galaxy-commits January 2012

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commit/galaxy-central: 2 new changesets
by Bitbucket 23 Jan '12

23 Jan '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/324d442b8fb0/ changeset: 324d442b8fb0 branch: sam_merge_patch user: natefoo date: 2012-01-23 20:22:50 summary: Closed branch sam_merge_patch affected #: 0 files https://bitbucket.org/galaxy/galaxy-central/changeset/d61fdfdce8bc/ changeset: d61fdfdce8bc user: natefoo date: 2012-01-23 20:23:22 summary: Merge closed branch affected #: 0 files 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: natefoo: Add tool_dependency_dir to the sample config.
by Bitbucket 23 Jan '12

23 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2e8f52ffe75d/ changeset: 2e8f52ffe75d user: natefoo date: 2012-01-23 18:29:00 summary: Add tool_dependency_dir to the sample config. affected #: 1 file diff -r 542cc69a44865797deb688a6b29c7aac603f6da2 -r 2e8f52ffe75ddf6e1009789745aabffa90edaac9 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -131,6 +131,11 @@ # Other tool config files must include the tool_path as an attribute in the <toolbox> tag. #tool_path = tools +# Path to the directory in which managed tool dependencies are placed. To use +# the dependency system, see the documentation at: +# http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies +#tool_dependency_dir = None + # Enable automatic installation of tools that used to be in the Galaxy # distribution but are now in the main Galaxy tool shed. The tools # that will be installed are configured in the config file named 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: dan: GATK Updates.
by Bitbucket 23 Jan '12

23 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/542cc69a4486/ changeset: 542cc69a4486 user: dan date: 2012-01-23 17:37:49 summary: GATK Updates. affected #: 7 files diff -r 84ee6eeedb41b507c5e79d6f3e0d2a50a694adb6 -r 542cc69a44865797deb688a6b29c7aac603f6da2 test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf --- a/test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf +++ b/test-data/gatk/gatk_unified_genotyper/gatk_unified_genotyper_out_1.vcf @@ -1,6 +1,6 @@ ##fileformat=VCFv4.1 ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> -##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> @@ -9,7 +9,7 @@ ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership"> -##INFO=<ID=DP,Number=1,Type=Integer,Description="Filtered Depth"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> ##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions"> ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> @@ -25,4 +25,4 @@ ##contig=<ID=phiX174,length=5386> ##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample -phiX174 1443 . AC . 0 . DP=10;MQ=37.74;MQ0=0;QD=0.00 GT:DP:PL ./.:10:0,0,0 +phiX174 1443 . AC . 0 . DB;DP=10;MQ=37.74;MQ0=0 GT ./. diff -r 84ee6eeedb41b507c5e79d6f3e0d2a50a694adb6 -r 542cc69a44865797deb688a6b29c7aac603f6da2 test-data/gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf --- a/test-data/gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf +++ b/test-data/gatk/gatk_variant_annotator/gatk_variant_annotator_out_1.vcf @@ -1,6 +1,6 @@ ##fileformat=VCFv4.1 ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> -##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> @@ -10,7 +10,7 @@ ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership"> -##INFO=<ID=DP,Number=1,Type=Integer,Description="Filtered Depth"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> ##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions"> ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> @@ -28,4 +28,4 @@ ##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta ##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample -phiX174 1443 . AC . 0 . DP=10;MQ=37.74;MQ0=0;QD=0.00 GT:DP:PL ./.:10:0,0,0 +phiX174 1443 . AC . 0 . DB;DP=10;MQ=37.74;MQ0=0 GT ./. diff -r 84ee6eeedb41b507c5e79d6f3e0d2a50a694adb6 -r 542cc69a44865797deb688a6b29c7aac603f6da2 test-data/gatk/gatk_variant_combine/gatk_variant_combine_out_1.vcf --- a/test-data/gatk/gatk_variant_combine/gatk_variant_combine_out_1.vcf +++ b/test-data/gatk/gatk_variant_combine/gatk_variant_combine_out_1.vcf @@ -1,7 +1,7 @@ ##fileformat=VCFv4.1 ##CombineVariants="analysis_type=CombineVariants input_file=[] sample_metadata=[] read_buffer_size=null phone_home=NO_ET read_filter=[] intervals=null excludeIntervals=null reference_sequence=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-bFIpbp/gatk_input.fasta rodBind=[] rodToIntervalTrackName=null BTI_merge_rule=UNION nonDeterministicRandomSeed=false downsampling_type=null downsample_to_fraction=null downsample_to_coverage=null baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=1 interval_merging=ALL read_group_black_list=null processingTracker=null restartProcessingTracker=false processingTrackerStatusFile=null processingTrackerID=-1 allow_intervals_with_unindexed_bam=false disable_experimental_low_memory_sharding=false logging_level=INFO log_to_file=null help=false variant=[(RodBinding name=from_variant_annotator source=/var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-bFIpbp/input_variant_from_variant_annotator.vcf)] out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED rod_priority_list=from_variant_annotator printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 mergeInfoWithMaxAC=false" ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> -##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> @@ -11,7 +11,7 @@ ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership"> -##INFO=<ID=DP,Number=1,Type=Integer,Description="Filtered Depth"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> ##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions"> ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> @@ -30,4 +30,4 @@ ##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta ##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-bFIpbp/gatk_input.fasta #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample -phiX174 1443 . AC . . PASS AC=0;AF=0.00;AN=0;DP=10;MQ=37.74;MQ0=0;QD=0.00;set=ReferenceInAll GT:DP:PL ./.:10:0,0,0 +phiX174 1443 . AC . . PASS AC=0;AF=0.00;AN=0;DB;DP=10;MQ=37.74;MQ0=0;set=ReferenceInAll GT ./. diff -r 84ee6eeedb41b507c5e79d6f3e0d2a50a694adb6 -r 542cc69a44865797deb688a6b29c7aac603f6da2 test-data/gatk/gatk_variant_eval/gatk_variant_eval_out_1.tabular --- a/test-data/gatk/gatk_variant_eval/gatk_variant_eval_out_1.tabular +++ b/test-data/gatk/gatk_variant_eval/gatk_variant_eval_out_1.tabular @@ -1,36 +1,30 @@ ##:GATKReport.v0.2 CompOverlap : The overlap between eval and comp sites -CompOverlap CompRod EvalRod JexlExpression Novelty nEvalVariants novelSites nVariantsAtComp compRate nConcordant concordantRate -CompOverlap dbsnp input_0 none all 0 0 0 0.00000000 0 0.00000000 -CompOverlap dbsnp input_0 none known 0 0 0 0.00000000 0 0.00000000 -CompOverlap dbsnp input_0 none novel 0 0 0 0.00000000 0 0.00000000 +CompOverlap CompRod EvalRod JexlExpression Novelty nEvalVariants novelSites nVariantsAtComp compRate nConcordant concordantRate +CompOverlap dbsnp input_0 none all 0 0 0 0.00 0 0.00 +CompOverlap dbsnp input_0 none known 0 0 0 0.00 0 0.00 +CompOverlap dbsnp input_0 none novel 0 0 0 0.00 0 0.00 ##:GATKReport.v0.2 CountVariants : Counts different classes of variants in the sample -CountVariants CompRod EvalRod JexlExpression Novelty nProcessedLoci nCalledLoci nRefLoci nVariantLoci variantRate variantRatePerBp nSNPs nMNPs nInsertions nDeletions nComplex nMixed nNoCalls nHets nHomRef nHomVar nSingletons nHomDerived heterozygosity heterozygosityPerBp hetHomRatio indelRate indelRatePerBp deletionInsertionRatio -CountVariants dbsnp input_0 none all 5386 1 1 0 0.00000000 0.00000000 0 0 0 0 0 0 1 0 0 0 0 0 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -CountVariants dbsnp input_0 none known 5386 1 1 0 0.00000000 0.00000000 0 0 0 0 0 0 1 0 0 0 0 0 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -CountVariants dbsnp input_0 none novel 5386 0 0 0 0.00000000 0.00000000 0 0 0 0 0 0 0 0 0 0 0 0 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 - -##:GATKReport.v0.2 SimpleMetricsByAC.metrics : TiTv by allele count -SimpleMetricsByAC.metrics CompRod EvalRod JexlExpression Novelty row AC nTi nTv n TiTv -SimpleMetricsByAC.metrics dbsnp input_0 none all ac0 0 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp input_0 none all ac1 1 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp input_0 none all ac2 2 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp input_0 none known ac0 0 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp input_0 none known ac1 1 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp input_0 none known ac2 2 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp input_0 none novel ac0 0 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp input_0 none novel ac1 1 0 0 0 0.0 -SimpleMetricsByAC.metrics dbsnp input_0 none novel ac2 2 0 0 0 0.0 +CountVariants CompRod EvalRod JexlExpression Novelty nProcessedLoci nCalledLoci nRefLoci nVariantLoci variantRate variantRatePerBp nSNPs nMNPs nInsertions nDeletions nComplex nSymbolic nMixed nNoCalls nHets nHomRef nHomVar nSingletons nHomDerived heterozygosity heterozygosityPerBp hetHomRatio indelRate indelRatePerBp deletionInsertionRatio +CountVariants dbsnp input_0 none all 5386 1 1 0 0.00000000 0.00000000 0 0 0 0 0 0 0 1 0 0 0 0 0 0.00e+00 0.00 0.00 0.00e+00 0.00 0.00 +CountVariants dbsnp input_0 none known 5386 1 1 0 0.00000000 0.00000000 0 0 0 0 0 0 0 1 0 0 0 0 0 0.00e+00 0.00 0.00 0.00e+00 0.00 0.00 +CountVariants dbsnp input_0 none novel 5386 0 0 0 0.00000000 0.00000000 0 0 0 0 0 0 0 0 0 0 0 0 0 0.00e+00 0.00 0.00 0.00e+00 0.00 0.00 ##:GATKReport.v0.2 TiTvVariantEvaluator : Ti/Tv Variant Evaluator -TiTvVariantEvaluator CompRod EvalRod JexlExpression Novelty nTi nTv tiTvRatio nTiInComp nTvInComp TiTvRatioStandard nTiDerived nTvDerived tiTvDerivedRatio -TiTvVariantEvaluator dbsnp input_0 none all 0 0 0.00000000 0 0 0.00000000 0 0 0.00000000 -TiTvVariantEvaluator dbsnp input_0 none known 0 0 0.00000000 0 0 0.00000000 0 0 0.00000000 -TiTvVariantEvaluator dbsnp input_0 none novel 0 0 0.00000000 0 0 0.00000000 0 0 0.00000000 +TiTvVariantEvaluator CompRod EvalRod JexlExpression Novelty nTi nTv tiTvRatio nTiInComp nTvInComp TiTvRatioStandard nTiDerived nTvDerived tiTvDerivedRatio +TiTvVariantEvaluator dbsnp input_0 none all 0 0 0.00 0 0 0.00 0 0 0.00 +TiTvVariantEvaluator dbsnp input_0 none known 0 0 0.00 0 0 0.00 0 0 0.00 +TiTvVariantEvaluator dbsnp input_0 none novel 0 0 0.00 0 0 0.00 0 0 0.00 ##:GATKReport.v0.2 ValidationReport : Assess site accuracy and sensitivity of callset against follow-up validation assay -ValidationReport CompRod EvalRod JexlExpression Novelty nComp TP FP FN TN sensitivity specificity PPV FDR CompMonoEvalNoCall CompMonoEvalFiltered CompMonoEvalMono CompMonoEvalPoly CompPolyEvalNoCall CompPolyEvalFiltered CompPolyEvalMono CompPolyEvalPoly CompFiltered nDifferentAlleleSites -ValidationReport dbsnp input_0 none all 43 0 0 0 43 NaN 100.00000000 NaN NaN 42 0 1 0 0 0 0 0 0 0 -ValidationReport dbsnp input_0 none known 1 0 0 0 1 NaN 100.00000000 NaN NaN 0 0 1 0 0 0 0 0 0 0 -ValidationReport dbsnp input_0 none novel 42 0 0 0 42 NaN 100.00000000 NaN NaN 42 0 0 0 0 0 0 0 0 0 +ValidationReport CompRod EvalRod JexlExpression Novelty nComp TP FP FN TN sensitivity specificity PPV FDR CompMonoEvalNoCall CompMonoEvalFiltered CompMonoEvalMono CompMonoEvalPoly CompPolyEvalNoCall CompPolyEvalFiltered CompPolyEvalMono CompPolyEvalPoly CompFiltered nDifferentAlleleSites +ValidationReport dbsnp input_0 none all 43 0 0 0 43 NaN 100.00 NaN NaN 42 0 1 0 0 0 0 0 0 0 +ValidationReport dbsnp input_0 none known 1 0 0 0 1 NaN 100.00 NaN NaN 0 0 1 0 0 0 0 0 0 0 +ValidationReport dbsnp input_0 none novel 42 0 0 0 42 NaN 100.00 NaN NaN 42 0 0 0 0 0 0 0 0 0 +##:GATKReport.v0.2 VariantSummary : 1000 Genomes Phase I summary of variants table +VariantSummary CompRod EvalRod JexlExpression Novelty nSamples nProcessedLoci nSNPs TiTvRatio SNPNoveltyRate nSNPsPerSample TiTvRatioPerSample SNPDPPerSample nIndels IndelNoveltyRate nIndelsPerSample IndelDPPerSample nSVs SVNoveltyRate nSVsPerSample +VariantSummary dbsnp input_0 none all 1 5386 0 0.00 NA 0 0.00 0.0 0 NA 0 0.0 0 NA 0 +VariantSummary dbsnp input_0 none known 1 5386 0 0.00 NA 0 0.00 0.0 0 NA 0 0.0 0 NA 0 +VariantSummary dbsnp input_0 none novel 1 5386 0 0.00 NA 0 0.00 0.0 0 NA 0 0.0 0 NA 0 + diff -r 84ee6eeedb41b507c5e79d6f3e0d2a50a694adb6 -r 542cc69a44865797deb688a6b29c7aac603f6da2 test-data/gatk/gatk_variant_select/gatk_variant_select_out_1.vcf --- a/test-data/gatk/gatk_variant_select/gatk_variant_select_out_1.vcf +++ b/test-data/gatk/gatk_variant_select/gatk_variant_select_out_1.vcf @@ -1,6 +1,6 @@ ##fileformat=VCFv4.1 ##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed"> -##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth (only filtered reads used for calling)"> +##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)"> ##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality"> ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"> @@ -10,7 +10,7 @@ ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> ##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities"> ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership"> -##INFO=<ID=DP,Number=1,Type=Integer,Description="Filtered Depth"> +##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered"> ##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?"> ##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions"> ##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias"> @@ -27,5 +27,6 @@ ##contig=<ID=phiX174,length=5386> ##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-aSMuO5/gatk_input.fasta ##reference=file:///var/folders/78/786YaG3QH58XnzrWynoDBk+++TI/-Tmp-/tmp-gatk-gaJtgB/gatk_input.fasta +##source=SelectVariants #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A Fake phiX Sample -phiX174 1443 . AC . 0 . AC=0;AF=0.00;AN=0;DP=0;MQ=37.74;MQ0=0;QD=0.00 GT:DP:PL ./.:10:0,0,0 +phiX174 1443 . AC . 0 . AC=0;AF=0.00;AN=0;DB;DP=0;MQ=37.74;MQ0=0 GT ./. diff -r 84ee6eeedb41b507c5e79d6f3e0d2a50a694adb6 -r 542cc69a44865797deb688a6b29c7aac603f6da2 tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -25,13 +25,13 @@ #if str( $annotations_type.annotations_type_selector ) == "use_all_annotations": --useAllAnnotations #else: - #if str( $annotations_type.annotations ) != "None": + #if $annotations_type.annotations: #for $annotation in str( $annotations_type.annotations.fields.gatk_value ).split( ',' ): --annotation "${annotation}" #end for #end if #end if - #if str( $exclude_annotations ) != "None": + #if $exclude_annotations: #for $annotation in str( $exclude_annotations.fields.gatk_value ).split( ',' ): --excludeAnnotation "${annotation}" #end for @@ -383,6 +383,7 @@ <param name="input_variant_bti" /><param name="annotations_type_selector" value="choose" /><param name="annotations" value="AlleleBalance,BaseQualityRankSumTest,DepthOfCoverage,HomopolymerRun,MappingQualityRankSumTest,MappingQualityZero,QualByDepth,RMSMappingQuality,SpanningDeletions,HaplotypeScore" /> + <param name="additional_annotations" value="0" /><param name="dbsnp_rod_bind_type_selector" value="set_dbsnp" /><param name="dbsnp_input_rod" value="gatk/fake_phiX_variant_locations.vcf" ftype="vcf" /><param name="snpEff_rod_bind_type_selector" value="exclude_snpEff" /> diff -r 84ee6eeedb41b507c5e79d6f3e0d2a50a694adb6 -r 542cc69a44865797deb688a6b29c7aac603f6da2 tools/gatk/variants_validate.xml --- a/tools/gatk/variants_validate.xml +++ b/tools/gatk/variants_validate.xml @@ -12,7 +12,7 @@ -T "ValidateVariants" -et "NO_ET" ##ET no phone home - --num_threads 4 ##hard coded, for now + ##--num_threads 4 ##hard coded, for now ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: natefoo: Ignore DrmCommunicationException when checking job state. Thanks Ed Kirton.
by Bitbucket 23 Jan '12

23 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/84ee6eeedb41/ changeset: 84ee6eeedb41 user: natefoo date: 2012-01-23 17:04:04 summary: Ignore DrmCommunicationException when checking job state. Thanks Ed Kirton. affected #: 1 file diff -r d56513828dc6f7c23b0e5b85f5ac33ce212587b7 -r 84ee6eeedb41b507c5e79d6f3e0d2a50a694adb6 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -278,6 +278,9 @@ log.debug("(%s/%s) job left DRM queue with following message: %s" % ( galaxy_job_id, job_id, e ) ) self.work_queue.put( ( 'finish', drm_job_state ) ) continue + except drmaa.DrmCommunicationException, e: + log.warning("(%s/%s) unable to communicate with DRM: %s" % ( galaxy_job_id, job_id, e )) + continue except Exception, e: # so we don't kill the monitor thread log.exception("(%s/%s) Unable to check job status" % ( galaxy_job_id, job_id ) ) 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: greg: Fix for loading tools from tool config(s).
by Bitbucket 23 Jan '12

23 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/d56513828dc6/ changeset: d56513828dc6 user: greg date: 2012-01-23 15:44:22 summary: Fix for loading tools from tool config(s). affected #: 1 file diff -r 73bae197e5fe3a420cd90326d80c7a2173e619a8 -r d56513828dc6f7c23b0e5b85f5ac33ce212587b7 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -107,10 +107,11 @@ self.load_section_tag_set( elem, self.tool_panel, tool_path ) elif elem.tag == 'label': self.load_label_tag_set( elem, self.tool_panel ) - shed_tool_conf_dict = dict( config_filename=config_filename, - tool_path=tool_path, - config_elems=config_elems ) - self.shed_tool_confs.append( shed_tool_conf_dict ) + if parsing_shed_tool_conf: + shed_tool_conf_dict = dict( config_filename=config_filename, + tool_path=tool_path, + config_elems=config_elems ) + self.shed_tool_confs.append( shed_tool_conf_dict ) def get_tool( self, tool_id, tool_version=None ): # Attempt to locate the tool in our in-memory dictionary. if tool_id in self.tools_by_id: 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.

1 0

commit/galaxy-central: jgoecks: Do not find valid chroms because this is computationally expensive and not currently used.
by Bitbucket 22 Jan '12

22 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/73bae197e5fe/ changeset: 73bae197e5fe user: jgoecks date: 2012-01-23 01:48:05 summary: Do not find valid chroms because this is computationally expensive and not currently used. affected #: 1 file diff -r 9b7a615b39648a2911c483f8d3b693931ca5c1b4 -r 73bae197e5fe3a420cd90326d80c7a2173e619a8 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -535,6 +535,8 @@ if msg: return msg + # NOTE: finding valid chroms is prohibitive for large summary trees and is not currently used by + # the client. valid_chroms = None # Check for data in the genome window. if data_sources.get( 'index' ): @@ -543,15 +545,14 @@ indexer = get_data_provider( tracks_dataset_type )( converted_dataset, dataset ) if not indexer.has_data( chrom ): return messages.NO_DATA - valid_chroms = indexer.valid_chroms() + #valid_chroms = indexer.valid_chroms() else: # Standalone data provider standalone_provider = get_data_provider( data_sources['data_standalone']['name'] )( dataset ) kwargs = {"stats": True} if not standalone_provider.has_data( chrom ): return messages.NO_DATA - valid_chroms = standalone_provider.valid_chroms() - + #valid_chroms = standalone_provider.valid_chroms() # Have data if we get here return { "status": messages.DATA, "valid_chroms": valid_chroms } 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.

1 0

commit/galaxy-central: jgoecks: Trackster: fix bugs in summary tree display & pack script.
by Bitbucket 22 Jan '12

22 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9b7a615b3964/ changeset: 9b7a615b3964 user: jgoecks date: 2012-01-22 22:21:59 summary: Trackster: fix bugs in summary tree display & pack script. affected #: 2 files diff -r 34db794299d3b79e1c9a92fff65e6222c70f4031 -r 9b7a615b39648a2911c483f8d3b693931ca5c1b4 static/scripts/packed/trackster.js --- a/static/scripts/packed/trackster.js +++ b/static/scripts/packed/trackster.js @@ -1,1 +1,1 @@ -var class_module=function(b,a){var c=function(){var f=arguments[0];for(var e=1;e<arguments.length;e++){var d=arguments[e];for(key in d){f[key]=d[key]}}return f};a.extend=c};var requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(var j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tipsy({gravity:"s"}).click(a)};var trackster_module=function(e,X){var p=e("class").extend,s=e("slotting"),L=e("painters");var ae=function(af,ag){this.document=af;this.default_font=ag!==undefined?ag:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};p(ae.prototype,{load_pattern:function(af,aj){var ag=this.patterns,ah=this.dummy_context,ai=new Image();ai.src=image_path+aj;ai.onload=function(){ag[af]=ah.createPattern(ai,"repeat")}},get_pattern:function(af){return this.patterns[af]},new_canvas:function(){var af=this.document.createElement("canvas");if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(af)}af.manager=this;return af}});var n={};var l=function(af,ag){n[af.attr("id")]=ag};var m=function(af,ah,aj,ai){aj=".group";var ag={};n[af.attr("id")]=ai;af.bind("drag",{handle:"."+ah,relative:true},function(ar,at){var aq=$(this);var aw=$(this).parent(),an=aw.children(),ap=n[$(this).attr("id")],am,al,au,ak,ao;al=$(this).parents(aj);if(al.length!==0){au=al.position().top;ak=au+al.outerHeight();if(at.offsetY<au){$(this).insertBefore(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable_before(ap,av);return}else{if(at.offsetY>ak){$(this).insertAfter(al);var av=n[al.attr("id")];av.remove_drawable(ap);av.container.add_drawable(ap);return}}}al=null;for(ao=0;ao<an.length;ao++){am=$(an.get(ao));au=am.position().top;ak=au+am.outerHeight();if(am.is(aj)&&this!==am.get(0)&&at.offsetY>=au&&at.offsetY<=ak){if(at.offsetY-au<ak-at.offsetY){am.find(".content-div").prepend(this)}else{am.find(".content-div").append(this)}if(ap.container){ap.container.remove_drawable(ap)}n[am.attr("id")].add_drawable(ap);return}}for(ao=0;ao<an.length;ao++){if(at.offsetY<$(an.get(ao)).position().top){break}}if(ao===an.length){if(this!==an.get(ao-1)){aw.append(this);n[aw.attr("id")].move_drawable(ap,ao)}}else{if(this!==an.get(ao)){$(this).insertBefore(an.get(ao));n[aw.attr("id")].move_drawable(ap,(at.deltaY>0?ao-1:ao))}}}).bind("dragstart",function(){ag["border-top"]=af.css("border-top");ag["border-bottom"]=af.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ag)})};X.moveable=m;var ad=16,F=9,C=20,T=F+2,y=100,I=12000,Q=200,A=5,u=10,K=5000,v=100,o="There was an error in indexing this dataset. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",D="No data for this chrom/contig.",t="Currently indexing... please wait",w="Tool cannot be rerun: ",a="Loading data...",Y="Ready for display",R=10,H=20;function Z(ag,af){if(!af){af=0}var ah=Math.pow(10,af);return Math.round(ag*ah)/ah}var c=function(af){this.num_elements=af;this.clear()};p(c.prototype,{get:function(ag){var af=this.key_ary.indexOf(ag);if(af!==-1){if(this.obj_cache[ag].stale){this.key_ary.splice(af,1);delete this.obj_cache[ag]}else{this.move_key_to_end(ag,af)}}return this.obj_cache[ag]},set:function(ag,ah){if(!this.obj_cache[ag]){if(this.key_ary.length>=this.num_elements){var af=this.key_ary.shift();delete this.obj_cache[af]}this.key_ary.push(ag)}this.obj_cache[ag]=ah;return ah},move_key_to_end:function(ag,af){this.key_ary.splice(af,1);this.key_ary.push(ag)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var S=function(ag,af,ah){c.call(this,ag);this.track=af;this.subset=(ah!==undefined?ah:true)};p(S.prototype,c.prototype,{load_data:function(ao,aj,am,ag,al){var an=this.track.view.chrom,ai={chrom:an,low:ao,high:aj,mode:am,resolution:ag,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ai,al);if(this.track.filters_manager){var ap=[];var af=this.track.filters_manager.filters;for(var ak=0;ak<af.length;ak++){ap[ap.length]=af[ak].name}ai.filter_cols=JSON.stringify(ap)}var ah=this;return $.getJSON(this.track.data_url,ai,function(aq){ah.set_data(ao,aj,aq)})},get_data:function(af,aj,ak,ag,ai){var ah=this.get(af,aj);if(ah&&(is_deferred(ah)||this.track.data_and_mode_compatible(ah,ak))){return ah}ah=this.load_data(af,aj,ak,ag,ai);this.set_data(af,aj,ah);return ah},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(an,ai,am,ah,al,aj){var ao=this.get(an,ai);if(!(ao&&this.track.data_and_mode_compatible(ao,am))){console.log("ERROR: no current data for: ",this.track,an,ai,am,ah,al);return}ao.stale=true;var ag=an;if(aj===this.DEEP_DATA_REQ){$.extend(al,{start_val:ao.data.length+1})}else{if(aj===this.BROAD_DATA_REQ){ag=(ao.max_high?ao.max_high:ao.data[ao.data.length-1][2])+1}}var af=this,ak=this.load_data(ag,ai,am,ah,al);new_data_available=$.Deferred();this.set_data(an,ai,new_data_available);$.when(ak).then(function(ap){if(ap.data){ap.data=ao.data.concat(ap.data);if(ap.max_low){ap.max_low=ao.max_low}if(ap.message){ap.message=ap.message.replace(/[0-9]+/,ap.data.length)}}af.set_data(an,ai,ap);new_data_available.resolve(ap)});return new_data_available},get:function(af,ag){return c.prototype.get.call(this,this.gen_key(af,ag))},set_data:function(ag,ah,af){return this.set(this.gen_key(ag,ah),af)},gen_key:function(af,ah){var ag=af+"_"+ah;return ag},split_key:function(af){return af.split("_")}});var G=function(ag,af,ah){S.call(this,ag,af,ah)};p(G.prototype,S.prototype,c.prototype,{get:S.prototype.get,load_data:function(af,ai,aj,ag,ah){if(ag>1){return{data:null}}return S.prototype.load_data.call(this,af,ai,aj,ag,ah)}});var q=function(ai,ag,af,ah,ak){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=ai;this.view=ag;this.container=af;this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ai}],saved_values:ah,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=ak;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(al){al.stopPropagation()});var aj=this;this.container_div.hover(function(){aj.icons_div.show()},function(){aj.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(af){if(af.content_visible){af.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");af.hide_contents();af.content_visible=false}else{af.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");af.content_visible=true;af.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ag){var ai=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},af=function(){ag.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ah=function(aj){if((aj.keyCode||aj.which)===27){ai()}else{if((aj.keyCode||aj.which)===13){af()}}};$(window).bind("keypress.check_enter_esc",ah);show_modal("Configure",ag.config.build_form(),{Cancel:ai,OK:af})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(af){$(".tipsy").remove();af.remove()}}];p(q.prototype,{init:function(){},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},from_dict:function(af){},update_icons:function(){},set_name:function(af){this.old_name=this.name;this.name=af;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.hide(0,function(){$(this).remove();view.update_intro_div();view.has_changes=true})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ag,ak,aj,ai,af){var ah=this;this.action_icons[ag]=$("<a/>").attr("href","javascript:void(0);").attr("title",ak).addClass("icon-button").addClass(aj).tipsy({gravity:"s"}).click(function(){ai(ah)}).appendTo(this.icons_div)},build_action_icons:function(af){var ah;for(var ag=0;ag<af.length;ag++){ah=af[ag];this.add_action_icon(ah.name,ah.title,ah.css_class,ah.on_click_fn,ah.prepend)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var x=function(aj,ai,ag,af,ah,ak){q.call(this,ai,ag,af,ah,ak);this.obj_type=aj;this.drawables=[]};p(x.prototype,q.prototype,{init:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af].init()}},_draw:function(){for(var af=0;af<this.drawables.length;af++){this.drawables[af]._draw()}},to_dict:function(){var ag=[];for(var af=0;af<this.drawables.length;af++){ag.push(this.drawables[af].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ag}},from_dict:function(al,af){var ak=new this.constructor(al.name,view,af,al.prefs,view.viewport_container,view);var ag,aj,ai;for(var ah=0;ah<al.drawables.length;ah++){ag=al.drawables[ah];aj=ag.obj_type;if(!aj){aj=ag.track_type}ai=addable_objects[aj].prototype.from_dict(ag,ak);ak.add_drawable(ai)}return ak},add_drawable:function(af){this.drawables.push(af);af.container=this},add_drawable_before:function(ah,af){var ag=this.drawables.indexOf(af);if(ag!=-1){this.drawables.splice(ag,0,ah);return true}return false},replace_drawable:function(ah,af,ag){var ai=this.drawables.indexOf(ah);if(ai!==-1){this.drawables[ai]=af;if(ag){ah.container_div.replaceWith(af.container_div)}}return ai},remove_drawable:function(ag){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);ag.container=null;return true}return false},move_drawable:function(ag,ah){var af=this.drawables.indexOf(ag);if(af!=-1){this.drawables.splice(af,1);this.drawables.splice(ah,0,ag);return true}return false}});var P=function(ai,ag,af,ah){x.call(this,"DrawableGroup",ai,ag,af,ah,"group-handle");this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this)};p(P.prototype,q.prototype,x.prototype,{action_icons_def:[{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(af){af.show_composite_track()}}].concat(q.prototype.action_icons_def),build_container_div:function(){var af=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(af)}return af},build_header_div:function(){var af=$("<div/>").addClass("track-header");af.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(af);return af},hide_contents:function(){this.content_div.hide()},show_contents:function(){this.content_div.show();this.request_draw()},update_icons:function(){var ah,aj=true,ai=this.drawables[0].get_type(),af=0;for(var ag=0;ag<this.drawables.length;ag++){ah=this.drawables[ag];if(ah.get_type()!==ai){can_composite=false;break}if(ah instanceof d){af++}}if(aj||af===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}},show_composite_track:function(){var af=new h("Composite Track",this.view,this,this.drawables);this.add_drawable(af);af.request_draw()},add_drawable:function(af){x.prototype.add_drawable.call(this,af);this.update_icons()},remove_drawable:function(af){x.prototype.remove_drawable.call(this,af);this.update_icons()},from_dict:function(ai,af){var ah=x.prototype.from_dict.call(this,ai,af);for(var ag=0;ag<ah.drawables.length;ag++){ah.content_div.append(ah.drawables[ag].container_div)}return ah}});var ac=function(af,ai,ah,ag){x.call(this,"View");this.container=af;this.chrom=null;this.vis_id=ah;this.dbkey=ag;this.title=ai;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.init();this.canvas_manager=new ae(af.get(0).ownerDocument);this.reset()};p(ac.prototype,x.prototype,{init:function(){var ah=this.container,af=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ah);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ah);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ah);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,af);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ai=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("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").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ag=function(aj){if(aj.type==="focusout"||(aj.keyCode||aj.which)===13||(aj.keyCode||aj.which)===27){if((aj.keyCode||aj.which)!==27){af.go_to($(this).val())}$(this).hide();$(this).val("");af.location_span.show();af.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ag).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){af.location_span.hide();af.chrom_select.hide();af.nav_input.val(af.chrom+":"+af.low+"-"+af.high);af.nav_input.css("display","inline-block");af.nav_input.select();af.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){af.zoom_out();af.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){af.zoom_in();af.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){af.change_chrom(af.chrom_select.val())});this.browser_content_div.click(function(aj){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(aj){af.zoom_in(aj.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(aj,ak){this.current_x=ak.offsetX}).bind("drag",function(aj,al){var am=al.offsetX-this.current_x;this.current_x=al.offsetX;var ak=Math.round(am/af.viewport_container.width()*(af.max_high-af.max_low));af.move_delta(-ak)});this.overview_close.click(function(){af.reset_overview()});this.viewport_container.bind("draginit",function(aj,ak){if(aj.clientX>af.viewport_container.width()-16){return false}}).bind("dragstart",function(aj,ak){ak.original_low=af.low;ak.current_height=aj.clientY;ak.current_x=ak.offsetX}).bind("drag",function(al,an){var aj=$(this);var ao=an.offsetX-an.current_x;var ak=aj.scrollTop()-(al.clientY-an.current_height);aj.scrollTop(ak);an.current_height=al.clientY;an.current_x=an.offsetX;var am=Math.round(ao/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}).bind("mousewheel",function(al,an,ak,aj){if(ak){ak*=50;var am=Math.round(-ak/af.viewport_container.width()*(af.high-af.low));af.move_delta(am)}});this.top_labeltrack.bind("dragstart",function(aj,ak){return $("<div />").css({height:af.browser_content_div.height()+af.top_labeltrack.height()+af.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(an,ao){$(ao.proxy).css({left:Math.min(an.pageX,ao.startX),width:Math.abs(an.pageX-ao.startX)});var ak=Math.min(an.pageX,ao.startX)-af.container.offset().left,aj=Math.max(an.pageX,ao.startX)-af.container.offset().left,am=(af.high-af.low),al=af.viewport_container.width();af.update_location(Math.round(ak/al*am)+af.low,Math.round(aj/al*am)+af.low)}).bind("dragend",function(ao,ap){var ak=Math.min(ao.pageX,ap.startX),aj=Math.max(ao.pageX,ap.startX),am=(af.high-af.low),al=af.viewport_container.width(),an=af.low;af.low=Math.round(ak/al*am)+an;af.high=Math.round(aj/al*am)+an;$(ap.proxy).remove();af.request_redraw()});this.add_label_track(new ab(this,{content_div:this.top_labeltrack}));this.add_label_track(new ab(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){af.resize_window()});$(document).bind("redraw",function(){af.redraw()});this.reset();$(window).trigger("resize")},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(af,ag){this.location_span.text(commatize(af)+" - "+commatize(ag));this.nav_input.val(this.chrom+":"+commatize(af)+"-"+commatize(ag))},load_chroms:function(ah){ah.num=v;ah.dbkey=this.dbkey;var af=this,ag=$.Deferred();$.ajax({url:chrom_url,data:ah,dataType:"json",success:function(aj){if(aj.chrom_info.length===0){alert("Invalid chromosome: "+ah.chrom);return}if(aj.reference){af.add_label_track(new z(af))}af.chrom_data=aj.chrom_info;var am='<option value="">Select Chrom/Contig</option>';for(var al=0,ai=af.chrom_data.length;al<ai;al++){var ak=af.chrom_data[al].chrom;am+='<option value="'+ak+'">'+ak+"</option>"}if(aj.prev_chroms){am+='<option value="previous">Previous '+v+"</option>"}if(aj.next_chroms){am+='<option value="next">Next '+v+"</option>"}af.chrom_select.html(am);af.chrom_start_index=aj.start_index;ag.resolve(aj)},error:function(){alert("Could not load chroms for this dbkey:",af.dbkey)}});return ag},change_chrom:function(ak,ag,am){if(!ak||ak==="None"){return}var ah=this;if(ak==="previous"){ah.load_chroms({low:this.chrom_start_index-v});return}if(ak==="next"){ah.load_chroms({low:this.chrom_start_index+v});return}var al=$.grep(ah.chrom_data,function(an,ao){return an.chrom===ak})[0];if(al===undefined){ah.load_chroms({chrom:ak},function(){ah.change_chrom(ak,ag,am)});return}else{if(ak!==ah.chrom){ah.chrom=ak;ah.chrom_select.val(ah.chrom);ah.max_high=al.len-1;ah.reset();ah.request_redraw(true);for(var aj=0,af=ah.drawables.length;aj<af;aj++){var ai=ah.drawables[aj];if(ai.init){ai.init()}}}if(ag!==undefined&&am!==undefined){ah.low=Math.max(ag,0);ah.high=Math.min(am,ah.max_high)}ah.reset_overview();ah.request_redraw()}},go_to:function(aj){aj=aj.replace(/ |,/g,"");var an=this,af,ai,ag=aj.split(":"),al=ag[0],am=ag[1];if(am!==undefined){try{var ak=am.split("-");af=parseInt(ak[0],10);ai=parseInt(ak[1],10)}catch(ah){return false}}an.change_chrom(al,af,ai)},move_fraction:function(ah){var af=this;var ag=af.high-af.low;this.move_delta(ah*ag)},move_delta:function(ah){var af=this;var ag=af.high-af.low;if(af.low-ah<af.max_low){af.low=af.max_low;af.high=af.max_low+ag}else{if(af.high-ah>af.max_high){af.high=af.max_high;af.low=af.max_high-ag}else{af.high-=ah;af.low-=ah}}af.request_redraw()},add_drawable:function(af){x.prototype.add_drawable.call(this,af);af.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(af){af.view=this;af.init();this.label_tracks.push(af)},remove_drawable:function(ah,ag){x.prototype.remove_drawable.call(this,ah);if(ag){var af=this;ah.container_div.hide(0,function(){$(this).remove();af.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(an,af,am,ag){var al=this,aj=(ag?[ag]:al.drawables),ah;var ag;for(var ak=0;ak<aj.length;ak++){ag=aj[ak];ah=-1;for(var ai=0;ai<al.tracks_to_be_redrawn.length;ai++){if(al.tracks_to_be_redrawn[ai][0]===ag){ah=ai;break}}if(ah<0){al.tracks_to_be_redrawn.push([ag,af,am])}else{al.tracks_to_be_redrawn[ak][1]=af;al.tracks_to_be_redrawn[ak][2]=am}}requestAnimationFrame(function(){al._redraw(an)})},_redraw:function(ap){var am=this.low,ai=this.high;if(am<this.max_low){am=this.max_low}if(ai>this.max_high){ai=this.max_high}var ao=this.high-this.low;if(this.high!==0&&ao<this.min_separation){ai=am+this.min_separation}this.low=Math.floor(am);this.high=Math.ceil(ai);this.resolution=Math.pow(A,Math.ceil(Math.log((this.high-this.low)/Q)/Math.log(A)));this.zoom_res=Math.pow(u,Math.max(0,Math.ceil(Math.log(this.resolution,u)/Math.log(u))));var af=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var al=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var aq=13;this.overview_box.css({left:af,width:Math.max(aq,al)}).show();if(al<aq){this.overview_box.css("left",af-(aq-al)/2)}if(this.overview_highlight){this.overview_highlight.css({left:af,width:al})}this.update_location(this.low,this.high);if(!ap){var ah,ag,an;for(var aj=0,ak=this.tracks_to_be_redrawn.length;aj<ak;aj++){ah=this.tracks_to_be_redrawn[aj][0];ag=this.tracks_to_be_redrawn[aj][1];an=this.tracks_to_be_redrawn[aj][2];if(ah){ah._draw(ag,an)}}this.tracks_to_be_redrawn=[];for(aj=0,ak=this.label_tracks.length;aj<ak;aj++){this.label_tracks[aj]._draw()}}},zoom_in:function(ag,ah){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ai=this.high-this.low,aj=ai/2+this.low,af=(ai/this.zoom_factor)/2;if(ag){aj=ag/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(aj-af);this.high=Math.round(aj+af);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ag=this.high-this.low,ah=ag/2+this.low,af=(ag*this.zoom_factor)/2;this.low=Math.round(ah-af);this.high=Math.round(ah+af);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(ah){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ah.dataset_id){return}this.overview_viewport.find(".track").remove()}var ag=ah.copy({content_div:this.overview_viewport}),af=this;ag.header_div.hide();ag.is_overview=true;af.overview_drawable=ag;this.overview_drawable.postdraw_actions=function(){af.overview_highlight.show().height(af.overview_drawable.content_div.height());af.overview_viewport.height(af.overview_drawable.content_div.height()+af.overview_box.outerHeight());af.overview_close.show();af.resize_window()};af.overview_drawable.request_draw();af.has_changes=true},reset_overview:function(){$(".tipsy").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 r=function(ah,al){this.track=ah;this.name=al.name;this.params=[];var at=al.params;for(var ai=0;ai<at.length;ai++){var an=at[ai],ag=an.name,ar=an.label,aj=unescape(an.html),au=an.value,ap=an.type;if(ap==="number"){this.params[this.params.length]=new f(ag,ar,aj,au,an.min,an.max)}else{if(ap=="select"){this.params[this.params.length]=new N(ag,ar,aj,au)}else{console.log("WARNING: unrecognized tool parameter type:",ag,ap)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(aw){aw.stopPropagation()}).click(function(aw){aw.stopPropagation()}).bind("dblclick",function(aw){aw.stopPropagation()});var aq=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var ao=this.params;var am=this;$.each(this.params,function(ax,aA){var az=$("<div>").addClass("param-row").appendTo(am.parent_div);var aw=$("<div>").addClass("param-label").text(aA.label).appendTo(az);var ay=$("<div/>").addClass("param-input").html(aA.html).appendTo(az);ay.find(":input").val(aA.value);$("<div style='clear: both;'/>").appendTo(az)});this.parent_div.find("input").click(function(){$(this).select()});var av=$("<div>").addClass("param-row").appendTo(this.parent_div);var ak=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(av);var af=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(av);var am=this;af.click(function(){am.run_on_region()});ak.click(function(){am.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var af={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();af[ag]=JSON.stringify(ah)});return af},get_param_values:function(){var ag=[];var af={};this.parent_div.find(":input").each(function(){var ah=$(this).attr("name"),ai=$(this).val();if(ah){ag[ag.length]=ai}});return ag},run_on_dataset:function(){var af=this;af.run({dataset_id:this.track.original_dataset_id,tool_id:af.name},null,function(ag){show_modal(af.name+" is Running",af.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ag={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},ak=this.track,ah=ag.tool_id+ak.tool_region_and_parameters_str(ag.chrom,ag.low,ag.high),af;if(ak.container===view){var aj=new P(this.name,this.track.view);var ai=ak.container.replace_drawable(ak,aj,false);aj.container_div.insertBefore(ak.view.content_div.children()[ai]);aj.add_drawable(ak);ak.container_div.appendTo(aj.content_div);af=aj}else{af=ak.container}var al=new ak.constructor(ah,view,af,"hda");al.init_for_tool_data();al.change_mode(ak.mode);af.add_drawable(al);al.content_div.text("Starting job.");this.run(ag,al,function(am){al.dataset_id=am.dataset_id;al.content_div.text("Running job.");al.init()})},run:function(ag,ah,ai){$.extend(ag,this.get_param_values_dict());var af=function(){$.getJSON(rerun_tool_url,ag,function(aj){if(aj==="no converter"){ah.container_div.addClass("error");ah.content_div.text(J)}else{if(aj.error){ah.container_div.addClass("error");ah.content_div.text(w+aj.message)}else{if(aj==="pending"){ah.container_div.addClass("pending");ah.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(af,2000)}else{ai(aj)}}}})};af()}});var N=function(ag,af,ah,ai){this.name=ag;this.label=af;this.html=ah;this.value=ai};var f=function(ah,ag,aj,ak,ai,af){N.call(this,ah,ag,aj,ak);this.min=ai;this.max=af};var g=function(ag,af,ah,ai){this.name=ag;this.index=af;this.tool_id=ah;this.tool_exp_name=ai};var V=function(ag,af,ah,ai){g.call(this,ag,af,ah,ai);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(V.prototype,{applies_to:function(af){if(af.length>this.index){return true}return false},keep:function(af){if(!this.applies_to(af)){return true}var ag=af[this.index];return(isNaN(ag)||(ag>=this.low&&ag<=this.high))},update_attrs:function(ag){var af=false;if(!this.applies_to(ag)){return af}if(ag[this.index]<this.min){this.min=Math.floor(ag[this.index]);af=true}if(ag[this.index]>this.max){this.max=Math.ceil(ag[this.index]);af=true}return af},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ah=function(ak,ai){var aj=ai-ak;return(aj<=2?0.01:1)};var ag=this.slider.slider("option","min"),af=this.slider.slider("option","max");if(this.min<ag||this.max>af){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ah(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var aa=function(ah,aq){this.track=ah;this.filters=[];for(var al=0;al<aq.length;al++){var af=aq[al],ag=af.name,ap=af.type,an=af.index,at=af.tool_id,ai=af.tool_exp_name;if(ap==="int"||ap==="float"){this.filters[al]=new V(ag,an,at,ai)}else{console.log("ERROR: unsupported filter: ",ag,ap)}}var ao=function(au,av,aw){au.click(function(){var ax=av.text();max=parseFloat(aw.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(aw.slider("option","values")){input_size=2*input_size+1;multi_value=true}av.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",ax).appendTo(av).focus().select().click(function(ay){ay.stopPropagation()}).blur(function(){$(this).remove();av.text(ax)}).keyup(function(aC){if(aC.keyCode===27){$(this).trigger("blur")}else{if(aC.keyCode===13){var aA=aw.slider("option","min"),ay=aw.slider("option","max"),aB=function(aD){return(isNaN(aD)||aD>ay||aD<aA)},az=$(this).val();if(!multi_value){az=parseFloat(az);if(aB(az)){alert("Parameter value must be in the range ["+aA+"-"+ay+"]");return $(this)}}else{az=az.split("-");az=[parseFloat(az[0]),parseFloat(az[1])];if(aB(az[0])||aB(az[1])){alert("Parameter value must be in the range ["+aA+"-"+ay+"]");return $(this)}}aw.slider((multi_value?"values":"value"),az)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()}).bind("keydown",function(au){au.stopPropagation()});var aj=this;$.each(this.filters,function(aA,av){av.container=$("<div/>").addClass("filter-row slider-row").appendTo(aj.parent_div);var au=$("<div/>").addClass("elt-label").appendTo(av.container);var aD=$("<span/>").addClass("slider-name").text(av.name+" ").appendTo(au);var aw=$("<span/>");var ax=$("<span/>").addClass("slider-value").appendTo(au).append("[").append(aw).append("]");var aC=$("<div/>").addClass("slider").appendTo(av.container);av.control_element=$("<div/>").attr("id",av.name+"-filter-control").appendTo(aC);var ay=[0,0];av.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aG,aH){var aF=aH.values;aw.text(aF[0]+"-"+aF[1]);av.low=aF[0];av.high=aF[1];aj.track.request_draw(true,true)},change:function(aF,aG){av.control_element.slider("option","slide").call(av.control_element,aF,aG)}});av.slider=av.control_element;av.slider_label=aw;ao(ax,aw,av.control_element);var aE=$("<div/>").addClass("display-controls").appendTo(av.container),az=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(aj.alpha_filter!==av){aj.alpha_filter=av;$(".layer-transparent").removeClass("active").hide();az.addClass("active").show()}else{aj.alpha_filter=null;az.removeClass("active")}aj.track.request_draw(true,true)}).appendTo(aE).hide(),aB=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(aj.height_filter!==av){aj.height_filter=av;$(".arrow-resize-090").removeClass("active").hide();aB.addClass("active").show()}else{aj.height_filter=null;aB.removeClass("active")}aj.track.request_draw(true,true)}).appendTo(aE).hide();av.container.hover(function(){az.show();aB.show()},function(){if(aj.alpha_filter!==av){az.hide()}if(aj.height_filter!==av){aB.hide()}});$("<div style='clear: both;'/>").appendTo(av.container)});if(this.filters.length!==0){var ar=$("<div/>").addClass("param-row").appendTo(this.parent_div);var am=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(ar);var ak=this;am.click(function(){ak.run_on_dataset()})}};p(aa.prototype,{reset_filters:function(){for(var af=0;af<this.filters.length;af++){filter=this.filters[af];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var an=function(ar,ap,aq){if(!(ap in ar)){ar[ap]=aq}return ar[ap]};var ah={},af,ag,ai;for(var aj=0;aj<this.filters.length;aj++){af=this.filters[aj];if(af.tool_id){if(af.min!=af.low){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" >= "+af.low}if(af.max!=af.high){ag=an(ah,af.tool_id,[]);ag[ag.length]=af.tool_exp_name+" <= "+af.high}}}var al=[];for(var ao in ah){al[al.length]=[ao,ah[ao]]}var am=al.length;(function ak(aw,at){var aq=at[0],ar=aq[0],av=aq[1],au="("+av.join(") and (")+")",ap={cond:au,input:aw,target_dataset_id:aw,tool_id:ar},at=at.slice(1);$.getJSON(run_tool_url,ap,function(ax){if(ax.error){show_modal("Filter Dataset","Error running tool "+ar,{Close:hide_modal})}else{if(at.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{ak(ax.dataset_id,at)}}})})(this.track.dataset_id,al)}});var B=function(af,ag){L.Scaler.call(this,ag);this.filter=af};B.prototype.gen_val=function(af){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(af[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var E=function(af){this.track=af.track;this.params=af.params;this.values={};this.restore_values((af.saved_values?af.saved_values:{}));this.onchange=af.onchange};p(E.prototype,{restore_values:function(af){var ag=this;$.each(this.params,function(ah,ai){if(af[ai.key]!==undefined){ag.values[ai.key]=af[ai.key]}else{ag.values[ai.key]=ai.default_value}})},build_form:function(){var ai=this;var af=$("<div />");var ah;function ag(al,aj){for(var an=0;an<al.length;an++){ah=al[an];if(ah.hidden){continue}var ak="param_"+an;var ar=ai.values[ah.key];var at=$("<div class='form-row' />").appendTo(aj);at.append($("<label />").attr("for",ak).text(ah.label+":"));if(ah.type==="bool"){at.append($('<input type="checkbox" />').attr("id",ak).attr("name",ak).attr("checked",ar))}else{if(ah.type==="text"){at.append($('<input type="text"/>').attr("id",ak).val(ar).click(function(){$(this).select()}))}else{if(ah.type=="select"){var ap=$("<select />").attr("id",ak);for(var am=0;am<ah.options.length;am++){$("<option/>").text(ah.options[am].label).attr("value",ah.options[am].value).appendTo(ap)}ap.val(ar);at.append(ap)}else{if(ah.type==="color"){var ao=$("<input />").attr("id",ak).attr("name",ak).val(ar);var aq=$("<div class='tipsy tipsy-west' style='position: absolute;' />").hide();(function(au,av){var ax=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(av);var aw=$("<div/>").appendTo(ax).farbtastic({width:100,height:100,callback:au,color:ar});$("<div />").append(au).append(av).appendTo(at).bind("click",function(ay){$(".tipsy").hide();av.css({left:$(this).position().left+$(au).width()+5,top:$(this).position().top-($(av).height()/2)+($(au).height()/2)}).show();$(document).bind("click.color-picker",function(){av.hide();$(document).unbind("click.color-picker")});ay.stopPropagation()})})(ao,aq)}else{at.append($("<input />").attr("id",ak).attr("name",ak).val(ar))}}}}if(ah.help){at.append($("<div class='help'/>").text(ah.help))}}}ag(this.params,af);return af},update_from_form:function(af){var ah=this;var ag=false;$.each(this.params,function(ai,ak){if(!ak.hidden){var al="param_"+ai;var aj=af.find("#"+al).val();if(ak.type==="float"){aj=parseFloat(aj)}else{if(ak.type==="int"){aj=parseInt(aj)}else{if(ak.type==="bool"){aj=af.find("#"+al).is(":checked")}}}if(aj!==ah.values[ak.key]){ah.values[ak.key]=aj;ag=true}}});if(ag){this.onchange()}}});var b=function(af,ai,ah,ag,aj){this.track=af;this.index=ai;this.low=ai*Q*ah;this.high=(ai+1)*Q*ah;this.resolution=ah;this.html_elt=$("<div class='track-tile'/>").append(ag);this.data=aj;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(af,ai,ah,ag,aj,ak){b.call(this,af,ai,ah,ag,aj);this.max_val=ak};p(k.prototype,b.prototype);var O=function(ai,an,aj,ah,al,at,am,au,ag,aq){b.call(this,ai,an,aj,ah,al);this.mode=am;this.feature_mapper=aq;this.has_icons=false;if(au||!ag){this.has_icons=true;var ao=this;ah=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:C-1,width:ah.width}).prependTo(this.html_elt);if(!ag){var ap=$("<a href='javascript:void(0);'/>").addClass("icon exclamation").attr("title","To minimize track height, not all features in this region are displayed. Click to display more.").tipsy({gravity:"s"}).appendTo(message_div).click(function(){$(".tipsy").hide();ao.track.slotters[at].max_rows*=2;ao.track.request_draw(true)})}if(au){var ar=al.length,ak=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ar+" features in this region were obtained from server. Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),af=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ar+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);ak.click(function(){ao.stale=true;ai.data_manager.get_more_data(ao.low,ao.high,ai.mode,ao.resolution,{},ai.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();ai.request_draw()}).dblclick(function(av){av.stopPropagation()});af.click(function(){ao.stale=true;ai.data_manager.get_more_data(ao.low,ao.high,ai.mode,ao.resolution,{},ai.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();ai.request_draw()}).dblclick(function(av){av.stopPropagation()})}}};p(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ag=this,af={};if(ag.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(ar){if(!this.hovered){return}var am=$(this).offset(),aq=ar.pageX-am.left,ap=ar.pageY-am.top,aw=ag.feature_mapper.get_feature_data(aq,ap),an=(aw?aw[0]:null);$(this).siblings(".feature-popup").each(function(){if(!an||$(this).attr("id")!==an.toString()){$(this).remove()}});if(aw){var ai=af[an];if(!ai){var an=aw[0],at={name:aw[3],start:aw[1],end:aw[2],strand:aw[4]},al=ag.track.filters_manager.filters,ak;for(var ao=0;ao<al.length;ao++){ak=al[ao];at[ak.name]=aw[ak.index]}var ai=$("<div/>").attr("id",an).addClass("feature-popup"),ax=$("<table/>"),av,au,ay;for(av in at){au=at[av];ay=$("<tr/>").appendTo(ax);$("<th/>").appendTo(ay).text(av);$("<td/>").attr("align","left").appendTo(ay).text(typeof(au)=="number"?Z(au,2):au)}ai.append($("<div class='feature-popup-inner'>").append(ax));af[an]=ai}ai.appendTo($(ag.html_elt).parent());var aj=aq+parseInt(ag.html_elt.css("left"))-ai.width()/2,ah=ap+parseInt(ag.html_elt.css("top"))+7;ai.css("left",aj+"px").css("top",ah+"px")}else{if(!ar.isPropagationStopped()){ar.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ar)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ai,ag,af,ah,ak,aj,al){q.call(this,ai,ag,af,{},"draghandle");this.data_url=(aj?aj:default_data_url);this.data_url_extra_params={};this.data_query_wait=(al?al:K);this.dataset_check_url=converted_datasets_state_url;this.data_manager=(ak?ak:new S(H,this));this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div)}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(af){af.view.set_overview(af)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(af){af.filters_div.toggle();af.filters_manager.reset_filters()}},{name:"tools_icon",title:"Tools",css_class:"tools-icon",on_click_fn:function(af){af.dynamic_tool_div.toggle();if(af.dynamic_tool_div.is(":visible")){af.set_name(af.name+af.tool_region_and_parameters_str())}else{af.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var af=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(af)}this.name_div=$("<div/>").addClass("track-name").appendTo(af).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return af},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);var ag=this;if(ag.display_modes!==undefined){var ak=(ag.config&&ag.config.values.mode?ag.config.values.mode:ag.display_modes[0]);ag.mode=ak;this.action_icons.mode_icon.attr("title","Set display mode (now: "+ag.mode+")");var ai={};for(var ah=0,af=ag.display_modes.length;ah<af;ah++){var aj=ag.display_modes[ah];ai[aj]=function(al){return function(){ag.change_mode(al);ag.icons_div.show();ag.container_div.mouseleave(function(){ag.icons_div.hide()})}}(aj)}make_popupmenu(this.action_icons.mode_icon,ai)}},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof ab){return"LabelTrack"}else{if(this instanceof z){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof W){return"ReadTrack"}else{if(this instanceof U){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var af=this;af.enabled=false;af.tile_cache.clear();af.data_manager.clear();af.content_div.css("height","auto");af.content_div.children().remove();af.container_div.removeClass("nodata error pending");if(!af.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:af.hda_ldda,dataset_id:af.dataset_id,chrom:af.view.chrom},function(ag){if(!ag||ag==="error"||ag.kind==="error"){af.container_div.addClass("error");af.content_div.text(o);if(ag.message){var ah=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})});af.content_div.append(ah)}}else{if(ag==="no converter"){af.container_div.addClass("error");af.content_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){af.container_div.addClass("nodata");af.content_div.text(D)}else{if(ag==="pending"){af.container_div.addClass("pending");af.content_div.text(t);setTimeout(function(){af.init()},af.data_query_wait)}else{if(ag.status==="data"){if(ag.valid_chroms){af.valid_chroms=ag.valid_chroms;af.update_icons()}af.content_div.text(Y);if(af.view.chrom){af.content_div.text("");af.content_div.css("height",af.height_px+"px");af.enabled=true;$.when(af.predraw_init()).done(function(){af.container_div.removeClass("nodata error pending");af.request_draw()})}}}}}}});this.update_icons()},predraw_init:function(){}});var M=function(aj,ah,ag,ai,am,al,ak){i.call(this,aj,ah,ag,ai,ak);var af=this,ah=af.view;m(af.container_div,af.drag_handle_class,".group",af);this.filters_manager=new aa(this,(am!==undefined?am:{}));this.filters_available=false;this.filters_visible=false;this.tool=(al!==undefined&&obj_length(al)>0?new r(this,al):undefined);this.tile_cache=new c(R);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(M.prototype,q.prototype,i.prototype,{copy:function(af){var ag=new this.constructor(this.name,this.view,af,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool,this.data_manager);ag.change_mode(this.mode);ag.enabled=this.enabled;return ag},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},from_dict:function(ah,ag){var af=new this.constructor(ah.name,view,ag,ah.hda_ldda,ah.dataset_id,ah.prefs,ah.filters,ah.tool);if(ah.mode){af.change_mode(ah.mode)}return af},change_mode:function(ag){var af=this;af.mode=ag;af.config.values.mode=ag;af.tile_cache.clear();af.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+af.mode+")");return af},update_icons:function(){var af=this;if(af.filters_available){af.action_icons.filters_icon.show()}else{af.action_icons.filters_icon.hide()}if(af.tool){af.action_icons.tools_icon.show()}else{af.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(ag,ah,af){return ag+"_"+ah+"_"+af},request_draw:function(ag,af){this.view.request_redraw(false,ag,af,this)},_draw:function(ah,ar){if(!this.can_draw()){return}var ap=this.view.low,al=this.view.high,an=al-ap,ai=this.view.container.width(),av=ai/an,ak=this.view.resolution,au=this.content_div;if(this.is_overview){ap=this.view.max_low;al=this.view.max_high;ak=Math.pow(A,Math.ceil(Math.log((view.max_high-view.max_low)/Q)/Math.log(A)));av=ai/(view.max_high-view.max_low)}if(!ar){this.content_div.children().addClass("remove")}this.max_height=0;var ag=Math.floor(ap/ak/Q);var ao=true;var at=[];var af=0;var am=function(aw){return(aw&&"track" in aw)};while((ag*Q*ak)<al){var aq=this.draw_helper(ah,ai,ag,ak,au,av);if(am(aq)){at.push(aq)}else{ao=false}ag+=1;af++}if(!ar){this.content_div.children(".remove").remove()}var aj=this;if(ao){aj.postdraw_actions(at,ai,av,ar)}},postdraw_actions:function(ai,aj,al,af){var ah=this;var ak=false;for(var ag=0;ag<ai.length;ag++){if(ai[ag].has_icons){ak=true;break}}if(ak){for(var ag=0;ag<ai.length;ag++){tile=ai[ag];if(!tile.has_icons){tile.html_elt.css("padding-top",C)}}}},draw_helper:function(af,ar,ax,av,ak,al,at){var aq=this,aA=this._gen_tile_cache_key(ar,al,ax),ay=ax*Q*av,ag=ay+Q*av;if(!at){at={}}var az=(af?undefined:aq.tile_cache.get(aA));if(az){aq.show_tile(az,ak,al);return az}var ao=true;var aw=aq.data_manager.get_data(ay,ag,aq.mode,av,aq.data_url_extra_params);if(is_deferred(aw)){ao=false}var am;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(ay,ag,aq.mode,av,view.reference_track.data_url_extra_params);if(is_deferred(am)){ao=false}}if(ao){p(aw,at.more_tile_data);var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}var ah=aq.view.canvas_manager.new_canvas(),ai=aq._get_tile_bounds(ax,av),ay=ai[0],ag=ai[1],ar=Math.ceil((ag-ay)*al)+aq.left_offset,ap=aq.get_canvas_height(aw,an,al,ar);ah.width=ar;ah.height=ap;var au=ah.getContext("2d");au.translate(this.left_offset,0);var az=aq.draw_tile(aw,au,an,av,ax,al,am);if(az!==undefined){aq.tile_cache.set(aA,az);aq.show_tile(az,ak,al)}return az}var aj=$.Deferred();$.when(aw,am).then(function(){view.request_redraw(false,false,false,aq);aj.resolve()});return aj},get_canvas_height:function(af,ah,ai,ag){return this.height_px},draw_tile:function(af,ah,ak,aj,ag,al,ai){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ah,aj,ak){var ag=this,af=ah.html_elt;ah.predisplay_actions();var ai=(ah.low-(this.is_overview?this.view.max_low:this.view.low))*ak;if(this.left_offset){ai-=this.left_offset}af.css({position:"absolute",top:0,left:ai,height:""});if(af.hasClass("remove")){af.removeClass("remove")}else{aj.append(af)}ag.max_height=Math.max(ag.max_height,af.height());ag.content_div.css("height",ag.max_height+"px");aj.children().css("height",ag.max_height+"px")},_get_tile_bounds:function(af,ag){var ai=af*Q*ag,aj=Q*ag,ah=(ai+aj<=this.view.max_high?ai+aj:this.view.max_high);return[ai,ah]},tool_region_and_parameters_str:function(ah,af,ai){var ag=this,aj=(ah!==undefined&&af!==undefined&&ai!==undefined?ah+":"+af+"-"+ai:"all");return" - region=["+aj+"], parameters=["+ag.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(af,ag){return true},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var ag=this;var af=function(){if(ag.data_manager.size()===0){setTimeout(af,300)}else{ag.data_url=default_data_url;ag.data_query_wait=K;ag.dataset_state_url=converted_datasets_state_url;$.getJSON(ag.dataset_state_url,{dataset_id:ag.dataset_id,hda_ldda:ag.hda_ldda},function(ah){})}};af()}}});var ab=function(ag,af){i.call(this,"label",ag,af,false,{});this.container_div.addClass("label-track")};p(ab.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ah=this.view,ai=ah.high-ah.low,al=Math.floor(Math.pow(10,Math.floor(Math.log(ai)/Math.log(10)))),af=Math.floor(ah.low/al)*al,aj=this.view.container.width(),ag=$("<div style='position: relative; height: 1.3em;'></div>");while(af<ah.high){var ak=(af-ah.low)/ai*aj;ag.append($("<div class='label'>"+commatize(af)+"</div>").css({position:"absolute",left:ak-1}));af+=al}this.content_div.children(":first").remove();this.content_div.append(ag)}});var h=function(ai,ah,ag,af){this.display_modes=af[0].display_modes;M.call(this,ai,ah,ag);this.drawables=[];this.left_offset=0;if(af){var al=[],ak;for(var aj=0;aj<af.length;aj++){ak=af[aj];al.push(ak.dataset_id);this.drawables[aj]=ak.copy();if(ak.left_offset>this.left_offset){this.left_offset=ak.left_offset}}this.enabled=true}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,M.prototype,{to_dict:x.prototype.to_dict,add_drawable:x.prototype.add_drawable,from_dict:function(al,af){var ak=new this.constructor(al.name,view,af,al.prefs,view.viewport_container,view);var ag,aj,ai;for(var ah=0;ah<al.drawables.length;ah++){ag=al.drawables[ah];aj=ag.obj_type;if(!aj){aj=ag.track_type}ai=addable_objects[aj].prototype.from_dict(ag);ak.add_drawable(ai)}return ak},change_mode:function(af){M.prototype.change_mode.call(this,af);for(var ag=0;ag<this.drawables.length;ag++){this.drawables[ag].change_mode(af)}},init:function(){this.enabled=true;this.request_draw()},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(ag,av,aB,ay,am,ao,aw){var au=this,aF=this._gen_tile_cache_key(av,ao,aB),aC=aB*Q*ay,ah=aC+Q*ay;if(!aw){aw={}}var aE=(ag?undefined:au.tile_cache.get(aF));if(aE){au.show_tile(aE,am,ao);return aE}var an=[],au,ar=true,az,ap;for(var aA=0;aA<this.drawables.length;aA++){au=this.drawables[aA];az=au.data_manager.get_data(aC,ah,au.mode,ay,au.data_url_extra_params);if(is_deferred(az)){ar=false}an.push(az);ap=null;if(view.reference_track&&ao>view.canvas_manager.char_width_px){ap=view.reference_track.data_manager.get_data(aC,ah,au.mode,ay,view.reference_track.data_url_extra_params);if(is_deferred(ap)){ar=false}}an.push(ap)}if(ar){p(az,aw.more_tile_data);this.tile_predraw_init();var aj=au.view.canvas_manager.new_canvas(),ak=au._get_tile_bounds(aB,ay),aC=ak[0],ah=ak[1],aD=0,av=Math.ceil((ah-aC)*ao)+this.left_offset,at=0,ai=[];var af=0;for(var aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];var aq=au.mode;if(aq==="Auto"){aq=au.get_mode(az);au.update_auto_mode(aq)}ai.push(aq);af=au.get_canvas_height(az,aq,ao,av);if(af>at){at=af}}aj.width=av;aj.height=(aw.height?aw.height:at);aD=0;var ax=aj.getContext("2d");ax.translate(this.left_offset,0);ax.globalAlpha=0.5;ax.globalCompositeOperation="source-over";for(var aA=0;aA<this.drawables.length;aA++,aD+=2){au=this.drawables[aA];az=an[aD];ap=an[aD+1];aE=au.draw_tile(az,ax,ai[aA],ay,aB,ao,ap)}this.tile_cache.set(aF,aE);this.show_tile(aE,am,ao);return aE}var al=$.Deferred(),au=this;$.when.apply($,an).then(function(){view.request_redraw(false,false,false,au);al.resolve()});return al},tile_predraw_init:function(){var ai=Number.MAX_VALUE,af=-ai,ag;for(var ah=0;ah<this.drawables.length;ah++){ag=this.drawables[ah];if(ag instanceof j){if(ag.prefs.min_value<ai){ai=ag.prefs.min_value}if(ag.prefs.max_value>af){af=ag.prefs.max_value}}}for(var ah=0;ah<this.drawables.length;ah++){ag=this.drawables[ah];ag.prefs.min_value=ai;ag.prefs.max_value=af}},postdraw_actions:function(ah,ak,am,ag){M.prototype.postdraw_actions.call(this,ah,ak,am,ag);var aj=-1;for(var ai=0;ai<ah.length;ai++){var af=ah[ai].html_elt.find("canvas").height();if(af>aj){aj=af}}for(var ai=0;ai<ah.length;ai++){var al=ah[ai];if(al.html_elt.find("canvas").height()!==aj){this.draw_helper(true,ak,al.index,al.resolution,al.html_elt.parent(),am,{height:aj});al.html_elt.remove()}}}});var z=function(af){M.call(this,"reference",af,{content_div:af.top_labeltrack},{});af.reference_track=this;this.left_offset=200;this.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=reference_url;this.data_url_extra_params={dbkey:af.dbkey};this.data_manager=new G(H,this,false)};p(z.prototype,q.prototype,M.prototype,{build_header_div:function(){},init:function(){this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(an,ao,ak,aj,ag,ap){var ai=this;if(ap>this.view.canvas_manager.char_width_px){if(an.data===null){ai.content_div.css("height","0px");return}var ah=ao.canvas;ao.font=ao.canvas.manager.default_font;ao.textAlign="center";an=an.data;for(var al=0,am=an.length;al<am;al++){var af=Math.round(al*ap);ao.fillText(an[al],af,10)}return new b(ai,ag,aj,ah,an)}this.content_div.css("height","0px")}});var j=function(af,am,ag,al,ao,an,aj,ak,ah){var ai=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,af,am,ag,an,aj,ak,ah);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=al;this.dataset_id=ao;this.original_dataset_id=ao;this.left_offset=0;this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"color",label:"Color",type:"color",default_value: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:this.height_px,hidden:true}],saved_values:an,onchange:function(){ai.set_name(ai.prefs.name);ai.vertical_range=ai.prefs.max_value-ai.prefs.min_value;$("#linetrack_"+ai.dataset_id+"_minval").text(ai.prefs.min_value);$("#linetrack_"+ai.dataset_id+"_maxval").text(ai.prefs.max_value);ai.tile_cache.clear();ai.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,M.prototype,{add_resize_handle:function(){var af=this;var ai=false;var ah=false;var ag=$("<div class='track-resize'>");$(af.container_div).hover(function(){if(af.content_visible){ai=true;ag.show()}},function(){ai=false;if(!ah){ag.hide()}});ag.hide().bind("dragstart",function(aj,ak){ah=true;ak.original_height=$(af.content_div).height()}).bind("drag",function(ak,al){var aj=Math.min(Math.max(al.original_height+al.deltaY,af.min_height_px),af.max_height_px);$(af.content_div).css("height",aj);af.height_px=aj;af.request_draw(true)}).bind("dragend",function(aj,ak){af.tile_cache.clear();ah=false;if(!ai){ag.hide()}af.config.values.height=af.height_px}).appendTo(af.container_div)},predraw_init:function(){var af=this;af.vertical_range=undefined;return $.getJSON(af.data_url,{stats:true,chrom:af.view.chrom,low:null,high:null,hda_ldda:af.hda_ldda,dataset_id:af.dataset_id},function(ag){af.container_div.addClass("line-track");var aj=ag.data;if(isNaN(parseFloat(af.prefs.min_value))||isNaN(parseFloat(af.prefs.max_value))){var ah=aj.min;var al=aj.max;ah=Math.floor(Math.min(0,Math.max(ah,aj.mean-2*aj.sd)));al=Math.ceil(Math.max(0,Math.min(al,aj.mean+2*aj.sd)));af.prefs.min_value=ah;af.prefs.max_value=al;$("#track_"+af.dataset_id+"_minval").val(af.prefs.min_value);$("#track_"+af.dataset_id+"_maxval").val(af.prefs.max_value)}af.vertical_range=af.prefs.max_value-af.prefs.min_value;af.total_frequency=aj.total_frequency;af.container_div.find(".yaxislabel").remove();var ak=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_minval").text(Z(af.prefs.min_value,3));var ai=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+af.dataset_id+"_maxval").text(Z(af.prefs.max_value,3));ai.css({position:"absolute",top:"24px",left:"10px"});ai.prependTo(af.container_div);ak.css({position:"absolute",bottom:"2px",left:"10px"});ak.prependTo(af.container_div)})},draw_tile:function(ap,an,ak,ai,ag,ao){if(this.vertical_range===undefined){return}var ah=an.canvas,af=this._get_tile_bounds(ag,ai),aj=af[0],am=af[1],al=new L.LinePainter(ap.data,aj,am,this.prefs,ak);al.draw(an,ah.width,ah.height,ao);return new b(this.track,ag,ai,ah,ap.data)}});var d=function(af,am,ag,al,ao,an,aj,ak,ah){var ai=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];M.call(this,af,am,ag,an,aj,ak,ah);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{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:"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},],saved_values:an,onchange:function(){ai.set_name(ai.prefs.name);ai.tile_cache.clear();ai.set_painter_from_config();ai.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=al;this.dataset_id=ao;this.original_dataset_id=ao;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()};p(d.prototype,q.prototype,M.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(at,an,aj,ah){M.prototype.postdraw_actions.call(this,at,ah);var am=this;if(ah){var ax=am.content_div.children();var aw=false;for(var ap=ax.length-1,aq=0;ap>=aq;ap--){var ai=$(ax[ap]);if(aw){ai.remove()}else{if(ai.children().length!==0){aw=true}}}}if(am.mode=="Histogram"){var ag=-1;for(var ap=0;ap<at.length;ap++){var ao=at[ap].max_val;if(ao>ag){ag=ao}}for(var ap=0;ap<at.length;ap++){var av=at[ap];if(av.max_val!==ag){av.html_elt.remove();am.draw_helper(true,an,av.index,av.resolution,av.html_elt.parent(),aj,{more_tile_data:{max:ag}})}}}if(am.filters_manager){var ak=am.filters_manager.filters;for(var ar=0;ar<ak.length;ar++){ak[ar].update_ui_elt()}var au=false,af,al;for(var ap=0;ap<at.length;ap++){if(at[ap].data.length){af=at[ap].data[0];for(var ar=0;ar<ak.length;ar++){al=ak[ar];if(al.applies_to(af)&&al.min!==al.max){au=true;break}}}}if(am.filters_available!==au){am.filters_available=au;if(!am.filters_available){am.filters_div.hide()}am.update_icons()}}},update_auto_mode:function(af){var af;if(this.mode=="Auto"){if(af=="no_detail"){af="feature spans"}else{if(af=="summary_tree"){af="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+af+")")}},incremental_slots:function(aj,af,ai){var ag=this.view.canvas_manager.dummy_context,ah=this.slotters[aj];if(!ah||(ah.mode!==ai)){ah=new (s.FeatureSlotter)(aj,ai,y,function(ak){return ag.measureText(ak)});this.slotters[aj]=ah}return ah.slot_features(af)},get_summary_tree_data:function(aj,am,ah,av){if(av>ah-am){av=ah-am}var aq=Math.floor((ah-am)/av),au=[],ai=0;var ak=0,al=0,ap,at=0,an=[],ar,ao;var ag=function(ay,ax,az,aw){ay[0]=ax+az*aw;ay[1]=ax+(az+1)*aw};while(at<av&&ak!==aj.length){var af=false;for(;at<av&&!af;at++){ag(an,am,at,aq);for(al=ak;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){af=true;break}}if(af){break}}data_start_index=al;au[au.length]=ar=[an[0],0];for(;al<aj.length;al++){ap=aj[al].slice(1,3);if(is_overlap(ap,an)){ar[1]++}else{break}}if(ar[1]>ai){ai=ar[1]}at++}return{max:ai,delta:aq,data:au}},get_mode:function(af){if(af.dataset_type==="summary_tree"){mode="summary_tree"}else{if(af.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(af,aj,ak,ag){if(aj==="summary_tree"||aj==="Histogram"){return this.summary_draw_height+T}else{var ai=this.incremental_slots(ak,af.data,aj);var ah=new (this.painter)(null,null,null,this.prefs,aj);return Math.max(ad,ah.get_required_height(ai,ag))}},draw_tile:function(ar,aw,au,ax,aB,an,ai){var av=this,ah=aw.canvas,ak=this._get_tile_bounds(aB,ax),aE=ak[0],ag=ak[1],aJ=25,aj=this.left_offset;if(au==="summary_tree"||au==="Histogram"){this.container_div.find(".yaxislabel").remove();var af=$("<div />").addClass("yaxislabel");af.text(ar.max);af.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});af.prependTo(this.container_div);if(ar.dataset_type!="summary_tree"){var ao=this.get_summary_tree_data(ar.data,aE,ag,200);if(ar.max){ao.max=ar.max}ar=ao}var aG=new L.SummaryTreePainter(ar,aE,ag,this.prefs);aw.translate(0,T);aG.draw(aw,ah.width,ah.height,an);return new k(av,aB,ax,ah,ar.data,ar.max)}var am=[],at=this.slotters[an].slots;all_slotted=true;if(ar.data){var ap=this.filters_manager.filters;for(var ay=0,aA=ar.data.length;ay<aA;ay++){var al=ar.data[ay];var az=false;var aq;for(var aD=0,aI=ap.length;aD<aI;aD++){aq=ap[aD];aq.update_attrs(al);if(!aq.keep(al)){az=true;break}}if(!az){am.push(al);if(!(al[0] in at)){all_slotted=false}}}}var aH=(this.filters_manager.alpha_filter?new B(this.filters_manager.alpha_filter):null);var aF=(this.filters_manager.height_filter?new B(this.filters_manager.height_filter):null);var aG=new (this.painter)(am,aE,ag,this.prefs,au,aH,aF,ai);var aC=null;aw.fillStyle=this.prefs.block_color;aw.font=aw.canvas.manager.default_font;aw.textAlign="right";this.container_div.find(".yaxislabel").remove();if(ar.data){aC=aG.draw(aw,ah.width,ah.height,an,at);aC.translation=-aj}return new O(av,aB,ax,ah,ar.data,an,au,ar.message,all_slotted,aC)},data_and_mode_compatible:function(af,ag){if(ag==="Auto"){return true}else{if(af.extra_info==="no_detail"||af.dataset_type==="summary_tree"){return false}else{return true}}},});var U=function(af,al,ag,ak,an,am,ai,aj,ah){d.call(this,af,al,ag,ak,an,am,ai,aj,ah);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:am,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};p(U.prototype,q.prototype,M.prototype,d.prototype);var W=function(af,al,ag,ak,ao,an,ai,ah){d.call(this,af,al,ag,ak,ao,an,ai,ah);var aj=get_random_color(),am=get_random_color([aj,"#ffffff"]);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:af},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:aj},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:am},{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},],saved_values:an,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};p(W.prototype,q.prototype,M.prototype,d.prototype);X.View=ac;X.DrawableGroup=P;X.LineTrack=j;X.FeatureTrack=d;X.ReadTrack=W;X.VcfTrack=U;X.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}else{}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(M,z,L,N){var E=this.view_start,O=this.view_end-this.view_start;var J=this.data.data,I=this.data.delta,G=this.data.max,B=L;delta_x_px=Math.ceil(I*N);M.save();for(var C=0,D=J.length;C<D;C++){var H=Math.floor((J[C][0]-E)*N);var F=J[C][1];if(!F){continue}var K=F/G*L;if(F!==0&&K<1){K=1}M.fillStyle=this.prefs.block_color;M.fillRect(H,B-K,delta_x_px,K);var A=4;if(this.prefs.show_counts&&(M.measureText(F).width+A)<delta_x_px){M.fillStyle=this.prefs.label_color;M.textAlign="center";M.fillText(F,H+(delta_x_px/2),10)}}M.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var 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T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var 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y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences&&this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}if(U+af>=L&&U+af<=aa){var 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requestAnimationFrame=(function(){return window.requestAnimationFrame||window.webkitRequestAnimationFrame||window.mozRequestAnimationFrame||window.oRequestAnimationFrame||window.msRequestAnimationFrame||function(b,a){window.setTimeout(b,1000/60)}})();var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(e,b){var g=e[0],f=e[1],d=b[0],c=b[1],a;if(g<d){if(f<d){a=BEFORE}else{if(f<=c){a=OVERLAP_START}else{a=CONTAINS}}}else{if(g>c){a=AFTER}else{if(f<=c){a=CONTAINED_BY}else{a=OVERLAP_END}}}return a};var is_overlap=function(c,b){var a=compute_overlap(c,b);return(a!==BEFORE&&a!==AFTER)};var is_deferred=function(a){return("isResolved" in a)};var get_random_color=function(a){if(!a){a="#ffffff"}if(typeof(a)==="string"){a=[a]}for(var j=0;j<a.length;j++){a[j]=parseInt(a[j].slice(1),16)}var n=function(t,s,i){return((t*299)+(s*587)+(i*114))/1000};var e=function(v,u,w,s,i,t){return(Math.max(v,s)-Math.min(v,s))+(Math.max(u,i)-Math.min(u,i))+(Math.max(w,t)-Math.min(w,t))};var g,o,f,k,q,h,r,c,d,b,p,m=false,l=0;do{g=Math.round(Math.random()*16777215);o=(g&16711680)>>16;f=(g&65280)>>8;k=g&255;d=n(o,f,k);m=true;for(var j=0;j<a.length;j++){q=a[j];h=(q&16711680)>>16;r=(q&65280)>>8;c=q&255;b=n(h,r,c);p=e(o,f,k,h,r,c);if((Math.abs(d-b)<40)||(p<200)){m=false;break}}l++}while(!m&&l<=10);return"#"+(16777216+g).toString(16).substr(1,6)};var create_action_icon=function(c,b,a){return $("<a/>").attr("href","javascript:void(0);").attr("title",c).addClass("icon-button").addClass(b).tipsy({gravity:"s"}).click(a)};var trackster_module=function(e,W){var p=e("class").extend,s=e("slotting"),L=e("painters");var ad=function(ae,af){this.document=ae;this.default_font=af!==undefined?af:"9px Monaco, Lucida Console, 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",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",D="No data for this chrom/contig.",t="Currently indexing... please wait",w="Tool cannot be rerun: ",a="Loading data...",X="Ready for display",R=10,H=20;function Y(af,ae){if(!ae){ae=0}var ag=Math.pow(10,ae);return Math.round(af*ag)/ag}var c=function(ae){this.num_elements=ae;this.clear()};p(c.prototype,{get:function(af){var ae=this.key_ary.indexOf(af);if(ae!==-1){if(this.obj_cache[af].stale){this.key_ary.splice(ae,1);delete this.obj_cache[af]}else{this.move_key_to_end(af,ae)}}return this.obj_cache[af]},set:function(af,ag){if(!this.obj_cache[af]){if(this.key_ary.length>=this.num_elements){var ae=this.key_ary.shift();delete this.obj_cache[ae]}this.key_ary.push(af)}this.obj_cache[af]=ag;return ag},move_key_to_end:function(af,ae){this.key_ary.splice(ae,1);this.key_ary.push(af)},clear:function(){this.obj_cache={};this.key_ary=[]},size:function(){return this.key_ary.length}});var S=function(af,ae,ag){c.call(this,af);this.track=ae;this.subset=(ag!==undefined?ag:true)};p(S.prototype,c.prototype,{load_data:function(an,ai,al,af,ak){var am=this.track.view.chrom,ah={chrom:am,low:an,high:ai,mode:al,resolution:af,dataset_id:this.track.dataset_id,hda_ldda:this.track.hda_ldda};$.extend(ah,ak);if(this.track.filters_manager){var ao=[];var ae=this.track.filters_manager.filters;for(var aj=0;aj<ae.length;aj++){ao[ao.length]=ae[aj].name}ah.filter_cols=JSON.stringify(ao)}var ag=this;return $.getJSON(this.track.data_url,ah,function(ap){ag.set_data(an,ai,ap)})},get_data:function(ae,ai,aj,af,ah){var ag=this.get(ae,ai);if(ag&&(is_deferred(ag)||this.track.data_and_mode_compatible(ag,aj))){return ag}ag=this.load_data(ae,ai,aj,af,ah);this.set_data(ae,ai,ag);return ag},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(am,ah,al,ag,ak,ai){var an=this.get(am,ah);if(!(an&&this.track.data_and_mode_compatible(an,al))){console.log("ERROR: no current data for: ",this.track,am,ah,al,ag,ak);return}an.stale=true;var af=am;if(ai===this.DEEP_DATA_REQ){$.extend(ak,{start_val:an.data.length+1})}else{if(ai===this.BROAD_DATA_REQ){af=(an.max_high?an.max_high:an.data[an.data.length-1][2])+1}}var ae=this,aj=this.load_data(af,ah,al,ag,ak);new_data_available=$.Deferred();this.set_data(am,ah,new_data_available);$.when(aj).then(function(ao){if(ao.data){ao.data=an.data.concat(ao.data);if(ao.max_low){ao.max_low=an.max_low}if(ao.message){ao.message=ao.message.replace(/[0-9]+/,ao.data.length)}}ae.set_data(am,ah,ao);new_data_available.resolve(ao)});return new_data_available},get:function(ae,af){return c.prototype.get.call(this,this.gen_key(ae,af))},set_data:function(af,ag,ae){return this.set(this.gen_key(af,ag),ae)},gen_key:function(ae,ag){var af=ae+"_"+ag;return af},split_key:function(ae){return ae.split("_")}});var G=function(af,ae,ag){S.call(this,af,ae,ag)};p(G.prototype,S.prototype,c.prototype,{get:S.prototype.get,load_data:function(ae,ah,ai,af,ag){if(af>1){return{data:null}}return S.prototype.load_data.call(this,ae,ah,ai,af,ag)}});var q=function(ah,af,ae,ag,aj){if(!q.id_counter){q.id_counter=0}this.id=q.id_counter++;this.name=ah;this.view=af;this.container=ae;this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ah}],saved_values:ag,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=aj;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(ak){ak.stopPropagation()});var ai=this;this.container_div.hover(function(){ai.icons_div.show()},function(){ai.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};q.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ae){if(ae.content_visible){ae.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ae.hide_contents();ae.content_visible=false}else{ae.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ae.content_visible=true;ae.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(af){var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(){af.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",ag);show_modal("Configure",af.config.build_form(),{Cancel:ah,OK:ae})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ae){$(".tipsy").remove();ae.remove()}}];p(q.prototype,{init:function(){},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},from_dict:function(ae){},update_icons:function(){},set_name:function(ae){this.old_name=this.name;this.name=ae;this.name_div.text(this.name)},revert_name:function(){this.name=this.old_name;this.name_div.text(this.name)},remove:function(){this.container.remove_drawable(this);this.container_div.hide(0,function(){$(this).remove();view.update_intro_div();view.has_changes=true})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(af,aj,ai,ah,ae){var ag=this;this.action_icons[af]=$("<a/>").attr("href","javascript:void(0);").attr("title",aj).addClass("icon-button").addClass(ai).tipsy({gravity:"s"}).click(function(){ah(ag)}).appendTo(this.icons_div)},build_action_icons:function(ae){var ag;for(var af=0;af<ae.length;af++){ag=ae[af];this.add_action_icon(ag.name,ag.title,ag.css_class,ag.on_click_fn,ag.prepend)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){}});var x=function(ai,ah,af,ae,ag,aj){q.call(this,ah,af,ae,ag,aj);this.obj_type=ai;this.drawables=[]};p(x.prototype,q.prototype,{init:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae].init()}},_draw:function(){for(var ae=0;ae<this.drawables.length;ae++){this.drawables[ae]._draw()}},to_dict:function(){var af=[];for(var ae=0;ae<this.drawables.length;ae++){af.push(this.drawables[ae].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:af}},from_dict:function(ak,ae){var aj=new this.constructor(ak.name,view,ae,ak.prefs,view.viewport_container,view);var af,ai,ah;for(var ag=0;ag<ak.drawables.length;ag++){af=ak.drawables[ag];ai=af.obj_type;if(!ai){ai=af.track_type}ah=addable_objects[ai].prototype.from_dict(af,aj);aj.add_drawable(ah)}return aj},add_drawable:function(ae){this.drawables.push(ae);ae.container=this},add_drawable_before:function(ag,ae){var af=this.drawables.indexOf(ae);if(af!=-1){this.drawables.splice(af,0,ag);return true}return false},replace_drawable:function(ag,ae,af){var ah=this.drawables.indexOf(ag);if(ah!==-1){this.drawables[ah]=ae;if(af){ag.container_div.replaceWith(ae.container_div)}}return ah},remove_drawable:function(af){var ae=this.drawables.indexOf(af);if(ae!=-1){this.drawables.splice(ae,1);af.container=null;return true}return false},move_drawable:function(af,ag){var ae=this.drawables.indexOf(af);if(ae!=-1){this.drawables.splice(ae,1);this.drawables.splice(ag,0,af);return true}return false}});var P=function(ah,af,ae,ag){x.call(this,"DrawableGroup",ah,af,ae,ag,"group-handle");this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);l(this.container_div,this);l(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this)};p(P.prototype,q.prototype,x.prototype,{action_icons_def:[{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ae){ae.show_composite_track()}}].concat(q.prototype.action_icons_def),build_container_div:function(){var ae=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ae)}return ae},build_header_div:function(){var ae=$("<div/>").addClass("track-header");ae.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ae);return ae},hide_contents:function(){this.content_div.hide()},show_contents:function(){this.content_div.show();this.request_draw()},update_icons:function(){var ag,ai=true,ah=this.drawables[0].get_type(),ae=0;for(var af=0;af<this.drawables.length;af++){ag=this.drawables[af];if(ag.get_type()!==ah){can_composite=false;break}if(ag instanceof d){ae++}}if(ai||ae===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".tipsy").remove()}},show_composite_track:function(){var ae=new h("Composite Track",this.view,this,this.drawables);this.add_drawable(ae);ae.request_draw()},add_drawable:function(ae){x.prototype.add_drawable.call(this,ae);this.update_icons()},remove_drawable:function(ae){x.prototype.remove_drawable.call(this,ae);this.update_icons()},from_dict:function(ah,ae){var ag=x.prototype.from_dict.call(this,ah,ae);for(var af=0;af<ag.drawables.length;af++){ag.content_div.append(ag.drawables[af].container_div)}return ag}});var ab=function(ae,ah,ag,af){x.call(this,"View");this.container=ae;this.chrom=null;this.vis_id=ag;this.dbkey=af;this.title=ah;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.init();this.canvas_manager=new ad(ae.get(0).ownerDocument);this.reset()};p(ab.prototype,x.prototype,{init:function(){var ag=this.container,ae=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ag);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ag);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ag);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;l(this.viewport_container,ae);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var ah=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){add_tracks()});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("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").addClass("no-autocomplete").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var af=function(ai){if(ai.type==="focusout"||(ai.keyCode||ai.which)===13||(ai.keyCode||ai.which)===27){if((ai.keyCode||ai.which)!==27){ae.go_to($(this).val())}$(this).hide();$(this).val("");ae.location_span.show();ae.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",af).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tipsy({gravity:"n"}).appendTo(this.nav_controls);this.location_span.click(function(){ae.location_span.hide();ae.chrom_select.hide();ae.nav_input.val(ae.chrom+":"+ae.low+"-"+ae.high);ae.nav_input.css("display","inline-block");ae.nav_input.select();ae.nav_input.focus()});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tipsy({gravity:"n"}).click(function(){ae.zoom_out();ae.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tipsy({gravity:"n"}).click(function(){ae.zoom_in();ae.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ae.change_chrom(ae.chrom_select.val())});this.browser_content_div.click(function(ai){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ai){ae.zoom_in(ai.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ai,aj){this.current_x=aj.offsetX}).bind("drag",function(ai,ak){var al=ak.offsetX-this.current_x;this.current_x=ak.offsetX;var aj=Math.round(al/ae.viewport_container.width()*(ae.max_high-ae.max_low));ae.move_delta(-aj)});this.overview_close.click(function(){ae.reset_overview()});this.viewport_container.bind("draginit",function(ai,aj){if(ai.clientX>ae.viewport_container.width()-16){return false}}).bind("dragstart",function(ai,aj){aj.original_low=ae.low;aj.current_height=ai.clientY;aj.current_x=aj.offsetX}).bind("drag",function(ak,am){var ai=$(this);var an=am.offsetX-am.current_x;var aj=ai.scrollTop()-(ak.clientY-am.current_height);ai.scrollTop(aj);am.current_height=ak.clientY;am.current_x=am.offsetX;var al=Math.round(an/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}).bind("mousewheel",function(ak,am,aj,ai){if(aj){aj*=50;var al=Math.round(-aj/ae.viewport_container.width()*(ae.high-ae.low));ae.move_delta(al)}});this.top_labeltrack.bind("dragstart",function(ai,aj){return $("<div />").css({height:ae.browser_content_div.height()+ae.top_labeltrack.height()+ae.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(am,an){$(an.proxy).css({left:Math.min(am.pageX,an.startX),width:Math.abs(am.pageX-an.startX)});var aj=Math.min(am.pageX,an.startX)-ae.container.offset().left,ai=Math.max(am.pageX,an.startX)-ae.container.offset().left,al=(ae.high-ae.low),ak=ae.viewport_container.width();ae.update_location(Math.round(aj/ak*al)+ae.low,Math.round(ai/ak*al)+ae.low)}).bind("dragend",function(an,ao){var aj=Math.min(an.pageX,ao.startX),ai=Math.max(an.pageX,ao.startX),al=(ae.high-ae.low),ak=ae.viewport_container.width(),am=ae.low;ae.low=Math.round(aj/ak*al)+am;ae.high=Math.round(ai/ak*al)+am;$(ao.proxy).remove();ae.request_redraw()});this.add_label_track(new aa(this,{content_div:this.top_labeltrack}));this.add_label_track(new aa(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){ae.resize_window()});$(document).bind("redraw",function(){ae.redraw()});this.reset();$(window).trigger("resize")},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},update_location:function(ae,af){this.location_span.text(commatize(ae)+" - "+commatize(af));this.nav_input.val(this.chrom+":"+commatize(ae)+"-"+commatize(af))},load_chroms:function(ag){ag.num=v;ag.dbkey=this.dbkey;var ae=this,af=$.Deferred();$.ajax({url:chrom_url,data:ag,dataType:"json",success:function(ai){if(ai.chrom_info.length===0){alert("Invalid chromosome: "+ag.chrom);return}if(ai.reference){ae.add_label_track(new z(ae))}ae.chrom_data=ai.chrom_info;var al='<option value="">Select Chrom/Contig</option>';for(var ak=0,ah=ae.chrom_data.length;ak<ah;ak++){var aj=ae.chrom_data[ak].chrom;al+='<option value="'+aj+'">'+aj+"</option>"}if(ai.prev_chroms){al+='<option value="previous">Previous '+v+"</option>"}if(ai.next_chroms){al+='<option value="next">Next '+v+"</option>"}ae.chrom_select.html(al);ae.chrom_start_index=ai.start_index;af.resolve(ai)},error:function(){alert("Could not load chroms for this dbkey:",ae.dbkey)}});return af},change_chrom:function(aj,af,al){if(!aj||aj==="None"){return}var ag=this;if(aj==="previous"){ag.load_chroms({low:this.chrom_start_index-v});return}if(aj==="next"){ag.load_chroms({low:this.chrom_start_index+v});return}var ak=$.grep(ag.chrom_data,function(am,an){return am.chrom===aj})[0];if(ak===undefined){ag.load_chroms({chrom:aj},function(){ag.change_chrom(aj,af,al)});return}else{if(aj!==ag.chrom){ag.chrom=aj;ag.chrom_select.val(ag.chrom);ag.max_high=ak.len-1;ag.reset();ag.request_redraw(true);for(var ai=0,ae=ag.drawables.length;ai<ae;ai++){var ah=ag.drawables[ai];if(ah.init){ah.init()}}}if(af!==undefined&&al!==undefined){ag.low=Math.max(af,0);ag.high=Math.min(al,ag.max_high)}ag.reset_overview();ag.request_redraw()}},go_to:function(ai){ai=ai.replace(/ |,/g,"");var am=this,ae,ah,af=ai.split(":"),ak=af[0],al=af[1];if(al!==undefined){try{var aj=al.split("-");ae=parseInt(aj[0],10);ah=parseInt(aj[1],10)}catch(ag){return false}}am.change_chrom(ak,ae,ah)},move_fraction:function(ag){var ae=this;var af=ae.high-ae.low;this.move_delta(ag*af)},move_delta:function(ag){var ae=this;var af=ae.high-ae.low;if(ae.low-ag<ae.max_low){ae.low=ae.max_low;ae.high=ae.max_low+af}else{if(ae.high-ag>ae.max_high){ae.high=ae.max_high;ae.low=ae.max_high-af}else{ae.high-=ag;ae.low-=ag}}ae.request_redraw()},add_drawable:function(ae){x.prototype.add_drawable.call(this,ae);ae.init();this.has_changes=true;this.update_intro_div()},add_label_track:function(ae){ae.view=this;ae.init();this.label_tracks.push(ae)},remove_drawable:function(ag,af){x.prototype.remove_drawable.call(this,ag);if(af){var ae=this;ag.container_div.hide(0,function(){$(this).remove();ae.update_intro_div()});this.has_changes=true}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(am,ae,al,af){var ak=this,ai=(af?[af]:ak.drawables),ag;var af;for(var aj=0;aj<ai.length;aj++){af=ai[aj];ag=-1;for(var ah=0;ah<ak.tracks_to_be_redrawn.length;ah++){if(ak.tracks_to_be_redrawn[ah][0]===af){ag=ah;break}}if(ag<0){ak.tracks_to_be_redrawn.push([af,ae,al])}else{ak.tracks_to_be_redrawn[aj][1]=ae;ak.tracks_to_be_redrawn[aj][2]=al}}requestAnimationFrame(function(){ak._redraw(am)})},_redraw:function(ao){var al=this.low,ah=this.high;if(al<this.max_low){al=this.max_low}if(ah>this.max_high){ah=this.max_high}var an=this.high-this.low;if(this.high!==0&&an<this.min_separation){ah=al+this.min_separation}this.low=Math.floor(al);this.high=Math.ceil(ah);this.resolution=Math.pow(A,Math.ceil(Math.log((this.high-this.low)/Q)/Math.log(A)));this.zoom_res=Math.pow(u,Math.max(0,Math.ceil(Math.log(this.resolution,u)/Math.log(u))));var ae=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ak=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ap=13;this.overview_box.css({left:ae,width:Math.max(ap,ak)}).show();if(ak<ap){this.overview_box.css("left",ae-(ap-ak)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ae,width:ak})}this.update_location(this.low,this.high);if(!ao){var ag,af,am;for(var ai=0,aj=this.tracks_to_be_redrawn.length;ai<aj;ai++){ag=this.tracks_to_be_redrawn[ai][0];af=this.tracks_to_be_redrawn[ai][1];am=this.tracks_to_be_redrawn[ai][2];if(ag){ag._draw(af,am)}}this.tracks_to_be_redrawn=[];for(ai=0,aj=this.label_tracks.length;ai<aj;ai++){this.label_tracks[ai]._draw()}}},zoom_in:function(af,ag){if(this.max_high===0||this.high-this.low<this.min_separation){return}var ah=this.high-this.low,ai=ah/2+this.low,ae=(ah/this.zoom_factor)/2;if(af){ai=af/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ai-ae);this.high=Math.round(ai+ae);this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var af=this.high-this.low,ag=af/2+this.low,ae=(af*this.zoom_factor)/2;this.low=Math.round(ag-ae);this.high=Math.round(ag+ae);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(ag){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ag.dataset_id){return}this.overview_viewport.find(".track").remove()}var af=ag.copy({content_div:this.overview_viewport}),ae=this;af.header_div.hide();af.is_overview=true;ae.overview_drawable=af;this.overview_drawable.postdraw_actions=function(){ae.overview_highlight.show().height(ae.overview_drawable.content_div.height());ae.overview_viewport.height(ae.overview_drawable.content_div.height()+ae.overview_box.outerHeight());ae.overview_close.show();ae.resize_window()};ae.overview_drawable.request_draw();ae.has_changes=true},reset_overview:function(){$(".tipsy").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 r=function(ag,ak){this.track=ag;this.name=ak.name;this.params=[];var ar=ak.params;for(var ah=0;ah<ar.length;ah++){var am=ar[ah],af=am.name,aq=am.label,ai=unescape(am.html),at=am.value,ao=am.type;if(ao==="number"){this.params[this.params.length]=new f(af,aq,ai,at,am.min,am.max)}else{if(ao=="select"){this.params[this.params.length]=new N(af,aq,ai,at)}else{console.log("WARNING: unrecognized tool parameter type:",af,ao)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(av){av.stopPropagation()}).click(function(av){av.stopPropagation()}).bind("dblclick",function(av){av.stopPropagation()});var ap=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var an=this.params;var al=this;$.each(this.params,function(aw,az){var ay=$("<div>").addClass("param-row").appendTo(al.parent_div);var av=$("<div>").addClass("param-label").text(az.label).appendTo(ay);var ax=$("<div/>").addClass("param-input").html(az.html).appendTo(ay);ax.find(":input").val(az.value);$("<div style='clear: both;'/>").appendTo(ay)});this.parent_div.find("input").click(function(){$(this).select()});var au=$("<div>").addClass("param-row").appendTo(this.parent_div);var aj=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(au);var ae=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(au);var al=this;ae.click(function(){al.run_on_region()});aj.click(function(){al.run_on_dataset()})};p(r.prototype,{get_param_values_dict:function(){var ae={};this.parent_div.find(":input").each(function(){var af=$(this).attr("name"),ag=$(this).val();ae[af]=JSON.stringify(ag)});return ae},get_param_values:function(){var af=[];var ae={};this.parent_div.find(":input").each(function(){var ag=$(this).attr("name"),ah=$(this).val();if(ag){af[af.length]=ah}});return af},run_on_dataset:function(){var ae=this;ae.run({dataset_id:this.track.original_dataset_id,tool_id:ae.name},null,function(af){show_modal(ae.name+" is Running",ae.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var af={dataset_id:this.track.original_dataset_id,chrom:this.track.view.chrom,low:this.track.view.low,high:this.track.view.high,tool_id:this.name},aj=this.track,ag=af.tool_id+aj.tool_region_and_parameters_str(af.chrom,af.low,af.high),ae;if(aj.container===view){var ai=new P(this.name,this.track.view);var ah=aj.container.replace_drawable(aj,ai,false);ai.container_div.insertBefore(aj.view.content_div.children()[ah]);ai.add_drawable(aj);aj.container_div.appendTo(ai.content_div);ae=ai}else{ae=aj.container}var ak=new aj.constructor(ag,view,ae,"hda");ak.init_for_tool_data();ak.change_mode(aj.mode);ae.add_drawable(ak);ak.content_div.text("Starting job.");this.run(af,ak,function(al){ak.dataset_id=al.dataset_id;ak.content_div.text("Running job.");ak.init()})},run:function(af,ag,ah){$.extend(af,this.get_param_values_dict());var ae=function(){$.getJSON(rerun_tool_url,af,function(ai){if(ai==="no converter"){ag.container_div.addClass("error");ag.content_div.text(J)}else{if(ai.error){ag.container_div.addClass("error");ag.content_div.text(w+ai.message)}else{if(ai==="pending"){ag.container_div.addClass("pending");ag.content_div.text("Converting input data so that it can be used quickly with tool.");setTimeout(ae,2000)}else{ah(ai)}}}})};ae()}});var N=function(af,ae,ag,ah){this.name=af;this.label=ae;this.html=ag;this.value=ah};var f=function(ag,af,ai,aj,ah,ae){N.call(this,ag,af,ai,aj);this.min=ah;this.max=ae};var g=function(af,ae,ag,ah){this.name=af;this.index=ae;this.tool_id=ag;this.tool_exp_name=ah};var U=function(af,ae,ag,ah){g.call(this,af,ae,ag,ah);this.low=-Number.MAX_VALUE;this.high=Number.MAX_VALUE;this.min=Number.MAX_VALUE;this.max=-Number.MAX_VALUE;this.container=null;this.slider=null;this.slider_label=null};p(U.prototype,{applies_to:function(ae){if(ae.length>this.index){return true}return false},keep:function(ae){if(!this.applies_to(ae)){return true}var af=ae[this.index];return(isNaN(af)||(af>=this.low&&af<=this.high))},update_attrs:function(af){var ae=false;if(!this.applies_to(af)){return ae}if(af[this.index]<this.min){this.min=Math.floor(af[this.index]);ae=true}if(af[this.index]>this.max){this.max=Math.ceil(af[this.index]);ae=true}return ae},update_ui_elt:function(){if(this.min!=this.max){this.container.show()}else{this.container.hide()}var ag=function(aj,ah){var ai=ah-aj;return(ai<=2?0.01:1)};var af=this.slider.slider("option","min"),ae=this.slider.slider("option","max");if(this.min<af||this.max>ae){this.slider.slider("option","min",this.min);this.slider.slider("option","max",this.max);this.slider.slider("option","step",ag(this.min,this.max));this.slider.slider("option","values",[this.min,this.max])}}});var Z=function(ag,ap){this.track=ag;this.filters=[];for(var ak=0;ak<ap.length;ak++){var ae=ap[ak],af=ae.name,ao=ae.type,am=ae.index,ar=ae.tool_id,ah=ae.tool_exp_name;if(ao==="int"||ao==="float"){this.filters[ak]=new U(af,am,ar,ah)}else{console.log("ERROR: unsupported filter: ",af,ao)}}var an=function(at,au,av){at.click(function(){var aw=au.text();max=parseFloat(av.slider("option","max")),input_size=(max<=1?4:max<=1000000?max.toString().length:6),multi_value=false;if(av.slider("option","values")){input_size=2*input_size+1;multi_value=true}au.text("");$("<input type='text'/>").attr("size",input_size).attr("maxlength",input_size).attr("value",aw).appendTo(au).focus().select().click(function(ax){ax.stopPropagation()}).blur(function(){$(this).remove();au.text(aw)}).keyup(function(aB){if(aB.keyCode===27){$(this).trigger("blur")}else{if(aB.keyCode===13){var az=av.slider("option","min"),ax=av.slider("option","max"),aA=function(aC){return(isNaN(aC)||aC>ax||aC<az)},ay=$(this).val();if(!multi_value){ay=parseFloat(ay);if(aA(ay)){alert("Parameter value must be in the range ["+az+"-"+ax+"]");return $(this)}}else{ay=ay.split("-");ay=[parseFloat(ay[0]),parseFloat(ay[1])];if(aA(ay[0])||aA(ay[1])){alert("Parameter value must be in the range ["+az+"-"+ax+"]");return $(this)}}av.slider((multi_value?"values":"value"),ay)}}})})};this.parent_div=$("<div/>").addClass("filters").hide();this.parent_div.bind("drag",function(at){at.stopPropagation()}).click(function(at){at.stopPropagation()}).bind("dblclick",function(at){at.stopPropagation()}).bind("keydown",function(at){at.stopPropagation()});var ai=this;$.each(this.filters,function(az,au){au.container=$("<div/>").addClass("filter-row slider-row").appendTo(ai.parent_div);var at=$("<div/>").addClass("elt-label").appendTo(au.container);var aC=$("<span/>").addClass("slider-name").text(au.name+" ").appendTo(at);var av=$("<span/>");var aw=$("<span/>").addClass("slider-value").appendTo(at).append("[").append(av).append("]");var aB=$("<div/>").addClass("slider").appendTo(au.container);au.control_element=$("<div/>").attr("id",au.name+"-filter-control").appendTo(aB);var ax=[0,0];au.control_element.slider({range:true,min:Number.MAX_VALUE,max:-Number.MIN_VALUE,values:[0,0],slide:function(aF,aG){var aE=aG.values;av.text(aE[0]+"-"+aE[1]);au.low=aE[0];au.high=aE[1];ai.track.request_draw(true,true)},change:function(aE,aF){au.control_element.slider("option","slide").call(au.control_element,aE,aF)}});au.slider=au.control_element;au.slider_label=av;an(aw,av,au.control_element);var aD=$("<div/>").addClass("display-controls").appendTo(au.container),ay=create_action_icon("Use filter for data transparency","layer-transparent",function(){if(ai.alpha_filter!==au){ai.alpha_filter=au;$(".layer-transparent").removeClass("active").hide();ay.addClass("active").show()}else{ai.alpha_filter=null;ay.removeClass("active")}ai.track.request_draw(true,true)}).appendTo(aD).hide(),aA=create_action_icon("Use filter for data height","arrow-resize-090",function(){if(ai.height_filter!==au){ai.height_filter=au;$(".arrow-resize-090").removeClass("active").hide();aA.addClass("active").show()}else{ai.height_filter=null;aA.removeClass("active")}ai.track.request_draw(true,true)}).appendTo(aD).hide();au.container.hover(function(){ay.show();aA.show()},function(){if(ai.alpha_filter!==au){ay.hide()}if(ai.height_filter!==au){aA.hide()}});$("<div style='clear: both;'/>").appendTo(au.container)});if(this.filters.length!==0){var aq=$("<div/>").addClass("param-row").appendTo(this.parent_div);var al=$("<input type='submit'/>").attr("value","Run on complete dataset").appendTo(aq);var aj=this;al.click(function(){aj.run_on_dataset()})}};p(Z.prototype,{reset_filters:function(){for(var ae=0;ae<this.filters.length;ae++){filter=this.filters[ae];filter.slider.slider("option","values",[filter.min,filter.max])}this.alpha_filter=null;this.height_filter=null},run_on_dataset:function(){var am=function(aq,ao,ap){if(!(ao in aq)){aq[ao]=ap}return aq[ao]};var ag={},ae,af,ah;for(var ai=0;ai<this.filters.length;ai++){ae=this.filters[ai];if(ae.tool_id){if(ae.min!=ae.low){af=am(ag,ae.tool_id,[]);af[af.length]=ae.tool_exp_name+" >= "+ae.low}if(ae.max!=ae.high){af=am(ag,ae.tool_id,[]);af[af.length]=ae.tool_exp_name+" <= "+ae.high}}}var ak=[];for(var an in ag){ak[ak.length]=[an,ag[an]]}var al=ak.length;(function aj(av,ar){var ap=ar[0],aq=ap[0],au=ap[1],at="("+au.join(") and (")+")",ao={cond:at,input:av,target_dataset_id:av,tool_id:aq},ar=ar.slice(1);$.getJSON(run_tool_url,ao,function(aw){if(aw.error){show_modal("Filter Dataset","Error running tool "+aq,{Close:hide_modal})}else{if(ar.length===0){show_modal("Filtering Dataset","Filter(s) are running on the complete dataset. Outputs are in dataset's history.",{Close:hide_modal})}else{aj(aw.dataset_id,ar)}}})})(this.track.dataset_id,ak)}});var B=function(ae,af){L.Scaler.call(this,af);this.filter=ae};B.prototype.gen_val=function(ae){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ae[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var E=function(ae){this.track=ae.track;this.params=ae.params;this.values={};this.restore_values((ae.saved_values?ae.saved_values:{}));this.onchange=ae.onchange};p(E.prototype,{restore_values:function(ae){var af=this;$.each(this.params,function(ag,ah){if(ae[ah.key]!==undefined){af.values[ah.key]=ae[ah.key]}else{af.values[ah.key]=ah.default_value}})},build_form:function(){var ah=this;var ae=$("<div />");var ag;function af(ak,ai){for(var am=0;am<ak.length;am++){ag=ak[am];if(ag.hidden){continue}var aj="param_"+am;var aq=ah.values[ag.key];var ar=$("<div class='form-row' />").appendTo(ai);ar.append($("<label />").attr("for",aj).text(ag.label+":"));if(ag.type==="bool"){ar.append($('<input type="checkbox" />').attr("id",aj).attr("name",aj).attr("checked",aq))}else{if(ag.type==="text"){ar.append($('<input type="text"/>').attr("id",aj).val(aq).click(function(){$(this).select()}))}else{if(ag.type=="select"){var ao=$("<select />").attr("id",aj);for(var al=0;al<ag.options.length;al++){$("<option/>").text(ag.options[al].label).attr("value",ag.options[al].value).appendTo(ao)}ao.val(aq);ar.append(ao)}else{if(ag.type==="color"){var an=$("<input />").attr("id",aj).attr("name",aj).val(aq);var ap=$("<div class='tipsy tipsy-west' style='position: absolute;' />").hide();(function(at,au){var aw=$("<div style='background-color: black; padding: 10px;'></div>").appendTo(au);var av=$("<div/>").appendTo(aw).farbtastic({width:100,height:100,callback:at,color:aq});$("<div />").append(at).append(au).appendTo(ar).bind("click",function(ax){$(".tipsy").hide();au.css({left:$(this).position().left+$(at).width()+5,top:$(this).position().top-($(au).height()/2)+($(at).height()/2)}).show();$(document).bind("click.color-picker",function(){au.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()})})(an,ap)}else{ar.append($("<input />").attr("id",aj).attr("name",aj).val(aq))}}}}if(ag.help){ar.append($("<div class='help'/>").text(ag.help))}}}af(this.params,ae);return ae},update_from_form:function(ae){var ag=this;var af=false;$.each(this.params,function(ah,aj){if(!aj.hidden){var ak="param_"+ah;var ai=ae.find("#"+ak).val();if(aj.type==="float"){ai=parseFloat(ai)}else{if(aj.type==="int"){ai=parseInt(ai)}else{if(aj.type==="bool"){ai=ae.find("#"+ak).is(":checked")}}}if(ai!==ag.values[aj.key]){ag.values[aj.key]=ai;af=true}}});if(af){this.onchange()}}});var b=function(ae,ah,ag,af,ai){this.track=ae;this.index=ah;this.low=ah*Q*ag;this.high=(ah+1)*Q*ag;this.resolution=ag;this.html_elt=$("<div class='track-tile'/>").append(af);this.data=ai;this.stale=false};b.prototype.predisplay_actions=function(){};var k=function(ae,ah,ag,af,ai,aj){b.call(this,ae,ah,ag,af,ai);this.max_val=aj};p(k.prototype,b.prototype);var O=function(ah,am,ai,ag,ak,ar,al,at,af,ap){b.call(this,ah,am,ai,ag,ak);this.mode=al;this.feature_mapper=ap;this.has_icons=false;if(at||!af){this.has_icons=true;var an=this;ag=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:C-1,width:ag.width}).prependTo(this.html_elt);if(!af){var ao=$("<a href='javascript:void(0);'/>").addClass("icon exclamation").attr("title","To minimize track height, not all features in this region are displayed. Click to display more.").tipsy({gravity:"s"}).appendTo(message_div).click(function(){$(".tipsy").hide();an.track.slotters[ar].max_rows*=2;an.track.request_draw(true)})}if(at){var aq=ak.length,aj=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+aq+" features in this region were obtained from server. Click to get more data including depth").tipsy({gravity:"s"}).appendTo(message_div),ae=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+aq+" features in this region were obtained from server. Click to get more data excluding depth").tipsy({gravity:"s"}).appendTo(message_div);aj.click(function(){an.stale=true;ah.data_manager.get_more_data(an.low,an.high,ah.mode,an.resolution,{},ah.data_manager.DEEP_DATA_REQ);$(".tipsy").hide();ah.request_draw()}).dblclick(function(au){au.stopPropagation()});ae.click(function(){an.stale=true;ah.data_manager.get_more_data(an.low,an.high,ah.mode,an.resolution,{},ah.data_manager.BROAD_DATA_REQ);$(".tipsy").hide();ah.request_draw()}).dblclick(function(au){au.stopPropagation()})}}};p(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var af=this,ae={};if(af.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).siblings(".feature-popup").remove()}).mousemove(function(aq){if(!this.hovered){return}var al=$(this).offset(),ap=aq.pageX-al.left,ao=aq.pageY-al.top,av=af.feature_mapper.get_feature_data(ap,ao),am=(av?av[0]:null);$(this).siblings(".feature-popup").each(function(){if(!am||$(this).attr("id")!==am.toString()){$(this).remove()}});if(av){var ah=ae[am];if(!ah){var am=av[0],ar={name:av[3],start:av[1],end:av[2],strand:av[4]},ak=af.track.filters_manager.filters,aj;for(var an=0;an<ak.length;an++){aj=ak[an];ar[aj.name]=av[aj.index]}var ah=$("<div/>").attr("id",am).addClass("feature-popup"),aw=$("<table/>"),au,at,ax;for(au in ar){at=ar[au];ax=$("<tr/>").appendTo(aw);$("<th/>").appendTo(ax).text(au);$("<td/>").attr("align","left").appendTo(ax).text(typeof(at)=="number"?Y(at,2):at)}ah.append($("<div class='feature-popup-inner'>").append(aw));ae[am]=ah}ah.appendTo($(af.html_elt).parent());var ai=ap+parseInt(af.html_elt.css("left"))-ah.width()/2,ag=ao+parseInt(af.html_elt.css("top"))+7;ah.css("left",ai+"px").css("top",ag+"px")}else{if(!aq.isPropagationStopped()){aq.stopPropagation();$(this).siblings().each(function(){$(this).trigger(aq)})}}}).mouseleave(function(){$(this).siblings(".feature-popup").remove()})};var i=function(ah,af,ae,ag,aj,ai,ak){q.call(this,ah,af,ae,{},"draghandle");this.data_url=(ai?ai:default_data_url);this.data_url_extra_params={};this.data_query_wait=(ak?ak:K);this.dataset_check_url=converted_datasets_state_url;this.data_manager=(aj?aj:new S(H,this));this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div)}};p(i.prototype,q.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},q.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ae){ae.view.set_overview(ae)}},q.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ae){ae.filters_div.toggle();ae.filters_manager.reset_filters()}},{name:"tools_icon",title:"Tools",css_class:"tools-icon",on_click_fn:function(ae){ae.dynamic_tool_div.toggle();if(ae.dynamic_tool_div.is(":visible")){ae.set_name(ae.name+ae.tool_region_and_parameters_str())}else{ae.revert_name()}$(".tipsy").remove()}},q.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&q.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ae=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ae)}this.name_div=$("<div/>").addClass("track-name").appendTo(ae).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ae},build_action_icons:function(){q.prototype.build_action_icons.call(this,this.action_icons_def);var af=this;if(af.display_modes!==undefined){var aj=(af.config&&af.config.values.mode?af.config.values.mode:af.display_modes[0]);af.mode=aj;this.action_icons.mode_icon.attr("title","Set display mode (now: "+af.mode+")");var ah={};for(var ag=0,ae=af.display_modes.length;ag<ae;ag++){var ai=af.display_modes[ag];ah[ai]=function(ak){return function(){af.change_mode(ak);af.icons_div.show();af.container_div.mouseleave(function(){af.icons_div.hide()})}}(ai)}make_popupmenu(this.action_icons.mode_icon,ah)}},hide_contents:function(){this.content_div.children().remove();this.content_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.content_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof aa){return"LabelTrack"}else{if(this instanceof z){return"ReferenceTrack"}else{if(this instanceof j){return"LineTrack"}else{if(this instanceof V){return"ReadTrack"}else{if(this instanceof T){return"VcfTrack"}else{if(this instanceof h){return"CompositeTrack"}else{if(this instanceof d){return"FeatureTrack"}}}}}}}return""},init:function(){var ae=this;ae.enabled=false;ae.tile_cache.clear();ae.data_manager.clear();ae.content_div.css("height","auto");ae.content_div.children().remove();ae.container_div.removeClass("nodata error pending");if(!ae.dataset_id){return}$.getJSON(converted_datasets_state_url,{hda_ldda:ae.hda_ldda,dataset_id:ae.dataset_id,chrom:ae.view.chrom},function(af){if(!af||af==="error"||af.kind==="error"){ae.container_div.addClass("error");ae.content_div.text(o);if(af.message){var ag=$(" <a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+af.message+"</pre>",{Close:hide_modal})});ae.content_div.append(ag)}}else{if(af==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(af==="no data"||(af.data!==undefined&&(af.data===null||af.data.length===0))){ae.container_div.addClass("nodata");ae.content_div.text(D)}else{if(af==="pending"){ae.container_div.addClass("pending");ae.content_div.text(t);setTimeout(function(){ae.init()},ae.data_query_wait)}else{if(af.status==="data"){if(af.valid_chroms){ae.valid_chroms=af.valid_chroms;ae.update_icons()}ae.content_div.text(X);if(ae.view.chrom){ae.content_div.text("");ae.content_div.css("height",ae.height_px+"px");ae.enabled=true;$.when(ae.predraw_init()).done(function(){ae.container_div.removeClass("nodata error pending");ae.request_draw()})}}}}}}});this.update_icons()},predraw_init:function(){}});var M=function(ai,ag,af,ah,al,ak,aj){i.call(this,ai,ag,af,ah,aj);var ae=this,ag=ae.view;m(ae.container_div,ae.drag_handle_class,".group",ae);this.filters_manager=new Z(this,(al!==undefined?al:{}));this.filters_available=false;this.filters_visible=false;this.tool=(ak!==undefined&&obj_length(ak)>0?new r(this,ak):undefined);this.tile_cache=new c(R);if(this.header_div){if(this.filters_manager){this.filters_div=this.filters_manager.parent_div;this.header_div.after(this.filters_div)}if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}};p(M.prototype,q.prototype,i.prototype,{copy:function(ae){var af=new this.constructor(this.name,this.view,ae,this.hda_ldda,this.dataset_id,this.prefs,this.filters,this.tool,this.data_manager);af.change_mode(this.mode);af.enabled=this.enabled;return af},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,}},from_dict:function(ag,af){var ae=new this.constructor(ag.name,view,af,ag.hda_ldda,ag.dataset_id,ag.prefs,ag.filters,ag.tool);if(ag.mode){ae.change_mode(ag.mode)}return ae},change_mode:function(af){var ae=this;ae.mode=af;ae.config.values.mode=af;ae.tile_cache.clear();ae.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ae.mode+")");return ae},update_icons:function(){var ae=this;if(ae.filters_available){ae.action_icons.filters_icon.show()}else{ae.action_icons.filters_icon.hide()}if(ae.tool){ae.action_icons.tools_icon.show()}else{ae.action_icons.tools_icon.hide()}},_gen_tile_cache_key:function(af,ag,ae){return af+"_"+ag+"_"+ae},request_draw:function(af,ae){this.view.request_redraw(false,af,ae,this)},_draw:function(ag,aq){if(!this.can_draw()){return}var ao=this.view.low,ak=this.view.high,am=ak-ao,ah=this.view.container.width(),au=ah/am,aj=this.view.resolution,at=this.content_div;if(this.is_overview){ao=this.view.max_low;ak=this.view.max_high;aj=Math.pow(A,Math.ceil(Math.log((view.max_high-view.max_low)/Q)/Math.log(A)));au=ah/(view.max_high-view.max_low)}if(!aq){this.content_div.children().addClass("remove")}this.max_height=0;var af=Math.floor(ao/aj/Q);var an=true;var ar=[];var ae=0;var al=function(av){return(av&&"track" in av)};while((af*Q*aj)<ak){var ap=this.draw_helper(ag,ah,af,aj,at,au);if(al(ap)){ar.push(ap)}else{an=false}af+=1;ae++}if(!aq){this.content_div.children(".remove").remove()}var ai=this;if(an){ai.postdraw_actions(ar,ah,au,aq)}},postdraw_actions:function(ah,ai,ak,ae){var ag=this;var aj=false;for(var af=0;af<ah.length;af++){if(ah[af].has_icons){aj=true;break}}if(aj){for(var af=0;af<ah.length;af++){tile=ah[af];if(!tile.has_icons){tile.html_elt.css("padding-top",C)}}}},draw_helper:function(ae,aq,aw,au,aj,ak,ar){var ap=this,az=this._gen_tile_cache_key(aq,ak,aw),ax=aw*Q*au,af=ax+Q*au;if(!ar){ar={}}var ay=(ae?undefined:ap.tile_cache.get(az));if(ay){ap.show_tile(ay,aj,ak);return ay}var an=true;var av=ap.data_manager.get_data(ax,af,ap.mode,au,ap.data_url_extra_params);if(is_deferred(av)){an=false}var al;if(view.reference_track&&ak>view.canvas_manager.char_width_px){al=view.reference_track.data_manager.get_data(ax,af,ap.mode,au,view.reference_track.data_url_extra_params);if(is_deferred(al)){an=false}}if(an){p(av,ar.more_tile_data);var am=ap.mode;if(am==="Auto"){am=ap.get_mode(av);ap.update_auto_mode(am)}var ag=ap.view.canvas_manager.new_canvas(),ah=ap._get_tile_bounds(aw,au),ax=ah[0],af=ah[1],aq=Math.ceil((af-ax)*ak)+ap.left_offset,ao=ap.get_canvas_height(av,am,ak,aq);ag.width=aq;ag.height=ao;var at=ag.getContext("2d");at.translate(this.left_offset,0);var ay=ap.draw_tile(av,at,am,au,aw,ak,al);if(ay!==undefined){ap.tile_cache.set(az,ay);ap.show_tile(ay,aj,ak)}return ay}var ai=$.Deferred();$.when(av,al).then(function(){view.request_redraw(false,false,false,ap);ai.resolve()});return ai},get_canvas_height:function(ae,ag,ah,af){return this.height_px},draw_tile:function(ae,ag,aj,ai,af,ak,ah){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ag,ai,aj){var af=this,ae=ag.html_elt;ag.predisplay_actions();var ah=(ag.low-(this.is_overview?this.view.max_low:this.view.low))*aj;if(this.left_offset){ah-=this.left_offset}ae.css({position:"absolute",top:0,left:ah,height:""});if(ae.hasClass("remove")){ae.removeClass("remove")}else{ai.append(ae)}af.max_height=Math.max(af.max_height,ae.height());af.content_div.css("height",af.max_height+"px");ai.children().css("height",af.max_height+"px")},_get_tile_bounds:function(ae,af){var ah=ae*Q*af,ai=Q*af,ag=(ah+ai<=this.view.max_high?ah+ai:this.view.max_high);return[ah,ag]},tool_region_and_parameters_str:function(ag,ae,ah){var af=this,ai=(ag!==undefined&&ae!==undefined&&ah!==undefined?ag+":"+ae+"-"+ah:"all");return" - region=["+ai+"], parameters=["+af.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ae,af){return true},init_for_tool_data:function(){this.data_url=raw_data_url;this.data_query_wait=1000;this.dataset_check_url=dataset_state_url;this.predraw_init=function(){var af=this;var ae=function(){if(af.data_manager.size()===0){setTimeout(ae,300)}else{af.data_url=default_data_url;af.data_query_wait=K;af.dataset_state_url=converted_datasets_state_url;$.getJSON(af.dataset_state_url,{dataset_id:af.dataset_id,hda_ldda:af.hda_ldda},function(ag){})}};ae()}}});var aa=function(af,ae){i.call(this,"label",af,ae,false,{});this.container_div.addClass("label-track")};p(aa.prototype,i.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ag=this.view,ah=ag.high-ag.low,ak=Math.floor(Math.pow(10,Math.floor(Math.log(ah)/Math.log(10)))),ae=Math.floor(ag.low/ak)*ak,ai=this.view.container.width(),af=$("<div style='position: relative; height: 1.3em;'></div>");while(ae<ag.high){var aj=(ae-ag.low)/ah*ai;af.append($("<div class='label'>"+commatize(ae)+"</div>").css({position:"absolute",left:aj-1}));ae+=ak}this.content_div.children(":first").remove();this.content_div.append(af)}});var h=function(ah,ag,af,ae){this.display_modes=ae[0].display_modes;M.call(this,ah,ag,af);this.drawables=[];this.left_offset=0;if(ae){var ak=[],aj;for(var ai=0;ai<ae.length;ai++){aj=ae[ai];ak.push(aj.dataset_id);this.drawables[ai]=aj.copy();if(aj.left_offset>this.left_offset){this.left_offset=aj.left_offset}}this.enabled=true}this.update_icons();this.obj_type="CompositeTrack"};p(h.prototype,M.prototype,{to_dict:x.prototype.to_dict,add_drawable:x.prototype.add_drawable,from_dict:function(ak,ae){var aj=new this.constructor(ak.name,view,ae,ak.prefs,view.viewport_container,view);var af,ai,ah;for(var ag=0;ag<ak.drawables.length;ag++){af=ak.drawables[ag];ai=af.obj_type;if(!ai){ai=af.track_type}ah=addable_objects[ai].prototype.from_dict(af);aj.add_drawable(ah)}return aj},change_mode:function(ae){M.prototype.change_mode.call(this,ae);for(var af=0;af<this.drawables.length;af++){this.drawables[af].change_mode(ae)}},init:function(){this.enabled=true;this.request_draw()},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide()},can_draw:q.prototype.can_draw,draw_helper:function(af,au,aA,ax,al,an,av){var at=this,aE=this._gen_tile_cache_key(au,an,aA),aB=aA*Q*ax,ag=aB+Q*ax;if(!av){av={}}var aD=(af?undefined:at.tile_cache.get(aE));if(aD){at.show_tile(aD,al,an);return aD}var am=[],at,aq=true,ay,ao;for(var az=0;az<this.drawables.length;az++){at=this.drawables[az];ay=at.data_manager.get_data(aB,ag,at.mode,ax,at.data_url_extra_params);if(is_deferred(ay)){aq=false}am.push(ay);ao=null;if(view.reference_track&&an>view.canvas_manager.char_width_px){ao=view.reference_track.data_manager.get_data(aB,ag,at.mode,ax,view.reference_track.data_url_extra_params);if(is_deferred(ao)){aq=false}}am.push(ao)}if(aq){p(ay,av.more_tile_data);this.tile_predraw_init();var ai=at.view.canvas_manager.new_canvas(),aj=at._get_tile_bounds(aA,ax),aB=aj[0],ag=aj[1],aC=0,au=Math.ceil((ag-aB)*an)+this.left_offset,ar=0,ah=[];var ae=0;for(var az=0;az<this.drawables.length;az++,aC+=2){at=this.drawables[az];ay=am[aC];var ap=at.mode;if(ap==="Auto"){ap=at.get_mode(ay);at.update_auto_mode(ap)}ah.push(ap);ae=at.get_canvas_height(ay,ap,an,au);if(ae>ar){ar=ae}}ai.width=au;ai.height=(av.height?av.height:ar);aC=0;var aw=ai.getContext("2d");aw.translate(this.left_offset,0);aw.globalAlpha=0.5;aw.globalCompositeOperation="source-over";for(var az=0;az<this.drawables.length;az++,aC+=2){at=this.drawables[az];ay=am[aC];ao=am[aC+1];aD=at.draw_tile(ay,aw,ah[az],ax,aA,an,ao)}this.tile_cache.set(aE,aD);this.show_tile(aD,al,an);return aD}var ak=$.Deferred(),at=this;$.when.apply($,am).then(function(){view.request_redraw(false,false,false,at);ak.resolve()});return ak},tile_predraw_init:function(){var ah=Number.MAX_VALUE,ae=-ah,af;for(var ag=0;ag<this.drawables.length;ag++){af=this.drawables[ag];if(af instanceof j){if(af.prefs.min_value<ah){ah=af.prefs.min_value}if(af.prefs.max_value>ae){ae=af.prefs.max_value}}}for(var ag=0;ag<this.drawables.length;ag++){af=this.drawables[ag];af.prefs.min_value=ah;af.prefs.max_value=ae}},postdraw_actions:function(ag,aj,al,af){M.prototype.postdraw_actions.call(this,ag,aj,al,af);var ai=-1;for(var ah=0;ah<ag.length;ah++){var ae=ag[ah].html_elt.find("canvas").height();if(ae>ai){ai=ae}}for(var ah=0;ah<ag.length;ah++){var ak=ag[ah];if(ak.html_elt.find("canvas").height()!==ai){this.draw_helper(true,aj,ak.index,ak.resolution,ak.html_elt.parent(),al,{height:ai});ak.html_elt.remove()}}}});var z=function(ae){M.call(this,"reference",ae,{content_div:ae.top_labeltrack},{});ae.reference_track=this;this.left_offset=200;this.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=reference_url;this.data_url_extra_params={dbkey:ae.dbkey};this.data_manager=new G(H,this,false)};p(z.prototype,q.prototype,M.prototype,{build_header_div:function(){},init:function(){this.enabled=true},can_draw:q.prototype.can_draw,draw_tile:function(am,an,aj,ai,af,ao){var ah=this;if(ao>this.view.canvas_manager.char_width_px){if(am.data===null){ah.content_div.css("height","0px");return}var ag=an.canvas;an.font=an.canvas.manager.default_font;an.textAlign="center";am=am.data;for(var ak=0,al=am.length;ak<al;ak++){var ae=Math.round(ak*ao);an.fillText(am[ak],ae,10)}return new b(ah,af,ai,ag,am)}this.content_div.css("height","0px")}});var j=function(ae,al,af,ak,an,am,ai,aj,ag){var ah=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ae,al,af,am,ai,aj,ag);this.min_height_px=16;this.max_height_px=400;this.height_px=32;this.hda_ldda=ak;this.dataset_id=an;this.original_dataset_id=an;this.left_offset=0;this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ae},{key:"color",label:"Color",type:"color",default_value: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:this.height_px,hidden:true}],saved_values:am,onchange:function(){ah.set_name(ah.prefs.name);ah.vertical_range=ah.prefs.max_value-ah.prefs.min_value;$("#linetrack_"+ah.dataset_id+"_minval").text(ah.prefs.min_value);$("#linetrack_"+ah.dataset_id+"_maxval").text(ah.prefs.max_value);ah.tile_cache.clear();ah.request_draw()}});this.prefs=this.config.values;this.height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value;this.add_resize_handle()};p(j.prototype,q.prototype,M.prototype,{add_resize_handle:function(){var ae=this;var ah=false;var ag=false;var af=$("<div class='track-resize'>");$(ae.container_div).hover(function(){if(ae.content_visible){ah=true;af.show()}},function(){ah=false;if(!ag){af.hide()}});af.hide().bind("dragstart",function(ai,aj){ag=true;aj.original_height=$(ae.content_div).height()}).bind("drag",function(aj,ak){var ai=Math.min(Math.max(ak.original_height+ak.deltaY,ae.min_height_px),ae.max_height_px);$(ae.content_div).css("height",ai);ae.height_px=ai;ae.request_draw(true)}).bind("dragend",function(ai,aj){ae.tile_cache.clear();ag=false;if(!ah){af.hide()}ae.config.values.height=ae.height_px}).appendTo(ae.container_div)},predraw_init:function(){var ae=this;ae.vertical_range=undefined;return $.getJSON(ae.data_url,{stats:true,chrom:ae.view.chrom,low:null,high:null,hda_ldda:ae.hda_ldda,dataset_id:ae.dataset_id},function(af){ae.container_div.addClass("line-track");var ai=af.data;if(isNaN(parseFloat(ae.prefs.min_value))||isNaN(parseFloat(ae.prefs.max_value))){var ag=ai.min;var ak=ai.max;ag=Math.floor(Math.min(0,Math.max(ag,ai.mean-2*ai.sd)));ak=Math.ceil(Math.max(0,Math.min(ak,ai.mean+2*ai.sd)));ae.prefs.min_value=ag;ae.prefs.max_value=ak;$("#track_"+ae.dataset_id+"_minval").val(ae.prefs.min_value);$("#track_"+ae.dataset_id+"_maxval").val(ae.prefs.max_value)}ae.vertical_range=ae.prefs.max_value-ae.prefs.min_value;ae.total_frequency=ai.total_frequency;ae.container_div.find(".yaxislabel").remove();var aj=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ae.dataset_id+"_minval").text(Y(ae.prefs.min_value,3));var ah=$("<div />").addClass("yaxislabel").attr("id","linetrack_"+ae.dataset_id+"_maxval").text(Y(ae.prefs.max_value,3));ah.css({position:"absolute",top:"24px",left:"10px"});ah.prependTo(ae.container_div);aj.css({position:"absolute",bottom:"2px",left:"10px"});aj.prependTo(ae.container_div)})},draw_tile:function(ao,am,aj,ah,af,an){if(this.vertical_range===undefined){return}var ag=am.canvas,ae=this._get_tile_bounds(af,ah),ai=ae[0],al=ae[1],ak=new L.LinePainter(ao.data,ai,al,this.prefs,aj);ak.draw(am,ag.width,ag.height,an);return new b(this.track,af,ah,ag,ao.data)}});var d=function(ae,al,af,ak,an,am,ai,aj,ag){var ah=this;this.display_modes=["Auto","Histogram","Dense","Squish","Pack"];M.call(this,ae,al,af,am,ai,aj,ag);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ae},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{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:"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},],saved_values:am,onchange:function(){ah.set_name(ah.prefs.name);ah.tile_cache.clear();ah.set_painter_from_config();ah.request_draw()}});this.prefs=this.config.values;this.height_px=0;this.container_div.addClass("feature-track");this.hda_ldda=ak;this.dataset_id=an;this.original_dataset_id=an;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()};p(d.prototype,q.prototype,M.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(ar,am,ai,ag){M.prototype.postdraw_actions.call(this,ar,ag);var al=this;if(ag){var aw=al.content_div.children();var av=false;for(var ao=aw.length-1,ap=0;ao>=ap;ao--){var ah=$(aw[ao]);if(av){ah.remove()}else{if(ah.children().length!==0){av=true}}}}if(al.mode=="Histogram"){var af=-1;for(var ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>af){af=an}}for(var ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==af){au.html_elt.remove();al.draw_helper(true,am,au.index,au.resolution,au.html_elt.parent(),ai,{more_tile_data:{max:af}})}}}if(al.filters_manager){var aj=al.filters_manager.filters;for(var aq=0;aq<aj.length;aq++){aj[aq].update_ui_elt()}var at=false,ae,ak;for(var ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ae=ar[ao].data[0];for(var aq=0;aq<aj.length;aq++){ak=aj[aq];if(ak.applies_to(ae)&&ak.min!==ak.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_div.hide()}al.update_icons()}}},update_auto_mode:function(ae){var ae;if(this.mode=="Auto"){if(ae=="no_detail"){ae="feature spans"}else{if(ae=="summary_tree"){ae="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ae+")")}},incremental_slots:function(ai,ae,ah){var af=this.view.canvas_manager.dummy_context,ag=this.slotters[ai];if(!ag||(ag.mode!==ah)){ag=new (s.FeatureSlotter)(ai,ah,y,function(aj){return af.measureText(aj)});this.slotters[ai]=ag}return ag.slot_features(ae)},get_summary_tree_data:function(ai,al,ag,au){if(au>ag-al){au=ag-al}var ap=Math.floor((ag-al)/au),at=[],ah=0;var aj=0,ak=0,ao,ar=0,am=[],aq,an;var af=function(ax,aw,ay,av){ax[0]=aw+ay*av;ax[1]=aw+(ay+1)*av};while(ar<au&&aj!==ai.length){var ae=false;for(;ar<au&&!ae;ar++){af(am,al,ar,ap);for(ak=aj;ak<ai.length;ak++){ao=ai[ak].slice(1,3);if(is_overlap(ao,am)){ae=true;break}}if(ae){break}}data_start_index=ak;at[at.length]=aq=[am[0],0];for(;ak<ai.length;ak++){ao=ai[ak].slice(1,3);if(is_overlap(ao,am)){aq[1]++}else{break}}if(aq[1]>ah){ah=aq[1]}ar++}return{max:ah,delta:ap,data:at}},get_mode:function(ae){if(ae.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ae.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(ae,ai,aj,af){if(ai==="summary_tree"||ai==="Histogram"){return this.summary_draw_height}else{var ah=this.incremental_slots(aj,ae.data,ai);var ag=new (this.painter)(null,null,null,this.prefs,ai);return Math.max(ac,ag.get_required_height(ah,af))}},draw_tile:function(aq,av,at,aw,aA,am,ah){var au=this,ag=av.canvas,aj=this._get_tile_bounds(aA,aw),aD=aj[0],af=aj[1],aI=25,ai=this.left_offset;if(at==="summary_tree"||at==="Histogram"){this.container_div.find(".yaxislabel").remove();var ae=$("<div />").addClass("yaxislabel");ae.text(aq.max);ae.css({position:"absolute",top:"24px",left:"10px",color:this.prefs.label_color});ae.prependTo(this.container_div);if(aq.dataset_type!="summary_tree"){var an=this.get_summary_tree_data(aq.data,aD,af,200);if(aq.max){an.max=aq.max}aq=an}var aF=new L.SummaryTreePainter(aq,aD,af,this.prefs);aF.draw(av,ag.width,ag.height,am);return new k(au,aA,aw,ag,aq.data,aq.max)}var al=[],ar=this.slotters[am].slots;all_slotted=true;if(aq.data){var ao=this.filters_manager.filters;for(var ax=0,az=aq.data.length;ax<az;ax++){var ak=aq.data[ax];var ay=false;var ap;for(var aC=0,aH=ao.length;aC<aH;aC++){ap=ao[aC];ap.update_attrs(ak);if(!ap.keep(ak)){ay=true;break}}if(!ay){al.push(ak);if(!(ak[0] in ar)){all_slotted=false}}}}var aG=(this.filters_manager.alpha_filter?new B(this.filters_manager.alpha_filter):null);var aE=(this.filters_manager.height_filter?new B(this.filters_manager.height_filter):null);var aF=new (this.painter)(al,aD,af,this.prefs,at,aG,aE,ah);var aB=null;av.fillStyle=this.prefs.block_color;av.font=av.canvas.manager.default_font;av.textAlign="right";this.container_div.find(".yaxislabel").remove();if(aq.data){aB=aF.draw(av,ag.width,ag.height,am,ar);aB.translation=-ai}return new O(au,aA,aw,ag,aq.data,am,at,aq.message,all_slotted,aB)},data_and_mode_compatible:function(ae,af){if(af==="Auto"){return true}else{if(ae.extra_info==="no_detail"||ae.dataset_type==="summary_tree"){return false}else{return true}}},});var T=function(ae,ak,af,aj,am,al,ah,ai,ag){d.call(this,ae,ak,af,aj,am,al,ah,ai,ag);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ae},{key:"block_color",label:"Block color",type:"color",default_value:get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},],saved_values:al,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};p(T.prototype,q.prototype,M.prototype,d.prototype);var V=function(ae,ak,af,aj,an,am,ah,ag){d.call(this,ae,ak,af,aj,an,am,ah,ag);var ai=get_random_color(),al=get_random_color([ai,"#ffffff"]);this.config=new E({track:this,params:[{key:"name",label:"Name",type:"text",default_value:ae},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:ai},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:al},{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},],saved_values:am,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};p(V.prototype,q.prototype,M.prototype,d.prototype);W.View=ab;W.DrawableGroup=P;W.LineTrack=j;W.FeatureTrack=d;W.ReadTrack=V;W.VcfTrack=T;W.CompositeTrack=h};var slotting_module=function(c,b){var e=c("class").extend;var d=2,a=5;b.FeatureSlotter=function(i,h,f,g){this.slots={};this.start_end_dct={};this.w_scale=i;this.mode=h;this.include_label=(h==="Pack");this.max_rows=f;this.measureText=g};e(b.FeatureSlotter.prototype,{slot_features:function(m){var p=this.w_scale,h=this.start_end_dct,x=[],z=[],n=0,y=this.max_rows;for(var v=0,w=m.length;v<w;v++){var k=m[v],o=k[0];if(this.slots[o]!==undefined){n=Math.max(n,this.slots[o]);z.push(this.slots[o])}else{x.push(v)}}var q=function(E,F){for(var D=0;D<=y;D++){var B=false,G=h[D];if(G!==undefined){for(var A=0,C=G.length;A<C;A++){var i=G[A];if(F>i[0]&&E<i[1]){B=true;break}}}if(!B){return D}}return -1};for(var v=0,w=x.length;v<w;v++){var k=m[x[v]],o=k[0],t=k[1],f=k[2],r=k[3],g=Math.floor(t*p),l=Math.ceil(f*p),u=this.measureText(r).width,j;if(r!==undefined&&this.include_label){u+=(d+a);if(g-u>=0){g-=u;j="left"}else{l+=u;j="right"}}var s=q(g,l);if(s>=0){if(h[s]===undefined){h[s]=[]}h[s].push([g,l]);this.slots[o]=s;n=Math.max(n,s)}else{}}return n+1}})};var painters_module=function(i,x){var u=i("class").extend;var p=function(I,A,G,z,F,D){if(D===undefined){D=4}var C=z-A;var B=F-G;var E=Math.floor(Math.sqrt(C*C+B*B)/D);var J=C/E;var H=B/E;var y;for(y=0;y<E;y++,A+=J,G+=H){if(y%2!==0){continue}I.fillRect(A,G,D,1)}};var q=function(B,A,z,E){var D=A-E/2,C=A+E/2,F=z-Math.sqrt(E*3/2);B.beginPath();B.moveTo(D,F);B.lineTo(C,F);B.lineTo(A,z);B.lineTo(D,F);B.strokeStyle=this.fillStyle;B.fill();B.stroke();B.closePath()};var d=function(y){this.default_val=(y?y:1)};d.prototype.gen_val=function(y){return this.default_val};var l=function(A,C,y,z,B){this.data=A;this.view_start=C;this.view_end=y;this.prefs=u({},this.default_prefs,z);this.mode=B};l.prototype.default_prefs={};l.prototype.draw=function(z,A,y,B){};var v=function(A,C,y,z,B){l.call(this,A,C,y,z,B)};v.prototype.default_prefs={show_counts:false};v.prototype.draw=function(L,z,K,M){var E=this.view_start,N=this.view_end-this.view_start,I=this.data.data,G=this.data.max,B=K;delta_x_px=Math.ceil(this.data.delta*M);L.save();for(var C=0,D=I.length;C<D;C++){var H=Math.floor((I[C][0]-E)*M);var F=I[C][1];if(!F){continue}var J=F/G*K;if(F!==0&&J<1){J=1}L.fillStyle=this.prefs.block_color;L.fillRect(H,B-J,delta_x_px,J);var A=4;if(this.prefs.show_counts&&(L.measureText(F).width+A)<delta_x_px){L.fillStyle=this.prefs.label_color;L.textAlign="center";L.fillText(F,H+(delta_x_px/2),10)}}L.restore()};var b=function(y,C,E,F,A){l.call(this,y,C,E,F,A);if(this.prefs.min_value===undefined){var G=Infinity;for(var z=0,B=this.data.length;z<B;z++){G=Math.min(G,this.data[z][1])}this.prefs.min_value=G}if(this.prefs.max_value===undefined){var D=-Infinity;for(var z=0,B=this.data.length;z<B;z++){D=Math.max(D,this.data[z][1])}this.prefs.max_value=D}};b.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};b.prototype.draw=function(S,Q,N,D){var I=false,K=this.prefs.min_value,F=this.prefs.max_value,M=F-K,B=N,C=this.view_start,P=this.view_end-this.view_start,L=this.mode,aa=this.data;S.save();var ac=Math.round(N+K/M*N);if(L!=="Intensity"){S.fillStyle="#aaa";S.fillRect(0,ac,Q,1)}S.beginPath();var Y,G,E;if(aa.length>1){E=Math.ceil((aa[1][0]-aa[0][0])*D)}else{E=10}var A=parseInt(this.prefs.color.slice(1),16),H=(A&16711680)>>16,R=(A&65280)>>8,V=A&255;for(var T=0,U=aa.length;T<U;T++){S.fillStyle=S.strokeStyle=this.prefs.color;Y=Math.round((aa[T][0]-C)*D);G=aa[T][1];var W=false,J=false;if(G===null){if(I&&L==="Filled"){S.lineTo(Y,B)}I=false;continue}if(G<K){J=true;G=K}else{if(G>F){W=true;G=F}}if(L==="Histogram"){G=Math.round(G/M*B);S.fillRect(Y,ac,E,-G)}else{if(L==="Intensity"){var z=(G-K)/M,O=Math.round(H+(255-H)*(1-z)),X=Math.round(R+(255-R)*(1-z)),ab=Math.round(V+(255-V)*(1-z));S.fillStyle="rgb("+O+","+X+","+ab+")";S.fillRect(Y,0,E,B)}else{G=Math.round(B-(G-K)/M*B);if(I){S.lineTo(Y,G)}else{I=true;if(L==="Filled"){S.moveTo(Y,B);S.lineTo(Y,G)}else{S.moveTo(Y,G)}}}}S.fillStyle=this.prefs.overflow_color;if(W||J){var Z;if(L==="Histogram"||L==="Intensity"){Z=E}else{Y-=2;Z=4}if(W){S.fillRect(Y,0,Z,3)}if(J){S.fillRect(Y,B-3,Z,3)}}S.fillStyle=this.prefs.color}if(L==="Filled"){if(I){S.lineTo(Y,ac);S.lineTo(0,ac)}S.fill()}else{S.stroke()}S.restore()};var m=function(y){this.feature_positions={};this.slot_height=y;this.translation=0;this.y_translation=0};m.prototype.map_feature_data=function(z,B,y,A){if(!this.feature_positions[B]){this.feature_positions[B]=[]}this.feature_positions[B].push({data:z,x_start:y,x_end:A})};m.prototype.get_feature_data=function(z,D){var C=Math.floor((D-this.y_translation)/this.slot_height),B;if(!this.feature_positions[C]){return null}z+=this.translation;for(var A=0;A<this.feature_positions[C].length;A++){B=this.feature_positions[C][A];if(z>=B.x_start&&z<=B.x_end){return B.data}}};var o=function(A,D,y,z,C,E,B){l.call(this,A,D,y,z,C);this.alpha_scaler=(E?E:new d());this.height_scaler=(B?B:new d())};o.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};u(o.prototype,{get_required_height:function(A,z){var y=y_scale=this.get_row_height(),B=this.mode;if(B==="no_detail"||B==="Squish"||B==="Pack"){y=A*y_scale}return y+this.get_top_padding(z)+this.get_bottom_padding(z)},get_top_padding:function(y){return 0},get_bottom_padding:function(y){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(K,I,G,E,F){var Q=this.data,D=this.view_start,M=this.view_end;K.save();K.fillStyle=this.prefs.block_color;K.textAlign="right";var H=this.view_end-this.view_start,L=this.get_row_height(),P=new m(L),B;for(var N=0,O=Q.length;N<O;N++){var A=Q[N],C=A[0],J=A[1],y=A[2],z=(F&&F[C]!==undefined?F[C]:null);if((J<M&&y>D)&&(this.mode=="Dense"||z!==null)){B=this.draw_element(K,this.mode,A,z,D,M,E,L,I);P.map_feature_data(A,z,B[0],B[1])}}K.restore();P.y_translation=this.get_top_padding(I);return P},draw_element:function(E,A,G,C,B,D,F,z,y){console.log("WARNING: Unimplemented function.");return[0,0]}});var c=10,h=3,k=5,w=10,f=1,s=9,e=3,a=9,j=2,g="#ccc";var r=function(A,D,y,z,C,E,B){o.call(this,A,D,y,z,C,E,B);this.draw_background_connector=true;this.draw_individual_connectors=false};u(r.prototype,o.prototype,{get_row_height:function(){var z=this.mode,y;if(z==="Dense"){y=c}else{if(z==="no_detail"){y=h}else{if(z==="Squish"){y=k}else{y=w}}}return y},draw_element:function(M,D,X,H,O,aj,an,ap,y){var T=X[0],al=X[1],ad=X[2]-1,Q=X[3],ae=Math.floor(Math.max(0,(al-O)*an)),N=Math.ceil(Math.min(y,Math.max(0,(ad-O)*an))),ac=ae,ao=N,aa=(D==="Dense"?0:(0+H))*ap+this.get_top_padding(y),L,ah,R=null,ar=null,B=this.prefs.block_color,ag=this.prefs.label_color;M.globalAlpha=this.alpha_scaler.gen_val(X);if(D==="Dense"){H=1}if(D==="no_detail"){M.fillStyle=B;M.fillRect(ae,aa+5,N-ae,f)}else{var K=X[4],Z=X[5],af=X[6],C=X[7],V=true;if(Z&&af){R=Math.floor(Math.max(0,(Z-O)*an));ar=Math.ceil(Math.min(y,Math.max(0,(af-O)*an)))}var am,U;if(D==="Squish"){am=1;U=e;V=false}else{if(D==="Dense"){am=5;U=s}else{am=5;U=a}}if(!C){M.fillStyle=B;M.fillRect(ae,aa+1,N-ae,U);if(K&&V){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}M.fillRect(ae,aa+1,N-ae,U)}}else{var J,W;if(D==="Squish"||D==="Dense"){J=aa+Math.floor(e/2)+1;W=1}else{if(K){J=aa;W=U}else{J+=(e/2)+1;W=1}}if(this.draw_background_connector){if(D==="Squish"||D==="Dense"){M.fillStyle=g}else{if(K){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand")}}}else{M.fillStyle=g}}M.fillRect(ae,J,N-ae,W)}var E;for(var ak=0,A=C.length;ak<A;ak++){var F=C[ak],z=Math.floor(Math.max(0,(F[0]-O)*an)),Y=Math.ceil(Math.min(y,Math.max((F[1]-1-O)*an))),S,ab;if(z>Y){continue}M.fillStyle=B;M.fillRect(z,aa+(U-am)/2+1,Y-z,am);if(R!==undefined&&af>Z&&!(z>ar||Y<R)){var ai=Math.max(z,R),I=Math.min(Y,ar);M.fillRect(ai,aa+1,I-ai,U);if(C.length==1&&D=="Pack"){if(K==="+"){M.fillStyle=M.canvas.manager.get_pattern("right_strand_inv")}else{if(K==="-"){M.fillStyle=M.canvas.manager.get_pattern("left_strand_inv")}}if(ai+14<I){ai+=2;I-=2}M.fillRect(ai,aa+1,I-ai,U)}}if(this.draw_individual_connectors&&S){this.draw_connector(M,S,ab,z,Y,aa)}S=z;ab=Y}if(D==="Pack"){M.globalAlpha=1;M.fillStyle="white";var G=this.height_scaler.gen_val(X),P=Math.ceil(U*G),aq=Math.round((U-P)/2);if(G!==1){M.fillRect(ae,J+1,N-ae,aq);M.fillRect(ae,J+U-aq+1,N-ae,aq)}}}M.globalAlpha=1;if(D==="Pack"&&al>O){M.fillStyle=ag;if(O===0&&ae-M.measureText(Q).width<0){M.textAlign="left";M.fillText(Q,N+j,aa+8);ao+=M.measureText(Q).width+j}else{M.textAlign="right";M.fillText(Q,ae-j,aa+8);ac-=M.measureText(Q).width+j}}}M.globalAlpha=1;return[ac,ao]}});var t=function(B,E,y,A,D,F,C,z){o.call(this,B,E,y,A,D,F,C);this.ref_seq=(z?z.data:null)};u(t.prototype,o.prototype,{get_row_height:function(){var y,z=this.mode;if(z==="Dense"){y=c}else{if(z==="Squish"){y=k}else{y=w;if(this.prefs.show_insertions){y*=2}}}return y},draw_read:function(K,A,ag,V,L,aa,ad,C,B,M){K.textAlign="center";var J=this,R=[L,aa],Z=0,W=0,D=0,F=K.canvas.manager.char_width_px,y=(B==="+"?this.prefs.block_color:this.prefs.reverse_strand_color);var O=[];if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){D=Math.round(ag/2)}if(!C){C=[[0,M.length]]}for(var G=0,I=C.length;G<I;G++){var z=C[G],E="MIDNSHP=X"[z[0]],S=z[1];if(E==="H"||E==="S"){Z-=S}var U=ad+Z,Y=Math.floor(Math.max(0,(U-L)*ag)),ab=Math.floor(Math.max(0,(U+S-L)*ag));if(Y===ab){ab+=1}switch(E){case"H":break;case"S":case"M":case"=":if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(D>0){K.fillStyle=y;K.fillRect(Y-D,V+1,ab-Y,9);K.fillStyle=g;for(var af=0,H=N.length;af<H;af++){if(this.prefs.show_differences&&this.ref_seq){var P=this.ref_seq[U-L+af];if(!P||P.toLowerCase()===N[af].toLowerCase()){continue}}if(U+af>=L&&U+af<=aa){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X,V+9)}}}else{K.fillStyle=y;K.fillRect(Y,V+4,ab-Y,e)}}W+=S;Z+=S;break;case"N":K.fillStyle=g;K.fillRect(Y-D,V+5,ab-Y,1);Z+=S;break;case"D":K.fillStyle="red";K.fillRect(Y-D,V+4,ab-Y,3);Z+=S;break;case"P":break;case"I":var ah=Y-D;if(is_overlap([U,U+S],R)){var N=M.slice(W,W+S);if(this.prefs.show_insertions){var T=Y-(ab-Y)/2;if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){K.fillStyle="yellow";K.fillRect(T-D,V-9,ab-Y,9);O[O.length]={type:"triangle",data:[ah,V+4,5]};K.fillStyle=g;switch(compute_overlap([U,U+S],R)){case (OVERLAP_START):N=N.slice(L-U);break;case (OVERLAP_END):N=N.slice(0,U-aa);break;case (CONTAINED_BY):break;case (CONTAINS):N=N.slice(L-U,U-aa);break}for(var af=0,H=N.length;af<H;af++){var X=Math.floor(Math.max(0,(U+af-L)*ag));K.fillText(N[af],X-(ab-Y)/2,V)}}else{K.fillStyle="yellow";K.fillRect(T,V+(this.mode!=="Dense"?2:5),ab-Y,(A!=="Dense"?e:s))}}else{if((A==="Pack"||this.mode==="Auto")&&M!==undefined&&ag>F){O.push({type:"text",data:[N.length,ah,V+9]})}else{}}}W+=S;break;case"X":W+=S;break}}K.fillStyle="yellow";var Q,ai,ae;for(var ac=0;ac<O.length;ac++){Q=O[ac];ai=Q.type;ae=Q.data;if(ai==="text"){K.save();K.font="bold "+K.font;K.fillText(ae[0],ae[1],ae[2]);K.restore()}else{if(ai=="triangle"){q(K,ae[0],ae[1],ae[2])}}}},draw_element:function(R,M,E,B,U,z,I,S,P){var H=E[0],Q=E[1],A=E[2],J=E[3],D=Math.floor(Math.max(0,(Q-U)*I)),F=Math.ceil(Math.min(P,Math.max(0,(A-U)*I))),C=(M==="Dense"?0:(0+B))*S,G=this.prefs.label_color,O=0;if((M==="Pack"||this.mode==="Auto")&&I>R.canvas.manager.char_width_px){var O=Math.round(I/2)}if(E[5] instanceof Array){var N=Math.floor(Math.max(0,(E[4][0]-U)*I)),L=Math.ceil(Math.min(P,Math.max(0,(E[4][1]-U)*I))),K=Math.floor(Math.max(0,(E[5][0]-U)*I)),y=Math.ceil(Math.min(P,Math.max(0,(E[5][1]-U)*I)));if(E[4][1]>=U&&E[4][0]<=z&&E[4][2]){this.draw_read(R,M,I,C,U,z,E[4][0],E[4][2],E[4][3],E[4][4])}if(E[5][1]>=U&&E[5][0]<=z&&E[5][2]){this.draw_read(R,M,I,C,U,z,E[5][0],E[5][2],E[5][3],E[5][4])}if(K>L){R.fillStyle=g;p(R,L-O,C+5,K-O,C+5)}}else{this.draw_read(R,M,I,C,U,z,Q,E[4],E[5],E[6])}if(M==="Pack"&&Q>U&&J!=="."){R.fillStyle=this.prefs.label_color;var T=1;if(T===0&&D-R.measureText(J).width<0){R.textAlign="left";R.fillText(J,F+j-O,C+8)}else{R.textAlign="right";R.fillText(J,D-j-O,C+8)}}return[0,0]}});var n=function(A,D,y,z,C,E,B){r.call(this,A,D,y,z,C,E,B);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};u(n.prototype,o.prototype,r.prototype,{calculate_longest_feature_length:function(){var z=0;for(var C=0,y=this.data.length;C<y;C++){var B=this.data[C],A=B[1],D=B[2];z=Math.max(z,D-A)}return z},get_top_padding:function(z){var y=this.view_end-this.view_start,A=z/y;return Math.min(128,Math.ceil((this.longest_feature_length/2)*A))},draw_connector:function(G,B,F,H,E,D){var y=(F+H)/2,C=H-y;var A=Math.PI,z=0;if(C>0){G.beginPath();G.arc(y,D,H-y,Math.PI,0);G.stroke()}}});x.Scaler=d;x.SummaryTreePainter=v;x.LinePainter=b;x.LinkedFeaturePainter=r;x.ReadPainter=t;x.ArcLinkedFeaturePainter=n};(function(d){var c={};var b=function(e){return c[e]};var a=function(f,g){var e={};g(b,e);c[f]=e};a("class",class_module);a("slotting",slotting_module);a("painters",painters_module);a("trackster",trackster_module);for(key in c.trackster){d[key]=c.trackster[key]}})(window); \ No newline at end of file diff -r 34db794299d3b79e1c9a92fff65e6222c70f4031 -r 9b7a615b39648a2911c483f8d3b693931ca5c1b4 static/scripts/trackster.js --- a/static/scripts/trackster.js +++ b/static/scripts/trackster.js @@ -373,7 +373,6 @@ CHAR_HEIGHT_PX = 9, // Padding at the top of tracks for error messages ERROR_PADDING = 20, - SUMMARY_TREE_TOP_PADDING = CHAR_HEIGHT_PX + 2, // Maximum number of rows un a slotted track MAX_FEATURE_DEPTH = 100, // Minimum width for window for squish to be used. @@ -4149,7 +4148,7 @@ get_canvas_height: function(result, mode, w_scale, canvas_width) { if (mode === "summary_tree" || mode === "Histogram") { // Extra padding at top of summary tree so label does not overlap data. - return this.summary_draw_height + SUMMARY_TREE_TOP_PADDING; + return this.summary_draw_height; } else { // All other modes require slotting. @@ -4199,8 +4198,6 @@ } // Paint summary tree into canvas var painter = new painters.SummaryTreePainter(result, tile_low, tile_high, this.prefs); - // FIXME: it shouldn't be necessary to build in padding. - ctx.translate(0, SUMMARY_TREE_TOP_PADDING); painter.draw(ctx, canvas.width, canvas.height, w_scale); return new SummaryTreeTile(track, tile_index, resolution, canvas, result.data, result.max); } @@ -4623,16 +4620,15 @@ SummaryTreePainter.prototype.default_prefs = { show_counts: false }; SummaryTreePainter.prototype.draw = function(ctx, width, height, w_scale) { - var view_start = this.view_start, - view_range = this.view_end - this.view_start; - - var points = this.data.data, delta = this.data.delta, max = this.data.max, + view_range = this.view_end - this.view_start, + points = this.data.data, + max = this.data.max, // Set base Y so that max label and data do not overlap. Base Y is where rectangle bases // start. However, height of each rectangle is relative to required_height; hence, the // max rectangle is required_height. base_y = height; - delta_x_px = Math.ceil(delta * w_scale); + delta_x_px = Math.ceil(this.data.delta * w_scale); ctx.save(); for (var i = 0, len = points.length; i < len; i++) { @@ -4640,10 +4636,10 @@ var y = points[i][1]; if (!y) { continue; } - var y_px = y / max * height + var y_px = y / max * height; if (y !== 0 && y_px < 1) { y_px = 1; } - ctx.fillStyle = this.prefs.block_color; + ctx.fillStyle = this.prefs.block_color; ctx.fillRect( x, base_y - y_px, delta_x_px, y_px ); // Draw number count if it can fit the number with some padding, otherwise things clump up 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.

1 0

commit/galaxy-central: 4 new changesets
by Bitbucket 22 Jan '12

22 Jan '12

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6345c9c5f79e/ changeset: 6345c9c5f79e user: jgoecks date: 2012-01-22 20:06:18 summary: Update test data for cufflinks v1.3.0 affected #: 3 files diff -r ef0a2b1c879b51c215afd445c248eb604645b29f -r 6345c9c5f79e80706a6466ae24b5480e56a26062 test-data/cufflinks_out1.gtf --- a/test-data/cufflinks_out1.gtf +++ b/test-data/cufflinks_out1.gtf @@ -1,4 +1,4 @@ -test_chromosome Cufflinks transcript 53 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "10465551.7182135005"; frac "1.000000"; conf_lo "8351190.978554"; conf_hi "12579912.457873"; cov "142.854781"; -test_chromosome Cufflinks exon 53 250 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "10465551.7182135005"; frac "1.000000"; conf_lo "8351190.978554"; conf_hi "12579912.457873"; cov "142.854781"; -test_chromosome Cufflinks exon 351 400 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; FPKM "10465551.7182135005"; frac "1.000000"; conf_lo "8351190.978554"; conf_hi "12579912.457873"; cov "142.854781"; -test_chromosome Cufflinks exon 501 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; FPKM "10465551.7182135005"; frac "1.000000"; conf_lo "8351190.978554"; conf_hi "12579912.457873"; cov "142.854781"; +test_chromosome Cufflinks transcript 53 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185"; +test_chromosome Cufflinks exon 53 250 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185"; +test_chromosome Cufflinks exon 351 400 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185"; +test_chromosome Cufflinks exon 501 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; FPKM "10679134.4063403048"; frac "1.000000"; conf_lo "8543307.525072"; conf_hi "12814961.287608"; cov "145.770185"; diff -r ef0a2b1c879b51c215afd445c248eb604645b29f -r 6345c9c5f79e80706a6466ae24b5480e56a26062 test-data/cufflinks_out4.txt --- /dev/null +++ b/test-data/cufflinks_out4.txt @@ -0,0 +1,1 @@ +100.000000 diff -r ef0a2b1c879b51c215afd445c248eb604645b29f -r 6345c9c5f79e80706a6466ae24b5480e56a26062 tools/ngs_rna/cufflinks_wrapper.xml --- a/tools/ngs_rna/cufflinks_wrapper.xml +++ b/tools/ngs_rna/cufflinks_wrapper.xml @@ -132,6 +132,7 @@ <output name="genes_expression" format="tabular" lines_diff="2" file="cufflinks_out3.fpkm_tracking"/><output name="transcripts_expression" format="tabular" lines_diff="2" file="cufflinks_out2.fpkm_tracking"/><output name="assembled_isoforms" file="cufflinks_out1.gtf"/> + <output name="global_model" file="cufflinks_out4.txt"/></test></tests> https://bitbucket.org/galaxy/galaxy-central/changeset/a533f050b897/ changeset: a533f050b897 user: jgoecks date: 2012-01-22 20:19:46 summary: Update test-data for cuffcompare v1.3.0 affected #: 2 files diff -r 6345c9c5f79e80706a6466ae24b5480e56a26062 -r a533f050b897cb68359b4e5d8974cfdcc60d1cfc test-data/cuffcompare_out5.gtf --- a/test-data/cuffcompare_out5.gtf +++ b/test-data/cuffcompare_out5.gtf @@ -5,86 +5,86 @@ 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 "TSS11"; -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 "TSS12"; -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 "TSS15"; -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 "TSS16"; -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 "TSS17"; -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 "TSS18"; -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 "TSS19"; -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 "TSS20"; -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 "TSS21"; -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 "TSS22"; -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 "TSS23"; -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 "TSS24"; -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 "TSS25"; -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 "TSS26"; -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 "TSS27"; -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 "TSS28"; -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 "TSS29"; -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 "TSS30"; -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 "TSS32"; -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 "TSS33"; -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 "TSS34"; -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 "TSS35"; -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 "TSS37"; -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 "TSS38"; -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 "TSS39"; -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 "TSS40"; -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 "TSS41"; -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 "TSS42"; -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 "TSS43"; -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 "TSS44"; -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 "TSS45"; -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 "TSS46"; -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 "TSS47"; -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 "TSS48"; -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 "TSS49"; -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 "TSS50"; -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 "TSS51"; -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 "TSS52"; -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 "TSS53"; -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 "TSS54"; -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 "TSS55"; -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 "TSS56"; -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 "TSS57"; -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 "TSS59"; -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 "TSS60"; -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 "TSS61"; -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 "TSS62"; -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 "TSS63"; -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 "TSS64"; -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 "TSS65"; -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 "TSS66"; -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 "TSS67"; -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 "TSS68"; -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 "TSS70"; -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 "TSS71"; -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 "TSS72"; -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 "TSS73"; -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 "TSS74"; -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 "TSS75"; -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 "TSS76"; -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 "TSS77"; -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 "TSS78"; -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 "TSS79"; -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 "TSS80"; -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 "TSS81"; -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 "TSS82"; -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 "TSS83"; -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 "TSS84"; -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 "TSS85"; -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 "TSS86"; -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 "TSS87"; -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 "TSS88"; -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 "TSS89"; -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 "TSS90"; -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 "TSS91"; -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 "TSS92"; -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 "TSS93"; -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 "TSS94"; -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 "TSS95"; -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 "TSS96"; -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 "TSS97"; -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 "TSS98"; -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 "TSS99"; +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 6345c9c5f79e80706a6466ae24b5480e56a26062 -r a533f050b897cb68359b4e5d8974cfdcc60d1cfc test-data/cuffcompare_out7.txt --- a/test-data/cuffcompare_out7.txt +++ b/test-data/cuffcompare_out7.txt @@ -1,5 +1,5 @@ -# Cuffcompare v1.1.0 | Command line was: -#cuffcompare -o cc_output -r /Users/jeremy/projects/galaxy-central/database/files/010/dataset_10115.dat -R ./input1 ./input2 +# Cuffcompare v1.3.0 | Command line was: +#cuffcompare -o cc_output -r /Users/jeremy/projects/galaxy-central/database/files/010/dataset_10703.dat -R ./input1 ./input2 # #= Summary for dataset: ./input1 : @@ -14,11 +14,15 @@ 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 - Missed exons: 2/3 ( 66.7%) - Wrong exons: 49/50 ( 98.0%) - Missed introns: 2/2 (100.0%) - Missed loci: 0/1 ( 0.0%) - Wrong loci: 49/50 ( 98.0%) + +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) https://bitbucket.org/galaxy/galaxy-central/changeset/e5c37f9787b7/ changeset: e5c37f9787b7 user: jgoecks date: 2012-01-22 20:35:13 summary: Update cuffdiff test data for v1.3.0 affected #: 4 files diff -r a533f050b897cb68359b4e5d8974cfdcc60d1cfc -r e5c37f9787b72231f31782e9e41f9e379afdb04c test-data/cuffdiff_out10.txt --- a/test-data/cuffdiff_out10.txt +++ b/test-data/cuffdiff_out10.txt @@ -5,10 +5,10 @@ XLOC_000004 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000005 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000006 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 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_000007 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000008 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000009 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000010 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000011 XLOC_000011 - chr1:3192441-3192494 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000012 XLOC_000012 - chr1:3192550-3192629 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000013 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 0 1 no @@ -23,11 +23,11 @@ XLOC_000022 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000023 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000024 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 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_000025 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000026 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000027 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000028 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 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_000029 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000030 XLOC_000030 - chr1:3201596-3201666 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000031 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000032 XLOC_000032 - chr1:3201725-3201809 q1 q2 NOTEST 0 0 0 0 0 1 no @@ -35,10 +35,10 @@ XLOC_000034 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000035 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000036 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 0 0 0 0 0 1 no -XLOC_000037 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 FAIL 0 0 0 0 0 1 no +XLOC_000037 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000038 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000039 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 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_000040 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000041 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000042 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000043 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 NOTEST 0 0 0 0 0 1 no @@ -47,7 +47,7 @@ XLOC_000046 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000047 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000048 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 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_000049 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000050 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000051 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000052 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 NOTEST 0 0 0 0 0 1 no @@ -57,8 +57,8 @@ XLOC_000056 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000057 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000058 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 NOTEST 0 0 0 0 0 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_000059 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 0 0 0 0 0 1 no +XLOC_000060 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000061 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000062 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 0 1 no XLOC_000063 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 0 1 no diff -r a533f050b897cb68359b4e5d8974cfdcc60d1cfc -r e5c37f9787b72231f31782e9e41f9e379afdb04c test-data/cuffdiff_out7.txt --- a/test-data/cuffdiff_out7.txt +++ b/test-data/cuffdiff_out7.txt @@ -1,91 +1,89 @@ tracking_id class_code nearest_ref_id gene_id gene_short_name tss_id locus length coverage q1_FPKM q1_conf_lo q1_conf_hi q1_status q2_FPKM q2_conf_lo q2_conf_hi q2_status TSS1 - - XLOC_000001 Xkr4 TSS1 chr1:3204754-3204833 - - 0 0 0 OK 8.3103e+06 0 2.00628e+07 OK -TSS11 - - XLOC_000008 - TSS11 chr1:3190858-3191434 - - 404373 101434 707312 OK 338500 95761.5 581239 OK -TSS12 - - XLOC_000009 - TSS12 chr1:3191512-3192077 - - 402276 96829.4 707722 OK 686974 410563 963384 OK -TSS15 - - XLOC_000010 - TSS15 chr1:3192250-3192336 - - 3.994e+06 0 1.1982e+07 OK 2.93812e+06 0 8.81435e+06 OK -TSS16 - - XLOC_000011 - TSS16 chr1:3192441-3192494 - - 0 0 0 OK 5.68095e+07 0 1.3715e+08 OK -TSS17 - - XLOC_000012 - TSS17 chr1:3192550-3192629 - - 0 0 0 OK 4.15515e+06 0 1.24654e+07 OK -TSS18 - - XLOC_000013 - TSS18 chr1:3192649-3192676 - - 0 0 0 OK 0 0 0 OK -TSS19 - - XLOC_000014 - TSS19 chr1:3192731-3192811 - - 0 0 0 OK 0 0 0 OK +TSS10 - - XLOC_000008 - TSS10 chr1:3190858-3191434 - - 474092 138279 809906 OK 369273 113039 625507 OK +TSS11 - - XLOC_000009 - TSS11 chr1:3191512-3192077 - - 502845 149756 855934 OK 739818 487934 991702 OK +TSS13 - - XLOC_000010 - TSS13 chr1:3192250-3192336 - - 3.994e+06 0 1.1982e+07 OK 2.93812e+06 0 8.81435e+06 OK +TSS14 - - XLOC_000011 - TSS14 chr1:3192441-3192494 - - 0 0 0 OK 8.52143e+07 0 1.83611e+08 OK +TSS15 - - XLOC_000012 - TSS15 chr1:3192550-3192629 - - 0 0 0 OK 4.15515e+06 0 1.24654e+07 OK +TSS16 - - XLOC_000013 - TSS16 chr1:3192649-3192676 - - 0 0 0 OK 0 0 0 OK +TSS17 - - XLOC_000014 - TSS17 chr1:3192731-3192811 - - 0 0 0 OK 0 0 0 OK +TSS18 - - XLOC_000015 - TSS18 chr1:3192940-3193042 - - 0 0 0 OK 6.02976e+06 0 1.34147e+07 OK +TSS19 - - XLOC_000016 - TSS19 chr1:3194185-3194226 - - 0 0 0 OK 2.1403e+08 0 6.42089e+08 OK TSS2 - - XLOC_000002 - TSS2 chr1:3111449-3111490 - - 0 0 0 OK 2.1403e+08 0 6.42089e+08 OK -TSS20 - - XLOC_000015 - TSS20 chr1:3192940-3193042 - - 0 0 0 OK 6.02976e+06 0 1.34147e+07 OK -TSS21 - - XLOC_000016 - TSS21 chr1:3194185-3194226 - - 0 0 0 OK 2.1403e+08 0 6.42089e+08 OK -TSS22 - - XLOC_000017 - TSS22 chr1:3194302-3194329 - - 0 0 0 OK 0 0 0 OK -TSS23 - - XLOC_000018 - TSS23 chr1:3194706-3194733 - - 0 0 0 OK 0 0 0 OK -TSS24 - - XLOC_000019 - TSS24 chr1:3195083-3195110 - - 0 0 0 OK 0 0 0 OK -TSS25 - - XLOC_000020 - TSS25 chr1:3195450-3195477 - - 0 0 0 OK 0 0 0 OK -TSS26 - - XLOC_000021 - TSS26 chr1:3197089-3197116 - - 0 0 0 OK 0 0 0 OK -TSS27 - - XLOC_000022 - TSS27 chr1:3197246-3197273 - - 0 0 0 OK 0 0 0 OK -TSS28 - - XLOC_000023 - TSS28 chr1:3197346-3197373 - - 0 0 0 OK 0 0 0 OK -TSS29 - - XLOC_000024 - TSS29 chr1:3197425-3197452 - - 0 0 0 OK 0 0 0 OK +TSS20 - - XLOC_000017 - TSS20 chr1:3194302-3194329 - - 0 0 0 OK 0 0 0 OK +TSS21 - - XLOC_000018 - TSS21 chr1:3194706-3194733 - - 0 0 0 OK 0 0 0 OK +TSS22 - - XLOC_000019 - TSS22 chr1:3195083-3195110 - - 0 0 0 OK 0 0 0 OK +TSS23 - - XLOC_000020 - TSS23 chr1:3195450-3195477 - - 0 0 0 OK 0 0 0 OK +TSS24 - - XLOC_000021 - TSS24 chr1:3197089-3197116 - - 0 0 0 OK 0 0 0 OK +TSS25 - - XLOC_000022 - TSS25 chr1:3197246-3197273 - - 0 0 0 OK 0 0 0 OK +TSS26 - - XLOC_000023 - TSS26 chr1:3197346-3197373 - - 0 0 0 OK 0 0 0 OK +TSS27 - - XLOC_000024 - TSS27 chr1:3197425-3197452 - - 0 0 0 OK 0 0 0 OK +TSS28 - - XLOC_000025 - TSS28 chr1:3200022-3200191 - - 959058 0 2.06648e+06 OK 705514 0 1.52017e+06 OK +TSS29 - - XLOC_000026 - TSS29 chr1:3200325-3200352 - - 0 0 0 OK 0 0 0 OK TSS3 - - XLOC_000003 - TSS3 chr1:3111545-3111576 - - 0 0 0 OK 0 0 0 OK -TSS30 - - XLOC_000025 - TSS30 chr1:3200022-3200191 - - 959058 0 2.06648e+06 OK 705514 0 1.52017e+06 OK -TSS32 - - XLOC_000026 - TSS32 chr1:3200325-3200352 - - 0 0 0 OK 0 0 0 OK -TSS33 - - XLOC_000027 - TSS33 chr1:3200430-3200457 - - 0 0 0 OK 0 0 0 OK -TSS34 - - XLOC_000028 - TSS34 chr1:3201007-3201039 - - 0 0 0 OK 0 0 0 OK -TSS35 - - XLOC_000029 - TSS35 chr1:3201077-3201481 - - 77513.9 0 167019 OK 285108 21736.5 548480 OK -TSS37 - - XLOC_000030 - TSS37 chr1:3201596-3201666 - - 1.89853e+07 0 4.58345e+07 OK 0 0 0 OK -TSS38 - - XLOC_000031 - TSS38 chr1:3201672-3201699 - - 0 0 0 OK 0 0 0 OK -TSS39 - - XLOC_000032 - TSS39 chr1:3201725-3201809 - - 1.31744e+07 0 2.83869e+07 OK 0 0 0 OK +TSS30 - - XLOC_000027 - TSS30 chr1:3200430-3200457 - - 0 0 0 OK 0 0 0 OK +TSS31 - - XLOC_000028 - TSS31 chr1:3201007-3201039 - - 0 0 0 OK 0 0 0 OK +TSS32 - - XLOC_000029 - TSS32 chr1:3201077-3201481 - - 77513.9 0 167019 OK 285108 21736.5 548480 OK +TSS33 - - XLOC_000030 - TSS33 chr1:3201596-3201666 - - 1.89853e+07 0 4.58345e+07 OK 0 0 0 OK +TSS34 - - XLOC_000031 - TSS34 chr1:3201672-3201699 - - 0 0 0 OK 0 0 0 OK +TSS35 - - XLOC_000032 - TSS35 chr1:3201725-3201809 - - 1.75659e+07 0 3.90796e+07 OK 0 0 0 OK +TSS36 - - XLOC_000033 Xkr4 TSS36 chr1:3211521-3211561 - - 0 0 0 OK 0 0 0 OK +TSS37 - - XLOC_000034 Xkr4 TSS37 chr1:3212213-3212292 - - 0 0 0 OK 8.3103e+06 0 2.00628e+07 OK +TSS38 - - XLOC_000035 Xkr4 TSS38 chr1:3212367-3212439 - - 0 0 0 OK 2.4671e+07 0 5.48867e+07 OK +TSS39 - - XLOC_000036 Xkr4 TSS39 chr1:3212717-3212801 - - 4.39147e+06 0 1.31744e+07 OK 0 0 0 OK TSS4 - - XLOC_000004 - TSS4 chr1:3174765-3174792 - - 0 0 0 OK 0 0 0 OK -TSS40 - - XLOC_000033 Xkr4 TSS40 chr1:3211521-3211561 - - 0 0 0 OK 0 0 0 OK -TSS41 - - XLOC_000034 Xkr4 TSS41 chr1:3212213-3212292 - - 0 0 0 OK 8.3103e+06 0 2.00628e+07 OK -TSS42 - - XLOC_000035 Xkr4 TSS42 chr1:3212367-3212439 - - 0 0 0 OK 2.4671e+07 0 5.48867e+07 OK -TSS43 - - XLOC_000036 Xkr4 TSS43 chr1:3212717-3212801 - - 4.39147e+06 0 1.31744e+07 OK 0 0 0 OK -TSS44 - - XLOC_000037 Xkr4 TSS44 chr1:3213095-3213242 - - 3.99739e+06 0 1.3943e+07 LOWDATA 1.82908e+06 0 5.48723e+06 OK -TSS45 - - XLOC_000037 Xkr4 TSS45 chr1:3213095-3213242 - - 1.36901e+06 0 5.30211e+06 LOWDATA 0 0 0 OK -TSS46 - - XLOC_000038 Xkr4 TSS46 chr1:3240606-3240633 - - 0 0 0 OK 0 0 0 OK -TSS47 - - XLOC_000039 Xkr4 TSS47 chr1:3242479-3242512 - - 0 0 0 OK 0 0 0 OK -TSS48 - - XLOC_000040 Xkr4 TSS48 chr1:3242633-3242923 - - 56312.4 0 168937 OK 372827 0 761430 OK -TSS49 - - XLOC_000041 Xkr4 TSS49 chr1:3242924-3243005 - - 0 0 0 OK 0 0 0 OK +TSS40 - - XLOC_000037 Xkr4 TSS40 chr1:3213095-3213242 - - 8.89174e+06 0 2.05036e+07 OK 1.82908e+06 0 5.48723e+06 OK +TSS41 - - XLOC_000038 Xkr4 TSS41 chr1:3240606-3240633 - - 0 0 0 OK 0 0 0 OK +TSS42 - - XLOC_000039 Xkr4 TSS42 chr1:3242479-3242512 - - 0 0 0 OK 0 0 0 OK +TSS43 - - XLOC_000040 Xkr4 TSS43 chr1:3242633-3242923 - - 56312.4 0 168937 OK 372827 0 761430 OK +TSS44 - - XLOC_000041 Xkr4 TSS44 chr1:3242924-3243005 - - 0 0 0 OK 0 0 0 OK +TSS45 - - XLOC_000042 Xkr4 TSS45 chr1:3243018-3243079 - - 0 0 0 OK 2.66226e+07 0 6.42725e+07 OK +TSS46 - - XLOC_000043 Xkr4 TSS46 chr1:3243108-3243154 - - 9.99919e+07 0 2.99976e+08 OK 0 0 0 OK +TSS47 - - XLOC_000044 Xkr4 TSS47 chr1:3243347-3243401 - - 0 0 0 OK 5.0951e+07 0 1.23007e+08 OK +TSS48 - - XLOC_000045 Xkr4 TSS48 chr1:3254079-3254106 - - 0 0 0 OK 0 0 0 OK +TSS49 - - XLOC_000046 Xkr4 TSS49 chr1:3256974-3257011 - - 0 0 0 OK 2.06814e+09 0 4.99293e+09 OK TSS5 - - XLOC_000005 - TSS5 chr1:3187401-3187428 - - 0 0 0 OK 0 0 0 OK -TSS50 - - XLOC_000042 Xkr4 TSS50 chr1:3243018-3243079 - - 0 0 0 OK 2.66226e+07 0 6.42725e+07 OK -TSS51 - - XLOC_000043 Xkr4 TSS51 chr1:3243108-3243154 - - 9.99919e+07 0 2.99976e+08 OK 0 0 0 OK -TSS52 - - XLOC_000044 Xkr4 TSS52 chr1:3243347-3243401 - - 0 0 0 OK 5.0951e+07 0 1.23007e+08 OK -TSS53 - - XLOC_000045 Xkr4 TSS53 chr1:3254079-3254106 - - 0 0 0 OK 0 0 0 OK -TSS54 - - XLOC_000046 Xkr4 TSS54 chr1:3256974-3257011 - - 0 0 0 OK 2.06814e+09 0 4.99293e+09 OK -TSS55 - - XLOC_000047 Xkr4 TSS55 chr1:3277155-3277182 - - 0 0 0 OK 0 0 0 OK -TSS56 - - XLOC_000048 Xkr4 TSS56 chr1:3277190-3277218 - - 0 0 0 OK 0 0 0 OK -TSS57 - - XLOC_000049 Xkr4 TSS57 chr1:3277913-3278390 - - 265614 16793 514436 OK 41870.3 0 90217.9 OK -TSS59 - - XLOC_000050 Xkr4 TSS59 chr1:3280117-3280144 - - 0 0 0 OK 0 0 0 OK +TSS50 - - XLOC_000047 Xkr4 TSS50 chr1:3277155-3277182 - - 0 0 0 OK 0 0 0 OK +TSS51 - - XLOC_000048 Xkr4 TSS51 chr1:3277190-3277218 - - 0 0 0 OK 0 0 0 OK +TSS52 - - XLOC_000049 Xkr4 TSS52 chr1:3277913-3278390 - - 265614 16793 514436 OK 41870.3 0 90217.9 OK +TSS54 - - XLOC_000050 Xkr4 TSS54 chr1:3280117-3280144 - - 0 0 0 OK 0 0 0 OK +TSS55 - - XLOC_000051 Xkr4 TSS55 chr1:3280498-3280525 - - 0 0 0 OK 0 0 0 OK +TSS56 - - XLOC_000052 Xkr4 TSS56 chr1:3280686-3280741 - - 0 0 0 OK 2.29576e+07 0 6.88728e+07 OK +TSS57 - - XLOC_000053 Xkr4 TSS57 chr1:3282504-3282531 - - 0 0 0 OK 0 0 0 OK +TSS58 - - XLOC_000054 Xkr4 TSS58 chr1:3282650-3282677 - - 0 0 0 OK 0 0 0 OK +TSS59 - - XLOC_000055 Xkr4 TSS59 chr1:3282760-3282832 - - 0 0 0 OK 0 0 0 OK TSS6 - - XLOC_000006 - TSS6 chr1:3188521-3188548 - - 0 0 0 OK 0 0 0 OK -TSS60 - - XLOC_000051 Xkr4 TSS60 chr1:3280498-3280525 - - 0 0 0 OK 0 0 0 OK -TSS61 - - XLOC_000052 Xkr4 TSS61 chr1:3280686-3280741 - - 0 0 0 OK 2.29576e+07 0 6.88728e+07 OK -TSS62 - - XLOC_000053 Xkr4 TSS62 chr1:3282504-3282531 - - 0 0 0 OK 0 0 0 OK -TSS63 - - XLOC_000054 Xkr4 TSS63 chr1:3282650-3282677 - - 0 0 0 OK 0 0 0 OK -TSS64 - - XLOC_000055 Xkr4 TSS64 chr1:3282760-3282832 - - 0 0 0 OK 0 0 0 OK -TSS65 - - XLOC_000056 Xkr4 TSS65 chr1:3284966-3284993 - - 0 0 0 OK 0 0 0 OK -TSS66 - - XLOC_000057 Xkr4 TSS66 chr1:3290488-3290553 - - 0 0 0 OK 9.79535e+06 0 2.9386e+07 OK -TSS67 - - XLOC_000058 Xkr4 TSS67 chr1:3290798-3290859 - - 1.8095e+07 0 5.4285e+07 OK 0 0 0 OK -TSS68 - - XLOC_000059 Xkr4 TSS68 chr1:3290919-3291273 - - 342218 0 691214 OK 75524 0 162732 OK -TSS7 - - XLOC_000007 - TSS7 chr1:3189810-3190789 - - 368900 151353 586447 OK 429265 337221 521309 OK -TSS70 - - XLOC_000060 Xkr4 TSS70 chr1:3299443-3299664 - - 937403 0 1.99795e+06 OK 137917 0 413751 OK -TSS71 - - XLOC_000060 Xkr4 TSS71 chr1:3299443-3299664 - - 0 0 0 OK 0 0 0 OK -TSS72 - - XLOC_000061 Xkr4 TSS72 chr1:3299691-3299733 - - 0 0 0 OK 0 0 0 OK -TSS73 - - XLOC_000062 Xkr4 TSS73 chr1:3300051-3300078 - - 0 0 0 OK 0 0 0 OK -TSS74 - - XLOC_000063 Xkr4 TSS74 chr1:3307748-3307775 - - 0 0 0 OK 0 0 0 OK -TSS75 - - XLOC_000064 Xkr4 TSS75 chr1:3318620-3318647 - - 0 0 0 OK 0 0 0 OK -TSS76 - - XLOC_000065 Xkr4 TSS76 chr1:3318999-3319051 - - 0 0 0 OK 0 0 0 OK -TSS77 - - XLOC_000066 Xkr4 TSS77 chr1:3330527-3330554 - - 0 0 0 OK 0 0 0 OK -TSS78 - - XLOC_000067 Xkr4 TSS78 chr1:3351240-3351311 - - 8.91489e+06 0 2.67447e+07 OK 0 0 0 OK -TSS79 - - XLOC_000068 Xkr4 TSS79 chr1:3355887-3356119 - - 0 0 0 OK 0 0 0 OK -TSS80 - - XLOC_000068 Xkr4 TSS80 chr1:3355887-3356119 - - 585828 0 1.30332e+06 OK 0 0 0 OK -TSS81 - - XLOC_000069 Xkr4 TSS81 chr1:3356180-3356225 - - 1.19208e+08 0 3.57623e+08 OK 0 0 0 OK -TSS82 - - XLOC_000070 Xkr4 TSS82 chr1:3363076-3363176 - - 4.42166e+06 0 1.06748e+07 OK 0 0 0 OK -TSS83 - - XLOC_000071 Xkr4 TSS83 chr1:3363214-3363278 - - 0 0 0 OK 0 0 0 OK -TSS84 - - XLOC_000072 Xkr4 TSS84 chr1:3363387-3363446 - - 4.28358e+07 0 1.03415e+08 OK 0 0 0 OK -TSS85 - - XLOC_000073 Xkr4 TSS85 chr1:3363753-3363849 - - 0 0 0 OK 0 0 0 OK -TSS86 - - XLOC_000074 Xkr4 TSS86 chr1:3364871-3364919 - - 7.29939e+07 0 2.18982e+08 OK 0 0 0 OK -TSS87 - - XLOC_000075 Xkr4 TSS87 chr1:3367135-3367162 - - 0 0 0 OK 0 0 0 OK -TSS88 - - XLOC_000076 Xkr4 TSS88 chr1:3367210-3367237 - - 0 0 0 OK 0 0 0 OK -TSS89 - - XLOC_000077 Xkr4 TSS89 chr1:3367333-3367382 - - 0 0 0 OK 0 0 0 OK -TSS90 - - XLOC_000078 Xkr4 TSS90 chr1:3369580-3369607 - - 0 0 0 OK 0 0 0 OK -TSS91 - - XLOC_000079 Xkr4 TSS91 chr1:3375001-3375028 - - 0 0 0 OK 0 0 0 OK -TSS92 - - XLOC_000080 Xkr4 TSS92 chr1:3377211-3377262 - - 0 0 0 OK 0 0 0 OK -TSS93 - - XLOC_000081 Xkr4 TSS93 chr1:3379888-3379915 - - 0 0 0 OK 0 0 0 OK -TSS94 - - XLOC_000082 Xkr4 TSS94 chr1:3386739-3386836 - - 0 0 0 OK 0 0 0 OK -TSS95 - - XLOC_000083 Xkr4 TSS95 chr1:3391325-3391352 - - 0 0 0 OK 0 0 0 OK -TSS96 - - XLOC_000084 Xkr4 TSS96 chr1:3435841-3435880 - - 0 0 0 OK 0 0 0 OK -TSS97 - - XLOC_000085 Xkr4 TSS97 chr1:3447761-3447788 - - 0 0 0 OK 0 0 0 OK -TSS98 - - XLOC_000086 Xkr4 TSS98 chr1:3450906-3450965 - - 0 0 0 OK 0 0 0 OK -TSS99 - - XLOC_000087 Xkr4 TSS99 chr1:3451051-3451109 - - 0 0 0 OK 0 0 0 OK +TSS60 - - XLOC_000056 Xkr4 TSS60 chr1:3284966-3284993 - - 0 0 0 OK 0 0 0 OK +TSS61 - - XLOC_000057 Xkr4 TSS61 chr1:3290488-3290553 - - 0 0 0 OK 9.79535e+06 0 2.9386e+07 OK +TSS62 - - XLOC_000058 Xkr4 TSS62 chr1:3290798-3290859 - - 1.8095e+07 0 5.4285e+07 OK 0 0 0 OK +TSS63 - - XLOC_000059 Xkr4 TSS63 chr1:3290919-3291273 - - 342218 0 691214 OK 75524 0 162732 OK +TSS65 - - XLOC_000060 Xkr4 TSS65 chr1:3299443-3299664 - - 937403 0 1.99795e+06 OK 137917 0 413751 OK +TSS66 - - XLOC_000060 Xkr4 TSS66 chr1:3299443-3299664 - - 0 0 0 OK 0 0 0 OK +TSS67 - - XLOC_000061 Xkr4 TSS67 chr1:3299691-3299733 - - 0 0 0 OK 0 0 0 OK +TSS68 - - XLOC_000062 Xkr4 TSS68 chr1:3300051-3300078 - - 0 0 0 OK 0 0 0 OK +TSS69 - - XLOC_000063 Xkr4 TSS69 chr1:3307748-3307775 - - 0 0 0 OK 0 0 0 OK +TSS7 - - XLOC_000007 - TSS7 chr1:3189810-3190789 - - 415851 231920 599782 OK 458870 363705 554035 OK +TSS70 - - XLOC_000064 Xkr4 TSS70 chr1:3318620-3318647 - - 0 0 0 OK 0 0 0 OK +TSS71 - - XLOC_000065 Xkr4 TSS71 chr1:3318999-3319051 - - 0 0 0 OK 0 0 0 OK +TSS72 - - XLOC_000066 Xkr4 TSS72 chr1:3330527-3330554 - - 0 0 0 OK 0 0 0 OK +TSS73 - - XLOC_000067 Xkr4 TSS73 chr1:3351240-3351311 - - 8.91489e+06 0 2.67447e+07 OK 0 0 0 OK +TSS74 - - XLOC_000068 Xkr4 TSS74 chr1:3355887-3356119 - - 585828 0 1.30332e+06 OK 0 0 0 OK +TSS75 - - XLOC_000069 Xkr4 TSS75 chr1:3356180-3356225 - - 1.19208e+08 0 3.57623e+08 OK 0 0 0 OK +TSS76 - - XLOC_000070 Xkr4 TSS76 chr1:3363076-3363176 - - 4.42166e+06 0 1.06748e+07 OK 0 0 0 OK +TSS77 - - XLOC_000071 Xkr4 TSS77 chr1:3363214-3363278 - - 0 0 0 OK 0 0 0 OK +TSS78 - - XLOC_000072 Xkr4 TSS78 chr1:3363387-3363446 - - 6.42536e+07 0 1.38447e+08 OK 0 0 0 OK +TSS79 - - XLOC_000073 Xkr4 TSS79 chr1:3363753-3363849 - - 0 0 0 OK 0 0 0 OK +TSS80 - - XLOC_000074 Xkr4 TSS80 chr1:3364871-3364919 - - 7.29939e+07 0 2.18982e+08 OK 0 0 0 OK +TSS81 - - XLOC_000075 Xkr4 TSS81 chr1:3367135-3367162 - - 0 0 0 OK 0 0 0 OK +TSS82 - - XLOC_000076 Xkr4 TSS82 chr1:3367210-3367237 - - 0 0 0 OK 0 0 0 OK +TSS83 - - XLOC_000077 Xkr4 TSS83 chr1:3367333-3367382 - - 0 0 0 OK 0 0 0 OK +TSS84 - - XLOC_000078 Xkr4 TSS84 chr1:3369580-3369607 - - 0 0 0 OK 0 0 0 OK +TSS85 - - XLOC_000079 Xkr4 TSS85 chr1:3375001-3375028 - - 0 0 0 OK 0 0 0 OK +TSS86 - - XLOC_000080 Xkr4 TSS86 chr1:3377211-3377262 - - 0 0 0 OK 0 0 0 OK +TSS87 - - XLOC_000081 Xkr4 TSS87 chr1:3379888-3379915 - - 0 0 0 OK 0 0 0 OK +TSS88 - - XLOC_000082 Xkr4 TSS88 chr1:3386739-3386836 - - 0 0 0 OK 0 0 0 OK +TSS89 - - XLOC_000083 Xkr4 TSS89 chr1:3391325-3391352 - - 0 0 0 OK 0 0 0 OK +TSS90 - - XLOC_000084 Xkr4 TSS90 chr1:3435841-3435880 - - 0 0 0 OK 0 0 0 OK +TSS91 - - XLOC_000085 Xkr4 TSS91 chr1:3447761-3447788 - - 0 0 0 OK 0 0 0 OK +TSS92 - - XLOC_000086 Xkr4 TSS92 chr1:3450906-3450965 - - 0 0 0 OK 0 0 0 OK +TSS93 - - XLOC_000087 Xkr4 TSS93 chr1:3451051-3451109 - - 0 0 0 OK 0 0 0 OK diff -r a533f050b897cb68359b4e5d8974cfdcc60d1cfc -r e5c37f9787b72231f31782e9e41f9e379afdb04c test-data/cuffdiff_out9.txt --- a/test-data/cuffdiff_out9.txt +++ b/test-data/cuffdiff_out9.txt @@ -1,91 +1,89 @@ test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 sqrt(JS) test_stat p_value q_value significant TSS1 XLOC_000001 Xkr4 chr1:3204754-3204833 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS11 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS12 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS15 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS16 XLOC_000011 - chr1:3192441-3192494 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS17 XLOC_000012 - chr1:3192550-3192629 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS18 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS19 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS10 XLOC_000008 - chr1:3190858-3191434 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS11 XLOC_000009 - chr1:3191512-3192077 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS13 XLOC_000010 - chr1:3192250-3192336 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS14 XLOC_000011 - chr1:3192441-3192494 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS15 XLOC_000012 - chr1:3192550-3192629 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS16 XLOC_000013 - chr1:3192649-3192676 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS17 XLOC_000014 - chr1:3192731-3192811 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS18 XLOC_000015 - chr1:3192940-3193042 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS19 XLOC_000016 - chr1:3194185-3194226 q1 q2 NOTEST 0 0 0 0 0 1 no TSS2 XLOC_000002 - chr1:3111449-3111490 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS20 XLOC_000015 - chr1:3192940-3193042 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS21 XLOC_000016 - chr1:3194185-3194226 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS22 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS23 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS24 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS25 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS26 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS27 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS28 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS29 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS20 XLOC_000017 - chr1:3194302-3194329 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS21 XLOC_000018 - chr1:3194706-3194733 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS22 XLOC_000019 - chr1:3195083-3195110 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS23 XLOC_000020 - chr1:3195450-3195477 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS24 XLOC_000021 - chr1:3197089-3197116 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS25 XLOC_000022 - chr1:3197246-3197273 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS26 XLOC_000023 - chr1:3197346-3197373 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS27 XLOC_000024 - chr1:3197425-3197452 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS28 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS29 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 0 1 no TSS3 XLOC_000003 - chr1:3111545-3111576 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS30 XLOC_000025 - chr1:3200022-3200191 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS32 XLOC_000026 - chr1:3200325-3200352 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS33 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS34 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS35 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS37 XLOC_000030 - chr1:3201596-3201666 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS38 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS39 XLOC_000032 - chr1:3201725-3201809 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS30 XLOC_000027 - chr1:3200430-3200457 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS31 XLOC_000028 - chr1:3201007-3201039 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS32 XLOC_000029 - chr1:3201077-3201481 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS33 XLOC_000030 - chr1:3201596-3201666 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS34 XLOC_000031 - chr1:3201672-3201699 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS35 XLOC_000032 - chr1:3201725-3201809 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS36 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS37 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS38 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS39 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 0 0 0 0 0 1 no TSS4 XLOC_000004 - chr1:3174765-3174792 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS40 XLOC_000033 Xkr4 chr1:3211521-3211561 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS41 XLOC_000034 Xkr4 chr1:3212213-3212292 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS42 XLOC_000035 Xkr4 chr1:3212367-3212439 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS43 XLOC_000036 Xkr4 chr1:3212717-3212801 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS44 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 FAIL 0 0 0 0 0 1 no -TSS45 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 FAIL 0 0 0 0 0 1 no -TSS46 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS47 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS48 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS49 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS40 XLOC_000037 Xkr4 chr1:3213095-3213242 q1 q2 OK 0 0 0.249945 0.143447 0.135175 0.135175 no +TSS41 XLOC_000038 Xkr4 chr1:3240606-3240633 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS42 XLOC_000039 Xkr4 chr1:3242479-3242512 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS43 XLOC_000040 Xkr4 chr1:3242633-3242923 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS44 XLOC_000041 Xkr4 chr1:3242924-3243005 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS45 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS46 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS47 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS48 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS49 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 NOTEST 0 0 0 0 0 1 no TSS5 XLOC_000005 - chr1:3187401-3187428 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS50 XLOC_000042 Xkr4 chr1:3243018-3243079 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS51 XLOC_000043 Xkr4 chr1:3243108-3243154 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS52 XLOC_000044 Xkr4 chr1:3243347-3243401 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS53 XLOC_000045 Xkr4 chr1:3254079-3254106 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS54 XLOC_000046 Xkr4 chr1:3256974-3257011 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS55 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS56 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS57 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS59 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS50 XLOC_000047 Xkr4 chr1:3277155-3277182 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS51 XLOC_000048 Xkr4 chr1:3277190-3277218 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS52 XLOC_000049 Xkr4 chr1:3277913-3278390 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS54 XLOC_000050 Xkr4 chr1:3280117-3280144 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS55 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS56 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS57 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS58 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS59 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 0 1 no TSS6 XLOC_000006 - chr1:3188521-3188548 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS60 XLOC_000051 Xkr4 chr1:3280498-3280525 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS61 XLOC_000052 Xkr4 chr1:3280686-3280741 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS62 XLOC_000053 Xkr4 chr1:3282504-3282531 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS63 XLOC_000054 Xkr4 chr1:3282650-3282677 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS64 XLOC_000055 Xkr4 chr1:3282760-3282832 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS65 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS66 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS67 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS68 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS7 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS70 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 1 1 no -TSS71 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS72 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS73 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS74 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS75 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS76 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS77 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS78 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS79 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS80 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS81 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS82 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS83 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS84 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS85 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS86 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS87 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS88 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS89 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS90 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS91 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS92 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS93 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS94 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS95 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS96 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS97 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS98 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 0 1 no -TSS99 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS60 XLOC_000056 Xkr4 chr1:3284966-3284993 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS61 XLOC_000057 Xkr4 chr1:3290488-3290553 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS62 XLOC_000058 Xkr4 chr1:3290798-3290859 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS63 XLOC_000059 Xkr4 chr1:3290919-3291273 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS65 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS66 XLOC_000060 Xkr4 chr1:3299443-3299664 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS67 XLOC_000061 Xkr4 chr1:3299691-3299733 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS68 XLOC_000062 Xkr4 chr1:3300051-3300078 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS69 XLOC_000063 Xkr4 chr1:3307748-3307775 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS7 XLOC_000007 - chr1:3189810-3190789 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS70 XLOC_000064 Xkr4 chr1:3318620-3318647 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS71 XLOC_000065 Xkr4 chr1:3318999-3319051 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS72 XLOC_000066 Xkr4 chr1:3330527-3330554 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS73 XLOC_000067 Xkr4 chr1:3351240-3351311 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS74 XLOC_000068 Xkr4 chr1:3355887-3356119 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS75 XLOC_000069 Xkr4 chr1:3356180-3356225 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS76 XLOC_000070 Xkr4 chr1:3363076-3363176 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS77 XLOC_000071 Xkr4 chr1:3363214-3363278 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS78 XLOC_000072 Xkr4 chr1:3363387-3363446 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS79 XLOC_000073 Xkr4 chr1:3363753-3363849 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS80 XLOC_000074 Xkr4 chr1:3364871-3364919 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS81 XLOC_000075 Xkr4 chr1:3367135-3367162 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS82 XLOC_000076 Xkr4 chr1:3367210-3367237 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS83 XLOC_000077 Xkr4 chr1:3367333-3367382 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS84 XLOC_000078 Xkr4 chr1:3369580-3369607 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS85 XLOC_000079 Xkr4 chr1:3375001-3375028 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS86 XLOC_000080 Xkr4 chr1:3377211-3377262 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS87 XLOC_000081 Xkr4 chr1:3379888-3379915 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS88 XLOC_000082 Xkr4 chr1:3386739-3386836 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS89 XLOC_000083 Xkr4 chr1:3391325-3391352 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS90 XLOC_000084 Xkr4 chr1:3435841-3435880 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS91 XLOC_000085 Xkr4 chr1:3447761-3447788 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS92 XLOC_000086 Xkr4 chr1:3450906-3450965 q1 q2 NOTEST 0 0 0 0 0 1 no +TSS93 XLOC_000087 Xkr4 chr1:3451051-3451109 q1 q2 NOTEST 0 0 0 0 0 1 no diff -r a533f050b897cb68359b4e5d8974cfdcc60d1cfc -r e5c37f9787b72231f31782e9e41f9e379afdb04c tools/ngs_rna/cuffdiff_wrapper.xml --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -151,7 +151,7 @@ <param name="aligned_reads2" value="cuffdiff_in2.sam" ftype="sam" /><param name="fdr" value="0.05" /> - <param name="min_alignment_count" value="0" ftype="sam" /> + <param name="min_alignment_count" value="0" /><param name="do_bias_correction" value="No" /><param name="do_normalization" value="No" /><param name="sPaired" value="single" ftype="sam" /> https://bitbucket.org/galaxy/galaxy-central/changeset/34db794299d3/ changeset: 34db794299d3 user: jgoecks date: 2012-01-22 20:39:19 summary: Remove unneeded ftype attribute. affected #: 1 file diff -r e5c37f9787b72231f31782e9e41f9e379afdb04c -r 34db794299d3b79e1c9a92fff65e6222c70f4031 tools/ngs_rna/cuffdiff_wrapper.xml --- a/tools/ngs_rna/cuffdiff_wrapper.xml +++ b/tools/ngs_rna/cuffdiff_wrapper.xml @@ -154,7 +154,7 @@ <param name="min_alignment_count" value="0" /><param name="do_bias_correction" value="No" /><param name="do_normalization" value="No" /> - <param name="sPaired" value="single" ftype="sam" /> + <param name="sPaired" value="single"/><!-- Line diffs are needed because cuffdiff does not produce deterministic output. TODO: can we find datasets that lead to deterministic behavior? 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: dan: Fix for setting up column assignments for dynamic options wrt tool data tables when the index file is missing.
by Bitbucket 20 Jan '12

20 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ef0a2b1c879b/ changeset: ef0a2b1c879b user: dan date: 2012-01-20 22:40:34 summary: Fix for setting up column assignments for dynamic options wrt tool data tables when the index file is missing. affected #: 1 file diff -r 8a597b83448f66523531c782b027dd000e277644 -r ef0a2b1c879b51c215afd445c248eb604645b29f lib/galaxy/tools/parameters/dynamic_options.py --- a/lib/galaxy/tools/parameters/dynamic_options.py +++ b/lib/galaxy/tools/parameters/dynamic_options.py @@ -411,16 +411,15 @@ app = tool_param.tool.app if tool_data_table_name in app.tool_data_tables: self.tool_data_table = app.tool_data_tables[ tool_data_table_name ] + # Column definitions are optional, but if provided override those from the table + if elem.find( "column" ) is not None: + self.parse_column_definitions( elem ) + else: + self.columns = self.tool_data_table.columns # Set self.missing_index_file if the index file to # which the tool_data_table refers does not exist. if self.tool_data_table.missing_index_file: self.missing_index_file = self.tool_data_table.missing_index_file - else: - # Column definitions are optional, but if provided override those from the table - if elem.find( "column" ) is not None: - self.parse_column_definitions( elem ) - else: - self.columns = self.tool_data_table.columns else: self.missing_tool_data_table_name = tool_data_table_name log.warn( "Data table named '%s' is required by tool but not configured" % tool_data_table_name ) 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: natefoo: Fix for the object store doctest.
by Bitbucket 20 Jan '12

20 Jan '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8a597b83448f/ changeset: 8a597b83448f user: natefoo date: 2012-01-20 22:20:13 summary: Fix for the object store doctest. affected #: 1 file diff -r ea34f05c3c212754ba79bdfb4959233cea2837b3 -r 8a597b83448f66523531c782b027dd000e277644 lib/galaxy/objectstore/__init__.py --- a/lib/galaxy/objectstore/__init__.py +++ b/lib/galaxy/objectstore/__init__.py @@ -195,11 +195,12 @@ >>> from galaxy.util.bunch import Bunch >>> import tempfile >>> file_path=tempfile.mkdtemp() - >>> s = DiskObjectStore(Bunch(umask=077), file_path=file_path) - >>> s.create(1) - >>> s.exists(1) + >>> obj = Bunch(id=1) + >>> s = DiskObjectStore(Bunch(umask=077, job_working_directory=file_path, new_file_path=file_path), file_path=file_path) + >>> s.create(obj) + >>> s.exists(obj) True - >>> assert s.get_filename(1) == file_path + '/000/dataset_1.dat' + >>> assert s.get_filename(obj) == file_path + '/000/dataset_1.dat' """ def __init__(self, config, file_path=None, extra_dirs=None): super(DiskObjectStore, self).__init__() 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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