.drawables.length;ad++){drawable=this.drawables[ad];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ae=new e(this.view,this.view,{name:this.name,drawables:this.drawables});var ad=this.container.replace_drawable(this,ae,true);ae.request_draw()},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);this.update_icons()},remove_drawable:function(ad){y.prototype.remove_drawable.call(this,ad);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ad=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ad},request_draw:function(ad){ac.each(this.drawables,function(ae){ae.request_draw(ad)})}});var Y=Backbone.View.extend({initialize:function(ad){o(ad,{obj_type:"View"});y.call(this,"View",ad.container,ad);this.chrom=null;this.vis_id=ad.vis_id;this.dbkey=ad.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ad.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var af=this.container,ad=this;this.top_container=$("<div/>").addClass("top-container").appendTo(af);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(af);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(af);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ad);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ag=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ad.dbkey},function(ah){ac.each(ah,function(ai){ad.add_drawable(n(ai,ad,ad))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ae=function(ah){if(ah.type==="focusout"||(ah.keyCode||ah.which)===13||(ah.keyCode||ah.which)===27){if((ah.keyCode||ah.which)!==27){ad.go_to($(this).val())}$(this).hide();$(this).val("");ad.location_span.show();ad.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ae).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ad.location_span.hide();ad.chrom_select.hide();ad.nav_input.val(ad.chrom+":"+ad.low+"-"+ad.high);ad.nav_input.css("display","inline-block");ad.nav_input.select();ad.nav_input.focus();ad.nav_input.autocomplete({source:function(aj,ah){var ak=[],ai=$.map(ad.get_tracks(c),function(al){return al.data_manager.search_features(aj.term).success(function(am){ak=ak.concat(am)})});$.when.apply($,ai).done(function(){ah($.map(ak,function(al){return{label:al[0],value:al[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ad.zoom_out();ad.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ad.zoom_in();ad.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ad.change_chrom(ad.chrom_select.val())});this.browser_content_div.click(function(ah){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ah){ad.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ad.viewport_container.width()*(ad.max_high-ad.max_low));ad.move_delta(-ai)});this.overview_close.click(function(){ad.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ad.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ad.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){ai*=50;var ak=Math.round(-ai/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("<div />").css({height:ad.browser_content_div.height()+ad.top_labeltrack.height()+ad.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX)-ad.container.offset().left,width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ad.container.offset().left,ah=Math.max(al.pageX,am.startX)-ad.container.offset().left,ak=(ad.high-ad.low),aj=ad.viewport_container.width();ad.update_location(Math.round(ai/aj*ak)+ad.low,Math.round(ah/aj*ak)+ad.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ad.high-ad.low),aj=ad.viewport_container.width(),al=ad.low;ad.low=Math.round(ai/aj*ak)+al;ad.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ad.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ad.resize_window()},500)});$(document).bind("redraw",function(){ad.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ad){return this.config.values[ad.toLowerCase()+"_color"]||this.config.values.n_color}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ae,ag,ad,ah){if(this.timer){clearTimeout(this.timer)}if(ah){var af=this;this.timer=setTimeout(function(){af.trigger("navigate",ae+":"+ag+"-"+ad)},500)}else{view.trigger("navigate",ae+":"+ag+"-"+ad)}},update_location:function(ad,af){this.location_span.text(commatize(ad)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ad)+"-"+commatize(af));var ae=view.chrom_select.val();if(ae!==""){this.trigger_navigate(ae,view.low,view.high,true)}},load_chroms:function(af){af.num=v;var ad=this,ae=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:af,dataType:"json",success:function(ah){if(ah.chrom_info.length===0){return}if(ah.reference){ad.add_label_track(new B(ad))}ad.chrom_data=ah.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,ag=ad.chrom_data.length;aj<ag;aj++){var ai=ad.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ah.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ah.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ad.chrom_select.html(ak);ad.chrom_start_index=ah.start_index;ae.resolve(ah.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ad.dbkey)}});return ae},change_chrom:function(ai,ae,ak){var af=this;if(!af.chrom_data){af.load_chroms_deferred.then(function(){af.change_chrom(ai,ae,ak)});return}if(!ai||ai==="None"){return}if(ai==="previous"){af.load_chroms({low:this.chrom_start_index-v});return}if(ai==="next"){af.load_chroms({low:this.chrom_start_index+v});return}var aj=$.grep(af.chrom_data,function(al,am){return al.chrom===ai})[0];if(aj===undefined){af.load_chroms({chrom:ai},function(){af.change_chrom(ai,ae,ak)});return}else{if(ai!==af.chrom){af.chrom=ai;af.chrom_select.val(af.chrom);af.max_high=aj.len-1;af.reset();for(var ah=0,ad=af.drawables.length;ah<ad;ah++){var ag=af.drawables[ah];if(ag.init){ag.init()}}if(af.reference_track){af.reference_track.init()}}if(ae&&ak){af.low=Math.max(ae,0);af.high=Math.min(ak,af.max_high)}else{af.low=0;af.high=af.max_high}af.reset_overview();af.request_redraw()}},go_to:function(ah){ah=ah.replace(/,/g,"");ah=ah.replace(/:|\-/g," ");var ae=ah.split(/\s+/),ag=ae[0],af=(ae[1]?parseInt(ae[1],10):null),ad=(ae[2]?parseInt(ae[2],10):null);if(!ad){af=af-15;ad=af+15}this.change_chrom(ag,af,ad)},move_fraction:function(af){var ad=this;var ae=ad.high-ad.low;this.move_delta(af*ae)},move_delta:function(ag){var ad=this;var af=ad.high-ad.low;if(ad.low-ag<ad.max_low){ad.low=ad.max_low;ad.high=ad.max_low+af}else{if(ad.high-ag>ad.max_high){ad.high=ad.max_high;ad.low=ad.max_high-af}else{ad.high-=ag;ad.low-=ag}}ad.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ad.request_redraw()},200);var ae=ad.chrom_select.val();this.trigger_navigate(ae,ad.low,ad.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div()},add_label_track:function(ad){ad.view=this;ad.init();this.label_tracks.push(ad)},remove_drawable:function(af,ae){y.prototype.remove_drawable.call(this,af);if(ae){var ad=this;af.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ae,af){var ad=this,ag=(af?[af]:ad.drawables);ac.each(ag,function(ah){var ai=ac.find(ad.tracks_to_be_redrawn,function(aj){return aj[0]===ah});if(ai){ai[1]=ae}else{ad.tracks_to_be_redrawn.push([ah,ae])}});if(!this.requested_redraw){requestAnimationFrame(function(){ad._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ad=this.low,ah=this.high;if(ad<this.max_low){ad=this.max_low}if(ah>this.max_high){ah=this.max_high}var ae=this.high-this.low;if(this.high!==0&&ae<this.min_separation){ah=ad+this.min_separation}this.low=Math.floor(ad);this.high=Math.ceil(ah);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ag=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=13;this.overview_box.css({left:ag,width:Math.max(af,ai)}).show();if(ai<af){this.overview_box.css("left",ag-(af-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ag,width:ai})}ac.each(this.tracks_to_be_redrawn,function(al){var aj=al[0],ak=al[1];if(aj){aj._draw(ak)}});this.tracks_to_be_redrawn=[];ac.each(this.label_tracks,function(aj){aj._draw()})},zoom_in:function(ae,af){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ag=this.high-this.low,ah=ag/2+this.low,ad=(ag/this.zoom_factor)/2;if(ae){ah=ae/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ah-ad);this.high=Math.round(ah+ad);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ae=this.high-this.low,af=ae/2+this.low,ad=(ae*this.zoom_factor)/2;this.low=Math.round(af-ad);this.high=Math.round(af+ad);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(af){if(this.overview_drawable){if(this.overview_drawable.dataset.id===af.dataset.id){return}this.overview_viewport.find(".track").remove()}var ae=af.copy({content_div:this.overview_viewport}),ad=this;ae.header_div.hide();ae.is_overview=true;ad.overview_drawable=ae;this.overview_drawable.postdraw_actions=function(){ad.overview_highlight.show().height(ad.overview_drawable.content_div.height());ad.overview_viewport.height(ad.overview_drawable.content_div.height()+ad.overview_box.outerHeight());ad.overview_close.show();ad.resize_window()};ad.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=R.Tool.extend({defaults:{track:null},initialize:function(ad){if(ad.tool_state!==undefined){this.set("hidden",ad.tool_state.hidden)}this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ad){return ac.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var af=this.$el.addClass("param-row"),ag=this.model;var ad=$("<div>").addClass("param-label").text(ag.get("label")).appendTo(af);var ae=$("<div/>").addClass("param-input").html(ag.get("html")).appendTo(af);ae.find(":input").val(ag.get("value"));$("<div style='clear: both;'/>").appendTo(af)},update_value:function(ad){this.model.set_value($(ad.target).val())}});var ab=Backbone.View.extend({initialize:function(ad){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ae=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ai){ai.stopPropagation()}).click(function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()}).keydown(function(ai){ai.stopPropagation()});var af=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(aj){var ai=new t({model:aj});ai.render();parent_div.append(ai.$el)});parent_div.find("input").click(function(){$(this).select()});var ag=$("<div>").addClass("param-row").appendTo(parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ag);var ad=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ag);ad.click(function(){ae.run_on_region()});ah.click(function(){ae.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ad=0;ad<this.params.length;ad++){this.params[ad].update_value()}},run_on_dataset:function(){var ad=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ad.id},null,function(ae){show_modal(ad.get("name")+" is Running",ad.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ae=this.model.get("track"),ah=this.model,aj=new w.GenomeRegion({chrom:ae.view.chrom,start:ae.view.low,end:ae.view.high}),ak={target_dataset_id:ae.dataset.id,action:"rerun",tool_id:ah.id,regions:[aj.toJSON()]},ai=ae,am=ak.tool_id+ai.tool_region_and_parameters_str(aj),ad;if(ai.container===view){var al=new P(view,view,{name:this.name});var ag=ai.container.replace_drawable(ai,al,false);al.container_div.insertBefore(ai.view.content_div.children()[ag]);al.add_drawable(ai);ai.container_div.appendTo(al.content_div);ad=al}else{ad=ai.container}var af=new ai.constructor(view,ad,{name:am,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ai.mode);af.set_filters_manager(ai.filters_manager.copy(af));af.update_icons();ad.add_drawable(af);af.tiles_div.text("Starting job.");this.run(ak,af,function(an){af.set_dataset(new X.Dataset(an));af.tiles_div.text("Running job.");af.init()})},run:function(ad,af,ag){ad.inputs=this.model.get_inputs_dict();var ae=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ad),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ah){return ah!=="pending"}});$.when(ae.go()).then(function(ah){if(ah==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ah.error){af.container_div.addClass("error");af.content_div.text(x+ah.message)}else{ag(ah)}}})}});var C=function(ad,ae){L.Scaler.call(this,ae);this.filter=ad};C.prototype.gen_val=function(ad){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ad[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ad){this.track=ad.track;this.params=ad.params;this.values={};this.restore_values((ad.saved_values?ad.saved_values:{}));this.onchange=ad.onchange};o(F.prototype,{set_param_default_value:function(ae,ad){var af=ac.find(this.params,function(ag){return ag.key===ae});if(af){af.default_value=ad}},set_param_value:function(ad,ae){var af=ac.find(this.params,function(ag){return ag.key===ad});if(af){if(typeof ae==="string"||ae instanceof String){if(ae.trim()===""){ae=af.default_value}else{if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae,10)}}}}}if(this.values[ad]!==ae){this.values[ad]=ae;return true}else{return false}},restore_values:function(ad){var ae=this;$.each(this.params,function(af,ag){if(ad[ag.key]!==undefined){ae.values[ag.key]=ad[ag.key]}else{ae.values[ag.key]=ag.default_value}})},build_form:function(){var ag=this;var ad=$("<div />");var af;function ae(al,ah){for(var ap=0;ap<al.length;ap++){af=al[ap];if(af.hidden){continue}var aj="param_"+ap;var au=ag.values[af.key];var aw=$("<div class='form-row' />").appendTo(ah);aw.append($("<label />").attr("for",aj).text(af.label+":"));if(af.type==="bool"){aw.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",au))}else{if(af.type==="text"){aw.append($('<input type="text"/>').attr("id",aj).val(au).click(function(){$(this).select()}))}else{if(af.type==="select"){var ar=$("<select />").attr("id",aj);for(var an=0;an<af.options.length;an++){$("<option/>").text(af.options[an].label).attr("value",af.options[an].value).appendTo(ar)}ar.val(au);aw.append(ar)}else{if(af.type==="color"){var av=$("<div/>").appendTo(aw),aq=$("<input />").attr("id",aj).attr("name",aj).val(au).css("float","left").appendTo(av).click(function(ay){$(".tooltip").removeClass("in");var ax=$(this).siblings(".tooltip").addClass("in");ax.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ax).height()/2)+($(this).height()/2)}).show();ax.click(function(az){az.stopPropagation()});$(document).bind("click.color-picker",function(){ax.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()}),ao=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(av).attr("title","Set new random color").tooltip(),at=$("<div class='tooltip right' style='position: absolute;' />").appendTo(av).hide(),ak=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(at),ai=$("<div class='tooltip-arrow'></div>").appendTo(at),am=$.farbtastic(ak,{width:100,height:100,callback:aq,color:au});av.append($("<div/>").css("clear","both"));(function(ax){ao.click(function(){ax.setColor(j.get_random_color())})})(am)}else{aw.append($("<input />").attr("id",aj).attr("name",aj).val(au))}}}}if(af.help){aw.append($("<div class='help'/>").text(af.help))}}}ae(this.params,ad);return ad},update_from_form:function(ad){var af=this;var ae=false;$.each(this.params,function(ag,ai){if(!ai.hidden){var aj="param_"+ag;var ah=ad.find("#"+aj).val();if(ai.type==="bool"){ah=ad.find("#"+aj).is(":checked")}ae=af.set_param_value(ai.key,ah)||ae}});if(ae){this.onchange();this.track.changed()}}});var b=function(ad,ag,ah,ae,af){this.track=ad;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.w_scale=ah;this.html_elt=$("<div class='track-tile'/>").append(ae).height($(ae).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ad,ag,ah,ae,af){b.call(this,ad,ag,ah,ae,af)};M.prototype.predisplay_actions=function(){};var O=function(ag,an,ap,af,ai,aj,aq,ae,am){b.call(this,ag,an,ap,af,ai);this.mode=aj;this.all_slotted=ae;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;af=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:af.width}).prependTo(this.html_elt);var al=new w.GenomeRegion({chrom:ag.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ad=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;ag.data_manager.get_more_data(al,ag.mode,1/ak.w_scale,{},ag.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();ag.request_draw()}).dblclick(function(ar){ar.stopPropagation()});ad.click(function(){ak.stale=true;ag.data_manager.get_more_data(al,ag.mode,1/ak.w_scale,{},ag.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();ag.request_draw()}).dblclick(function(ar){ar.stopPropagation()})}};o(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ae=this,ad={};if(ae.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ap){if(!this.hovered){return}var ak=$(this).offset(),ao=ap.pageX-ak.left,an=ap.pageY-ak.top,au=ae.feature_mapper.get_feature_data(ao,an),al=(au?au[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!al||$(this).attr("id")!==al.toString()){$(this).remove()}});if(au){var ag=ad[al];if(!ag){var al=au[0],aq={name:au[3],start:au[1],end:au[2],strand:au[4]},aj=ae.track.filters_manager.filters,ai;for(var am=0;am<aj.length;am++){ai=aj[am];aq[ai.name]=au[ai.index]}var ag=$("<div/>").attr("id",al).addClass("feature-popup"),av=$("<table/>"),at,ar,aw;for(at in aq){ar=aq[at];aw=$("<tr/>").appendTo(av);$("<th/>").appendTo(aw).text(at);$("<td/>").attr("align","left").appendTo(aw).text(typeof(ar)==="number"?V(ar,2):ar)}ag.append($("<div class='feature-popup-inner'>").append(av));ad[al]=ag}ag.appendTo($(this).parents(".track-content").children(".overlay"));var ah=ao+parseInt(ae.html_elt.css("left"))-ag.width()/2,af=an+parseInt(ae.html_elt.css("top"))+7;ag.css("left",ah+"px").css("top",af+"px")}else{if(!ap.isPropagationStopped()){ap.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ap)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ae,ad,af){o(af,{drag_handle_class:"draghandle"});p.call(this,ae,ad,af);this.dataset=null;if(af.dataset){this.dataset=(af.dataset instanceof Backbone.Model?af.dataset:X.Dataset.findOrCreate(af.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in af?af.data_query_wait:K);this.data_manager=("data_manager" in af?af.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ae.dbkey,chroms_info:{chrom_info:ae.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in af)||af.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ad){ad.view.set_overview(ad)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters()}else{ad.filters_manager.init_filters()}ad.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ad){ad.tool.toggle();if(ad.tool.is_visible()){ad.set_name(ad.name+ad.tool_region_and_parameters_str())}else{ad.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ad){var ag='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',af=ac.template(ag,{track:ad});var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){var ak=$('select[name="regions"] option:selected').val(),am,aj=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),al=ac.map($(".bookmark"),function(an){return new w.GenomeRegion({from_str:$(an).children(".position").text()})});if(ak==="cur"){am=[aj]}else{if(ak==="bookmarks"){am=al}else{am=[aj].concat(al)}}hide_modal();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(am).toJSON())})},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){ae()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",af,{No:ai,Yes:ae})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ad=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ad)}this.name_div=$("<div/>").addClass("track-name").appendTo(ad).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ad},set_dataset:function(ad){this.dataset=ad;this.data_manager.set("dataset",ad)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ad=this;var ag=false;var af=false;var ae=$("<div class='track-resize'>");$(ad.container_div).hover(function(){if(ad.content_visible){ag=true;ae.show()}},function(){ag=false;if(!af){ae.hide()}});ae.hide().bind("dragstart",function(ah,ai){af=true;ai.original_height=$(ad.content_div).height()}).bind("drag",function(ai,aj){var ah=Math.min(Math.max(aj.original_height+aj.deltaY,ad.min_height_px),ad.max_height_px);$(ad.tiles_div).css("height",ah);ad.visible_height_px=(ad.max_height_px===ah?0:ah);ad.on_resize()}).bind("dragend",function(ah,ai){ad.tile_cache.clear();af=false;if(!ag){ae.hide()}ad.config.values.height=ad.visible_height_px;ad.changed()}).appendTo(ad.container_div)},set_display_modes:function(ag,aj){this.display_modes=ag;this.mode=(aj?aj:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ae=this,ah={};for(var af=0,ad=ae.display_modes.length;af<ad;af++){var ai=ae.display_modes[af];ah[ai]=function(ak){return function(){ae.change_mode(ak);ae.icons_div.show();ae.container_div.mouseleave(function(){ae.icons_div.hide()})}}(ai)}make_popupmenu(this.action_icons.mode_icon,ah)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(af){var ae=this;ae.enabled=false;ae.tile_cache.clear();ae.data_manager.clear();ae.tiles_div.css("height","auto");ae.tiles_div.text("").children().remove();ae.container_div.removeClass("nodata error pending");if(!ae.dataset.id){return}var ad=$.Deferred(),ag={hda_ldda:ae.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ae.view.chrom,retry:af};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){ae.container_div.addClass("error");ae.tiles_div.text(m);if(ah.message){ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ah.message+"</pre>",{Close:hide_modal})}));ae.tiles_div.append($("<span/>").text(" "));ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ae.init(true)}))}}else{if(ah==="no converter"){ae.container_div.addClass("error");ae.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){ae.container_div.addClass("nodata");ae.tiles_div.text(E)}else{if(ah==="pending"){ae.container_div.addClass("pending");ae.tiles_div.html(u);setTimeout(function(){ae.init()},ae.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){ae.valid_chroms=ah.valid_chroms;ae.update_icons()}ae.tiles_div.text(U);if(ae.view.chrom){ae.tiles_div.text("");ae.tiles_div.css("height",ae.visible_height_px+"px");ae.enabled=true;$.when.apply($,ae.predraw_init()).done(function(){ad.resolve();ae.container_div.removeClass("nodata error pending");ae.request_draw()})}else{ad.resolve()}}}}}}});this.update_icons();return ad},predraw_init:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){ad.container_div.addClass("line-track");var ag=ae.data;if(ag&&ag.min&&ag.max){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.config.set_param_default_value("min_value",af);ad.config.set_param_default_value("max_value",ah);ad.prefs.min_value=af;ad.prefs.max_value=ah}})},get_drawables:function(){return this}});var N=function(af,ae,ah){f.call(this,af,ae,ah);var ad=this;k(ad.container_div,ad.drag_handle_class,".group",ad);this.filters_manager=new h.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ah.tool?new q(ac.extend(ah.tool,{track:this,tool_state:ah.tool_state})):null);this.tile_cache=new w.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ag=new ab({model:this.tool});ag.render();this.dynamic_tool_div=ag.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};o(N.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ad){$(".tooltip").remove();ad.slotters[ad.view.resolution_px_b].max_rows*=2;ad.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ad){var ae=this.to_dict();o(ae,{data_manager:this.data_manager});var af=new this.constructor(this.view,ad,ae);af.change_mode(this.mode);af.enabled=this.enabled;return af},set_filters_manager:function(ad){this.filters_manager=ad;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){var ag=ae.data;if(isNaN(parseFloat(ad.prefs.min_value))||isNaN(parseFloat(ad.prefs.max_value))){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.prefs.min_value=af;ad.prefs.max_value=ah}})},change_mode:function(ae){var ad=this;ad.mode=ae;ad.config.values.mode=ae;if(ae==="Auto"){this.data_manager.clear()}ad.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ad.mode+")");return ad},update_icons:function(){var ad=this;if(ad.filters_available){ad.action_icons.filters_icon.show()}else{ad.action_icons.filters_icon.hide()}if(ad.tool){ad.action_icons.tools_icon.show();ad.action_icons.param_space_viz_icon.show()}else{ad.action_icons.tools_icon.hide();ad.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ae,ad){return ae+"_"+ad},request_draw:function(ad){if(ad&&ad.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ad,this)},before_draw:function(){this.max_height_px=0},_draw:function(ar){if(!this.can_draw()){return}var ao=ar&&ar.clear_after,am=this.view.low,ah=this.view.high,ak=ah-am,ae=this.view.container.width(),aq=this.view.resolution_px_b,ag=1/aq;if(this.is_overview){am=this.view.max_low;ah=this.view.max_high;aq=ae/(view.max_high-view.max_low);ag=1/aq}this.before_draw();this.tiles_div.children().addClass("remove");var ad=Math.floor(am/(ag*S)),al,an,ai,aj=[],ap=[];while((ad*S*ag)<ah){al=Math.floor(ad*S*ag);an=new w.GenomeRegion({chrom:this.view.chrom,start:al,end:Math.min(al+Math.ceil(S*ag),this.view.max_high)});ai=this.draw_helper(an,aq,ar);aj.push(ai);$.when(ai).then(function(at){ap.push(at)});ad+=1}if(!ao){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;$.when.apply($,aj).then(function(){af.tiles_div.children(".remove").remove();ap=ac.filter(ap,function(at){return at!==null});if(ap.length!==0){af.postdraw_actions(ap,ae,aq,ao)}})},_add_yaxis_label:function(ag,ai){var ae=this,ah=(ag==="max"?"top":"bottom"),aj=(ag==="max"?"max":"min"),ad=(ag==="max"?"max_value":"min_value"),ai=ai||function(){ae.request_draw({clear_tile_cache:true})},af=this.container_div.find(".yaxislabel."+ah);if(af.length!==0){af.text(ae.prefs[ad])}else{af=$("<div/>").text(ae.prefs[ad]).make_text_editable({num_cols:12,on_finish:function(ak){$(".tooltip").remove();ae.config.set_param_value(ad,ak);ai()},help_text:"Set "+aj+" value"}).addClass("yaxislabel "+ah).css("color",this.prefs.label_color);this.container_div.prepend(af)}},postdraw_actions:function(ag,ah,aj,ad){var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length>0){this.max_height_px=0;var ae=this;ac.each(ag,function(ak){if(!(ak instanceof M)){ak.html_elt.remove();ae.draw_helper(ak.region,aj,{force:true,mode:"Coverage"})}});ae._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ai=ac.find(ag,function(ak){return ak.has_icons});if(ai){ac.each(ag,function(ak){if(!ak.has_icons){ak.html_elt.css("padding-top",D)}})}}},get_mode:function(ad){return this.mode},update_auto_mode:function(ad){},_get_drawables:function(){return[this]},draw_helper:function(am,ap,aq){if(!aq){aq={}}var ae=aq.force,ao=!(aq.data_fetch===false),aj=aq.mode||this.mode,ag=1/ap,af=this,ah=this._get_drawables(),an=this._gen_tile_cache_key(ap,am),ai=function(ar){return(ar&&"track" in ar)};var ak=(ae?undefined:af.tile_cache.get_elt(an));if(ak){if(ai(ak)){af.show_tile(ak,ap)}return ak}if(!ao){return null}var al=function(){var ar=(ac.find(A,function(au){return au===aj})?"Coverage":aj);var at=ac.map(ah,function(au){return au.data_manager.get_data(am,ar,ag,af.data_url_extra_params)});if(view.reference_track){at.push(view.reference_track.data_manager.get_data(am,aj,ag,view.reference_track.data_url_extra_params))}return at};var ad=$.Deferred();af.tile_cache.set_elt(an,ad);$.when.apply($,al()).then(function(){var ar=al(),ax=ar,aD;if(view.reference_track){aD=view.reference_track.data_manager.subset_entry(ar.pop(),am)}var ay=[],av=[];ac.each(ah,function(aI,aF){var aH=aI.mode,aG=ax[aF];if(aH==="Auto"){aH=aI.get_mode(aG);aI.update_auto_mode(aH)}ay.push(aH);av.push(aI.get_canvas_height(aG,aH,ap,at))});var aw=af.view.canvas_manager.new_canvas(),az=am.get("start"),aE=am.get("end"),au=0,at=Math.ceil((aE-az)*ap)+af.left_offset,aB=ac.max(av),aA;aw.width=at;aw.height=(aq.height||aB);var aC=aw.getContext("2d");aC.translate(af.left_offset,0);if(ah.length>1){aC.globalAlpha=0.5;aC.globalCompositeOperation="source-over"}ac.each(ah,function(aG,aF){aA=aG.draw_tile(ax[aF],aC,ay[aF],am,ap,aD)});if(aA!==undefined){af.tile_cache.set_elt(an,aA);af.show_tile(aA,ap)}ad.resolve(aA)});return ad},get_canvas_height:function(ad,af,ag,ae){return this.visible_height_px},_draw_line_track_tile:function(ad,af,ai,ah,aj){var ag=af.canvas,ae=new L.LinePainter(ad.data,ah.get("start"),ah.get("end"),this.prefs,ai);ae.draw(af,ag.width,ag.height,aj);return new M(this,ah,aj,ag,ad.data)},draw_tile:function(ad,ae,ah,ag,ai,af){},show_tile:function(af,ai){var ae=this,ad=af.html_elt;af.predisplay_actions();var ah=(af.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ah-=this.left_offset}ad.css({position:"absolute",top:0,left:ah});if(ad.hasClass("remove")){ad.removeClass("remove")}else{this.tiles_div.append(ad)}af.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},tool_region_and_parameters_str:function(ag){var ad=this,af=(ag!==undefined?ag.toString():"all"),ae=ac.values(ad.tool.get_inputs_dict()).join(", ");return" - region=["+af+"], parameters=["+ae+"]"},data_and_mode_compatible:function(ad,ae){if(ae==="Auto"){return true}else{if(ae==="Coverage"){return ad.dataset_type==="bigwig"}else{if(ad.dataset_type==="bigwig"||ad.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ad){if(ad.message||ad.extra_info==="no_detail"){return false}else{if(ad.dataset_type==="bigwig"){return(ad.data[1][0]-ad.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ae,ad){var af={resize:false};f.call(this,ae,ad,af);this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ah){var af=this.view,ag=af.high-af.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ag)/Math.log(10)))),ad=Math.floor(af.low/ak)*ak,ai=this.view.container.width(),ae=$("<div style='position: relative; height: 1.3em;'></div>");while(ad<af.high){var aj=(ad-af.low)/ag*ai;ae.append($("<div class='label'>"+commatize(ad)+"</div>").css({position:"absolute",left:aj-1}));ad+=ak}this.content_div.children(":first").remove();this.content_div.append(ae)}});var e=function(ae,ad,ah){this.display_modes=A;N.call(this,ae,ad,ah);this.drawables=[];if("drawables" in ah){var ag;for(var af=0;af<ah.drawables.length;af++){ag=ah.drawables[af];this.drawables[af]=n(ag,ae,null);if(ag.left_offset>this.left_offset){this.left_offset=ag.left_offset}}this.enabled=true}ac.each(this.drawables,function(ai){if(ai instanceof c||ai instanceof T){ai.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ad){$(".tooltip").remove();ad.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ad){N.prototype.change_mode.call(this,ad);for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].change_mode(ad)}},init:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].init())}var ad=this;$.when.apply($,af).then(function(){ad.enabled=true;ad.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ag=new P(this.view,this.container,{name:this.name}),ad;for(var af=0;af<this.drawables.length;af++){ad=this.drawables[af];ad.update_icons();ag.add_drawable(ad);ad.container=ag;ag.content_div.append(ad.container_div)}var ae=this.container.replace_drawable(this,ag,true);ag.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ae=ac.min(ac.map(this.drawables,function(af){return af.prefs.min_value})),ad=ac.max(ac.map(this.drawables,function(af){return af.prefs.max_value}));this.prefs.min_value=ae;this.prefs.max_value=ad;ac.each(this.drawables,function(af){af.prefs.min_value=ae;af.prefs.max_value=ad})},update_all_min_max:function(){var ad=this;ac.each(this.drawables,function(ae){ae.prefs.min_value=ad.prefs.min_value;ae.prefs.max_value=ad.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(aj,ad,am,ai){N.prototype.postdraw_actions.call(this,aj,ad,am,ai);var ah=-1;for(var af=0;af<aj.length;af++){var ak=aj[af].html_elt.find("canvas").height();if(ak>ah){ah=ak}}for(var af=0;af<aj.length;af++){var ag=aj[af];if(ag.html_elt.find("canvas").height()!==ah){this.draw_helper(ag.region,am,{force:true,height:ah});ag.html_elt.remove()}}var ae=this,al=function(){ae.update_all_min_max()};this._add_yaxis_label("min",al);this._add_yaxis_label("max",al)}});var B=function(ad){N.call(this,ad,{content_div:ad.top_labeltrack},{resize:false});ad.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=galaxy_config.root+"api/genomes//"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ae,af,ad){if(af>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ae,af,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ad){return true},draw_tile:function(af,al,ag,ai,am){var ae=this.data_manager.subset_entry(af,ai),ak=ae.data;var ad=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ah=0,aj=ak.length;ah<aj;ah++){al.fillStyle=this.view.get_base_color(ak[ah]);al.fillText(ak[ah],Math.floor(ah*am),10)}return new b(this,ai,am,ad,ae)}});var g=function(af,ae,ag){var ad=this;this.display_modes=A;this.mode="Histogram";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:j.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(g.prototype,p.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ad,ae,ag,af,ah){return this._draw_line_track_tile(ad,ae,ag,af,ah)},can_subset:function(ad){return(ad.data[1][0]-ad.data[0][0]===1)},postdraw_actions:function(ae,af,ag,ad){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(af,ae,ag){var ad=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);this.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(r.prototype,p.prototype,N.prototype,{draw_tile:function(ad,af,ai,ah,aj){var ag=af.canvas,ae=new L.DiagonalHeatmapPainter(ad.data,ah.get("start"),ah.get("end"),this.prefs,ai);ae.draw(af,ag.width,ag.height,aj);return new b(this,ah,aj,ag,ad.data)}});var c=function(ag,af,ai){var ae=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ag,af,ai);var ah=j.get_random_color(),ad=j.get_random_color([ah,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ai.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.set_painter_from_config();ae.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(an,af,ao,am){N.prototype.postdraw_actions.call(this,an,af,ao,am);var ah=this,ai;if(ah.filters_manager){var ag=ah.filters_manager.filters;for(var ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<an.length;ai++){if(an[ai].data.length){al=an[ai].data[0];for(var ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(an[0] instanceof O){var ad=true;for(ai=0;ai<an.length;ai++){if(!an[ai].all_slotted){ad=false;break}}if(!ad){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ad){var ad;if(this.mode==="Auto"){if(ad==="no_detail"){ad="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ad+")")}},incremental_slots:function(ah,ad,ag){var ae=this.view.canvas_manager.dummy_context,af=this.slotters[ah];if(!af||(af.mode!==ag)){af=new (s.FeatureSlotter)(ah,ag,z,function(ai){return ae.measureText(ai)});this.slotters[ah]=af}return af.slot_features(ad)},get_mode:function(ad){if(ad.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ad,ah,ai,ae){if(ah==="Coverage"||ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=this.incremental_slots(ai,ad.data,ah);var af=new (this.painter)(null,null,null,this.prefs,ah);return Math.max(aa,af.get_required_height(ag,ae))}},draw_tile:function(an,ar,ap,ag,ak,af){var aq=this,ae=ar.canvas,ay=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,ar,ap,ag,ak)}var aj=[],ao=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var at=0,av=an.data.length;at<av;at++){var ai=an.data[at];var au=false;var am;for(var ax=0,aC=al.length;ax<aC;ax++){am=al[ax];am.update_attrs(ai);if(!am.keep(ai)){au=true;break}}if(!au){aj.push(ai);if(!(ai[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(aj,ay,ad,this.prefs,ap,aB,az,af,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){aw=aA.draw(ar,ae.width,ae.height,ak,ao);aw.translation=-ah}return new O(aq,ag,ak,ae,an.data,ap,an.message,all_slotted,aw)}});var Z=function(ae,ad,af){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Histogram color",type:"color",default_value:j.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,N.prototype,{draw_tile:function(ad,ag,ai,ah,aj){if(ad.dataset_type==="bigwig"){return this._draw_line_track_tile(ad,ag,"Histogram",ah,aj)}else{var af=this.view,ae=new (this.painter)(ad.data,ah.get("start"),ah.get("end"),this.prefs,ai,function(ak){return af.get_base_color(ak)});ae.draw(ag,ag.canvas.width,ag.canvas.height,aj);return new b(this,ah,aj,ag.canvas,ad.data)}},get_canvas_height:function(ad,ah,ai,af){if(ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=new (this.painter)(null,null,null,this.prefs,ah);var ae=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ae===0&&ad.data.length!==0){ae=ad.data[0][7].match(/,/g);if(ae===null){ae=1}else{ae=ae.length+1}}return ag.get_required_height(ae)}},predraw_init:function(){var ad=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ad.push(this.dataset.fetch())}return ad},postdraw_actions:function(ag,ah,aj,ae){N.prototype.postdraw_actions.call(this,ag,ah,aj,ae);var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length===0&&this.prefs.show_labels){var ad;if(this.container_div.find(".yaxislabel.variant").length===0){ad=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ad+"px",top:(this.prefs.summary_height-ad)/2+"px"}));if(this.prefs.show_sample_data){var ai=this.dataset.get("metadata").get("sample_names").join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ad=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ad,"line-height":ad});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(af,ae,ah){c.call(this,af,ae,ah);var ag=j.get_random_color(),ad=j.get_random_color([ag,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=(af.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};o(T.prototype,p.prototype,N.prototype,c.prototype);var d={CompositeTrack:e,DrawableGroup:P,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var n=function(af,ae,ad){if("copy" in af){return af.copy(ad)}else{var ag=af.obj_type;if(!ag){ag=af.track_type}return new d[ag](ae,ad,af)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:T,VariantTrack:Z,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ac,w,j,s,L,h,X,R){var o=ac.extend;var l={};var i=function(ad,ae){l[ad.attr("id")]=ae};var k=function(ad,af,ah,ag){ah=".group";var ae={};l[ad.attr("id")]=ag;ad.bind("drag",{handle:"."+af,relative:true},function(ap,aq){var ao=$(this),au=$(this).parent(),al=au.children(),an=l[$(this).attr("id")],ak,aj,ar,ai,am;aj=$(this).parents(ah);if(aj.length!==0){ar=aj.position().top;ai=ar+aj.outerHeight();if(aq.offsetY<ar){$(this).insertBefore(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable_before(an,at);return}else{if(aq.offsetY>ai){$(this).insertAfter(aj);var at=l[aj.attr("id")];at.remove_drawable(an);at.container.add_drawable(an);return}}}aj=null;for(am=0;am<al.length;am++){ak=$(al.get(am));ar=ak.position().top;ai=ar+ak.outerHeight();if(ak.is(ah)&&this!==ak.get(0)&&aq.offsetY>=ar&&aq.offsetY<=ai){if(aq.offsetY-ar<ai-aq.offsetY){ak.find(".content-div").prepend(this)}else{ak.find(".content-div").append(this)}if(an.container){an.container.remove_drawable(an)}l[ak.attr("id")].add_drawable(an);return}}for(am=0;am<al.length;am++){ak=$(al.get(am));if(aq.offsetY<ak.position().top&&!(ak.hasClass("reference-track")||ak.hasClass("intro"))){break}}if(am===al.length){if(this!==al.get(am-1)){au.append(this);l[au.attr("id")].move_drawable(an,am)}}else{if(this!==al.get(am)){$(this).insertBefore(al.get(am));l[au.attr("id")].move_drawable(an,(aq.deltaY>0?am-1:am))}}}).bind("dragstart",function(){ae["border-top"]=ad.css("border-top");ae["border-bottom"]=ad.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ae)})};var aa=16,G=9,D=20,z=100,I=12000,S=400,K=5000,v=100,m="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",u="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",x="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20,A=["Histogram","Line","Filled","Intensity"];function V(ae,ad){if(!ad){ad=0}var af=Math.pow(10,ad);return Math.round(ae*af)/af}var p=function(ae,ad,ag){if(!p.id_counter){p.id_counter=0}this.id=p.id_counter++;this.name=ag.name;this.view=ae;this.container=ad;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ag.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ah){ah.stopPropagation()});var af=this;this.container_div.hover(function(){af.icons_div.show()},function(){af.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};p.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ad){if(ad.content_visible){ad.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ad.hide_contents();ad.content_visible=false}else{ad.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ad.content_visible=true;ad.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ae){var ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){ae.config.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ah){if((ah.keyCode||ah.which)===27){ag()}else{if((ah.keyCode||ah.which)===13){ad()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ae.config.build_form(),buttons:{Cancel:ag,Ok:ad}})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ad){$(".tooltip").remove();ad.remove()}}];o(p.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(ad){},to_dict:function(){},set_name:function(ad){this.old_name=this.name;this.name=ad;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ad=this.view;this.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ae,aj,ai,ah,ad,ag){var af=this;this.action_icons[ae]=$("<a/>").attr("href","javascript:void(0);").attr("title",aj).addClass("icon-button").addClass(ai).tooltip().click(function(){ah(af)}).appendTo(this.icons_div);if(ag){this.action_icons[ae].hide()}},build_action_icons:function(ad){var af;for(var ae=0;ae<ad.length;ae++){af=ad[ae];this.add_action_icon(af.name,af.title,af.css_class,af.on_click_fn,af.prepend,af.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var y=function(ae,ad,af){p.call(this,ae,ad,af);this.obj_type=af.obj_type;this.drawables=[]};o(y.prototype,p.prototype,{unpack_drawables:function(af){this.drawables=[];var ae;for(var ad=0;ad<af.length;ad++){ae=n(af[ad],this.view,this);this.add_drawable(ae)}},init:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].init()}},_draw:function(ad){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw(ad)}},to_dict:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ae}},add_drawable:function(ad){this.drawables.push(ad);ad.container=this;this.changed()},add_drawable_before:function(af,ad){this.changed();var ae=this.drawables.indexOf(ad);if(ae!==-1){this.drawables.splice(ae,0,af);return true}return false},replace_drawable:function(af,ad,ae){var ag=this.drawables.indexOf(af);if(ag!==-1){this.drawables[ag]=ad;if(ae){af.container_div.replaceWith(ad.container_div)}this.changed()}return ag},remove_drawable:function(ae){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);ae.container=null;this.changed();return true}return false},move_drawable:function(ae,af){var ad=this.drawables.indexOf(ae);if(ad!==-1){this.drawables.splice(ad,1);this.drawables.splice(af,0,ae);this.changed();return true}return false},get_drawables:function(){return this.drawables},get_tracks:function(ag){var ad=this.drawables.slice(0),ae=[],af;while(ad.length!==0){af=ad.shift();if(af instanceof ag){ae.push(af)}else{if(af.drawables){ad=ad.concat(af.drawables)}}}return ae}});var P=function(ae,ad,ag){o(ag,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});y.call(this,ae,ad,ag);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);i(this.container_div,this);i(this.content_div,this);k(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new h.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in ag){this.unpack_drawables(ag.drawables)}if("filters" in ag){var af=this.filters_manager;this.filters_manager=new h.FiltersManager(this,ag.filters);af.parent_div.replaceWith(this.filters_manager.parent_div);if(ag.filters.visible){this.setup_multitrack_filtering()}}};o(P.prototype,p.prototype,y.prototype,{action_icons_def:[p.prototype.action_icons_def[0],p.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ad){$(".tooltip").remove();ad.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters();ad._restore_filter_managers()}else{ad.setup_multitrack_filtering();ad.request_draw({clear_tile_cache:true})}ad.filters_manager.toggle()}},p.prototype.action_icons_def[2]],build_container_div:function(){var ad=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ad)}return ad},build_header_div:function(){var ad=$("<div/>").addClass("track-header");ad.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ad);return ad},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var af=this.drawables.length;if(af===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(af===1){if(this.drawables[0] instanceof e){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var am,al,aj,ap=true,ah=this.drawables[0].get_type(),ad=0;for(am=0;am<af;am++){aj=this.drawables[am];if(aj.get_type()!==ah){can_composite=false;break}if(aj instanceof c){ad++}}if(ap||ad===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tooltip").remove()}if(ad>1&&ad===this.drawables.length){var aq={},ae;aj=this.drawables[0];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];aq[ae.name]=[ae]}for(am=1;am<this.drawables.length;am++){aj=this.drawables[am];for(al=0;al<aj.filters_manager.filters.length;al++){ae=aj.filters_manager.filters[al];if(ae.name in aq){aq[ae.name].push(ae)}}}this.filters_manager.remove_all();var ag,ai,ak,an;for(var ao in aq){ag=aq[ao];if(ag.length===ad){ai=new h.NumberFilter({name:ag[0].name,index:ag[0].index});this.filters_manager.add_filter(ai)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].filters_manager=this.saved_filters_managers[ad]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ad=0;ad<this.drawables.length;ad++){drawable=this.drawables[ad];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ae=new e(this.view,this.view,{name:this.name,drawables:this.drawables});var ad=this.container.replace_drawable(this,ae,true);ae.request_draw()},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);this.update_icons()},remove_drawable:function(ad){y.prototype.remove_drawable.call(this,ad);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ad=o(y.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ad},request_draw:function(ad){ac.each(this.drawables,function(ae){ae.request_draw(ad)})}});var Y=Backbone.View.extend({initialize:function(ad){o(ad,{obj_type:"View"});y.call(this,"View",ad.container,ad);this.chrom=null;this.vis_id=ad.vis_id;this.dbkey=ad.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new w.CanvasManager(this.container.get(0).ownerDocument);this.reset();this.config=new F({track:this,params:[{key:"a_color",label:"A Color",type:"color",default_value:"#FF0000"},{key:"c_color",label:"C Color",type:"color",default_value:"#00FF00"},{key:"g_color",label:"G Color",type:"color",default_value:"#0000FF"},{key:"t_color",label:"T Color",type:"color",default_value:"#FF00FF"},{key:"n_color",label:"N Color",type:"color",default_value:"#AAAAAA"}],saved_values:ad.prefs,onchange:function(){track.request_redraw({clear_tile_cache:true})}})},render:function(){this.requested_redraw=false;var af=this.container,ad=this;this.top_container=$("<div/>").addClass("top-container").appendTo(af);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(af);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(af);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;i(this.viewport_container,ad);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ag=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){w.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ad.dbkey},function(ah){ac.each(ah,function(ai){ad.add_drawable(n(ai,ad,ad))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ae=function(ah){if(ah.type==="focusout"||(ah.keyCode||ah.which)===13||(ah.keyCode||ah.which)===27){if((ah.keyCode||ah.which)!==27){ad.go_to($(this).val())}$(this).hide();$(this).val("");ad.location_span.show();ad.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ae).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ad.location_span.hide();ad.chrom_select.hide();ad.nav_input.val(ad.chrom+":"+ad.low+"-"+ad.high);ad.nav_input.css("display","inline-block");ad.nav_input.select();ad.nav_input.focus();ad.nav_input.autocomplete({source:function(aj,ah){var ak=[],ai=$.map(ad.get_tracks(c),function(al){return al.data_manager.search_features(aj.term).success(function(am){ak=ak.concat(am)})});$.when.apply($,ai).done(function(){ah($.map(ak,function(al){return{label:al[0],value:al[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ad.zoom_out();ad.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ad.zoom_in();ad.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ad.change_chrom(ad.chrom_select.val())});this.browser_content_div.click(function(ah){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ah){ad.zoom_in(ah.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ah,ai){this.current_x=ai.offsetX}).bind("drag",function(ah,aj){var ak=aj.offsetX-this.current_x;this.current_x=aj.offsetX;var ai=Math.round(ak/ad.viewport_container.width()*(ad.max_high-ad.max_low));ad.move_delta(-ai)});this.overview_close.click(function(){ad.reset_overview()});this.viewport_container.bind("draginit",function(ah,ai){if(ah.clientX>ad.viewport_container.width()-16){return false}}).bind("dragstart",function(ah,ai){ai.original_low=ad.low;ai.current_height=ah.clientY;ai.current_x=ai.offsetX}).bind("drag",function(aj,al){var ah=$(this);var am=al.offsetX-al.current_x;var ai=ah.scrollTop()-(aj.clientY-al.current_height);ah.scrollTop(ai);al.current_height=aj.clientY;al.current_x=al.offsetX;var ak=Math.round(am/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}).bind("mousewheel",function(aj,al,ai,ah){if(ai){ai*=50;var ak=Math.round(-ai/ad.viewport_container.width()*(ad.high-ad.low));ad.move_delta(ak)}});this.top_labeltrack.bind("dragstart",function(ah,ai){return $("<div />").css({height:ad.browser_content_div.height()+ad.top_labeltrack.height()+ad.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(al,am){$(am.proxy).css({left:Math.min(al.pageX,am.startX)-ad.container.offset().left,width:Math.abs(al.pageX-am.startX)});var ai=Math.min(al.pageX,am.startX)-ad.container.offset().left,ah=Math.max(al.pageX,am.startX)-ad.container.offset().left,ak=(ad.high-ad.low),aj=ad.viewport_container.width();ad.update_location(Math.round(ai/aj*ak)+ad.low,Math.round(ah/aj*ak)+ad.low)}).bind("dragend",function(am,an){var ai=Math.min(am.pageX,an.startX),ah=Math.max(am.pageX,an.startX),ak=(ad.high-ad.low),aj=ad.viewport_container.width(),al=ad.low;ad.low=Math.round(ai/aj*ak)+al;ad.high=Math.round(ah/aj*ak)+al;$(an.proxy).remove();ad.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ad.resize_window()},500)});$(document).bind("redraw",function(){ad.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ad){return this.config.values[ad.toLowerCase()+"_color"]||this.config.values.n_color}});o(Y.prototype,y.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ae,ag,ad,ah){if(this.timer){clearTimeout(this.timer)}if(ah){var af=this;this.timer=setTimeout(function(){af.trigger("navigate",ae+":"+ag+"-"+ad)},500)}else{view.trigger("navigate",ae+":"+ag+"-"+ad)}},update_location:function(ad,af){this.location_span.text(commatize(ad)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ad)+"-"+commatize(af));var ae=view.chrom_select.val();if(ae!==""){this.trigger_navigate(ae,view.low,view.high,true)}},load_chroms:function(af){af.num=v;var ad=this,ae=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:af,dataType:"json",success:function(ah){if(ah.chrom_info.length===0){return}if(ah.reference){ad.add_label_track(new B(ad))}ad.chrom_data=ah.chrom_info;var ak='<option value="">Select Chrom/Contig</option>';for(var aj=0,ag=ad.chrom_data.length;aj<ag;aj++){var ai=ad.chrom_data[aj].chrom;ak+='<option value="'+ai+'">'+ai+"</option>"}if(ah.prev_chroms){ak+='<option value="previous">Previous '+v+"</option>"}if(ah.next_chroms){ak+='<option value="next">Next '+v+"</option>"}ad.chrom_select.html(ak);ad.chrom_start_index=ah.start_index;ae.resolve(ah.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ad.dbkey)}});return ae},change_chrom:function(ai,ae,ak){var af=this;if(!af.chrom_data){af.load_chroms_deferred.then(function(){af.change_chrom(ai,ae,ak)});return}if(!ai||ai==="None"){return}if(ai==="previous"){af.load_chroms({low:this.chrom_start_index-v});return}if(ai==="next"){af.load_chroms({low:this.chrom_start_index+v});return}var aj=$.grep(af.chrom_data,function(al,am){return al.chrom===ai})[0];if(aj===undefined){af.load_chroms({chrom:ai},function(){af.change_chrom(ai,ae,ak)});return}else{if(ai!==af.chrom){af.chrom=ai;af.chrom_select.val(af.chrom);af.max_high=aj.len-1;af.reset();for(var ah=0,ad=af.drawables.length;ah<ad;ah++){var ag=af.drawables[ah];if(ag.init){ag.init()}}if(af.reference_track){af.reference_track.init()}}if(ae&&ak){af.low=Math.max(ae,0);af.high=Math.min(ak,af.max_high)}else{af.low=0;af.high=af.max_high}af.reset_overview();af.request_redraw()}},go_to:function(ah){ah=ah.replace(/,/g,"");ah=ah.replace(/:|\-/g," ");var ae=ah.split(/\s+/),ag=ae[0],af=(ae[1]?parseInt(ae[1],10):null),ad=(ae[2]?parseInt(ae[2],10):null);if(!ad){af=af-15;ad=af+15}this.change_chrom(ag,af,ad)},move_fraction:function(af){var ad=this;var ae=ad.high-ad.low;this.move_delta(af*ae)},move_delta:function(ag){var ad=this;var af=ad.high-ad.low;if(ad.low-ag<ad.max_low){ad.low=ad.max_low;ad.high=ad.max_low+af}else{if(ad.high-ag>ad.max_high){ad.high=ad.max_high;ad.low=ad.max_high-af}else{ad.high-=ag;ad.low-=ag}}ad.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ad.request_redraw()},200);var ae=ad.chrom_select.val();this.trigger_navigate(ae,ad.low,ad.high,true)},add_drawable:function(ad){y.prototype.add_drawable.call(this,ad);ad.init();this.changed();this.update_intro_div()},add_label_track:function(ad){ad.view=this;ad.init();this.label_tracks.push(ad)},remove_drawable:function(af,ae){y.prototype.remove_drawable.call(this,af);if(ae){var ad=this;af.container_div.hide(0,function(){$(this).remove();ad.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ae,af){var ad=this,ag=(af?[af]:ad.drawables);ac.each(ag,function(ah){var ai=ac.find(ad.tracks_to_be_redrawn,function(aj){return aj[0]===ah});if(ai){ai[1]=ae}else{ad.tracks_to_be_redrawn.push([ah,ae])}});if(!this.requested_redraw){requestAnimationFrame(function(){ad._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ad=this.low,ah=this.high;if(ad<this.max_low){ad=this.max_low}if(ah>this.max_high){ah=this.max_high}var ae=this.high-this.low;if(this.high!==0&&ae<this.min_separation){ah=ad+this.min_separation}this.low=Math.floor(ad);this.high=Math.ceil(ah);this.update_location(this.low,this.high);this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ag=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var af=13;this.overview_box.css({left:ag,width:Math.max(af,ai)}).show();if(ai<af){this.overview_box.css("left",ag-(af-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ag,width:ai})}ac.each(this.tracks_to_be_redrawn,function(al){var aj=al[0],ak=al[1];if(aj){aj._draw(ak)}});this.tracks_to_be_redrawn=[];ac.each(this.label_tracks,function(aj){aj._draw()})},zoom_in:function(ae,af){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var ag=this.high-this.low,ah=ag/2+this.low,ad=(ag/this.zoom_factor)/2;if(ae){ah=ae/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ah-ad);this.high=Math.round(ah+ad);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ae=this.high-this.low,af=ae/2+this.low,ad=(ae*this.zoom_factor)/2;this.low=Math.round(af-ad);this.high=Math.round(af+ad);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(af){if(this.overview_drawable){if(this.overview_drawable.dataset.id===af.dataset.id){return}this.overview_viewport.find(".track").remove()}var ae=af.copy({content_div:this.overview_viewport}),ad=this;ae.header_div.hide();ae.is_overview=true;ad.overview_drawable=ae;this.overview_drawable.postdraw_actions=function(){ad.overview_highlight.show().height(ad.overview_drawable.content_div.height());ad.overview_viewport.height(ad.overview_drawable.content_div.height()+ad.overview_box.outerHeight());ad.overview_close.show();ad.resize_window()};ad.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var q=R.Tool.extend({defaults:{track:null},initialize:function(ad){if(ad.tool_state!==undefined){this.set("hidden",ad.tool_state.hidden)}this.remove_inputs(["data","hidden_data","conditional"])},state_dict:function(ad){return ac.extend(this.get_inputs_dict(),{hidden:!this.is_visible()})}});var t=Backbone.View.extend({events:{"change input":"update_value"},render:function(){var af=this.$el.addClass("param-row"),ag=this.model;var ad=$("<div>").addClass("param-label").text(ag.get("label")).appendTo(af);var ae=$("<div/>").addClass("param-input").html(ag.get("html")).appendTo(af);ae.find(":input").val(ag.get("value"));$("<div style='clear: both;'/>").appendTo(af)},update_value:function(ad){this.model.set_value($(ad.target).val())}});var ab=Backbone.View.extend({initialize:function(ad){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ae=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ai){ai.stopPropagation()}).click(function(ai){ai.stopPropagation()}).bind("dblclick",function(ai){ai.stopPropagation()}).keydown(function(ai){ai.stopPropagation()});var af=$("<div class='tool-name'>").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(aj){var ai=new t({model:aj});ai.render();parent_div.append(ai.$el)});parent_div.find("input").click(function(){$(this).select()});var ag=$("<div>").addClass("param-row").appendTo(parent_div);var ah=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(ag);var ad=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(ag);ad.click(function(){ae.run_on_region()});ah.click(function(){ae.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ad=0;ad<this.params.length;ad++){this.params[ad].update_value()}},run_on_dataset:function(){var ad=this.model;this.run({target_dataset_id:this.model.get("track").dataset.id,action:"rerun",tool_id:ad.id},null,function(ae){Galaxy.modal.show({title:ad.get("name")+" is Running",body:ad.get("name")+" is running on the complete dataset. Tool outputs are in dataset's history.",buttons:{Close:function(){Galaxy.modal.hide()}}})})},run_on_region:function(){var ae=this.model.get("track"),ah=this.model,aj=new w.GenomeRegion({chrom:ae.view.chrom,start:ae.view.low,end:ae.view.high}),ak={target_dataset_id:ae.dataset.id,action:"rerun",tool_id:ah.id,regions:[aj.toJSON()]},ai=ae,am=ak.tool_id+ai.tool_region_and_parameters_str(aj),ad;if(ai.container===view){var al=new P(view,view,{name:this.name});var ag=ai.container.replace_drawable(ai,al,false);al.container_div.insertBefore(ai.view.content_div.children()[ag]);al.add_drawable(ai);ai.container_div.appendTo(al.content_div);ad=al}else{ad=ai.container}var af=new ai.constructor(view,ad,{name:am,hda_ldda:"hda"});af.init_for_tool_data();af.change_mode(ai.mode);af.set_filters_manager(ai.filters_manager.copy(af));af.update_icons();ad.add_drawable(af);af.tiles_div.text("Starting job.");this.run(ak,af,function(an){af.set_dataset(new X.Dataset(an));af.tiles_div.text("Running job.");af.init()})},run:function(ad,af,ag){ad.inputs=this.model.get_inputs_dict();var ae=new j.ServerStateDeferred({ajax_settings:{url:galaxy_config.root+"api/tools",data:JSON.stringify(ad),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ah){return ah!=="pending"}});$.when(ae.go()).then(function(ah){if(ah==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ah.error){af.container_div.addClass("error");af.content_div.text(x+ah.message)}else{ag(ah)}}})}});var C=function(ad,ae){L.Scaler.call(this,ae);this.filter=ad};C.prototype.gen_val=function(ad){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ad[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ad){this.track=ad.track;this.params=ad.params;this.values={};this.restore_values((ad.saved_values?ad.saved_values:{}));this.onchange=ad.onchange};o(F.prototype,{set_param_default_value:function(ae,ad){var af=ac.find(this.params,function(ag){return ag.key===ae});if(af){af.default_value=ad}},set_param_value:function(ad,ae){var af=ac.find(this.params,function(ag){return ag.key===ad});if(af){if(typeof ae==="string"||ae instanceof String){if(ae.trim()===""){ae=af.default_value}else{if(af.type==="float"){ae=parseFloat(ae)}else{if(af.type==="int"){ae=parseInt(ae,10)}}}}}if(this.values[ad]!==ae){this.values[ad]=ae;return true}else{return false}},restore_values:function(ad){var ae=this;$.each(this.params,function(af,ag){if(ad[ag.key]!==undefined){ae.values[ag.key]=ad[ag.key]}else{ae.values[ag.key]=ag.default_value}})},build_form:function(){var ag=this;var ad=$("<div />");var af;function ae(al,ah){for(var ap=0;ap<al.length;ap++){af=al[ap];if(af.hidden){continue}var aj="param_"+ap;var au=ag.values[af.key];var aw=$("<div class='form-row' />").appendTo(ah);aw.append($("<label />").attr("for",aj).text(af.label+":"));if(af.type==="bool"){aw.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",au))}else{if(af.type==="text"){aw.append($('<input type="text"/>').attr("id",aj).val(au).click(function(){$(this).select()}))}else{if(af.type==="select"){var ar=$("<select />").attr("id",aj);for(var an=0;an<af.options.length;an++){$("<option/>").text(af.options[an].label).attr("value",af.options[an].value).appendTo(ar)}ar.val(au);aw.append(ar)}else{if(af.type==="color"){var av=$("<div/>").appendTo(aw),aq=$("<input />").attr("id",aj).attr("name",aj).val(au).css("float","left").appendTo(av).click(function(ay){$(".tooltip").removeClass("in");var ax=$(this).siblings(".tooltip").addClass("in");ax.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(ax).height()/2)+($(this).height()/2)}).show();ax.click(function(az){az.stopPropagation()});$(document).bind("click.color-picker",function(){ax.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()}),ao=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(av).attr("title","Set new random color").tooltip(),at=$("<div class='tooltip right' style='position: absolute;' />").appendTo(av).hide(),ak=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(at),ai=$("<div class='tooltip-arrow'></div>").appendTo(at),am=$.farbtastic(ak,{width:100,height:100,callback:aq,color:au});av.append($("<div/>").css("clear","both"));(function(ax){ao.click(function(){ax.setColor(j.get_random_color())})})(am)}else{aw.append($("<input />").attr("id",aj).attr("name",aj).val(au))}}}}if(af.help){aw.append($("<div class='help'/>").text(af.help))}}}ae(this.params,ad);return ad},update_from_form:function(ad){var af=this;var ae=false;$.each(this.params,function(ag,ai){if(!ai.hidden){var aj="param_"+ag;var ah=ad.find("#"+aj).val();if(ai.type==="bool"){ah=ad.find("#"+aj).is(":checked")}ae=af.set_param_value(ai.key,ah)||ae}});if(ae){this.onchange();this.track.changed()}}});var b=function(ad,ag,ah,ae,af){this.track=ad;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.w_scale=ah;this.html_elt=$("<div class='track-tile'/>").append(ae).height($(ae).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var M=function(ad,ag,ah,ae,af){b.call(this,ad,ag,ah,ae,af)};M.prototype.predisplay_actions=function(){};var O=function(ag,an,ap,af,ai,aj,aq,ae,am){b.call(this,ag,an,ap,af,ai);this.mode=aj;this.all_slotted=ae;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;af=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:af.width}).prependTo(this.html_elt);var al=new w.GenomeRegion({chrom:ag.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ad=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;ag.data_manager.get_more_data(al,ag.mode,1/ak.w_scale,{},ag.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();ag.request_draw()}).dblclick(function(ar){ar.stopPropagation()});ad.click(function(){ak.stale=true;ag.data_manager.get_more_data(al,ag.mode,1/ak.w_scale,{},ag.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();ag.request_draw()}).dblclick(function(ar){ar.stopPropagation()})}};o(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ae=this,ad={};if(ae.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ap){if(!this.hovered){return}var ak=$(this).offset(),ao=ap.pageX-ak.left,an=ap.pageY-ak.top,au=ae.feature_mapper.get_feature_data(ao,an),al=(au?au[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!al||$(this).attr("id")!==al.toString()){$(this).remove()}});if(au){var ag=ad[al];if(!ag){var al=au[0],aq={name:au[3],start:au[1],end:au[2],strand:au[4]},aj=ae.track.filters_manager.filters,ai;for(var am=0;am<aj.length;am++){ai=aj[am];aq[ai.name]=au[ai.index]}var ag=$("<div/>").attr("id",al).addClass("feature-popup"),av=$("<table/>"),at,ar,aw;for(at in aq){ar=aq[at];aw=$("<tr/>").appendTo(av);$("<th/>").appendTo(aw).text(at);$("<td/>").attr("align","left").appendTo(aw).text(typeof(ar)==="number"?V(ar,2):ar)}ag.append($("<div class='feature-popup-inner'>").append(av));ad[al]=ag}ag.appendTo($(this).parents(".track-content").children(".overlay"));var ah=ao+parseInt(ae.html_elt.css("left"))-ag.width()/2,af=an+parseInt(ae.html_elt.css("top"))+7;ag.css("left",ah+"px").css("top",af+"px")}else{if(!ap.isPropagationStopped()){ap.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ap)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var f=function(ae,ad,af){o(af,{drag_handle_class:"draghandle"});p.call(this,ae,ad,af);this.dataset=null;if(af.dataset){this.dataset=(af.dataset instanceof Backbone.Model?af.dataset:X.Dataset.findOrCreate(af.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in af?af.data_query_wait:K);this.data_manager=("data_manager" in af?af.data_manager:new w.GenomeDataManager({dataset:this.dataset,genome:new w.Genome({key:ae.dbkey,chroms_info:{chrom_info:ae.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in af)||af.resize){this.add_resize_handle()}}};o(f.prototype,p.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},p.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ad){ad.view.set_overview(ad)}},p.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ad){if(ad.filters_manager.visible()){ad.filters_manager.clear_filters()}else{ad.filters_manager.init_filters()}ad.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ad){ad.tool.toggle();if(ad.tool.is_visible()){ad.set_name(ad.name+ad.tool_region_and_parameters_str())}else{ad.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ad){var ag='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',af=ac.template(ag,{track:ad});var ai=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){var ak=$('select[name="regions"] option:selected').val(),am,aj=new w.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),al=ac.map($(".bookmark"),function(an){return new w.GenomeRegion({from_str:$(an).children(".position").text()})});if(ak==="cur"){am=[aj]}else{if(ak==="bookmarks"){am=al}else{am=[aj].concat(al)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ad.dataset.id,hda_ldda:ad.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(am).toJSON())})},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){ae()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:af,buttons:{No:ai,Yes:ae}})}},p.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&p.prototype.can_draw.call(this)},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ad=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ad)}this.name_div=$("<div/>").addClass("track-name").appendTo(ad).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ad},set_dataset:function(ad){this.dataset=ad;this.data_manager.set("dataset",ad)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ad=this;var ag=false;var af=false;var ae=$("<div class='track-resize'>");$(ad.container_div).hover(function(){if(ad.content_visible){ag=true;ae.show()}},function(){ag=false;if(!af){ae.hide()}});ae.hide().bind("dragstart",function(ah,ai){af=true;ai.original_height=$(ad.content_div).height()}).bind("drag",function(ai,aj){var ah=Math.min(Math.max(aj.original_height+aj.deltaY,ad.min_height_px),ad.max_height_px);$(ad.tiles_div).css("height",ah);ad.visible_height_px=(ad.max_height_px===ah?0:ah);ad.on_resize()}).bind("dragend",function(ah,ai){ad.tile_cache.clear();af=false;if(!ag){ae.hide()}ad.config.values.height=ad.visible_height_px;ad.changed()}).appendTo(ad.container_div)},set_display_modes:function(ag,aj){this.display_modes=ag;this.mode=(aj?aj:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ae=this,ah={};for(var af=0,ad=ae.display_modes.length;af<ad;af++){var ai=ae.display_modes[af];ah[ai]=function(ak){return function(){ae.change_mode(ak);ae.icons_div.show();ae.container_div.mouseleave(function(){ae.icons_div.hide()})}}(ai)}make_popupmenu(this.action_icons.mode_icon,ah)},build_action_icons:function(){p.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof W){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof g){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof Z){return"VariantTrack"}else{if(this instanceof e){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(af){var ae=this;ae.enabled=false;ae.tile_cache.clear();ae.data_manager.clear();ae.tiles_div.css("height","auto");ae.tiles_div.text("").children().remove();ae.container_div.removeClass("nodata error pending");if(!ae.dataset.id){return}var ad=$.Deferred(),ag={hda_ldda:ae.dataset.get("hda_ldda"),data_type:this.dataset_check_type,chrom:ae.view.chrom,retry:af};$.getJSON(this.dataset.url(),ag,function(ah){if(!ah||ah==="error"||ah.kind==="error"){ae.container_div.addClass("error");ae.tiles_div.text(m);if(ah.message){ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"<pre>"+ah.message+"</pre>",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ae.tiles_div.append($("<span/>").text(" "));ae.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ae.init(true)}))}}else{if(ah==="no converter"){ae.container_div.addClass("error");ae.tiles_div.text(J)}else{if(ah==="no data"||(ah.data!==undefined&&(ah.data===null||ah.data.length===0))){ae.container_div.addClass("nodata");ae.tiles_div.text(E)}else{if(ah==="pending"){ae.container_div.addClass("pending");ae.tiles_div.html(u);setTimeout(function(){ae.init()},ae.data_query_wait)}else{if(ah==="data"||ah.status==="data"){if(ah.valid_chroms){ae.valid_chroms=ah.valid_chroms;ae.update_icons()}ae.tiles_div.text(U);if(ae.view.chrom){ae.tiles_div.text("");ae.tiles_div.css("height",ae.visible_height_px+"px");ae.enabled=true;$.when.apply($,ae.predraw_init()).done(function(){ad.resolve();ae.container_div.removeClass("nodata error pending");ae.request_draw()})}else{ad.resolve()}}}}}}});this.update_icons();return ad},predraw_init:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){ad.container_div.addClass("line-track");var ag=ae.data;if(ag&&ag.min&&ag.max){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.config.set_param_default_value("min_value",af);ad.config.set_param_default_value("max_value",ah);ad.prefs.min_value=af;ad.prefs.max_value=ah}})},get_drawables:function(){return this}});var N=function(af,ae,ah){f.call(this,af,ae,ah);var ad=this;k(ad.container_div,ad.drag_handle_class,".group",ad);this.filters_manager=new h.FiltersManager(this,("filters" in ah?ah.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ah.tool?new q(ac.extend(ah.tool,{track:this,tool_state:ah.tool_state})):null);this.tile_cache=new w.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var ag=new ab({model:this.tool});ag.render();this.dynamic_tool_div=ag.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(ah.mode){this.change_mode(ah.mode)}};o(N.prototype,p.prototype,f.prototype,{action_icons_def:f.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ad){$(".tooltip").remove();ad.slotters[ad.view.resolution_px_b].max_rows*=2;ad.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ad){var ae=this.to_dict();o(ae,{data_manager:this.data_manager});var af=new this.constructor(this.view,ad,ae);af.change_mode(this.mode);af.enabled=this.enabled;return af},set_filters_manager:function(ad){this.filters_manager=ad;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ad=this;return $.getJSON(ad.dataset.url(),{data_type:"data",stats:true,chrom:ad.view.chrom,low:0,high:ad.view.max_high,hda_ldda:ad.dataset.get("hda_ldda")},function(ae){var ag=ae.data;if(isNaN(parseFloat(ad.prefs.min_value))||isNaN(parseFloat(ad.prefs.max_value))){var af=ag.min,ah=ag.max;af=Math.floor(Math.min(0,Math.max(af,ag.mean-2*ag.sd)));ah=Math.ceil(Math.max(0,Math.min(ah,ag.mean+2*ag.sd)));ad.prefs.min_value=af;ad.prefs.max_value=ah}})},change_mode:function(ae){var ad=this;ad.mode=ae;ad.config.values.mode=ae;if(ae==="Auto"){this.data_manager.clear()}ad.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ad.mode+")");return ad},update_icons:function(){var ad=this;if(ad.filters_available){ad.action_icons.filters_icon.show()}else{ad.action_icons.filters_icon.hide()}if(ad.tool){ad.action_icons.tools_icon.show();ad.action_icons.param_space_viz_icon.show()}else{ad.action_icons.tools_icon.hide();ad.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ae,ad){return ae+"_"+ad},request_draw:function(ad){if(ad&&ad.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ad,this)},before_draw:function(){this.max_height_px=0},_draw:function(ar){if(!this.can_draw()){return}var ao=ar&&ar.clear_after,am=this.view.low,ah=this.view.high,ak=ah-am,ae=this.view.container.width(),aq=this.view.resolution_px_b,ag=1/aq;if(this.is_overview){am=this.view.max_low;ah=this.view.max_high;aq=ae/(view.max_high-view.max_low);ag=1/aq}this.before_draw();this.tiles_div.children().addClass("remove");var ad=Math.floor(am/(ag*S)),al,an,ai,aj=[],ap=[];while((ad*S*ag)<ah){al=Math.floor(ad*S*ag);an=new w.GenomeRegion({chrom:this.view.chrom,start:al,end:Math.min(al+Math.ceil(S*ag),this.view.max_high)});ai=this.draw_helper(an,aq,ar);aj.push(ai);$.when(ai).then(function(at){ap.push(at)});ad+=1}if(!ao){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;$.when.apply($,aj).then(function(){af.tiles_div.children(".remove").remove();ap=ac.filter(ap,function(at){return at!==null});if(ap.length!==0){af.postdraw_actions(ap,ae,aq,ao)}})},_add_yaxis_label:function(ag,ai){var ae=this,ah=(ag==="max"?"top":"bottom"),aj=(ag==="max"?"max":"min"),ad=(ag==="max"?"max_value":"min_value"),ai=ai||function(){ae.request_draw({clear_tile_cache:true})},af=this.container_div.find(".yaxislabel."+ah);if(af.length!==0){af.text(ae.prefs[ad])}else{af=$("<div/>").text(ae.prefs[ad]).make_text_editable({num_cols:12,on_finish:function(ak){$(".tooltip").remove();ae.config.set_param_value(ad,ak);ai()},help_text:"Set "+aj+" value"}).addClass("yaxislabel "+ah).css("color",this.prefs.label_color);this.container_div.prepend(af)}},postdraw_actions:function(ag,ah,aj,ad){var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length>0){this.max_height_px=0;var ae=this;ac.each(ag,function(ak){if(!(ak instanceof M)){ak.html_elt.remove();ae.draw_helper(ak.region,aj,{force:true,mode:"Coverage"})}});ae._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ai=ac.find(ag,function(ak){return ak.has_icons});if(ai){ac.each(ag,function(ak){if(!ak.has_icons){ak.html_elt.css("padding-top",D)}})}}},get_mode:function(ad){return this.mode},update_auto_mode:function(ad){},_get_drawables:function(){return[this]},draw_helper:function(am,ap,aq){if(!aq){aq={}}var ae=aq.force,ao=!(aq.data_fetch===false),aj=aq.mode||this.mode,ag=1/ap,af=this,ah=this._get_drawables(),an=this._gen_tile_cache_key(ap,am),ai=function(ar){return(ar&&"track" in ar)};var ak=(ae?undefined:af.tile_cache.get_elt(an));if(ak){if(ai(ak)){af.show_tile(ak,ap)}return ak}if(!ao){return null}var al=function(){var ar=(ac.find(A,function(au){return au===aj})?"Coverage":aj);var at=ac.map(ah,function(au){return au.data_manager.get_data(am,ar,ag,af.data_url_extra_params)});if(view.reference_track){at.push(view.reference_track.data_manager.get_data(am,aj,ag,view.reference_track.data_url_extra_params))}return at};var ad=$.Deferred();af.tile_cache.set_elt(an,ad);$.when.apply($,al()).then(function(){var ar=al(),ax=ar,aD;if(view.reference_track){aD=view.reference_track.data_manager.subset_entry(ar.pop(),am)}var ay=[],av=[];ac.each(ah,function(aI,aF){var aH=aI.mode,aG=ax[aF];if(aH==="Auto"){aH=aI.get_mode(aG);aI.update_auto_mode(aH)}ay.push(aH);av.push(aI.get_canvas_height(aG,aH,ap,at))});var aw=af.view.canvas_manager.new_canvas(),az=am.get("start"),aE=am.get("end"),au=0,at=Math.ceil((aE-az)*ap)+af.left_offset,aB=ac.max(av),aA;aw.width=at;aw.height=(aq.height||aB);var aC=aw.getContext("2d");aC.translate(af.left_offset,0);if(ah.length>1){aC.globalAlpha=0.5;aC.globalCompositeOperation="source-over"}ac.each(ah,function(aG,aF){aA=aG.draw_tile(ax[aF],aC,ay[aF],am,ap,aD)});if(aA!==undefined){af.tile_cache.set_elt(an,aA);af.show_tile(aA,ap)}ad.resolve(aA)});return ad},get_canvas_height:function(ad,af,ag,ae){return this.visible_height_px},_draw_line_track_tile:function(ad,af,ai,ah,aj){var ag=af.canvas,ae=new L.LinePainter(ad.data,ah.get("start"),ah.get("end"),this.prefs,ai);ae.draw(af,ag.width,ag.height,aj);return new M(this,ah,aj,ag,ad.data)},draw_tile:function(ad,ae,ah,ag,ai,af){},show_tile:function(af,ai){var ae=this,ad=af.html_elt;af.predisplay_actions();var ah=(af.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ah-=this.left_offset}ad.css({position:"absolute",top:0,left:ah});if(ad.hasClass("remove")){ad.removeClass("remove")}else{this.tiles_div.append(ad)}af.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,af.html_elt.height());af.html_elt.parent().children().css("height",this.max_height_px+"px");var ag=this.max_height_px;if(this.visible_height_px!==0){ag=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",ag+"px")},tool_region_and_parameters_str:function(ag){var ad=this,af=(ag!==undefined?ag.toString():"all"),ae=ac.values(ad.tool.get_inputs_dict()).join(", ");return" - region=["+af+"], parameters=["+ae+"]"},data_and_mode_compatible:function(ad,ae){if(ae==="Auto"){return true}else{if(ae==="Coverage"){return ad.dataset_type==="bigwig"}else{if(ad.dataset_type==="bigwig"||ad.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ad){if(ad.message||ad.extra_info==="no_detail"){return false}else{if(ad.dataset_type==="bigwig"){return(ad.data[1][0]-ad.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ae,ad){var af={resize:false};f.call(this,ae,ad,af);this.container_div.addClass("label-track")};o(W.prototype,f.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ah){var af=this.view,ag=af.high-af.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ag)/Math.log(10)))),ad=Math.floor(af.low/ak)*ak,ai=this.view.container.width(),ae=$("<div style='position: relative; height: 1.3em;'></div>");while(ad<af.high){var aj=(ad-af.low)/ag*ai;ae.append($("<div class='label'>"+commatize(ad)+"</div>").css({position:"absolute",left:aj-1}));ad+=ak}this.content_div.children(":first").remove();this.content_div.append(ae)}});var e=function(ae,ad,ah){this.display_modes=A;N.call(this,ae,ad,ah);this.drawables=[];if("drawables" in ah){var ag;for(var af=0;af<ah.drawables.length;af++){ag=ah.drawables[af];this.drawables[af]=n(ag,ae,null);if(ag.left_offset>this.left_offset){this.left_offset=ag.left_offset}}this.enabled=true}ac.each(this.drawables,function(ai){if(ai instanceof c||ai instanceof T){ai.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};o(e.prototype,N.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ad){$(".tooltip").remove();ad.show_group()}}].concat(N.prototype.action_icons_def),to_dict:y.prototype.to_dict,add_drawable:y.prototype.add_drawable,unpack_drawables:y.prototype.unpack_drawables,change_mode:function(ad){N.prototype.change_mode.call(this,ad);for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].change_mode(ad)}},init:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].init())}var ad=this;$.when.apply($,af).then(function(){ad.enabled=true;ad.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:p.prototype.can_draw,_get_drawables:function(){return this.drawables},show_group:function(){var ag=new P(this.view,this.container,{name:this.name}),ad;for(var af=0;af<this.drawables.length;af++){ad=this.drawables[af];ad.update_icons();ag.add_drawable(ad);ad.container=ag;ag.content_div.append(ad.container_div)}var ae=this.container.replace_drawable(this,ag,true);ag.request_draw({clear_tile_cache:true})},before_draw:function(){N.prototype.before_draw.call(this);var ae=ac.min(ac.map(this.drawables,function(af){return af.prefs.min_value})),ad=ac.max(ac.map(this.drawables,function(af){return af.prefs.max_value}));this.prefs.min_value=ae;this.prefs.max_value=ad;ac.each(this.drawables,function(af){af.prefs.min_value=ae;af.prefs.max_value=ad})},update_all_min_max:function(){var ad=this;ac.each(this.drawables,function(ae){ae.prefs.min_value=ad.prefs.min_value;ae.prefs.max_value=ad.prefs.max_value});this.request_draw({clear_tile_cache:true})},postdraw_actions:function(aj,ad,am,ai){N.prototype.postdraw_actions.call(this,aj,ad,am,ai);var ah=-1;for(var af=0;af<aj.length;af++){var ak=aj[af].html_elt.find("canvas").height();if(ak>ah){ah=ak}}for(var af=0;af<aj.length;af++){var ag=aj[af];if(ag.html_elt.find("canvas").height()!==ah){this.draw_helper(ag.region,am,{force:true,height:ah});ag.html_elt.remove()}}var ae=this,al=function(){ae.update_all_min_max()};this._add_yaxis_label("min",al);this._add_yaxis_label("max",al)}});var B=function(ad){N.call(this,ad,{content_div:ad.top_labeltrack},{resize:false});ad.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=galaxy_config.root+"api/genomes//"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new w.GenomeReferenceDataManager({data_url:this.data_url,can_subset:this.can_subset});this.hide_contents()};o(B.prototype,p.prototype,N.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},predraw_init:function(){},can_draw:p.prototype.can_draw,draw_helper:function(ae,af,ad){if(af>this.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ae,af,ad)}else{this.tiles_div.hide();return null}},can_subset:function(ad){return true},draw_tile:function(af,al,ag,ai,am){var ae=this.data_manager.subset_entry(af,ai),ak=ae.data;var ad=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";for(var ah=0,aj=ak.length;ah<aj;ah++){al.fillStyle=this.view.get_base_color(ak[ah]);al.fillText(ak[ah],Math.floor(ah*am),10)}return new b(this,ai,am,ad,ae)}});var g=function(af,ae,ag){var ad=this;this.display_modes=A;this.mode="Histogram";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:j.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(g.prototype,p.prototype,N.prototype,{before_draw:function(){},draw_tile:function(ad,ae,ag,af,ah){return this._draw_line_track_tile(ad,ae,ag,af,ah)},can_subset:function(ad){return(ad.data[1][0]-ad.data[0][0]===1)},postdraw_actions:function(ae,af,ag,ad){this._add_yaxis_label("max");this._add_yaxis_label("min")}});var r=function(af,ae,ag){var ad=this;this.display_modes=["Heatmap"];this.mode="Heatmap";N.call(this,af,ae,ag);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:ag.prefs,onchange:function(){ad.set_name(ad.prefs.name);this.request_redraw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height};o(r.prototype,p.prototype,N.prototype,{draw_tile:function(ad,af,ai,ah,aj){var ag=af.canvas,ae=new L.DiagonalHeatmapPainter(ad.data,ah.get("start"),ah.get("end"),this.prefs,ai);ae.draw(af,ag.width,ag.height,aj);return new b(this,ah,aj,ag,ad.data)}});var c=function(ag,af,ai){var ae=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ag,af,ai);var ah=j.get_random_color(),ad=j.get_random_color([ah,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ah},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ai.prefs,onchange:function(){ae.set_name(ae.prefs.name);ae.set_painter_from_config();ae.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};o(c.prototype,p.prototype,N.prototype,{set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},postdraw_actions:function(an,af,ao,am){N.prototype.postdraw_actions.call(this,an,af,ao,am);var ah=this,ai;if(ah.filters_manager){var ag=ah.filters_manager.filters;for(var ak=0;ak<ag.length;ak++){ag[ak].update_ui_elt()}var aj=false,al,ae;for(ai=0;ai<an.length;ai++){if(an[ai].data.length){al=an[ai].data[0];for(var ak=0;ak<ag.length;ak++){ae=ag[ak];if(ae.applies_to(al)&&ae.min!==ae.max){aj=true;break}}}}if(ah.filters_available!==aj){ah.filters_available=aj;if(!ah.filters_available){ah.filters_manager.hide()}ah.update_icons()}}if(an[0] instanceof O){var ad=true;for(ai=0;ai<an.length;ai++){if(!an[ai].all_slotted){ad=false;break}}if(!ad){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ad){var ad;if(this.mode==="Auto"){if(ad==="no_detail"){ad="feature spans"}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ad+")")}},incremental_slots:function(ah,ad,ag){var ae=this.view.canvas_manager.dummy_context,af=this.slotters[ah];if(!af||(af.mode!==ag)){af=new (s.FeatureSlotter)(ah,ag,z,function(ai){return ae.measureText(ai)});this.slotters[ah]=af}return af.slot_features(ad)},get_mode:function(ad){if(ad.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ad,ah,ai,ae){if(ah==="Coverage"||ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=this.incremental_slots(ai,ad.data,ah);var af=new (this.painter)(null,null,null,this.prefs,ah);return Math.max(aa,af.get_required_height(ag,ae))}},draw_tile:function(an,ar,ap,ag,ak,af){var aq=this,ae=ar.canvas,ay=ag.get("start"),ad=ag.get("end"),ah=this.left_offset;if(an.dataset_type==="bigwig"){return this._draw_line_track_tile(an,ar,ap,ag,ak)}var aj=[],ao=this.slotters[ak].slots;all_slotted=true;if(an.data){var al=this.filters_manager.filters;for(var at=0,av=an.data.length;at<av;at++){var ai=an.data[at];var au=false;var am;for(var ax=0,aC=al.length;ax<aC;ax++){am=al[ax];am.update_attrs(ai);if(!am.keep(ai)){au=true;break}}if(!au){aj.push(ai);if(!(ai[0] in ao)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null),az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null),aA=new (this.painter)(aj,ay,ad,this.prefs,ap,aB,az,af,function(aD){return aq.view.get_base_color(aD)});var aw=null;ar.fillStyle=this.prefs.block_color;ar.font=ar.canvas.manager.default_font;ar.textAlign="right";if(an.data){aw=aA.draw(ar,ae.width,ae.height,ak,ao);aw.translation=-ah}return new O(aq,ag,ak,ae,an.data,ap,an.message,all_slotted,aw)}});var Z=function(ae,ad,af){this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];N.call(this,ae,ad,af);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Histogram color",type:"color",default_value:j.get_random_color()},{key:"show_sample_data",label:"Show sample data",type:"bool",default_value:true},{key:"show_labels",label:"Show summary and sample labels",type:"bool",default_value:true},{key:"summary_height",label:"Locus summary height",type:"float",default_value:20},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=L.VariantPainter;this.summary_draw_height=30;this.left_offset=30};o(Z.prototype,p.prototype,N.prototype,{draw_tile:function(ad,ag,ai,ah,aj){if(ad.dataset_type==="bigwig"){return this._draw_line_track_tile(ad,ag,"Histogram",ah,aj)}else{var af=this.view,ae=new (this.painter)(ad.data,ah.get("start"),ah.get("end"),this.prefs,ai,function(ak){return af.get_base_color(ak)});ae.draw(ag,ag.canvas.width,ag.canvas.height,aj);return new b(this,ah,aj,ag.canvas,ad.data)}},get_canvas_height:function(ad,ah,ai,af){if(ad.dataset_type==="bigwig"){return this.summary_draw_height}else{var ag=new (this.painter)(null,null,null,this.prefs,ah);var ae=(this.dataset.get_metadata("sample_names")?this.dataset.get_metadata("sample_names").length:0);if(ae===0&&ad.data.length!==0){ae=ad.data[0][7].match(/,/g);if(ae===null){ae=1}else{ae=ae.length+1}}return ag.get_required_height(ae)}},predraw_init:function(){var ad=[f.prototype.predraw_init.call(this)];if(!this.dataset.get_metadata("sample_names")){ad.push(this.dataset.fetch())}return ad},postdraw_actions:function(ag,ah,aj,ae){N.prototype.postdraw_actions.call(this,ag,ah,aj,ae);var af=ac.filter(ag,function(ak){return(ak instanceof M)});if(af.length===0&&this.prefs.show_labels){var ad;if(this.container_div.find(".yaxislabel.variant").length===0){ad=this.prefs.summary_height/2;this.tiles_div.prepend($("<div/>").text("Summary").addClass("yaxislabel variant top").css({"font-size":ad+"px",top:(this.prefs.summary_height-ad)/2+"px"}));if(this.prefs.show_sample_data){var ai=this.dataset.get("metadata").get("sample_names").join("<br/>");this.tiles_div.prepend($("<div/>").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ad=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ad,"line-height":ad});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(af,ae,ah){c.call(this,af,ae,ah);var ag=j.get_random_color(),ad=j.get_random_color([ag,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ad},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"}],saved_values:ah.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.request_draw({clear_tile_cache:true})}});this.prefs=this.config.values;this.painter=(af.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};o(T.prototype,p.prototype,N.prototype,c.prototype);var d={CompositeTrack:e,DrawableGroup:P,DiagonalHeatmapTrack:r,FeatureTrack:c,LineTrack:g,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var n=function(af,ae,ad){if("copy" in af){return af.copy(ad)}else{var ag=af.obj_type;if(!ag){ag=af.track_type}return new d[ag](ae,ad,af)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:g,FeatureTrack:c,DiagonalHeatmapTrack:r,ReadTrack:T,VariantTrack:Z,CompositeTrack:e,object_from_template:n}}); \ No newline at end of file diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/scripts/packed/viz/trackster_ui.js --- a/static/scripts/packed/viz/trackster_ui.js +++ b/static/scripts/packed/viz/trackster_ui.js @@ -1,1 +1,1 @@ -define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(a,f,e,c,d,h){var j=d.object_from_template;var b=function(l,k){if(!k){k={}}var m=new IconButtonCollection(f.map(l,function(n){return new IconButton(f.extend(n,k))}));return new IconButtonMenuView({collection:m})};var g=a.Base.extend({initialize:function(k){this.baseURL=k},createButtonMenu:function(){var k=this,l=b([{icon_class:"plus-button",title:"Add tracks",on_click:function(){h.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(m){f.each(m,function(n){view.add_drawable(j(n,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new d.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=k.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){show_modal("Saving...","progress");var m=[];$(".bookmark").each(function(){m.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var n=(view.overview_drawable?view.overview_drawable.name:null),o={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:n},bookmarks:m};$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.name,dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(o)}}).success(function(p){hide_modal();view.vis_id=p.vis_id;view.has_changes=false;window.history.pushState({},"",p.url+window.location.hash)}).error(function(){show_modal("Could Not Save","Could not save visualization. Please try again later.",{Close:hide_modal})})}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=l;return l},add_bookmarks:function(){var k=this,l=this.baseURL;show_modal("Select dataset for new bookmarks","progress");$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(m){show_modal("Select dataset for new bookmarks",m,{Cancel:function(){hide_modal()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var n,o=$(this).val();if($(this).attr("name")==="id"){n={hda_id:o}}else{n={ldda_id:o}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:n,dataType:"json"}).then(function(p){for(i=0;i<p.data.length;i++){var q=p.data[i];k.add_bookmark(q[0],q[1])}})});hide_modal()}})}})},add_bookmark:function(o,m,k){var q=$("#right .unified-panel-body"),s=$("<div/>").addClass("bookmark").appendTo(q);var t=$("<div/>").addClass("position").appendTo(s),p=$("<a href=''/>").text(o).appendTo(t).click(function(){view.go_to(o);return false}),n=$("<div/>").text(m).appendTo(s);if(k){var r=$("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){s.slideUp("fast");s.remove();view.has_changes=true;return false}),l=$("<a href=''/>").addClass("icon-button delete").appendTo(r);n.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return s},create_visualization:function(p,k,o,q,n){var m=this,l=new d.TracksterView(p);l.editor=true;$.when(l.load_chroms_deferred).then(function(B){if(k){var z=k.chrom,r=k.start,w=k.end,t=k.overview;if(z&&(r!==undefined)&&w){l.change_chrom(z,r,w)}else{l.change_chrom(B[0].chrom)}}else{l.change_chrom(B[0].chrom)}if(o){var u,s,v;for(var x=0;x<o.length;x++){l.add_drawable(j(o[x],l,l))}}l.update_intro_div();var A;for(var x=0;x<l.drawables.length;x++){if(l.drawables[x].name===t){l.set_overview(l.drawables[x]);break}}if(q){var y;for(var x=0;x<q.length;x++){y=q[x];m.add_bookmark(y.position,y.annotation,n)}}l.has_changes=false});return l},init_keyboard_nav:function(k){$(document).keydown(function(l){if($(l.srcElement).is(":input")){return}switch(l.which){case 37:k.move_fraction(0.25);break;case 38:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()-20);break;case 39:k.move_fraction(-0.25);break;case 40:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()+20);break}})}});return{object_from_template:j,TracksterUI:g}}); \ No newline at end of file +define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(a,f,e,c,d,h){var j=d.object_from_template;var b=function(l,k){if(!k){k={}}var m=new IconButtonCollection(f.map(l,function(n){return new IconButton(f.extend(n,k))}));return new IconButtonMenuView({collection:m})};var g=a.Base.extend({initialize:function(k){this.baseURL=k},createButtonMenu:function(){var k=this,l=b([{icon_class:"plus-button",title:"Add tracks",on_click:function(){h.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(m){f.each(m,function(n){view.add_drawable(j(n,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new d.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=k.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var m=[];$(".bookmark").each(function(){m.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var n=(view.overview_drawable?view.overview_drawable.name:null),o={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:n},bookmarks:m};$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.name,dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(o)}}).success(function(p){Galaxy.modal.hide();view.vis_id=p.vis_id;view.has_changes=false;window.history.pushState({},"",p.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=l;return l},add_bookmarks:function(){var k=this,l=this.baseURL;Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"});$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(m){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:m,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var n,o=$(this).val();if($(this).attr("name")==="id"){n={hda_id:o}}else{n={ldda_id:o}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:n,dataType:"json"}).then(function(p){for(i=0;i<p.data.length;i++){var q=p.data[i];k.add_bookmark(q[0],q[1])}})});Galaxy.modal.hide()}}})}})},add_bookmark:function(o,m,k){var q=$("#right .unified-panel-body"),s=$("<div/>").addClass("bookmark").appendTo(q);var t=$("<div/>").addClass("position").appendTo(s),p=$("<a href=''/>").text(o).appendTo(t).click(function(){view.go_to(o);return false}),n=$("<div/>").text(m).appendTo(s);if(k){var r=$("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){s.slideUp("fast");s.remove();view.has_changes=true;return false}),l=$("<a href=''/>").addClass("icon-button delete").appendTo(r);n.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return s},create_visualization:function(p,k,o,q,n){var m=this,l=new d.TracksterView(p);l.editor=true;$.when(l.load_chroms_deferred).then(function(B){if(k){var z=k.chrom,r=k.start,w=k.end,t=k.overview;if(z&&(r!==undefined)&&w){l.change_chrom(z,r,w)}else{l.change_chrom(B[0].chrom)}}else{l.change_chrom(B[0].chrom)}if(o){var u,s,v;for(var x=0;x<o.length;x++){l.add_drawable(j(o[x],l,l))}}l.update_intro_div();var A;for(var x=0;x<l.drawables.length;x++){if(l.drawables[x].name===t){l.set_overview(l.drawables[x]);break}}if(q){var y;for(var x=0;x<q.length;x++){y=q[x];m.add_bookmark(y.position,y.annotation,n)}}l.has_changes=false});return l},init_keyboard_nav:function(k){$(document).keydown(function(l){if($(l.srcElement).is(":input")){return}switch(l.which){case 37:k.move_fraction(0.25);break;case 38:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()-20);break;case 39:k.move_fraction(-0.25);break;case 40:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()+20);break}})}});return{object_from_template:j,TracksterUI:g}}); \ No newline at end of file diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/scripts/packed/viz/visualization.js --- a/static/scripts/packed/viz/visualization.js +++ b/static/scripts/packed/viz/visualization.js @@ -1,1 +1,1 @@ -define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(s,i,l,o){var a=function(u,x,w,v){$.ajax({url:u,data:w,error:function(){alert("Grid failed")},success:function(y){show_modal("Select datasets for new tracks",y,{Cancel:function(){hide_modal()},Add:function(){var z=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var A={data_type:"track_config",hda_ldda:"hda"},B=$(this).val();if($(this).attr("name")!=="id"){A.hda_ldda="ldda"}z[z.length]=$.ajax({url:x+"/"+B,data:A,dataType:"json"})});$.when.apply($,z).then(function(){var A=(arguments[0] instanceof Array?$.map(arguments,function(B){return B[0]}):[arguments[0]]);v(A)});hide_modal()}})}})};var j=function(u){return("promise" in u)};var f=function(u){this.default_font=u!==undefined?u:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};s.extend(f.prototype,{load_pattern:function(u,y){var v=this.patterns,w=this.dummy_context,x=new Image();x.src=galaxy_config.root+"static/images"+y;x.onload=function(){v[u]=w.createPattern(x,"repeat")}},get_pattern:function(u){return this.patterns[u]},new_canvas:function(){var u=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(u)}u.manager=this;return u}});var q=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(u){this.clear()},get_elt:function(w){var x=this.attributes.obj_cache,y=this.attributes.key_ary,v=w.toString(),u=s.indexOf(y,function(z){return z.toString()===v});if(u!==-1){if(x[v].stale){y.splice(u,1);delete x[v]}else{this.move_key_to_end(w,u)}}return x[v]},set_elt:function(w,y){var z=this.attributes.obj_cache,A=this.attributes.key_ary,v=w.toString(),x=this.attributes.num_elements;if(!z[v]){if(A.length>=x){var u=A.shift();delete z[u.toString()]}A.push(w)}z[v]=y;return y},move_key_to_end:function(v,u){this.attributes.key_ary.splice(u,1);this.attributes.key_ary.push(v)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=q.extend({defaults:s.extend({},q.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(u,v){return true},can_subset:function(u){return false}}),initialize:function(u){q.prototype.initialize.call(this);var v=this.get("init_data");if(v){this.add_data(v)}},add_data:function(u){if(this.get("num_elements")<u.length){this.set("num_elements",u.length)}var v=this;s.each(u,function(w){v.set_data(w.region,w)})},data_is_ready:function(){var x=this.get("dataset"),w=$.Deferred(),u=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),v=new l.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:x.get("hda_ldda"),data_type:u},dataType:"json"},interval:5000,success_fn:function(y){return y!=="pending"}});$.when(v.go()).then(function(y){w.resolve(y==="ok"||y==="data")});return w},search_features:function(u){var v=this.get("dataset"),w={query:u,hda_ldda:v.get("hda_ldda"),data_type:"features"};return $.getJSON(v.url(),w)},load_data:function(C,B,v,A){var y=this.get("dataset"),x={data_type:this.get("data_type"),chrom:C.get("chrom"),low:C.get("start"),high:C.get("end"),mode:B,resolution:v,hda_ldda:y.get("hda_ldda")};$.extend(x,A);var E=this.get("filters_manager");if(E){var F=[];var u=E.filters;for(var z=0;z<u.length;z++){F.push(u[z].name)}x.filter_cols=JSON.stringify(F)}var w=this,D=$.getJSON(y.url(),x,function(G){G.region=C;w.set_data(C,G)});this.set_data(C,D);return D},get_data:function(B,A,w,y){var C=this.get_elt(B);if(C&&(j(C)||this.get("data_mode_compatible")(C,A))){return C}var D=this.get("key_ary"),u=this.get("obj_cache"),v,z;for(var x=0;x<D.length;x++){v=D[x];if(v.contains(B)){z=true;C=u[v.toString()];if(j(C)||(this.get("data_mode_compatible")(C,A)&&this.get("can_subset")(C))){this.move_key_to_end(v,x);if(!j(C)){var F=this.subset_entry(C,B);this.set(B,F);C=F}return C}}}if(!z&&B.length()<this.attributes.min_region_size){var E=this.most_recently_added();if(!E||(B.get("start")>E.get("start"))){B.set("end",B.get("start")+this.attributes.min_region_size)}else{B.set("start",B.get("end")-this.attributes.min_region_size)}B.set("genome",this.attributes.genome);B.trim()}return this.load_data(B,A,w,y)},set_data:function(v,u){this.set_elt(v,u)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(C,B,x,A,y){var E=this._mark_stale(C);if(!(E&&this.get("data_mode_compatible")(E,B))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var w=C.get("start");if(y===this.DEEP_DATA_REQ){$.extend(A,{start_val:E.data.length+1})}else{if(y===this.BROAD_DATA_REQ){w=(E.max_high?E.max_high:E.data[E.data.length-1][2])+1}}var D=C.copy().set("start",w);var v=this,z=this.load_data(D,B,x,A),u=$.Deferred();this.set_data(C,u);$.when(z).then(function(F){if(F.data){F.data=E.data.concat(F.data);if(F.max_low){F.max_low=E.max_low}if(F.message){F.message=F.message.replace(/[0-9]+/,F.data.length)}}v.set_data(C,F);u.resolve(F)});return u},can_get_more_detailed_data:function(v){var u=this.get_elt(v);return(u.dataset_type==="bigwig"&&u.data.length<8000)},get_more_detailed_data:function(x,z,v,y,w){var u=this._mark_stale(x);if(!u){console.log("ERROR getting more detailed data: no current data");return}if(!w){w={}}if(u.dataset_type==="bigwig"){w.num_samples=1000*y}return this.load_data(x,z,v,w)},_mark_stale:function(v){var u=this.get_elt(v);if(!u){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),v.toString())}u.stale=true;return u},get_genome_wide_data:function(u){var w=this,y=true,x=s.map(u.get("chroms_info").chrom_info,function(A){var z=w.get_elt(new g({chrom:A.chrom,start:0,end:A.len}));if(!z){y=false}return z});if(y){return x}var v=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(z){w.add_data(z.data);v.resolve(z.data)});return v},subset_entry:function(w,x){var u={bigwig:function(y,z){return s.filter(y,function(A){return A[0]>=z.get("start")&&A[0]<=z.get("end")})},refseq:function(z,A){var B=A.get("start")-w.region.get("start"),y=w.data.length-(w.region.get("end")-A.get("end"));return w.data.slice(B,y)}};var v=w.data;if(!w.region.same(x)&&w.dataset_type in u){v=u[w.dataset_type](w.data,x)}return{region:x,data:v,dataset_type:w.dataset_type}}});var p=d.extend({initialize:function(u){var v=new Backbone.Model();v.urlRoot=u.data_url;this.set("dataset",v)},load_data:function(w,x,u,v){return(w.length()<=100000?d.prototype.load_data.call(this,w,x,u,v):{data:null,region:w})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(u){this.id=u.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(u){var v=s.find(this.get_chroms_info(),function(w){return w.chrom===u});return new g({chrom:v.chrom,end:v.len})},get_chrom_len:function(u){return s.find(this.get_chroms_info(),function(v){return v.chrom===u}).len}});var g=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(u){return this.attributes.chrom===u.get("chrom")&&this.attributes.start===u.get("start")&&this.attributes.end===u.get("end")},initialize:function(v){if(v.from_str){var x=v.from_str.split(":"),w=x[0],u=x[1].split("-");this.set({chrom:w,start:parseInt(u[0],10),end:parseInt(u[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end");this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new g({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(B){var v=this.get("chrom"),A=B.get("chrom"),z=this.get("start"),x=B.get("start"),y=this.get("end"),w=B.get("end"),u;if(v&&A&&v!==A){return g.overlap_results.DIF_CHROMS}if(z<x){if(y<x){u=g.overlap_results.BEFORE}else{if(y<w){u=g.overlap_results.OVERLAP_START}else{u=g.overlap_results.CONTAINS}}}else{if(z>x){if(z>w){u=g.overlap_results.AFTER}else{if(y<=w){u=g.overlap_results.CONTAINED_BY}else{u=g.overlap_results.OVERLAP_END}}}else{u=(y>=w?g.overlap_results.CONTAINS:g.overlap_results.CONTAINED_BY)}}return u},trim:function(u){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var v=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>v){this.attributes.end=v-1}}return this},contains:function(u){return this.compute_overlap(u)===g.overlap_results.CONTAINS},overlaps:function(u){return s.intersection([this.compute_overlap(u)],[g.overlap_results.DIF_CHROMS,g.overlap_results.BEFORE,g.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var m=Backbone.Collection.extend({model:g});var e=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:g}]});var r=Backbone.Collection.extend({model:e});var t=Backbone.RelationalModel.extend({relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:i.Dataset}],initialize:function(u){this.set("config",o.ConfigSettingCollection.from_config_dict(u.prefs));this.get("config").add([{key:"name",value:this.get("name")},{key:"color"}]);var v=this.get("preloaded_data");if(v){v=v.data}else{v=[]}this.set("data_manager",new d({dataset:this.get("dataset"),init_data:v}))}});var n=Backbone.RelationalModel.extend({defaults:{title:"",type:""},url:galaxy_config.root+"visualization/save",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=n.extend({defaults:s.extend({},n.prototype.defaults,{dbkey:"",tracks:null,bookmarks:null,viewport:null}),relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:t}],add_tracks:function(u){this.get("tracks").add(u)}});var b=Backbone.Model.extend({});var h=Backbone.Router.extend({initialize:function(v){this.view=v.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var u=this;u.view.on("navigate",function(w){u.navigate(w)})},change_location:function(u){this.view.go_to(u)}});return{BackboneTrack:t,BrowserBookmark:e,BrowserBookmarkCollection:r,Cache:q,CanvasManager:f,Genome:c,GenomeDataManager:d,GenomeRegion:g,GenomeRegionCollection:m,GenomeVisualization:k,GenomeReferenceDataManager:p,TrackBrowserRouter:h,TrackConfig:b,Visualization:n,select_datasets:a}}); \ No newline at end of file +define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(s,i,l,o){var a=function(u,x,w,v){$.ajax({url:u,data:w,error:function(){alert("Grid failed")},success:function(y){Galaxy.modal.show({title:"Select datasets for new tracks",body:y,buttons:{Cancel:function(){Galaxy.modal.hide()},Add:function(){var z=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var A={data_type:"track_config",hda_ldda:"hda"},B=$(this).val();if($(this).attr("name")!=="id"){A.hda_ldda="ldda"}z[z.length]=$.ajax({url:x+"/"+B,data:A,dataType:"json"})});$.when.apply($,z).then(function(){var A=(arguments[0] instanceof Array?$.map(arguments,function(B){return B[0]}):[arguments[0]]);v(A)});Galaxy.modal.hide()}}})}})};var j=function(u){return("promise" in u)};var f=function(u){this.default_font=u!==undefined?u:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};s.extend(f.prototype,{load_pattern:function(u,y){var v=this.patterns,w=this.dummy_context,x=new Image();x.src=galaxy_config.root+"static/images"+y;x.onload=function(){v[u]=w.createPattern(x,"repeat")}},get_pattern:function(u){return this.patterns[u]},new_canvas:function(){var u=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(u)}u.manager=this;return u}});var q=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(u){this.clear()},get_elt:function(w){var x=this.attributes.obj_cache,y=this.attributes.key_ary,v=w.toString(),u=s.indexOf(y,function(z){return z.toString()===v});if(u!==-1){if(x[v].stale){y.splice(u,1);delete x[v]}else{this.move_key_to_end(w,u)}}return x[v]},set_elt:function(w,y){var z=this.attributes.obj_cache,A=this.attributes.key_ary,v=w.toString(),x=this.attributes.num_elements;if(!z[v]){if(A.length>=x){var u=A.shift();delete z[u.toString()]}A.push(w)}z[v]=y;return y},move_key_to_end:function(v,u){this.attributes.key_ary.splice(u,1);this.attributes.key_ary.push(v)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=q.extend({defaults:s.extend({},q.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:200,filters_manager:null,data_type:"data",data_mode_compatible:function(u,v){return true},can_subset:function(u){return false}}),initialize:function(u){q.prototype.initialize.call(this);var v=this.get("init_data");if(v){this.add_data(v)}},add_data:function(u){if(this.get("num_elements")<u.length){this.set("num_elements",u.length)}var v=this;s.each(u,function(w){v.set_data(w.region,w)})},data_is_ready:function(){var x=this.get("dataset"),w=$.Deferred(),u=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),v=new l.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:x.get("hda_ldda"),data_type:u},dataType:"json"},interval:5000,success_fn:function(y){return y!=="pending"}});$.when(v.go()).then(function(y){w.resolve(y==="ok"||y==="data")});return w},search_features:function(u){var v=this.get("dataset"),w={query:u,hda_ldda:v.get("hda_ldda"),data_type:"features"};return $.getJSON(v.url(),w)},load_data:function(C,B,v,A){var y=this.get("dataset"),x={data_type:this.get("data_type"),chrom:C.get("chrom"),low:C.get("start"),high:C.get("end"),mode:B,resolution:v,hda_ldda:y.get("hda_ldda")};$.extend(x,A);var E=this.get("filters_manager");if(E){var F=[];var u=E.filters;for(var z=0;z<u.length;z++){F.push(u[z].name)}x.filter_cols=JSON.stringify(F)}var w=this,D=$.getJSON(y.url(),x,function(G){G.region=C;w.set_data(C,G)});this.set_data(C,D);return D},get_data:function(B,A,w,y){var C=this.get_elt(B);if(C&&(j(C)||this.get("data_mode_compatible")(C,A))){return C}var D=this.get("key_ary"),u=this.get("obj_cache"),v,z;for(var x=0;x<D.length;x++){v=D[x];if(v.contains(B)){z=true;C=u[v.toString()];if(j(C)||(this.get("data_mode_compatible")(C,A)&&this.get("can_subset")(C))){this.move_key_to_end(v,x);if(!j(C)){var F=this.subset_entry(C,B);this.set(B,F);C=F}return C}}}if(!z&&B.length()<this.attributes.min_region_size){var E=this.most_recently_added();if(!E||(B.get("start")>E.get("start"))){B.set("end",B.get("start")+this.attributes.min_region_size)}else{B.set("start",B.get("end")-this.attributes.min_region_size)}B.set("genome",this.attributes.genome);B.trim()}return this.load_data(B,A,w,y)},set_data:function(v,u){this.set_elt(v,u)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(C,B,x,A,y){var E=this._mark_stale(C);if(!(E&&this.get("data_mode_compatible")(E,B))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var w=C.get("start");if(y===this.DEEP_DATA_REQ){$.extend(A,{start_val:E.data.length+1})}else{if(y===this.BROAD_DATA_REQ){w=(E.max_high?E.max_high:E.data[E.data.length-1][2])+1}}var D=C.copy().set("start",w);var v=this,z=this.load_data(D,B,x,A),u=$.Deferred();this.set_data(C,u);$.when(z).then(function(F){if(F.data){F.data=E.data.concat(F.data);if(F.max_low){F.max_low=E.max_low}if(F.message){F.message=F.message.replace(/[0-9]+/,F.data.length)}}v.set_data(C,F);u.resolve(F)});return u},can_get_more_detailed_data:function(v){var u=this.get_elt(v);return(u.dataset_type==="bigwig"&&u.data.length<8000)},get_more_detailed_data:function(x,z,v,y,w){var u=this._mark_stale(x);if(!u){console.log("ERROR getting more detailed data: no current data");return}if(!w){w={}}if(u.dataset_type==="bigwig"){w.num_samples=1000*y}return this.load_data(x,z,v,w)},_mark_stale:function(v){var u=this.get_elt(v);if(!u){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),v.toString())}u.stale=true;return u},get_genome_wide_data:function(u){var w=this,y=true,x=s.map(u.get("chroms_info").chrom_info,function(A){var z=w.get_elt(new g({chrom:A.chrom,start:0,end:A.len}));if(!z){y=false}return z});if(y){return x}var v=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(z){w.add_data(z.data);v.resolve(z.data)});return v},subset_entry:function(w,x){var u={bigwig:function(y,z){return s.filter(y,function(A){return A[0]>=z.get("start")&&A[0]<=z.get("end")})},refseq:function(z,A){var B=A.get("start")-w.region.get("start"),y=w.data.length-(w.region.get("end")-A.get("end"));return w.data.slice(B,y)}};var v=w.data;if(!w.region.same(x)&&w.dataset_type in u){v=u[w.dataset_type](w.data,x)}return{region:x,data:v,dataset_type:w.dataset_type}}});var p=d.extend({initialize:function(u){var v=new Backbone.Model();v.urlRoot=u.data_url;this.set("dataset",v)},load_data:function(w,x,u,v){return(w.length()<=100000?d.prototype.load_data.call(this,w,x,u,v):{data:null,region:w})}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(u){this.id=u.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(u){var v=s.find(this.get_chroms_info(),function(w){return w.chrom===u});return new g({chrom:v.chrom,end:v.len})},get_chrom_len:function(u){return s.find(this.get_chroms_info(),function(v){return v.chrom===u}).len}});var g=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,str_val:null,genome:null},same:function(u){return this.attributes.chrom===u.get("chrom")&&this.attributes.start===u.get("start")&&this.attributes.end===u.get("end")},initialize:function(v){if(v.from_str){var x=v.from_str.split(":"),w=x[0],u=x[1].split("-");this.set({chrom:w,start:parseInt(u[0],10),end:parseInt(u[1],10)})}this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end");this.on("change",function(){this.attributes.str_val=this.get("chrom")+":"+this.get("start")+"-"+this.get("end")},this)},copy:function(){return new g({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){return this.attributes.str_val},toJSON:function(){return{chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")}},compute_overlap:function(B){var v=this.get("chrom"),A=B.get("chrom"),z=this.get("start"),x=B.get("start"),y=this.get("end"),w=B.get("end"),u;if(v&&A&&v!==A){return g.overlap_results.DIF_CHROMS}if(z<x){if(y<x){u=g.overlap_results.BEFORE}else{if(y<w){u=g.overlap_results.OVERLAP_START}else{u=g.overlap_results.CONTAINS}}}else{if(z>x){if(z>w){u=g.overlap_results.AFTER}else{if(y<=w){u=g.overlap_results.CONTAINED_BY}else{u=g.overlap_results.OVERLAP_END}}}else{u=(y>=w?g.overlap_results.CONTAINS:g.overlap_results.CONTAINED_BY)}}return u},trim:function(u){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var v=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>v){this.attributes.end=v-1}}return this},contains:function(u){return this.compute_overlap(u)===g.overlap_results.CONTAINS},overlaps:function(u){return s.intersection([this.compute_overlap(u)],[g.overlap_results.DIF_CHROMS,g.overlap_results.BEFORE,g.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var m=Backbone.Collection.extend({model:g});var e=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:g}]});var r=Backbone.Collection.extend({model:e});var t=Backbone.RelationalModel.extend({relations:[{type:Backbone.HasOne,key:"dataset",relatedModel:i.Dataset}],initialize:function(u){this.set("config",o.ConfigSettingCollection.from_config_dict(u.prefs));this.get("config").add([{key:"name",value:this.get("name")},{key:"color"}]);var v=this.get("preloaded_data");if(v){v=v.data}else{v=[]}this.set("data_manager",new d({dataset:this.get("dataset"),init_data:v}))}});var n=Backbone.RelationalModel.extend({defaults:{title:"",type:""},url:galaxy_config.root+"visualization/save",save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=n.extend({defaults:s.extend({},n.prototype.defaults,{dbkey:"",tracks:null,bookmarks:null,viewport:null}),relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:t}],add_tracks:function(u){this.get("tracks").add(u)}});var b=Backbone.Model.extend({});var h=Backbone.Router.extend({initialize:function(v){this.view=v.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var u=this;u.view.on("navigate",function(w){u.navigate(w)})},change_location:function(u){this.view.go_to(u)}});return{BackboneTrack:t,BrowserBookmark:e,BrowserBookmarkCollection:r,Cache:q,CanvasManager:f,Genome:c,GenomeDataManager:d,GenomeRegion:g,GenomeRegionCollection:m,GenomeVisualization:k,GenomeReferenceDataManager:p,TrackBrowserRouter:h,TrackConfig:b,Visualization:n,select_datasets:a}}); \ No newline at end of file diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/scripts/viz/circster.js --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -992,7 +992,7 @@ icon_class: 'disk--arrow', title: 'Save', on_click: function() { // show saving dialog box - show_modal("Saving...", "progress"); + Galaxy.modal.show({title: "Saving...", body: "progress" }); // link configuration var view = galaxy_config.app.viz_config; @@ -1010,15 +1010,19 @@ 'vis_json' : JSON.stringify(view) } }).success(function(vis_info) { - hide_modal(); + Galaxy.modal.hide(); view.vis_id = vis_info.vis_id; view.has_changes = false; // needed to set URL when first saving a visualization window.history.pushState({}, "", vis_info.url + window.location.hash); - }) - .error(function() { - show_modal( "Could Not Save", "Could not save visualization. Please try again later.", { "Close" : hide_modal } ); + }).error(function() { + // show dialog + Galaxy.modal.show({ + title : "Could Not Save", + body : "Could not save visualization. Please try again later.", + buttons : { "Cancel": function() { Galaxy.modal.hide() } } + }); }); } },{ diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -115,12 +115,15 @@ success: function(response) { // show dialog - show_modal("New Visualization", self.template_view_new(response), - { - "Cancel": function() { window.location = galaxy_config.root + "visualization/list"; }, - "Create": function() { self.create_browser($("#new-title").val(), $("#new-dbkey").val()); } + Galaxy.modal.show({ + title : "New Visualization", + body : self.template_view_new(response), + buttons : { + "Cancel": function() { window.location = galaxy_config.root + "visualization/list"; }, + "Create": function() { self.create_browser($("#new-title").val(), $("#new-dbkey").val()); Galaxy.modal.hide(); } + } }); - + // select default if (galaxy_config.app.default_dbkey) $("#new-dbkey option[value='" + galaxy_config.app.default_dbkey + "']").attr("selected", true); @@ -188,9 +191,6 @@ // modify view setting view.editor = true; - - // hide modal dialog - hide_modal(); }, // initialization for editor-specific functions. diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -285,11 +285,11 @@ title: "Edit settings", css_class: "settings-icon", on_click_fn: function(drawable) { - var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); }, + var cancel_fn = function() { Galaxy.modal.hide(); $(window).unbind("keypress.check_enter_esc"); }, ok_fn = function() { - drawable.config.update_from_form( $(".dialog-box") ); - hide_modal(); - $(window).unbind("keypress.check_enter_esc"); + drawable.config.update_from_form( $(Galaxy.modal.el) ); + Galaxy.modal.hide(); + $(window).unbind("keypress.check_enter_esc"); }, check_enter_esc = function(e) { if ((e.keyCode || e.which) === 27) { // Escape key @@ -299,11 +299,10 @@ } }; - $(window).bind("keypress.check_enter_esc", check_enter_esc); - show_modal("Configure", drawable.config.build_form(), { - "Cancel": cancel_fn, - "OK": ok_fn - }); + $(window).bind("keypress.check_enter_esc", check_enter_esc); + + // show dialog + Galaxy.modal.show({title: "Configure", body: drawable.config.build_form(), buttons : {'Cancel' : cancel_fn, 'Ok' : ok_fn } }); } }, // Remove. @@ -1761,9 +1760,7 @@ null, // Success callback. function(track_data) { - show_modal(tool.get('name') + " is Running", - tool.get('name') + " is running on the complete dataset. Tool outputs are in dataset's history.", - { "Close" : hide_modal } ); + Galaxy.modal.show({title: tool.get('name') + " is Running", body: tool.get('name') + " is running on the complete dataset. Tool outputs are in dataset's history.", buttons : {'Close' : function() { Galaxy.modal.hide(); } } }); } ); }, @@ -2023,11 +2020,10 @@ var tip = $(this).siblings(".tooltip").addClass( "in" ); tip.css( { // left: $(this).position().left + ( $(input).width() / 2 ) - 60, - // top: $(this).position().top + $(this.height) + // top: $(this).position().top + $(this.height) left: $(this).position().left + $(this).width() + 5, - top: $(this).position().top - ( $(tip).height() / 2 ) + ( $(this).height() / 2 ) + top: $(this).position().top + Galaxy.modal.scrollTop() - ( $(tip).height() / 2 ) + ( $(this).height() / 2 ) } ).show(); - // Click management: // Keep showing tip if clicking in tip. @@ -2431,7 +2427,7 @@ '<option value="both">current viewing area and bookmarks</option>' + '</select>', html = _.template(template, { track: track }); - var cancel_fn = function() { hide_modal(); $(window).unbind("keypress.check_enter_esc"); }, + var cancel_fn = function() { Galaxy.modal.hide(); $(window).unbind("keypress.check_enter_esc"); }, ok_fn = function() { var regions_to_use = $('select[name="regions"] option:selected').val(), regions, @@ -2458,7 +2454,7 @@ regions = [ view_region ].concat(bookmarked_regions); } - hide_modal(); + Galaxy.modal.hide(); // Go to visualization. window.location.href = @@ -2476,12 +2472,9 @@ ok_fn(); } }; - - show_modal("Visualize tool parameter space and output from different parameter settings?", html, { - "No": cancel_fn, - "Yes": ok_fn - }); + // show dialog + Galaxy.modal.show({title: "Visualize tool parameter space and output from different parameter settings?", body: html, buttons : {'No' : cancel_fn, 'Yes' : ok_fn } }); } }, // Remove track. @@ -2689,7 +2682,7 @@ // Add links to (a) show error and (b) try again. track.tiles_div.append( $("<a href='javascript:void(0);'></a>").text("View error").click(function() { - show_modal( "Trackster Error", "<pre>" + result.message + "</pre>", { "Close" : hide_modal } ); + Galaxy.modal.show({title: "Trackster Error", body: "<pre>" + result.message + "</pre>", buttons : {'Close' : function() { Galaxy.modal.hide(); } } }); }) ); track.tiles_div.append( $('<span/>').text(' ') ); @@ -2951,17 +2944,6 @@ track.action_icons.tools_icon.hide(); track.action_icons.param_space_viz_icon.hide(); } - - // - // List chrom/contigs with data option. - // - /* - if (track.valid_chroms) { - track_dropdown["List chrom/contigs with data"] = function() { - show_modal("Chrom/contigs with data", "<p>" + track.valid_chroms.join("<br/>") + "</p>", { "Close": function() { hide_modal(); } }); - }; - } - */ }, /** diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/scripts/viz/trackster_ui.js --- a/static/scripts/viz/trackster_ui.js +++ b/static/scripts/viz/trackster_ui.js @@ -62,9 +62,9 @@ } }, { icon_class: 'disk--arrow', title: 'Save', on_click: function() { - // Show saving dialog box - show_modal("Saving...", "progress"); - + // show dialog + Galaxy.modal.show({title: "Saving...", body: "progress" }); + // Save bookmarks. var bookmarks = []; $(".bookmark").each(function() { @@ -94,15 +94,19 @@ 'vis_json' : JSON.stringify(viz_config) } }).success(function(vis_info) { - hide_modal(); + Galaxy.modal.hide(); view.vis_id = vis_info.vis_id; view.has_changes = false; // Needed to set URL when first saving a visualization. window.history.pushState({}, "", vis_info.url + window.location.hash); - }) - .error(function() { - show_modal( "Could Not Save", "Could not save visualization. Please try again later.", { "Close" : hide_modal } ); + }).error(function() { + // show dialog + Galaxy.modal.show({ + title : "Could Not Save", + body : "Could not save visualization. Please try again later.", + buttons : { "Cancel": function() { Galaxy.modal.hide() } } + }); }); } } ], @@ -119,43 +123,54 @@ add_bookmarks: function() { var self = this, baseURL = this.baseURL; - show_modal( "Select dataset for new bookmarks", "progress" ); + + // show modal while loading history + Galaxy.modal.show({title: "Select dataset for new bookmarks", body: "progress" }); + $.ajax({ url: this.baseURL + "/visualization/list_histories", data: { "f-dbkey": view.dbkey }, error: function() { alert( "Grid failed" ); }, success: function(table_html) { - show_modal( - "Select dataset for new bookmarks", - table_html, { - "Cancel": function() { - hide_modal(); + + // show modal to select bookmarks + Galaxy.modal.show( + { + title : "Select dataset for new bookmarks", + body : table_html, + buttons : + { + "Cancel": function() + { + Galaxy.modal.hide(); }, - "Insert": function() { + + "Insert": function() + { // Just use the first selected - $('input[name=id]:checked,input[name=ldda_ids]:checked').first().each(function(){ + $('input[name=id]:checked,input[name=ldda_ids]:checked').first().each(function() + { var data, id = $(this).val(); - if ($(this).attr("name") === "id") { - data = { hda_id: id }; - } else { - data = { ldda_id: id}; + if ($(this).attr("name") === "id") + data = { hda_id: id }; + else + data = { ldda_id: id}; + + $.ajax({ + url: this.baseURL + "/visualization/bookmarks_from_dataset", + data: data, + dataType: "json" + }).then( function(data) { + for( i = 0; i < data.data.length; i++ ) { + var row = data.data[i]; + self.add_bookmark( row[0], row[1] ); } - - $.ajax({ - url: this.baseURL + "/visualization/bookmarks_from_dataset", - data: data, - dataType: "json" - }).then( function(data) { - for( i = 0; i < data.data.length; i++ ) { - var row = data.data[i]; - self.add_bookmark( row[0], row[1] ); - } - }); + }); }); - hide_modal(); + Galaxy.modal.hide(); } } - ); + }); } }); }, diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -20,11 +20,13 @@ data: filters, error: function() { alert( "Grid failed" ); }, success: function(table_html) { - show_modal( - "Select datasets for new tracks", - table_html, { + Galaxy.modal.show({ + title : "Select datasets for new tracks", + body : table_html, + buttons : + { "Cancel": function() { - hide_modal(); + Galaxy.modal.hide(); }, "Add": function() { var requests = []; @@ -55,10 +57,10 @@ ); success_fn(track_defs); }); - hide_modal(); + Galaxy.modal.hide(); } } - ); + }); } }); }; diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -55,7 +55,7 @@ small{font-size:85%} cite{font-style:normal} .text-muted{color:#999} -.text-primary{color:#00f} +.text-primary{color:#5f6990} .text-warning{color:#80571e} .text-danger{color:#7e2a27} .text-success{color:#295f29} @@ -184,12 +184,12 @@ .btn:hover,.btn:focus{color:#333;text-decoration:none} .btn:active,.btn.active{outline:0;background-image:none;-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,0.125);box-shadow:inset 0 3px 5px rgba(0,0,0,0.125)} .btn.disabled,.btn[disabled],fieldset[disabled] .btn{cursor:not-allowed;pointer-events:none;opacity:.65;filter:alpha(opacity=65);-webkit-box-shadow:none;box-shadow:none} -.btn-default{color:#333;background-color:#fff;border-color:#bfbfbf}.btn-default:hover,.btn-default:focus,.btn-default:active,.btn-default.active,.open .dropdown-toggle.btn-default{color:#333;background-color:#ebebeb;border-color:#a1a1a1} +.btn-default{color:#333;background-color:#f2f2f2;border-color:#bfbfbf}.btn-default:hover,.btn-default:focus,.btn-default:active,.btn-default.active,.open .dropdown-toggle.btn-default{color:#333;background-color:#dedede;border-color:#a1a1a1} .btn-default:active,.btn-default.active,.open .dropdown-toggle.btn-default{background-image:none} -.btn-default.disabled,.btn-default[disabled],fieldset[disabled] .btn-default,.btn-default.disabled:hover,.btn-default[disabled]:hover,fieldset[disabled] .btn-default:hover,.btn-default.disabled:focus,.btn-default[disabled]:focus,fieldset[disabled] .btn-default:focus,.btn-default.disabled:active,.btn-default[disabled]:active,fieldset[disabled] .btn-default:active,.btn-default.disabled.active,.btn-default[disabled].active,fieldset[disabled] .btn-default.active{background-color:#fff;border-color:#bfbfbf} -.btn-primary{color:#fff;background-color:#00f;border-color:#003}.btn-primary:hover,.btn-primary:focus,.btn-primary:active,.btn-primary.active,.open .dropdown-toggle.btn-primary{color:#fff;background-color:#0000d6;border-color:#000} +.btn-default.disabled,.btn-default[disabled],fieldset[disabled] .btn-default,.btn-default.disabled:hover,.btn-default[disabled]:hover,fieldset[disabled] .btn-default:hover,.btn-default.disabled:focus,.btn-default[disabled]:focus,fieldset[disabled] .btn-default:focus,.btn-default.disabled:active,.btn-default[disabled]:active,fieldset[disabled] .btn-default:active,.btn-default.disabled.active,.btn-default[disabled].active,fieldset[disabled] .btn-default.active{background-color:#f2f2f2;border-color:#bfbfbf} +.btn-primary{color:#fff;background-color:#5f6990;border-color:#0e0f15}.btn-primary:hover,.btn-primary:focus,.btn-primary:active,.btn-primary.active,.open .dropdown-toggle.btn-primary{color:#fff;background-color:#4e5777;border-color:#000} .btn-primary:active,.btn-primary.active,.open .dropdown-toggle.btn-primary{background-image:none} -.btn-primary.disabled,.btn-primary[disabled],fieldset[disabled] .btn-primary,.btn-primary.disabled:hover,.btn-primary[disabled]:hover,fieldset[disabled] .btn-primary:hover,.btn-primary.disabled:focus,.btn-primary[disabled]:focus,fieldset[disabled] .btn-primary:focus,.btn-primary.disabled:active,.btn-primary[disabled]:active,fieldset[disabled] .btn-primary:active,.btn-primary.disabled.active,.btn-primary[disabled].active,fieldset[disabled] .btn-primary.active{background-color:#00f;border-color:#003} +.btn-primary.disabled,.btn-primary[disabled],fieldset[disabled] .btn-primary,.btn-primary.disabled:hover,.btn-primary[disabled]:hover,fieldset[disabled] .btn-primary:hover,.btn-primary.disabled:focus,.btn-primary[disabled]:focus,fieldset[disabled] .btn-primary:focus,.btn-primary.disabled:active,.btn-primary[disabled]:active,fieldset[disabled] .btn-primary:active,.btn-primary.disabled.active,.btn-primary[disabled].active,fieldset[disabled] .btn-primary.active{background-color:#5f6990;border-color:#0e0f15} .btn-warning{color:#fff;background-color:#bf822c;border-color:#191106}.btn-warning:hover,.btn-warning:focus,.btn-warning:active,.btn-warning.active,.open .dropdown-toggle.btn-warning{color:#fff;background-color:#9d6b24;border-color:#000} .btn-warning:active,.btn-warning.active,.open .dropdown-toggle.btn-warning{background-image:none} .btn-warning.disabled,.btn-warning[disabled],fieldset[disabled] .btn-warning,.btn-warning.disabled:hover,.btn-warning[disabled]:hover,fieldset[disabled] .btn-warning:hover,.btn-warning.disabled:focus,.btn-warning[disabled]:focus,fieldset[disabled] .btn-warning:focus,.btn-warning.disabled:active,.btn-warning[disabled]:active,fieldset[disabled] .btn-warning:active,.btn-warning.disabled.active,.btn-warning[disabled].active,fieldset[disabled] .btn-warning.active{background-color:#bf822c;border-color:#191106} @@ -422,8 +422,8 @@ .dropdown-menu{position:absolute;top:100%;left:0;z-index:1000;display:none;float:left;min-width:160px;padding:5px 0;margin:2px 0 0;list-style:none;font-size:12px;background-color:#fff;border:1px solid #ccc;border:1px solid rgba(0,0,0,0.15);border-radius:3px;-webkit-box-shadow:0 6px 12px rgba(0,0,0,0.175);box-shadow:0 6px 12px rgba(0,0,0,0.175);background-clip:padding-box}.dropdown-menu.pull-right{right:0;left:auto} .dropdown-menu .divider{height:1px;margin:7.5px 0;overflow:hidden;background-color:#e5e5e5} .dropdown-menu>li>a{display:block;padding:3px 20px;clear:both;font-weight:normal;line-height:1.428571429;color:#333;white-space:nowrap} -.dropdown-menu>li>a:hover,.dropdown-menu>li>a:focus{text-decoration:none;color:#fff;background-color:#303030} -.dropdown-menu>.active>a,.dropdown-menu>.active>a:hover,.dropdown-menu>.active>a:focus{color:#fff;text-decoration:none;outline:0;background-color:#303030} +.dropdown-menu>li>a:hover,.dropdown-menu>li>a:focus{text-decoration:none;color:#fff;background-color:#5f6990} +.dropdown-menu>.active>a,.dropdown-menu>.active>a:hover,.dropdown-menu>.active>a:focus{color:#fff;text-decoration:none;outline:0;background-color:#5f6990} .dropdown-menu>.disabled>a,.dropdown-menu>.disabled>a:hover,.dropdown-menu>.disabled>a:focus{color:#999} .dropdown-menu>.disabled>a:hover,.dropdown-menu>.disabled>a:focus{text-decoration:none;background-color:transparent;background-image:none;filter:progid:DXImageTransform.Microsoft.gradient(enabled = false);cursor:not-allowed} .open>.dropdown-menu{display:block} @@ -513,7 +513,7 @@ @media (min-width:768px){.nav-tabs.nav-justified>li>a{border-bottom:1px solid #bfbfbf;border-radius:3px 3px 0 0} .nav-tabs.nav-justified>.active>a,.nav-tabs.nav-justified>.active>a:hover,.nav-tabs.nav-justified>.active>a:focus{border-bottom-color:#fff}} .nav-pills>li{float:left}.nav-pills>li>a{border-radius:5px} .nav-pills>li+li{margin-left:2px} -.nav-pills>li.active>a,.nav-pills>li.active>a:hover,.nav-pills>li.active>a:focus{color:#fff;background-color:#303030} +.nav-pills>li.active>a,.nav-pills>li.active>a:hover,.nav-pills>li.active>a:focus{color:#fff;background-color:#5f6990} .nav-stacked>li{float:none}.nav-stacked>li+li{margin-top:2px;margin-left:0} .nav-justified{width:100%}.nav-justified>li{float:none}.nav-justified>li>a{text-align:center;margin-bottom:5px} @media (min-width:768px){.nav-justified>li{display:table-cell;width:1%}.nav-justified>li>a{margin-bottom:0}} @@ -597,7 +597,7 @@ .pagination>li:first-child>a,.pagination>li:first-child>span{margin-left:0;border-bottom-left-radius:3px;border-top-left-radius:3px} .pagination>li:last-child>a,.pagination>li:last-child>span{border-bottom-right-radius:3px;border-top-right-radius:3px} .pagination>li>a:hover,.pagination>li>span:hover,.pagination>li>a:focus,.pagination>li>span:focus{background-color:#eee} -.pagination>.active>a,.pagination>.active>span,.pagination>.active>a:hover,.pagination>.active>span:hover,.pagination>.active>a:focus,.pagination>.active>span:focus{z-index:2;color:#fff;background-color:#00f;border-color:#00f;cursor:default} +.pagination>.active>a,.pagination>.active>span,.pagination>.active>a:hover,.pagination>.active>span:hover,.pagination>.active>a:focus,.pagination>.active>span:focus{z-index:2;color:#fff;background-color:#5f6990;border-color:#5f6990;cursor:default} .pagination>.disabled>span,.pagination>.disabled>span:hover,.pagination>.disabled>span:focus,.pagination>.disabled>a,.pagination>.disabled>a:hover,.pagination>.disabled>a:focus{color:#999;background-color:#fff;border-color:#bfbfbf;cursor:not-allowed} .pagination-lg>li>a,.pagination-lg>li>span{padding:8px 14px;font-size:15px} .pagination-lg>li:first-child>a,.pagination-lg>li:first-child>span{border-bottom-left-radius:5px;border-top-left-radius:5px} @@ -637,7 +637,7 @@ .alert-danger{background-color:#f9c7c5;border-color:#dd1c15;color:#7e2a27}.alert-danger hr{border-top-color:#c61913} .alert-danger .alert-link{color:#571d1b} @-webkit-keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}@-moz-keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}@-o-keyframes progress-bar-stripes{from{background-position:0 0} to{background-position:40px 0}}@keyframes progress-bar-stripes{from{background-position:40px 0} to{background-position:0 0}}.progress{overflow:hidden;height:17px;margin-bottom:17px;background-color:#f5f5f5;border-radius:3px;-webkit-box-shadow:inset 0 1px 2px rgba(0,0,0,0.1);box-shadow:inset 0 1px 2px rgba(0,0,0,0.1)} -.progress-bar{float:left;width:0%;height:100%;font-size:11px;color:#fff;text-align:center;background-color:#00f;-webkit-box-shadow:inset 0 -1px 0 rgba(0,0,0,0.15);box-shadow:inset 0 -1px 0 rgba(0,0,0,0.15);-webkit-transition:width .6s ease;transition:width .6s ease} +.progress-bar{float:left;width:0%;height:100%;font-size:11px;color:#fff;text-align:center;background-color:#5f6990;-webkit-box-shadow:inset 0 -1px 0 rgba(0,0,0,0.15);box-shadow:inset 0 -1px 0 rgba(0,0,0,0.15);-webkit-transition:width .6s ease;transition:width .6s ease} .progress-striped .progress-bar{background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(.25, rgba(255,255,255,0.15)), color-stop(.25, transparent), color-stop(.5, transparent), color-stop(.5, rgba(255,255,255,0.15)), color-stop(.75, rgba(255,255,255,0.15)), color-stop(.75, transparent), to(transparent));background-image:-webkit-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-size:40px 40px} .progress.active .progress-bar{-webkit-animation:progress-bar-stripes 2s linear infinite;-moz-animation:progress-bar-stripes 2s linear infinite;-ms-animation:progress-bar-stripes 2s linear infinite;-o-animation:progress-bar-stripes 2s linear infinite;animation:progress-bar-stripes 2s linear infinite} .progress-bar-success{background-color:#3f943f}.progress-striped .progress-bar-success{background-image:-webkit-gradient(linear, 0 100%, 100% 0, color-stop(.25, rgba(255,255,255,0.15)), color-stop(.25, transparent), color-stop(.5, transparent), color-stop(.5, rgba(255,255,255,0.15)), color-stop(.75, rgba(255,255,255,0.15)), color-stop(.75, transparent), to(transparent));background-image:-webkit-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-image:-moz-linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent);background-image:linear-gradient(45deg, rgba(255,255,255,0.15) 25%, transparent 25%, transparent 50%, rgba(255,255,255,0.15) 50%, rgba(255,255,255,0.15) 75%, transparent 75%, transparent)} @@ -659,8 +659,8 @@ .list-group-item>.badge+.badge{margin-right:5px} a.list-group-item{color:#555}a.list-group-item .list-group-item-heading{color:#333} a.list-group-item:hover,a.list-group-item:focus{text-decoration:none;background-color:#f5f5f5} -.list-group-item.active,.list-group-item.active:hover,.list-group-item.active:focus{z-index:2;color:#fff;background-color:#303030;border-color:#303030}.list-group-item.active .list-group-item-heading,.list-group-item.active:hover .list-group-item-heading,.list-group-item.active:focus .list-group-item-heading{color:inherit} -.list-group-item.active .list-group-item-text,.list-group-item.active:hover .list-group-item-text,.list-group-item.active:focus .list-group-item-text{color:#969696} +.list-group-item.active,.list-group-item.active:hover,.list-group-item.active:focus{z-index:2;color:#fff;background-color:#5f6990;border-color:#5f6990}.list-group-item.active .list-group-item-heading,.list-group-item.active:hover .list-group-item-heading,.list-group-item.active:focus .list-group-item-heading{color:inherit} +.list-group-item.active .list-group-item-text,.list-group-item.active:hover .list-group-item-text,.list-group-item.active:focus .list-group-item-text{color:#d6d9e4} .list-group-item-heading{margin-top:0;margin-bottom:5px} .list-group-item-text{margin-bottom:0;line-height:1.3} .panel{margin-bottom:17px;background-color:#fff;border:1px solid transparent;border-radius:3px;-webkit-box-shadow:0 1px 1px rgba(0,0,0,0.05);box-shadow:0 1px 1px rgba(0,0,0,0.05)} @@ -681,8 +681,8 @@ .panel-group .panel-footer{border-top:0}.panel-group .panel-footer+.panel-collapse .panel-body{border-bottom:1px solid #bfbfbf} .panel-default{border-color:#bfbfbf}.panel-default>.panel-heading{color:#333;background-color:#f5f5f5;border-color:#bfbfbf}.panel-default>.panel-heading+.panel-collapse .panel-body{border-top-color:#bfbfbf} .panel-default>.panel-footer+.panel-collapse .panel-body{border-bottom-color:#bfbfbf} -.panel-primary{border-color:#00f}.panel-primary>.panel-heading{color:#fff;background-color:#00f;border-color:#00f}.panel-primary>.panel-heading+.panel-collapse .panel-body{border-top-color:#00f} -.panel-primary>.panel-footer+.panel-collapse .panel-body{border-bottom-color:#00f} +.panel-primary{border-color:#5f6990}.panel-primary>.panel-heading{color:#fff;background-color:#5f6990;border-color:#5f6990}.panel-primary>.panel-heading+.panel-collapse .panel-body{border-top-color:#5f6990} +.panel-primary>.panel-footer+.panel-collapse .panel-body{border-bottom-color:#5f6990} .panel-success{border-color:#20b420}.panel-success>.panel-heading{color:#295f29;background-color:#aff1af;border-color:#20b420}.panel-success>.panel-heading+.panel-collapse .panel-body{border-top-color:#20b420} .panel-success>.panel-footer+.panel-collapse .panel-body{border-bottom-color:#20b420} .panel-warning{border-color:#e28709}.panel-warning>.panel-heading{color:#80571e;background-color:#fce1ba;border-color:#e28709}.panel-warning>.panel-heading+.panel-collapse .panel-body{border-top-color:#e28709} @@ -753,9 +753,9 @@ .affix{position:fixed} .navbar-fixed-top .navbar-brand{font-family:Verdana;font-weight:bold;font-size:160%} pre{overflow:auto;word-wrap:normal;white-space:pre} -.btn.active,.btn:active{color:inherit} .dropdown-menu{max-width:auto} input[type="checkbox"],input[type="radio"]{margin-left:0.5ex;margin-right:0.5ex} +.modal-dialog{width:690px} .modal-body{overflow:auto} .nav-tabs{margin-bottom:15px} a{text-decoration:underline} @@ -1124,7 +1124,7 @@ .galaxy-frame .frame .f-pin{left:6px;top:1px} .galaxy-frame .frame .f-resize{background:#fff;width:16px;height:16px;color:#2c3143;right:0px;bottom:0px;text-align:center;line-height:16px;border:0px} .upload-info{font-weight:normal;text-align:center} -.upload-box{width:100%;height:250px;max-height:250px;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:20px}.upload-box .panel{display:none}.upload-box .panel .panel-heading{position:relative;height:19px;padding:5px}.upload-box .panel .panel-heading .title{position:absolute;top:2px;font-weight:normal;text-align:left;margin:0px;max-width:300px;overflow:hidden} +.upload-box{width:100%;height:95%;max-height:95%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:20px}.upload-box .panel{display:none}.upload-box .panel .panel-heading{position:relative;height:19px;padding:5px}.upload-box .panel .panel-heading .title{position:absolute;top:2px;font-weight:normal;text-align:left;margin:0px;max-width:300px;overflow:hidden} .upload-box .panel .panel-heading .info{position:absolute;top:3px;font-weight:normal;right:20px;text-align:right;margin:0px} .upload-box .panel .panel-heading .symbol{position:absolute;cursor:pointer;top:0px;right:3px} .upload-box .panel .panel-body{position:relative;padding:5px} @@ -1146,6 +1146,9 @@ #center{left:250px;right:250px;overflow:hidden;z-index:1} #right-border{right:250px} #right{width:250px;right:0px;z-index:200;border-left:solid #999 1px} +body.has-message-box #left,body.has-inactivity-box #left,body.has-message-box #left-border,body.has-inactivity-box #left-border,body.has-message-box #center,body.has-inactivity-box #center,body.has-message-box #right-border,body.has-inactivity-box #right-border,body.has-message-box #right,body.has-inactivity-box #right{top:64px} +body.has-message-box.has-inactivity-box #left,body.has-message-box.has-inactivity-box #left-border,body.has-message-box.has-inactivity-box #center,body.has-message-box.has-inactivity-box #right-border,body.has-message-box.has-inactivity-box #right{top:94px} +body.has-message-box.has-inactivity-box #inactivebox{top:64px} .subnavbar{background-image:-webkit-gradient(linear, 0 0, 0 100%, from(#fff), color-stop(25%, #fff), to(#e6e6e6));background-image:-webkit-linear-gradient(#fff, #fff 25%, #e6e6e6);background-image:-moz-linear-gradient(top, #fff, #fff 25%, #e6e6e6);background-image:linear-gradient(#fff, #fff 25%, #e6e6e6);background-repeat:no-repeat;filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#ffffffff', endColorstr='#ffe6e6e6', GradientType=0);border-bottom:solid #bfbfbf 1px;border-top:solid #bfbfbf 1px;padding:5px;color:#555} .unified-panel-header{-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;height:30px;z-index:1000;text-shadow:rgba(255,255,255,0.8) 0 1px 0;background:#eee;border-bottom:solid #999 1px;margin:0;padding:0;padding-right:10px;padding-left:10px;font-weight:bold;color:#555}.unified-panel-header a{color:#555} .unified-panel-header-inner{padding-top:8px} @@ -1165,7 +1168,7 @@ .panel-header-button .caret{margin-top:7px} .panel-header-button.popup{padding-right:1.75em;background:url(../images/dropdownarrow.png) no-repeat right 7px} #DD-helper{background:white;opacity:0;z-index:900;position:absolute;top:0;left:0;width:100%;height:100%} -.panel-error-message,.panel-warning-message,.panel-done-message,.panel-info-message{height:24px;line-height:24px;padding:0px;padding-left:26px;background-color:#f9c7c5;background-image:url(error_small.png);background-repeat:no-repeat;background-position:6px 50%} +.panel-error-message,.panel-warning-message,.panel-done-message,.panel-info-message{height:30px;line-height:30px;padding:0px;padding-left:26px;background-color:#f9c7c5;background-image:url(error_small.png);background-repeat:no-repeat;background-position:6px 50%} .panel-warning-message{background-image:url(warn_small.png);background-color:#fce1ba} .panel-done-message{background-image:url(ok_small.png);background-color:#aff1af} .panel-info-message{background-image:url(info_small.png);background-color:#a6e4f7} @@ -1179,7 +1182,7 @@ #masthead .iconbar .toggle{color:#BCC800} .quota-meter-container{position:absolute;top:0;right:0;height:32px} .quota-meter{position:absolute;top:8px;right:8px;height:16px;width:100px;background-color:#f5f5f5} -.quota-meter-bar{position:absolute;top:0;left:0;height:16px;background-color:#00f} +.quota-meter-bar{position:absolute;top:0;left:0;height:16px;background-color:#5f6990} .quota-meter-bar-warn{background-color:#bf822c} .quota-meter-bar-error{background-color:#b93e3a} .quota-meter-text{position:absolute;top:50%;left:0;width:100px;height:16px;margin-top:-6px;text-align:center;z-index:9001;color:#000;white-space:nowrap} @@ -1216,21 +1219,24 @@ select,input,textarea{font:inherit} .form-row select,.form-row textarea,.form-row input[type="text"],.form-row input[type="file"],.form-row input[type="password"]{max-width:90%} textarea,input[type="text"],input[type="password"]{font-size:12px;line-height:1.428571429;border:1px solid #aaa;padding:3px} -input[type="submit"],button{display:inline-block;padding:4px 10px;margin-bottom:0;font-size:12px;font-weight:normal;line-height:1.428571429;text-align:center;vertical-align:middle;cursor:pointer;border:1px solid transparent;border-radius:3px;white-space:nowrap;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;color:#333;background-color:#fff;border-color:#bfbfbf}input[type="submit"]:focus,button:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} +input[type="submit"],button{display:inline-block;padding:4px 10px;margin-bottom:0;font-size:12px;font-weight:normal;line-height:1.428571429;text-align:center;vertical-align:middle;cursor:pointer;border:1px solid transparent;border-radius:3px;white-space:nowrap;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;color:#333;background-color:#f2f2f2;border-color:#bfbfbf}input[type="submit"]:focus,button:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} input[type="submit"]:hover,button:hover,input[type="submit"]:focus,button:focus{color:#333;text-decoration:none} input[type="submit"]:active,button:active,input[type="submit"].active,button.active{outline:0;background-image:none;-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,0.125);box-shadow:inset 0 3px 5px rgba(0,0,0,0.125)} input[type="submit"].disabled,button.disabled,input[type="submit"][disabled],button[disabled],fieldset[disabled] input[type="submit"],fieldset[disabled] button{cursor:not-allowed;pointer-events:none;opacity:.65;filter:alpha(opacity=65);-webkit-box-shadow:none;box-shadow:none} input[type="submit"] [class^="fa-icon-"],button [class^="fa-icon-"],input[type="submit"] [class*=" fa-icon-"],button [class*=" fa-icon-"]{display:inline;line-height:.6em}input[type="submit"] [class^="fa-icon-"].fa-icon-spin,button [class^="fa-icon-"].fa-icon-spin,input[type="submit"] [class*=" fa-icon-"].fa-icon-spin,button [class*=" fa-icon-"].fa-icon-spin{display:inline-block} input[type="submit"] [class^="fa-icon-"].pull-left.fa-icon-2x,button [class^="fa-icon-"].pull-left.fa-icon-2x,input[type="submit"] [class*=" fa-icon-"].pull-left.fa-icon-2x,button [class*=" fa-icon-"].pull-left.fa-icon-2x,input[type="submit"] [class^="fa-icon-"].pull-right.fa-icon-2x,button [class^="fa-icon-"].pull-right.fa-icon-2x,input[type="submit"] [class*=" fa-icon-"].pull-right.fa-icon-2x,button [class*=" fa-icon-"].pull-right.fa-icon-2x{margin-top:.35em} input[type="submit"] [class^="fa-icon-"].fa-icon-spin.icon-large,button [class^="fa-icon-"].fa-icon-spin.icon-large,input[type="submit"] [class*=" fa-icon-"].fa-icon-spin.icon-large,button [class*=" fa-icon-"].fa-icon-spin.icon-large{height:.75em} -input[type="submit"]:hover,button:hover,input[type="submit"]:focus,button:focus,input[type="submit"]:active,button:active,input[type="submit"].active,button.active,.open .dropdown-toggleinput[type="submit"],.open .dropdown-togglebutton{color:#333;background-color:#ebebeb;border-color:#a1a1a1} +input[type="submit"]:hover,button:hover,input[type="submit"]:focus,button:focus,input[type="submit"]:active,button:active,input[type="submit"].active,button.active,.open .dropdown-toggleinput[type="submit"],.open .dropdown-togglebutton{color:#333;background-color:#dedede;border-color:#a1a1a1} input[type="submit"]:active,button:active,input[type="submit"].active,button.active,.open .dropdown-toggleinput[type="submit"],.open .dropdown-togglebutton{background-image:none} -input[type="submit"].disabled,button.disabled,input[type="submit"][disabled],button[disabled],fieldset[disabled] input[type="submit"],fieldset[disabled] button,input[type="submit"].disabled:hover,button.disabled:hover,input[type="submit"][disabled]:hover,button[disabled]:hover,fieldset[disabled] input[type="submit"]:hover,fieldset[disabled] button:hover,input[type="submit"].disabled:focus,button.disabled:focus,input[type="submit"][disabled]:focus,button[disabled]:focus,fieldset[disabled] input[type="submit"]:focus,fieldset[disabled] button:focus,input[type="submit"].disabled:active,button.disabled:active,input[type="submit"][disabled]:active,button[disabled]:active,fieldset[disabled] input[type="submit"]:active,fieldset[disabled] button:active,input[type="submit"].disabled.active,button.disabled.active,input[type="submit"][disabled].active,button[disabled].active,fieldset[disabled] input[type="submit"].active,fieldset[disabled] button.active{background-color:#fff;border-color:#bfbfbf} +input[type="submit"].disabled,button.disabled,input[type="submit"][disabled],button[disabled],fieldset[disabled] input[type="submit"],fieldset[disabled] button,input[type="submit"].disabled:hover,button.disabled:hover,input[type="submit"][disabled]:hover,button[disabled]:hover,fieldset[disabled] input[type="submit"]:hover,fieldset[disabled] button:hover,input[type="submit"].disabled:focus,button.disabled:focus,input[type="submit"][disabled]:focus,button[disabled]:focus,fieldset[disabled] input[type="submit"]:focus,fieldset[disabled] button:focus,input[type="submit"].disabled:active,button.disabled:active,input[type="submit"][disabled]:active,button[disabled]:active,fieldset[disabled] input[type="submit"]:active,fieldset[disabled] button:active,input[type="submit"].disabled.active,button.disabled.active,input[type="submit"][disabled].active,button[disabled].active,fieldset[disabled] input[type="submit"].active,fieldset[disabled] button.active{background-color:#f2f2f2;border-color:#bfbfbf} +input[type="submit"].btn-primary,button.btn-primary{color:#fff;background-color:#5f6990;border-color:#0e0f15}input[type="submit"].btn-primary:hover,button.btn-primary:hover,input[type="submit"].btn-primary:focus,button.btn-primary:focus,input[type="submit"].btn-primary:active,button.btn-primary:active,input[type="submit"].btn-primary.active,button.btn-primary.active,.open .dropdown-toggleinput[type="submit"].btn-primary,.open .dropdown-togglebutton.btn-primary{color:#fff;background-color:#4e5777;border-color:#000} +input[type="submit"].btn-primary:active,button.btn-primary:active,input[type="submit"].btn-primary.active,button.btn-primary.active,.open .dropdown-toggleinput[type="submit"].btn-primary,.open .dropdown-togglebutton.btn-primary{background-image:none} +input[type="submit"].btn-primary.disabled,button.btn-primary.disabled,input[type="submit"].btn-primary[disabled],button.btn-primary[disabled],fieldset[disabled] input[type="submit"].btn-primary,fieldset[disabled] button.btn-primary,input[type="submit"].btn-primary.disabled:hover,button.btn-primary.disabled:hover,input[type="submit"].btn-primary[disabled]:hover,button.btn-primary[disabled]:hover,fieldset[disabled] input[type="submit"].btn-primary:hover,fieldset[disabled] button.btn-primary:hover,input[type="submit"].btn-primary.disabled:focus,button.btn-primary.disabled:focus,input[type="submit"].btn-primary[disabled]:focus,button.btn-primary[disabled]:focus,fieldset[disabled] input[type="submit"].btn-primary:focus,fieldset[disabled] button.btn-primary:focus,input[type="submit"].btn-primary.disabled:active,button.btn-primary.disabled:active,input[type="submit"].btn-primary[disabled]:active,button.btn-primary[disabled]:active,fieldset[disabled] input[type="submit"].btn-primary:active,fieldset[disabled] button.btn-primary:active,input[type="submit"].btn-primary.disabled.active,button.btn-primary.disabled.active,input[type="submit"].btn-primary[disabled].active,button.btn-primary[disabled].active,fieldset[disabled] input[type="submit"].btn-primary.active,fieldset[disabled] button.btn-primary.active{background-color:#5f6990;border-color:#0e0f15} .search-query{display:inline-block;padding:4px;font-size:12px;line-height:1.428571429;color:#555;border:1px solid #aaa;padding-left:14px !important;padding-right:14px !important;margin-bottom:0;-webkit-border-radius:14px;-moz-border-radius:14px;border-radius:14px;max-width:auto} .search-query:focus{border-color:rgba(24,132,218,0.8);-webkit-box-shadow:inset 0 1px 1px rgba(0,0,0,0.075),0 0 8px rgba(82,168,236,0.6);box-shadow:inset 0 1px 1px rgba(0,0,0,0.075),0 0 8px rgba(82,168,236,0.6);outline:0;outline:thin dotted \9;} .search-spinner{position:absolute;display:none;right:6px;top:9px} #search-clear-btn{position:absolute;right:6px;top:8px;display:block;font-size:1.4em;text-decoration:none;color:#888;font-family:FontAwesome;font-size:1.1666666666666667em;background-image:none !important;background-position:0% 0%;background-repeat:repeat}#search-clear-btn:before{content:"\f057"} -.errormessagelarge,.warningmessagelarge,.donemessagelarge,.infomessagelarge{padding:15px;margin-bottom:17px;border:1px solid transparent;border-radius:3px;min-height:36px;padding-left:52px;background-image:url(error_large.png);background-repeat:no-repeat;background-position:10px 10px}.errormessagelarge h4,.warningmessagelarge h4,.donemessagelarge h4,.infomessagelarge h4{margin-top:0;color:inherit} +.errormessagelarge,.warningmessagelarge,.donemessagelarge,.infomessagelarge{padding:15px;margin-bottom:17px;border:1px solid transparent;border-radius:3px;min-height:36px;padding-left:52px;background-image:url(error_large.png);background-repeat:no-repeat;background-position:10px 8px}.errormessagelarge h4,.warningmessagelarge h4,.donemessagelarge h4,.infomessagelarge h4{margin-top:0;color:inherit} .errormessagelarge .alert-link,.warningmessagelarge .alert-link,.donemessagelarge .alert-link,.infomessagelarge .alert-link{font-weight:bold} .errormessagelarge>p,.warningmessagelarge>p,.donemessagelarge>p,.infomessagelarge>p,.errormessagelarge>ul,.warningmessagelarge>ul,.donemessagelarge>ul,.infomessagelarge>ul{margin-bottom:0} .errormessagelarge>p+p,.warningmessagelarge>p+p,.donemessagelarge>p+p,.infomessagelarge>p+p{margin-top:5px} @@ -1317,40 +1323,40 @@ .state-fg-ok{color:#66AA66} .state-fg-error{color:#AA6666} .state-fg-deleted{color:#3399FF} -button{display:inline-block;padding:4px 10px;margin-bottom:0;font-size:12px;font-weight:normal;line-height:1.428571429;text-align:center;vertical-align:middle;cursor:pointer;border:1px solid transparent;border-radius:3px;white-space:nowrap;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;color:#333;background-color:#fff;border-color:#bfbfbf}button:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} +button{display:inline-block;padding:4px 10px;margin-bottom:0;font-size:12px;font-weight:normal;line-height:1.428571429;text-align:center;vertical-align:middle;cursor:pointer;border:1px solid transparent;border-radius:3px;white-space:nowrap;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;color:#333;background-color:#f2f2f2;border-color:#bfbfbf}button:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} button:hover,button:focus{color:#333;text-decoration:none} button:active,button.active{outline:0;background-image:none;-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,0.125);box-shadow:inset 0 3px 5px rgba(0,0,0,0.125)} button.disabled,button[disabled],fieldset[disabled] button{cursor:not-allowed;pointer-events:none;opacity:.65;filter:alpha(opacity=65);-webkit-box-shadow:none;box-shadow:none} button [class^="fa-icon-"],button [class*=" fa-icon-"]{display:inline;line-height:.6em}button [class^="fa-icon-"].fa-icon-spin,button [class*=" fa-icon-"].fa-icon-spin{display:inline-block} button [class^="fa-icon-"].pull-left.fa-icon-2x,button [class*=" fa-icon-"].pull-left.fa-icon-2x,button [class^="fa-icon-"].pull-right.fa-icon-2x,button [class*=" fa-icon-"].pull-right.fa-icon-2x{margin-top:.35em} button [class^="fa-icon-"].fa-icon-spin.icon-large,button [class*=" fa-icon-"].fa-icon-spin.icon-large{height:.75em} -button:hover,button:focus,button:active,button.active,.open .dropdown-togglebutton{color:#333;background-color:#ebebeb;border-color:#a1a1a1} +button:hover,button:focus,button:active,button.active,.open .dropdown-togglebutton{color:#333;background-color:#dedede;border-color:#a1a1a1} button:active,button.active,.open .dropdown-togglebutton{background-image:none} -button.disabled,button[disabled],fieldset[disabled] button,button.disabled:hover,button[disabled]:hover,fieldset[disabled] button:hover,button.disabled:focus,button[disabled]:focus,fieldset[disabled] button:focus,button.disabled:active,button[disabled]:active,fieldset[disabled] button:active,button.disabled.active,button[disabled].active,fieldset[disabled] button.active{background-color:#fff;border-color:#bfbfbf} -.action-button{display:inline-block;padding:4px 10px;margin-bottom:0;font-size:12px;font-weight:normal;line-height:1.428571429;text-align:center;vertical-align:middle;cursor:pointer;border:1px solid transparent;border-radius:3px;white-space:nowrap;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;color:#333;background-color:#fff;border-color:#bfbfbf}.action-button:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} +button.disabled,button[disabled],fieldset[disabled] button,button.disabled:hover,button[disabled]:hover,fieldset[disabled] button:hover,button.disabled:focus,button[disabled]:focus,fieldset[disabled] button:focus,button.disabled:active,button[disabled]:active,fieldset[disabled] button:active,button.disabled.active,button[disabled].active,fieldset[disabled] button.active{background-color:#f2f2f2;border-color:#bfbfbf} +.action-button{display:inline-block;padding:4px 10px;margin-bottom:0;font-size:12px;font-weight:normal;line-height:1.428571429;text-align:center;vertical-align:middle;cursor:pointer;border:1px solid transparent;border-radius:3px;white-space:nowrap;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none;color:#333;background-color:#f2f2f2;border-color:#bfbfbf}.action-button:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} .action-button:hover,.action-button:focus{color:#333;text-decoration:none} .action-button:active,.action-button.active{outline:0;background-image:none;-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,0.125);box-shadow:inset 0 3px 5px rgba(0,0,0,0.125)} .action-button.disabled,.action-button[disabled],fieldset[disabled] .action-button{cursor:not-allowed;pointer-events:none;opacity:.65;filter:alpha(opacity=65);-webkit-box-shadow:none;box-shadow:none} .action-button [class^="fa-icon-"],.action-button [class*=" fa-icon-"]{display:inline;line-height:.6em}.action-button [class^="fa-icon-"].fa-icon-spin,.action-button [class*=" fa-icon-"].fa-icon-spin{display:inline-block} .action-button [class^="fa-icon-"].pull-left.fa-icon-2x,.action-button [class*=" fa-icon-"].pull-left.fa-icon-2x,.action-button [class^="fa-icon-"].pull-right.fa-icon-2x,.action-button [class*=" fa-icon-"].pull-right.fa-icon-2x{margin-top:.35em} .action-button [class^="fa-icon-"].fa-icon-spin.icon-large,.action-button [class*=" fa-icon-"].fa-icon-spin.icon-large{height:.75em} -.action-button:hover,.action-button:focus,.action-button:active,.action-button.active,.open .dropdown-toggle.action-button{color:#333;background-color:#ebebeb;border-color:#a1a1a1} +.action-button:hover,.action-button:focus,.action-button:active,.action-button.active,.open .dropdown-toggle.action-button{color:#333;background-color:#dedede;border-color:#a1a1a1} .action-button:active,.action-button.active,.open .dropdown-toggle.action-button{background-image:none} -.action-button.disabled,.action-button[disabled],fieldset[disabled] .action-button,.action-button.disabled:hover,.action-button[disabled]:hover,fieldset[disabled] .action-button:hover,.action-button.disabled:focus,.action-button[disabled]:focus,fieldset[disabled] .action-button:focus,.action-button.disabled:active,.action-button[disabled]:active,fieldset[disabled] .action-button:active,.action-button.disabled.active,.action-button[disabled].active,fieldset[disabled] .action-button.active{background-color:#fff;border-color:#bfbfbf} +.action-button.disabled,.action-button[disabled],fieldset[disabled] .action-button,.action-button.disabled:hover,.action-button[disabled]:hover,fieldset[disabled] .action-button:hover,.action-button.disabled:focus,.action-button[disabled]:focus,fieldset[disabled] .action-button:focus,.action-button.disabled:active,.action-button[disabled]:active,fieldset[disabled] .action-button:active,.action-button.disabled.active,.action-button[disabled].active,fieldset[disabled] .action-button.active{background-color:#f2f2f2;border-color:#bfbfbf} a.action-button{color:#333;text-decoration:none} .action-button>img{vertical-align:middle} -.action-button:active{outline:0;background-image:none;-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,0.125);box-shadow:inset 0 3px 5px rgba(0,0,0,0.125);color:inherit} -.menubutton{padding:4px 10px;margin-bottom:0;font-size:12px;font-weight:normal;line-height:1.428571429;text-align:center;vertical-align:middle;border:1px solid transparent;border-radius:3px;white-space:nowrap;user-select:none;color:#333;background-color:#fff;border-color:#bfbfbf;display:inline-block;cursor:pointer;position:relative;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none}.menubutton:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} +.action-button:active{outline:0;background-image:none;-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,0.125);box-shadow:inset 0 3px 5px rgba(0,0,0,0.125)} +.menubutton{padding:4px 10px;margin-bottom:0;font-size:12px;font-weight:normal;line-height:1.428571429;text-align:center;vertical-align:middle;border:1px solid transparent;border-radius:3px;white-space:nowrap;user-select:none;color:#333;background-color:#f2f2f2;border-color:#bfbfbf;display:inline-block;cursor:pointer;position:relative;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;user-select:none}.menubutton:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} .menubutton:hover,.menubutton:focus{color:#333;text-decoration:none} .menubutton:active,.menubutton.active{outline:0;background-image:none;-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,0.125);box-shadow:inset 0 3px 5px rgba(0,0,0,0.125)} .menubutton.disabled,.menubutton[disabled],fieldset[disabled] .menubutton{cursor:not-allowed;pointer-events:none;opacity:.65;filter:alpha(opacity=65);-webkit-box-shadow:none;box-shadow:none} .menubutton [class^="fa-icon-"],.menubutton [class*=" fa-icon-"]{display:inline;line-height:.6em}.menubutton [class^="fa-icon-"].fa-icon-spin,.menubutton [class*=" fa-icon-"].fa-icon-spin{display:inline-block} .menubutton [class^="fa-icon-"].pull-left.fa-icon-2x,.menubutton [class*=" fa-icon-"].pull-left.fa-icon-2x,.menubutton [class^="fa-icon-"].pull-right.fa-icon-2x,.menubutton [class*=" fa-icon-"].pull-right.fa-icon-2x{margin-top:.35em} .menubutton [class^="fa-icon-"].fa-icon-spin.icon-large,.menubutton [class*=" fa-icon-"].fa-icon-spin.icon-large{height:.75em} -.menubutton:hover,.menubutton:focus,.menubutton:active,.menubutton.active,.open .dropdown-toggle.menubutton{color:#333;background-color:#ebebeb;border-color:#a1a1a1} +.menubutton:hover,.menubutton:focus,.menubutton:active,.menubutton.active,.open .dropdown-toggle.menubutton{color:#333;background-color:#dedede;border-color:#a1a1a1} .menubutton:active,.menubutton.active,.open .dropdown-toggle.menubutton{background-image:none} -.menubutton.disabled,.menubutton[disabled],fieldset[disabled] .menubutton,.menubutton.disabled:hover,.menubutton[disabled]:hover,fieldset[disabled] .menubutton:hover,.menubutton.disabled:focus,.menubutton[disabled]:focus,fieldset[disabled] .menubutton:focus,.menubutton.disabled:active,.menubutton[disabled]:active,fieldset[disabled] .menubutton:active,.menubutton.disabled.active,.menubutton[disabled].active,fieldset[disabled] .menubutton.active{background-color:#fff;border-color:#bfbfbf} -.menubutton:active{outline:0;background-image:none;-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,0.125);box-shadow:inset 0 3px 5px rgba(0,0,0,0.125);color:inherit} +.menubutton.disabled,.menubutton[disabled],fieldset[disabled] .menubutton,.menubutton.disabled:hover,.menubutton[disabled]:hover,fieldset[disabled] .menubutton:hover,.menubutton.disabled:focus,.menubutton[disabled]:focus,fieldset[disabled] .menubutton:focus,.menubutton.disabled:active,.menubutton[disabled]:active,fieldset[disabled] .menubutton:active,.menubutton.disabled.active,.menubutton[disabled].active,fieldset[disabled] .menubutton.active{background-color:#f2f2f2;border-color:#bfbfbf} +.menubutton:active{outline:0;background-image:none;-webkit-box-shadow:inset 0 3px 5px rgba(0,0,0,0.125);box-shadow:inset 0 3px 5px rgba(0,0,0,0.125)} .menubutton:focus{outline:thin dotted #333;outline:5px auto -webkit-focus-ring-color;outline-offset:-2px} .menubutton a{text-decoration:none} .menubutton .label,.menubutton>label{position:relative;display:inline-block;border-right:none;text-decoration:none;text-align:left;max-height:2.857142858;line-height:1.428571429;overflow:hidden;text-overflow:ellipsis} @@ -1406,7 +1412,7 @@ div.historyItemButtons .icon-button.edit:hover{background-image:url(sprite-history-buttons.png);background-position:0px -112px;width:16px;height:16px} div.historyItemButtons .icon-button.edit_disabled{background-image:url(sprite-history-buttons.png);background-position:0px -128px;width:16px;height:16px} div.historyItemBody div{padding-top:2px} -pre.peek{background:white;color:black;width:100%;font-size:10px;overflow:auto}pre.peek th{color:white;background:#00f} +pre.peek{background:white;color:black;width:100%;font-size:10px;overflow:auto}pre.peek th{color:white;background:#5f6990} pre.peek table,pre.peek th,pre.peek tr,pre.peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px} .toolMenuContainer{color:#000;background:#dfe5f9;min-height:100%;padding:5px 10px} div.toolSectionPad{margin:0;padding:0;height:5px;font-size:0px} diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/style/src/less/base.less --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -57,6 +57,14 @@ // ==== Panel layout styles ==== +@panel-message-height: 30px; + +@layout_top_padding: 0px; +@border-default-color_padding: 0px; + +@panel_header_height: 30px; +@panel_footer_height: 25px; + #background { position: absolute; background: #fff; @@ -74,7 +82,7 @@ top: @navbar-height + @layout_top_padding + 1; left:0; width:100%; - height: @panel_header_height !important; + height: @panel-message-height !important; overflow: hidden; border-bottom: solid #999 1px; font-size: 90%; @@ -85,18 +93,12 @@ top: @navbar-height + @layout_top_padding + 1; left:0; width:100%; - height: @panel_header_height !important; + height: @panel-message-height !important; overflow: hidden; border-bottom: solid #999 1px; font-size: 90%; } -@layout_top_padding: 0px; -@border-default-color_padding: 0px; - -@panel_header_height: 30px; -@panel_footer_height: 25px; - // Panels #left, #left-border, #center, #right-border, #right { @@ -134,6 +136,23 @@ border-left: solid @layout-border-color 1px; } +// If the message box or inactivity box is visible +body.has-message-box, body.has-inactivity-box { + #left, #left-border, #center, #right-border, #right { + top: @panel-message-height + @navbar-height + @layout_top_padding + 1; + } +} + +// If both are visible +body.has-message-box.has-inactivity-box { + #left, #left-border, #center, #right-border, #right { + top: 2 * @panel-message-height + @navbar-height + @layout_top_padding + 1; + } + #inactivebox { + top: @panel-message-height + @navbar-height + @layout_top_padding + 1; + } +} + .subnavbar { #gradient > .vertical-three-colors(@white, @white, 25%, darken(@white, 10%)); border-bottom: solid @border-default-color 1px; @@ -299,8 +318,8 @@ .panel-error-message, .panel-warning-message, .panel-done-message, .panel-info-message { - height: 24px; - line-height: 24px; + height: @panel-message-height; + line-height: @panel-message-height; padding: 0px; padding-left: 26px; background-color: @state-danger-bg; @@ -671,9 +690,14 @@ padding: 3px; } +// Always style buttons and submits as bootstrap buttons input[type="submit"], button { .btn(); .btn-default(); + // The above overrides the button variants (primary, danger, etc) because it occurs later, redefine btn-primary (bit of a hack) + &.btn-primary { + .btn-primary(); + } } .search-query { @@ -726,7 +750,7 @@ padding-left: 52px; background-image: url(error_large.png); background-repeat: no-repeat; - background-position: 10px 10px; + background-position: 10px 8px; } .errormessagelarge { diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/style/src/less/galaxy_bootstrap/overrides.less --- a/static/style/src/less/galaxy_bootstrap/overrides.less +++ b/static/style/src/less/galaxy_bootstrap/overrides.less @@ -16,10 +16,6 @@ @btn:hover(); } -.btn.active, .btn:active { - color: inherit; -} - .dropdown-menu { max-width: auto; } @@ -31,6 +27,10 @@ // Modal -- wider by default, scroll like Trello +.modal-dialog { + width: 690px; +} + /* NOTE: these styles do not currently work. diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/style/src/less/galaxy_bootstrap/variables.less --- a/static/style/src/less/galaxy_bootstrap/variables.less +++ b/static/style/src/less/galaxy_bootstrap/variables.less @@ -2,9 +2,7 @@ // Caveat: currently only works for light colored backgrounds, less provides functions (contrast) that could be used to improve this // Base color -- Based on the Galaxy masthead color - @base-color-1: #2C3143; - @base-color-2: lighten(@base-color-1,25%); @base-color-3: lighten(@base-color-1,50%); @@ -164,7 +162,7 @@ @btn-font-weight: normal; @btn-default-color: #333; -@btn-default-bg: @white; +@btn-default-bg: darken(@white,5%); @btn-default-border: @border-default-color; @btn-primary-color: @white; diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/style/src/less/theme/blue.less --- a/static/style/src/less/theme/blue.less +++ b/static/style/src/less/theme/blue.less @@ -11,9 +11,6 @@ @table-border-color: darken(@table-heading-bg,20%); @link-color: #303030; -@component-active-bg: @link-color; - -@brand-primary: blue; @input-border: #aaa; diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 static/style/src/less/upload.less --- a/static/style/src/less/upload.less +++ b/static/style/src/less/upload.less @@ -7,8 +7,8 @@ .upload-box { width : 100%; - height : 250px; - max-height : 250px; + height : 95%; + max-height : 95%; text-align : center; overflow : scroll; font-size : @font-size-base; diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako --- a/templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako +++ b/templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako @@ -60,7 +60,14 @@ </div><div class="toolForm"><div class="toolFormBody"> - <form name="select_shed_tool_panel_config" id="select_shed_tool_panel_config" action="${h.url_for( controller='admin_toolshed', action='prepare_for_install', tool_shed_url=tool_shed_url, encoded_repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, includes_tool_dependencies=includes_tool_dependencies )}" method="post" > + <form name="select_shed_tool_panel_config" id="select_shed_tool_panel_config" action="${h.url_for( controller='admin_toolshed', action='prepare_for_install' )}" method="post" > + <div class="form-row"> + <input type="hidden" name="encoded_repo_info_dicts" value="${encoded_repo_info_dicts}" /> + <input type="hidden" name="includes_tools" value="${includes_tools}" /> + <input type="hidden" name="includes_tool_dependencies" value="${includes_tool_dependencies}" /> + <input type="hidden" name="includes_tools_for_display_in_tool_panel" value="${includes_tools_for_display_in_tool_panel}" /> + <input type="hidden" name="tool_shed_url" value="${tool_shed_url}" /> + </div><div style="clear: both"></div><% readme_files_dict = containers_dict.get( 'readme_files', None ) %> %if readme_files_dict: diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 templates/admin/tool_shed_repository/select_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako @@ -60,7 +60,14 @@ </div><div class="toolForm"><div class="toolFormBody"> - <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='prepare_for_install', tool_shed_url=tool_shed_url, encoded_repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, includes_tool_dependencies=includes_tool_dependencies )}" method="post" > + <form name="select_tool_panel_section" id="select_tool_panel_section" action="${h.url_for( controller='admin_toolshed', action='prepare_for_install' )}" method="post" > + <div class="form-row"> + <input type="hidden" name="includes_tools" value="${includes_tools}" /> + <input type="hidden" name="includes_tool_dependencies" value="${includes_tool_dependencies}" /> + <input type="hidden" name="includes_tools_for_display_in_tool_panel" value="${includes_tools_for_display_in_tool_panel}" /> + <input type="hidden" name="tool_shed_url" value="${tool_shed_url}" /> + <input type="hidden" name="encoded_repo_info_dicts" value="${encoded_repo_info_dicts}" /> + </div><div style="clear: both"></div><% readme_files_dict = containers_dict.get( 'readme_files', None ) %> %if readme_files_dict: diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -29,20 +29,6 @@ right: 0 !important; %endif } -## This is some dirty hack happening - %if self.message_box_visible or self.show_inactivity_warning: - #left, #left-border, #center, #right-border, #right - { - top: 64px; - } - %endif - %if self.message_box_visible and self.show_inactivity_warning: - #left, #left-border, #center, #right-border, #right - { - top: 94px; - } - #inactivebox{top:64px;} - %endif </style></%def> @@ -261,7 +247,8 @@ <div id="top-modal-dialog" class="modal-dialog"><div class="modal-content"><div class="modal-header"> - <span><h4 class='title'>${title}</h4></span> + <button type='button' class='close' style="display: none;">×</button> + <h4 class='title'>${title}</h4></div><div class="modal-body">${content}</div><div class="modal-footer"> @@ -293,7 +280,15 @@ ${self.javascripts()} </head> - <body scroll="no" class="full-content ${self.body_class}"> + <% + body_class = self.body_class + if self.message_box_visible: + body_class += " has-message-box" + if self.show_inactivity_warning: + body_class += " has-inactivity-box" + %> + + <body scroll="no" class="full-content ${body_class}"> %if self.require_javascript: <noscript><div class="overlay overlay-background"> @@ -311,16 +306,14 @@ <div id="masthead" class="navbar navbar-fixed-top navbar-inverse"> ${self.masthead()} </div> - %if self.message_box_visible and app.config.message_box_content: <div id="messagebox" class="panel-${app.config.message_box_class}-message"> - ${app.config.message_box_content} + ${app.config.message_box_content} </div> - %endif - %if self.show_inactivity_warning: - <div id="inactivebox" class="panel-warning-message"> + %if self.show_inactivity_warning: + <div id="inactivebox" class="panel-warning-message"> ${app.config.inactivity_box_content} - </div> - %endif + </div> + %endif ${self.overlay(visible=self.overlay_visible)} %if self.has_left_panel: <div id="left"> diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 templates/webapps/galaxy/cloud/index.mako --- a/templates/webapps/galaxy/cloud/index.mako +++ b/templates/webapps/galaxy/cloud/index.mako @@ -118,37 +118,39 @@ }); } }); - $('#loading_indicator').ajaxStart(function(){ - $(this).show('fast'); + $(document).ajaxStart(function(){ + $('#loading_indicator').show('fast'); }).ajaxStop(function(){ - $(this).hide('fast'); + $('#loading_indicator').hide('fast'); }); $('form').ajaxForm({ type: 'POST', dataType: 'json', beforeSubmit: function(data, form){ - if ($('#id_password').val() != $('#id_password_confirm').val()){ - //Passwords don't match. - form.prepend('<div class="errormessage">Passwords do not match</div>'); - return false; - }else{ - //Clear errors - $('.errormessage').remove() - //Hide the form, show pending box with spinner. - $('#launchFormContainer').hide('fast'); - $('#responsePanel').show('fast'); - } - //Dig up zone info for selected cluster, set hidden input. - //This is not necessary to present to the user though the interface may prove useful. + // Dig up zone info for selected cluster, set hidden input. + // This is not necessary to present to the user though the interface may prove useful. var ei_val = _.find(data, function(f_obj){return f_obj.name === 'existing_instance'}); if( ei_val && (ei_val.value !== "New Cluster")){ var cluster = _.find(cloudlaunch_clusters, function(cluster){return cluster.name === ei_val.value}); var zdata = _.find(data, function(f_obj){return f_obj.name === 'zone'}); zdata.value = cluster.zone; + }else if($('#id_cluster_name').val() === ''){ + // If we're not using an existing cluster, this must be set. + form.prepend('<div class="errormessage">You must specify a cluster name</div>'); + return false; } + if ($('#id_password').val() != $('#id_password_confirm').val()){ + //Passwords don't match. + form.prepend('<div class="errormessage">Passwords do not match</div>'); + return false; + } + // Lastly, clear errors and flip to the response panel. + $('.errormessage').remove() + $('#launchFormContainer').hide('fast'); + $('#responsePanel').show('fast'); }, success: function(data){ - //Success Message, link to key download if required, link to server itself. + // Success Message, link to key download if required, link to server itself. $('#launchPending').hide('fast'); //Set appropriate fields (dns, key, ami) and then display. if(data.kp_material_tag){ @@ -183,7 +185,7 @@ <div class="page-container" style="padding: 10px;"><div id="loading_indicator"></div><h2>Launch a Galaxy Cloud Instance</h2> - <div id="launchFormContainer" class="toolForm"> + <div id="launchFormContainer"><form id="cloudlaunch_form" action="${h.url_for( controller='/cloudlaunch', action='launch_instance')}" method="post"><p>To launch a Galaxy Cloud Cluster, enter your AWS Secret diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 templates/webapps/galaxy/galaxy.masthead.mako --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -34,10 +34,11 @@ $('<link href="' + galaxy_config.root + 'static/style/galaxy.frame.masthead.css" rel="stylesheet">').appendTo('head'); ## load galaxy js-modules - require(['galaxy.master', 'galaxy.frame'], function(master, frame) + require(['galaxy.master', 'galaxy.frame', 'galaxy.modal'], function(master, frame, modal) { Galaxy.master = new master.GalaxyMaster(); Galaxy.frame_manager = new frame.GalaxyFrameManager(); + Galaxy.modal = new modal.GalaxyModal(); }); </script> diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 templates/webapps/galaxy/galaxy.panels.mako --- a/templates/webapps/galaxy/galaxy.panels.mako +++ b/templates/webapps/galaxy/galaxy.panels.mako @@ -152,34 +152,6 @@ </script></%def> -## overlay -<%def name="overlay( title='', content='')"> - <%def name="title()"></%def> - <%def name="content()"></%def> - <% - display = "style='display: none;'" - overlay_class = "" - %> - - <div id="top-modal" class="modal fade ${overlay_class}" ${display}> - <div id="top-modal-backdrop" class="modal-backdrop fade ${overlay_class}" style="z-index: -1"></div> - <div id="top-modal-dialog" class="modal-dialog" border="0" ${display}> - <div class="modal-content"> - <div class="modal-header"> - <span><h3 class='title'>${title}</h3></span> - </div> - <div class="modal-body">${content}</div> - <div class="modal-footer"> - <div class="buttons" style="float: right;"></div> - <div class="extra_buttons" style=""></div> - <div style="clear: both;"></div> - </div> - </div> - </div> - - </div> -</%def> - ## document <html><head> @@ -197,14 +169,6 @@ </head><body scroll="no" class="full-content"> - <noscript> - <div class="overlay overlay-background"> - <div class="modal dialog-box" border="0"> - <div class="modal-header"><h3 class="title">Javascript Required</h3></div> - <div class="modal-body">The Galaxy analysis interface requires a browser with Javascript enabled. <br> Please enable Javascript and refresh this page</div> - </div> - </div> - </noscript><div id="everything" style="position: absolute; top: 0; left: 0; width: 100%; height: 100%;"> ## background displays first <div id="background"></div> @@ -219,9 +183,6 @@ <div id="messagebox" class="panel-message"></div> %endif - ## overlay - ${self.overlay()} - ## left panel %if self.galaxy_config['left_panel']: <div id="left"> diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -276,7 +276,8 @@ else: folder_label = "%s<i> - click the name to preview the tool and use the pop-up menu to inspect all metadata</i>" % folder_label elif folder.invalid_tools: - folder_label = "%s<i> - click the tool config file name to see why the tool is invalid</i>" % folder_label + if trans.webapp.name == 'tool_shed': + folder_label = "%s<i> - click the tool config file name to see why the tool is invalid</i>" % folder_label elif folder.tool_dependencies: if folder.description: folder_label = "%s<i> - %s</i>" % ( folder_label, folder.description ) diff -r 8f0476edc6a2bf1fd217ad3d9b7ff0b8d39b951f -r 47f3bec46ced8ee624da7431b79e7d95874c28e2 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -134,6 +134,25 @@ </toolbox> ''' + +job_conf_xml = '''<?xml version="1.0"?> + +<job_conf> + <plugins> + <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/> + </plugins> + <handlers> + <handler id="main"/> + </handlers> + <destinations> + <destination id="local" runner="local"/> + </destinations> + <limits> + <limit type="walltime">00:10:00</limit> + </limits> +</job_conf> +''' + # If we have a tool_data_table_conf.test.xml, set it up to be loaded when the UniverseApplication is started. # This allows one to specify a set of tool data that is used exclusively for testing, and not loaded into any # Galaxy instance. By default, this will be in the test-data-repo/location directory generated by buildbot_setup.sh. @@ -588,6 +607,7 @@ shed_tool_data_table_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_DATA_TABLE_CONF', os.path.join( galaxy_test_tmp_dir, 'test_shed_tool_data_table_conf.xml' ) ) galaxy_tool_data_table_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_DATA_TABLE_CONF', tool_data_table_conf ) galaxy_tool_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_CONF', os.path.join( galaxy_test_tmp_dir, 'test_tool_conf.xml' ) ) + galaxy_job_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_JOB_CONF', os.path.join( galaxy_test_tmp_dir, 'test_job_conf.xml' ) ) galaxy_shed_tool_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_SHED_TOOL_CONF', os.path.join( galaxy_test_tmp_dir, 'test_shed_tool_conf.xml' ) ) galaxy_migrated_tool_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_MIGRATED_TOOL_CONF', os.path.join( galaxy_test_tmp_dir, 'test_migrated_tool_conf.xml' ) ) galaxy_tool_sheds_conf_file = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF', os.path.join( galaxy_test_tmp_dir, 'test_tool_sheds_conf.xml' ) ) @@ -635,6 +655,8 @@ # ---- Start up a Galaxy instance ------------------------------------------------------ # Generate the tool_conf.xml file. file( galaxy_tool_conf_file, 'w' ).write( tool_conf_xml ) + # Generate the job_conf.xml file. + file( galaxy_job_conf_file, 'w' ).write( job_conf_xml ) # Generate the tool_sheds_conf.xml file, but only if a the user has not specified an existing one in the environment. if 'GALAXY_INSTALL_TEST_TOOL_SHEDS_CONF' not in os.environ: file( galaxy_tool_sheds_conf_file, 'w' ).write( tool_sheds_conf_xml ) @@ -656,6 +678,7 @@ datatype_converters_config_file = "datatype_converters_conf.xml.sample", file_path = galaxy_file_path, id_secret = galaxy_encode_secret, + job_config_file = galaxy_job_conf_file, job_queue_workers = 5, log_destination = "stdout", migrated_tools_config = galaxy_migrated_tool_conf_file, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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galaxy-commits October 2013