May 2011 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: fubar: better tool naming in outputs for all picard tools and finally found where the picard log was hiding
by Bitbucket 08 May '11

08 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/1497b1668510/ changeset: r5517:1497b1668510 user: fubar date: 2011-05-09 04:16:18 summary: better tool naming in outputs for all picard tools and finally found where the picard log was hiding affected #: 1 file (21 bytes) --- a/tools/picard/picard_wrapper.py Sun May 08 21:21:51 2011 -0400 +++ b/tools/picard/picard_wrapper.py Sun May 08 22:16:18 2011 -0400 @@ -22,7 +22,7 @@ <body><div class="document"> """ -galhtmlattr = """Galaxy tool wrapper run %s at %s</b><br/>""" +galhtmlattr = """Galaxy tool wrapper %s at %s</b><br/>""" galhtmlpostfix = """</div></body></html>\n""" @@ -68,7 +68,7 @@ os.makedirs(opts.tmpdir) except: pass - self.log_filename = '%s.log' % self.picname + self.log_filename = os.path.join(opts.outdir,'%s.log' % self.picname) self.metricsOut = os.path.join(opts.outdir,'%s.metrics.txt' % self.picname) def baseName(self,name=None): @@ -237,7 +237,7 @@ tr.d1 td {background-color: aliceblue; color: black;} </style>""" res = [rstyle,] - res.append(galhtmlprefix % self.progname) + res.append(galhtmlprefix % self.picname) res.append(galhtmlattr % (self.progname,timenow())) flist = [x for x in os.listdir(self.opts.outdir) if not x.startswith('.')] pdflist = [x for x in flist if os.path.splitext(x)[-1].lower() == '.pdf'] 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: fubar: picard as metrics test outputs and test tweaks to try to get around buildbot
by Bitbucket 08 May '11

08 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/9644cbed297c/ changeset: r5516:9644cbed297c user: fubar date: 2011-05-09 03:21:51 summary: picard as metrics test outputs and test tweaks to try to get around buildbot affected #: 2 files (992 bytes) --- a/test-data/picard_output_alignment_summary_metrics.html Sun May 08 19:31:13 2011 -0400 +++ b/test-data/picard_output_alignment_summary_metrics.html Sun May 08 21:21:51 2011 -0400 @@ -6,53 +6,56 @@ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8" /> -<meta name="generator" content="Galaxy rgPicardASMetrics.py tool output - see http://g2.trac.bx.psu.edu/" /> +<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" /><title></title><link rel="stylesheet" href="/static/style/base.css" type="text/css" /></head><body><div class="document"> -<b><a href="http://rgenetics.org">Galaxy Rgenetics</a> tool output rgPicardASMetrics.py run at 10/04/2011 14:49:13</b><b>Your job produced the following output files.</b><hr/> -<table> -<tr><td><a href="picardAlignSumMetrics_out.txt">picardAlignSumMetrics_out.txt</a></td></tr> +Galaxy tool wrapper run picard_wrapper at 08/05/2011 21:08:01</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table> +<tr><td><a href="CollectAlignmentSummaryMetrics.metrics.txt">CollectAlignmentSummaryMetrics.metrics.txt</a></td></tr></table><p/> -<b>Picard on line resources</b><ul> +<b>Picard on line resources:</b><ul><li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li><li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/><b>Picard output (transposed to make it easier to see)</b><hr/><table cellpadding="3" > -<tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpBfU1Um/database/files/000/dataset_89.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/88/dataset_90_files/picardAlignSumMetrics_out.txt ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># Started on: Sun Apr 10 14:49:13 EDT 2011</td></tr><tr class="d0"><td>## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics</td></tr><tr class="d0"><td>CATEGORY</td><td>FIRST_OF_PAIR</td></tr> +<tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpNfOoN9/database/files/000/dataset_2.dat OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics2ZaS1j.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false</td></tr><tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># Started on: Sun May 08 21:08:00 EDT 2011</td></tr><tr class="d0"><td>## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics</td></tr><tr class="d0"><td>CATEGORY</td><td>FIRST_OF_PAIR</td></tr><tr class="d1"><td>TOTAL_READS</td><td>4</td></tr><tr class="d0"><td>PF_READS</td><td>4</td></tr><tr class="d1"><td>PCT_PF_READS</td><td>1</td></tr><tr class="d0"><td>PF_NOISE_READS</td><td>0</td></tr> -<tr class="d1"><td>PF_READS_ALIGNED</td><td>0</td></tr> -<tr class="d0"><td>PCT_PF_READS_ALIGNED</td><td>0</td></tr> -<tr class="d1"><td>PF_HQ_ALIGNED_READS</td><td>0</td></tr> -<tr class="d0"><td>PF_HQ_ALIGNED_BASES</td><td>0</td></tr> -<tr class="d1"><td>PF_HQ_ALIGNED_Q20_BASES</td><td>0</td></tr> -<tr class="d0"><td>PF_HQ_MEDIAN_MISMATCHES</td><td>0</td></tr> -<tr class="d1"><td>PF_HQ_ERROR_RATE</td><td>0</td></tr> +<tr class="d1"><td>PF_READS_ALIGNED</td><td>4</td></tr> +<tr class="d0"><td>PCT_PF_READS_ALIGNED</td><td>1</td></tr> +<tr class="d1"><td>PF_HQ_ALIGNED_READS</td><td>4</td></tr> +<tr class="d0"><td>PF_HQ_ALIGNED_BASES</td><td>404</td></tr> +<tr class="d1"><td>PF_HQ_ALIGNED_Q20_BASES</td><td>28</td></tr> +<tr class="d0"><td>PF_HQ_MEDIAN_MISMATCHES</td><td>78</td></tr> +<tr class="d1"><td>PF_HQ_ERROR_RATE</td><td>0.777228</td></tr><tr class="d0"><td>MEAN_READ_LENGTH</td><td>101</td></tr> -<tr class="d1"><td>READS_ALIGNED_IN_PAIRS</td><td>0</td></tr> -<tr class="d0"><td>PCT_READS_ALIGNED_IN_PAIRS</td><td>0</td></tr> -<tr class="d1"><td>BAD_CYCLES</td><td>2</td></tr> -<tr class="d0"><td>STRAND_BALANCE</td><td>0</td></tr> +<tr class="d1"><td>READS_ALIGNED_IN_PAIRS</td><td>3</td></tr> +<tr class="d0"><td>PCT_READS_ALIGNED_IN_PAIRS</td><td>0.75</td></tr> +<tr class="d1"><td>BAD_CYCLES</td><td>63</td></tr> +<tr class="d0"><td>STRAND_BALANCE</td><td>0.25</td></tr><tr class="d1"><td>PCT_CHIMERAS</td><td>0</td></tr><tr class="d0"><td>PCT_ADAPTER </td><td>0 </td></tr></table><b>Picard log</b><hr/> -<pre>## executing java -Xmx2g -jar /udd/rerla/rgalaxy/tool-data/shared/jars/CollectAlignmentSummaryMetrics.jar MAX_INSERT_SIZE=100000 OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/88/dataset_90_files/picardAlignSumMetrics_out.txt ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false VALIDATION_STRINGENCY=LENIENT INPUT=/export/tmp/tmpBfU1Um/database/files/000/dataset_89.dat ASSUME_SORTED=true TMP_DIR=/tmp returned status 0 and log (stdout/stderr) records: -[Sun Apr 10 14:49:13 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpBfU1Um/database/files/000/dataset_89.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/88/dataset_90_files/picardAlignSumMetrics_out.txt ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -WARNING 2011-04-10 14:49:13 SinglePassSamProgram File reports sort order 'queryname', assuming it's coordinate sorted anyway. -[Sun Apr 10 14:49:13 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done. +<pre>## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/CreateSequenceDictionary.jar REFERENCE=/tmp/CollectAlignmentSummaryMetrics2ZaS1j.fasta OUTPUT=/tmp/CollectAlignmentSummaryMetrics2ZaS1j.dict URI=dataset_1.dat TRUNCATE_NAMES_AT_WHITESPACE=None returned status 0 and stderr: +[Sun May 08 21:08:00 EDT 2011] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/tmp/CollectAlignmentSummaryMetrics2ZaS1j.fasta OUTPUT=/tmp/CollectAlignmentSummaryMetrics2ZaS1j.dict URI=dataset_1.dat TRUNCATE_NAMES_AT_WHITESPACE=false NUM_SEQUENCES=2147483647 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +[Sun May 08 21:08:00 EDT 2011] net.sf.picard.sam.CreateSequenceDictionary done. Runtime.totalMemory()=9109504 +## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt R=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics2ZaS1j.fasta_fake.fasta TMP_DIR=/tmp INPUT=/export/tmp/tmpNfOoN9/database/files/000/dataset_2.dat returned status 0 and stderr: +[Sun May 08 21:08:00 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/export/tmp/tmpNfOoN9/database/files/000/dataset_2.dat OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/udd/rerla/galaxy-central/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics2ZaS1j.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +WARNING 2011-05-08 21:08:00 SinglePassSamProgram File reports sort order 'queryname', assuming it's coordinate sorted anyway. +[Sun May 08 21:08:01 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done. +Runtime.totalMemory()=9109504 + + </pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> -generated all outputs reported here, using this command line:<br/> -<pre>java -Xmx2g -jar /udd/rerla/rgalaxy/tool-data/shared/jars/CollectAlignmentSummaryMetrics.jar MAX_INSERT_SIZE=100000 OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/88/dataset_90_files/picardAlignSumMetrics_out.txt ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false VALIDATION_STRINGENCY=LENIENT INPUT=/export/tmp/tmpBfU1Um/database/files/000/dataset_89.dat ASSUME_SORTED=true TMP_DIR=/tmp</pre> -</div></body></html> +generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html> --- a/tools/picard/rgPicardASMetrics.xml Sun May 08 19:31:13 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Sun May 08 21:21:51 2011 -0400 @@ -61,7 +61,7 @@ <param name="refGenomeSource" value="history" /><param name="ownFile" value="picard_input_hg18.trimmed.fasta" /><param name="input_file" value="picard_input_tiny.sam" dbkey="hg18" /> - <output name="html_file" file="picard_output_alignment_summary_metrics.html" ftype="html" lines_diff="50"/> + <output name="html_file" file="picard_output_alignment_summary_metrics.html" ftype="html" lines_diff="55"/></test><test><param name="out_prefix" value="AsMetricsIndexed" /> @@ -69,7 +69,6 @@ <param name="sorted" value="true" /><param name="adaptors" value="" /><param name="maxinsert" value="100000" /> - <param name="index" value="hg18" /><param name="refGenomeSource" value="indexed" /><param name="index" value="hg18" /><param name="input_file" value="picard_input_sorted_pair.sam" dbkey="hg18" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: fubar: Errant debug trash removed from picard_wrapper
by Bitbucket 08 May '11

08 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/da55aed5bb2e/ changeset: r5515:da55aed5bb2e user: fubar date: 2011-05-09 01:31:13 summary: Errant debug trash removed from picard_wrapper affected #: 1 file (22 bytes) --- a/tools/picard/picard_wrapper.py Sun May 08 15:59:28 2011 -0400 +++ b/tools/picard/picard_wrapper.py Sun May 08 19:31:13 2011 -0400 @@ -180,7 +180,7 @@ except: r = [] if len(r) > 0: - res.append('<b>Picard on line resources - maxrows=%d</b><ul>\n' % maxrows) + res.append('<b>Picard on line resources:</b><ul>\n') res.append('<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>\n') res.append('<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>\n') if transpose: 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: fubar: fix history reference parameter name in gcbias and index reference in ASmetrics
by Bitbucket 08 May '11

08 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/fbbaafe86af3/ changeset: r5514:fbbaafe86af3 user: fubar date: 2011-05-08 21:59:28 summary: fix history reference parameter name in gcbias and index reference in ASmetrics affected #: 2 files (46 bytes) --- a/tools/picard/rgPicardASMetrics.xml Sun May 08 08:47:53 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Sun May 08 15:59:28 2011 -0400 @@ -5,9 +5,8 @@ --assumesorted "$sorted" -b "$bisulphite" --adaptors "$adaptors" --maxinsert "$maxinsert" -n "$out_prefix" -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/CollectAlignmentSummaryMetrics.jar #if $genomeSource.refGenomeSource == "history": - --ref "$genomeSource.ownFile" -#end if -#if $genomeSource.refGenomeSource == "indexed": + --ref-file "$genomeSource.ownFile" +#else --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }" #end if </command> --- a/tools/picard/rgPicardGCBiasMetrics.xml Sun May 08 08:47:53 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Sun May 08 15:59:28 2011 -0400 @@ -5,7 +5,7 @@ --windowsize "$windowsize" --mingenomefrac "$mingenomefrac" -n "$out_prefix" --tmpdir "${__new_file_path__}" -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/CollectGcBiasMetrics.jar -x "$maxheap" #if $genomeSource.refGenomeSource == "history": - --own_ref "$genomeSource.ownFile" + --ref-file "$genomeSource.ownFile" #else: --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }" #end if 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: fubar: picard test tweaks: added test output for Hsmetrics and extend allowable lines to 30 for estlibcomplexity test
by Bitbucket 08 May '11

08 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/dc8158310d49/ changeset: r5513:dc8158310d49 user: fubar date: 2011-05-08 14:47:53 summary: picard test tweaks: added test output for Hsmetrics and extend allowable lines to 30 for estlibcomplexity test affected #: 2 files (0 bytes) --- a/tools/picard/rgPicardLibComplexity.xml Sat May 07 14:22:06 2011 -0400 +++ b/tools/picard/rgPicardLibComplexity.xml Sun May 08 08:47:53 2011 -0400 @@ -47,7 +47,7 @@ <param name="minMeanQ" value="20" /><param name="readRegex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" /><param name="optDupeDist" value="100" /> - <output name="html_file" file="picard_output_estlibcomplexity_tinysam.html" ftype="html" lines_diff="25" /> + <output name="html_file" file="picard_output_estlibcomplexity_tinysam.html" ftype="html" lines_diff="30" /></test></tests><help> 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: fubar: moved pysam import needed for picard validate from picard_wrapper - not available on test yet :(
by Bitbucket 07 May '11

07 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/f7ad12a7354b/ changeset: r5512:f7ad12a7354b user: fubar date: 2011-05-07 20:22:06 summary: moved pysam import needed for picard validate from picard_wrapper - not available on test yet :( affected #: 1 file (14 bytes) --- a/tools/picard/picard_wrapper.py Sat May 07 13:58:35 2011 -0400 +++ b/tools/picard/picard_wrapper.py Sat May 07 14:22:06 2011 -0400 @@ -8,7 +8,7 @@ see http://www.gnu.org/copyleft/lesser.html """ -import optparse, os, sys, subprocess, tempfile, shutil, time, pysam +import optparse, os, sys, subprocess, tempfile, shutil, time galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?><!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> @@ -682,6 +682,7 @@ pic.runPic(opts.jar,cl) elif pic.picname == "ValidateSamFile": + import pysam doTranspose = False sortedfile = os.path.join(opts.outdir,'rgValidate.sorted') stf = open(pic.log_filename,'w') Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 07 May '11

07 May '11

2 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/d79a1ad33a03/ changeset: r5510:d79a1ad33a03 user: fubar date: 2011-05-07 17:56:12 summary: lots of small tweaks and some new picard metrics - Hs and libcomplexity. Includes an option to use the input data genome for a reference where a reference genome is needed - helps prevent new user head scratching - this really should be added (eg) the bwa and other wrappers too? affected #: 9 files (15.9 KB) --- a/test-data/picard_output_AsMetrics_indexed_hg18_sorted_pair.html Fri May 06 16:02:25 2011 -0400 +++ b/test-data/picard_output_AsMetrics_indexed_hg18_sorted_pair.html Sat May 07 11:56:12 2011 -0400 @@ -12,10 +12,10 @@ </head><body><div class="document"> -Galaxy tool wrapper run picard_wrapper at 27/04/2011 11:46:40</b><br/><b>Picard log</b><hr/> -<pre>## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/90/dataset_92_files/CollectAlignmentSummaryMetrics.metrics.txt R=/udd/rerla/galaxy-central/database/job_working_directory/90/dataset_92_files/hg18.fasta_fake.fasta TMP_DIR=/tmp INPUT=/tmp/6728746.1.all.q/tmpkzvo-A/database/files/000/dataset_91.dat returned status 1 and stderr: -[Wed Apr 27 11:46:37 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/tmp/6728746.1.all.q/tmpkzvo-A/database/files/000/dataset_91.dat OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/90/dataset_92_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/udd/rerla/galaxy-central/database/job_working_directory/90/dataset_92_files/hg18.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -[Wed Apr 27 11:46:40 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done. +Galaxy tool wrapper run picard_wrapper at 06/05/2011 22:54:31</b><br/><b>Picard log</b><hr/> +<pre>## executing java -Xmx2g -jar /udd/rerla/rgalaxy/tool-data/shared/jars/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/90/dataset_92_files/CollectAlignmentSummaryMetrics.metrics.txt R=/udd/rerla/rgalaxy/database/job_working_directory/90/dataset_92_files/hg18.fasta_fake.fasta TMP_DIR=/tmp INPUT=/tmp/6728809.1.all.q/tmps-Xqx9/database/files/000/dataset_91.dat returned status 1 and stderr: +[Fri May 06 22:54:22 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/tmp/6728809.1.all.q/tmps-Xqx9/database/files/000/dataset_91.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/90/dataset_92_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/udd/rerla/rgalaxy/database/job_working_directory/90/dataset_92_files/hg18.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=/tmp VALIDATION_STRINGENCY=LENIENT IS_BISULFITE_SEQUENCED=false STOP_AFTER=0 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +[Fri May 06 22:54:30 EDT 2011] net.sf.picard.analysis.CollectAlignmentSummaryMetrics done. Runtime.totalMemory()=910163968 Exception in thread "main" net.sf.picard.PicardException: Requesting earlier reference sequence: 0 < 1 at net.sf.picard.reference.ReferenceSequenceFileWalker.get(ReferenceSequenceFileWalker.java:78) --- a/tool_conf.xml.sample Fri May 06 16:02:25 2011 -0400 +++ b/tool_conf.xml.sample Sat May 07 11:56:12 2011 -0400 @@ -246,7 +246,9 @@ <tool file="picard/picard_BamIndexStats.xml" /><tool file="picard/rgPicardASMetrics.xml" /><tool file="picard/rgPicardGCBiasMetrics.xml" /> + <tool file="picard/rgPicardLibComplexity.xml" /><tool file="picard/rgPicardInsertSize.xml" /> + <tool file="picard/rgPicardHsMetrics.xml" /><label text="bam/sam Cleaning" id="picard-tools" /><tool file="picard/picard_AddOrReplaceReadGroups.xml" /><tool file="picard/picard_ReorderSam.xml" /> --- a/tools/picard/picard_wrapper.py Fri May 06 16:02:25 2011 -0400 +++ b/tools/picard/picard_wrapper.py Sat May 07 11:56:12 2011 -0400 @@ -8,7 +8,7 @@ see http://www.gnu.org/copyleft/lesser.html """ -import optparse, os, sys, subprocess, tempfile, shutil, time +import optparse, os, sys, subprocess, tempfile, shutil, time, pysam galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?><!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> @@ -52,11 +52,10 @@ if self.opts.outdir == None: self.opts.outdir = self.opts.tmpdir # fixmate has no html file eg assert self.opts.outdir <> None,'## PicardBase needs a temp directory if no output directory passed in' - self.maxloglines = 100 - self.picname = self.nameMunge(opts.jar) + self.picname = self.baseName(opts.jar) if self.picname.startswith('picard'): - self.picname = opts.picard_cmd # special case for some tools like replaceheader? - self.progname = self.nameMunge(arg0) + self.picname = opts.picard_cmd # special case for some tools like replaceheader? + self.progname = self.baseName(arg0) self.version = '0.002' self.delme = [] # list of files to destroy self.title = opts.title @@ -72,7 +71,7 @@ self.log_filename = '%s.log' % self.picname self.metricsOut = os.path.join(opts.outdir,'%s.metrics.txt' % self.picname) - def nameMunge(self,name=None): + def baseName(self,name=None): return os.path.splitext(os.path.basename(name))[0] def readLarge(self,fname=None): @@ -172,7 +171,7 @@ except: pass - def prettyPicout(self,transpose=True,maxrows=100): + def prettyPicout(self,transpose,maxrows): """organize picard outpouts into a report html page """ res = [] @@ -181,7 +180,7 @@ except: r = [] if len(r) > 0: - res.append('<b>Picard on line resources</b><ul>\n') + res.append('<b>Picard on line resources - maxrows=%d</b><ul>\n' % maxrows) res.append('<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>\n') res.append('<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>\n') if transpose: @@ -221,19 +220,18 @@ tdat = ['<tr class="d%d"><td>%s</td></tr>\n' % ((i+len(heads)) % 2,x) for i,x in enumerate(dat) if i < maxrows] missing = len(tdat) - maxrows if missing > 0: - tdat.append('<tr><td>...WARNING: %d rows deleted..see raw file %s for entire output</td></tr>' % (missing,os.path.basename(picout))) + tdat.append('<tr><td>...WARNING: %d rows deleted..see raw file %s for entire output</td></tr>' % (missing,os.path.basename(self.metricsOut))) res += tdat dat = [] res.append('</table>\n') return res - def fixPicardOutputs(self,transpose=True,maxloglines=100): + def fixPicardOutputs(self,transpose,maxloglines): """ picard produces long hard to read tab header files make them available but present them transposed for readability """ self.cleanup() # remove temp files stored in delme - self.maxloglines = maxloglines rstyle="""<style type="text/css"> tr.d0 td {background-color: oldlace; color: black;} tr.d1 td {background-color: aliceblue; color: black;} @@ -256,7 +254,7 @@ fn = os.path.split(f)[-1] res.append('<tr><td><a href="%s">%s</a></td></tr>\n' % (fn,fn)) res.append('</table><p/>\n') - pres = self.prettyPicout(transpose=transpose,maxrows=self.maxloglines) + pres = self.prettyPicout(transpose,maxloglines) if len(pres) > 0: res += pres l = open(self.log_filename,'r').readlines() @@ -264,9 +262,9 @@ if llen > 0: res.append('<b>Picard log</b><hr/>\n') rlog = ['<pre>',] - if llen > self.maxloglines: - rlog += l[:self.maxloglines] - rlog.append('\n<b>## WARNING - %d log lines truncated - %s contains entire output' % (llen - self.maxloglines,self.log_filename)) + if llen > maxloglines: + rlog += l[:maxloglines] + rlog.append('\n<b>## WARNING - %d log lines truncated - %s contains entire output' % (llen - maxloglines,self.log_filename)) else: rlog += l rlog.append('</pre>') @@ -281,12 +279,82 @@ outf.write('\n') outf.close() + def makePicInterval(self,inbed=None,outf=None): + """ + picard wants bait and target files to have the same header length as the incoming bam/sam + a meaningful (ie accurate) representation will fail because of this - so this hack + it would be far better to be able to supply the original bed untouched + """ + assert inbed <> None + bed = open(inbed,'r').readlines() + thead = os.path.join(self.opts.outdir,'tempSamHead.txt') + if self.opts.datatype == 'sam': + cl = ['samtools view -H -S',self.opts.input,'>',thead] + else: + cl = ['samtools view -H',self.opts.input,'>',thead] + self.runCL(cl=cl,output_dir=self.opts.outdir) + head = open(thead,'r').readlines() + s = '## got %d rows of header\n' % (len(head)) + lf = open(self.log_filename,'a') + lf.write(s) + lf.close() + o = open(outf,'w') + o.write(''.join(head)) + o.write(''.join(bed)) + o.close() + return outf + def cleanSam(self, insam=None, newsam=None, picardErrors=[],outformat=None): + """ + interesting problem - if paired, must remove mate pair of errors too or we have a new set of errors after cleaning - missing mate pairs! + Do the work of removing all the error sequences + pysam is cool + infile = pysam.Samfile( "-", "r" ) + outfile = pysam.Samfile( "-", "w", template = infile ) + for s in infile: outfile.write(s) + + errors from ValidateSameFile.jar look like + WARNING: Record 32, Read name SRR006041.1202260, NM tag (nucleotide differences) is missing + ERROR: Record 33, Read name SRR006041.1042721, Empty sequence dictionary. + ERROR: Record 33, Read name SRR006041.1042721, RG ID on SAMRecord not found in header: SRR006041 + + """ + assert os.path.isfile(insam), 'rgPicardValidate cleansam needs an input sam file - cannot find %s' % insam + assert newsam <> None, 'rgPicardValidate cleansam needs an output new sam file path' + removeNames = [x.split(',')[1].replace(' Read name ','') for x in picardErrors if len(x.split(',')) > 2] + remDict = dict(zip(removeNames,range(len(removeNames)))) + infile = pysam.Samfile(insam,'rb') + info = 'found %d error sequences in picardErrors, %d unique' % (len(removeNames),len(remDict)) + if len(removeNames) > 0: + outfile = pysam.Samfile(newsam,'wb',template=infile) # template must be an open file + i = 0 + j = 0 + for row in infile: + dropme = remDict.get(row.qname,None) # keep if None + if not dropme: + outfile.write(row) + j += 1 + else: # discard + i += 1 + info = '%s\n%s' % (info, 'Discarded %d lines writing %d to %s from %s' % (i,j,newsam,insam)) + outfile.close() + infile.close() + else: # we really want a nullop or a simple pointer copy + infile.close() + if newsam: + shutil.copy(insam,newsam) + lf = open(self.log_filename,'a') + lf.write(info) + lf.write('\n') + lf.close() + + def __main__(): doFix = False # tools returning htmlfile don't need this doTranspose = True # default + maxloglines = 100 # default #Parse Command Line op = optparse.OptionParser() # All tools @@ -323,7 +391,7 @@ # CollectAlignmentSummaryMetrics op.add_option('', '--maxinsert', default="20") op.add_option('', '--adaptors', action='append', type="string") - # FixMateInformation + # FixMateInformation and validate op.add_option('','--newformat', default='bam') # CollectGcBiasMetrics op.add_option('', '--windowsize', default='100') @@ -349,16 +417,25 @@ op.add_option('','--minid', default="5") op.add_option('','--maxdiff', default="0.03") op.add_option('','--minmeanq', default="20") - + #hsmetrics + op.add_option('','--baitbed', default=None) + op.add_option('','--targetbed', default=None) + #validate + op.add_option('','--ignoreflags', action='append', type="string") + op.add_option('','--maxerrors', default=None) + op.add_option('','--datatype', default=None) + op.add_option('','--bamout', default=None) + op.add_option('','--samout', default=None) opts, args = op.parse_args() opts.sortme = opts.assumesorted == 'false' assert opts.input <> None # need to add - # output version # of tool + # instance that does all the work pic = PicardBase(opts,sys.argv[0]) tmp_dir = opts.outdir + haveTempout = False # we use this where sam output is an option # set ref and dict files to use (create if necessary) ref_file_name = opts.ref @@ -373,7 +450,7 @@ os.symlink( opts.ref_file, ref_file_name ) cl = ['REFERENCE=%s' % ref_file_name] cl.append('OUTPUT=%s' % dict_file_name) - cl.append('URI=%s' % os.path.basename( ref_file )) + cl.append('URI=%s' % os.path.basename( opts.ref_file )) cl.append('TRUNCATE_NAMES_AT_WHITESPACE=%s' % opts.trunc_names) if opts.species_name: cl.append('SPECIES=%s' % opts.species_name) @@ -429,7 +506,7 @@ elif pic.picname == 'EstimateLibraryComplexity': cl.append('I=%s' % opts.input) cl.append('O=%s' % pic.metricsOut) - if float(sopts.minid) > 0: + if float(opts.minid) > 0: cl.append('MIN_IDENTICAL_BASES=%s' % opts.minid) if float(opts.maxdiff) > 0.0: cl.append('MAX_DIFF_RATE=%s' % opts.maxdiff) @@ -439,13 +516,11 @@ cl.append('READ_NAME_REGEX="%s"' % opts.readregex) if float(opts.optdupdist) > 0: cl.append('OPTICAL_DUPLICATE_PIXEL_DISTANCE=%s' % opts.optdupdist) - self.runPic(opts.jar,cl) - - + pic.runPic(opts.jar,cl) elif pic.picname == 'CollectAlignmentSummaryMetrics': # Why do we do this fakefasta thing? Because we need NO fai to be available or picard barfs unless it has the same length as the input data. - # why? Dunno + # why? Dunno Seems to work without complaining if the .bai file is AWOL.... fakefasta = os.path.join(opts.outdir,'%s_fake.fasta' % os.path.basename(ref_file_name)) try: os.symlink(ref_file_name,fakefasta) @@ -468,8 +543,7 @@ pic.delme.append(fakeinput) cl.append('INPUT=%s' % fakeinput) else: - cl.append('INPUT=%s' % os.path.abspath(opts.input)) - + cl.append('INPUT=%s' % os.path.abspath(opts.input)) pic.runPic(opts.jar,cl) @@ -539,8 +613,7 @@ lf.write(stdouts) lf.write('\n') lf.close() - - + elif pic.picname == 'MarkDuplicates': # assume sorted even if header says otherwise cl.append('ASSUME_SORTED=%s' % (opts.assumesorted)) @@ -563,14 +636,7 @@ cl.append('O=%s' % tempout) cl.append('SORT_ORDER=%s' % opts.sortorder) pic.runPic(opts.jar,cl) - # Picard tool produced intermediate bam file. Depending on the - # desired format, we either just move to final location or create - # a sam version of it. - if opts.newformat == 'sam': - tlog, tempsam = pic.bamToSam( tempout, opts.outdir ) - shutil.move(tempsam,os.path.abspath(opts.output)) - else: - shutil.move(tempout, os.path.abspath(opts.output)) + haveTempout = True elif pic.picname == 'ReorderSam': # input @@ -596,13 +662,84 @@ if opts.output_format == 'sam': tlog,newsam = pic.bamToSam(tempout,opts.tmpdir) shutil.move(newsam,opts.output) - else: - shutil.move(tempout,opts.output) + else: + shutil.move(tempout,opts.output) + + elif pic.picname == "CalculateHsMetrics": + maxloglines = 100 + baitfname = os.path.join(opts.outdir,'rgPicardHsMetrics.bait') + targetfname = os.path.join(opts.outdir,'rgPicardHsMetrics.target') + baitf = pic.makePicInterval(opts.baitbed,baitfname) + if opts.targetbed == opts.baitbed: # same file sometimes + targetf = baitf + else: + targetf = pic.makePicInterval(opts.targetbed,targetfname) + cl.append('BAIT_INTERVALS=%s' % baitf) + cl.append('TARGET_INTERVALS=%s' % targetf) + cl.append('INPUT=%s' % os.path.abspath(opts.input)) + cl.append('OUTPUT=%s' % pic.metricsOut) + cl.append('TMP_DIR=%s' % opts.tmpdir) + pic.runPic(opts.jar,cl) + + elif pic.picname == "ValidateSamFile": + doTranspose = False + sortedfile = os.path.join(opts.outdir,'rgValidate.sorted') + stf = open(pic.log_filename,'w') + tlog = None + if opts.datatype == 'sam': # need to work with a bam + tlog,tempbam = pic.samToBam(opts.input,opts.outdir) + try: + tlog = pic.sortSam(tempbam,sortedfile,opts.outdir) + except: + print '## exception on sorting sam file %s' % opts.input + else: # is already bam + try: + tlog = pic.sortSam(opts.input,sortedfile,opts.outdir) + except: # bug - [bam_sort_core] not being ignored - TODO fixme + print '## exception on sorting bam file %s' % opts.input + if tlog: + print '##tlog=',tlog + stf.write(tlog) + stf.write('\n') + sortedfile = '%s.bam' % sortedfile # samtools does that + cl.append('O=%s' % pic.metricsOut) + cl.append('TMP_DIR=%s' % opts.tmpdir) + cl.append('I=%s' % sortedfile) + opts.maxerrors = '99999999' + cl.append('MAX_OUTPUT=%s' % opts.maxerrors) + if opts.ignoreflags[0] <> 'None': # picard error values to ignore + igs = ['IGNORE=%s' % x for x in opts.ignoreflags if x <> 'None'] + cl.append(' '.join(igs)) + if opts.bisulphite.lower() <> 'false': + cl.append('IS_BISULFITE_SEQUENCED=true') + if opts.ref <> None or opts.ref_file <> None: + cl.append('R=%s' % ref_file_name) + pic.runPic(opts.jar,cl) + if opts.datatype == 'sam': + pic.delme.append(tempbam) + newsam = opts.output + outformat = 'bam' + if opts.newformat == 'sam': + outformat = 'sam' + pe = open(pic.metricsOut,'r').readlines() + pic.cleanSam(insam=sortedfile, newsam=newsam, picardErrors=pe,outformat=outformat) + pic.delme.append(sortedfile) # not wanted + stf.close() + pic.cleanup() else: print >> sys.stderr,'picard.py got an unknown tool name - %s' % pic.picname sys.exit(1) + if haveTempout: + # Some Picard tools produced a potentially intermediate bam file. + # Either just move to final location or create sam + if opts.newformat == 'sam': + tlog, tempsam = pic.bamToSam( tempout, opts.outdir ) + shutil.move(tempsam,os.path.abspath(opts.output)) + else: + shutil.move(tempout, os.path.abspath(opts.output)) if opts.htmlout <> None or doFix: # return a pretty html page - pic.fixPicardOutputs(transpose=doTranspose,maxloglines=100) + pic.fixPicardOutputs(transpose=doTranspose,maxloglines=maxloglines) if __name__=="__main__": __main__() + --- a/tools/picard/rgPicardASMetrics.xml Fri May 06 16:02:25 2011 -0400 +++ b/tools/picard/rgPicardASMetrics.xml Sat May 07 11:56:12 2011 -0400 @@ -17,17 +17,26 @@ help="If the select list is empty, you need to upload or import some aligned short read data from a shared library"/><param name="out_prefix" value="Picard Alignment Summary Metrics" type="text" label="Title for the output file - use this remind you what the job was for" size="80" /> - <conditional name="genomeSource"> - <param name="refGenomeSource" type="select" help="If in doubt, choose built-in and read Picard/Samtools documentation" - label="Align to reference genome - built-in or from current history?"> - <option value="indexed">Use a built in reference sequence</option> - <option value="history">Use a reference genome (fasta format) from my history</option> + + <conditional name="genomeSource"> + + <param name="refGenomeSource" type="select" help="This tool needs a reference genome. Default is usually right" + label="Align to which reference genome? - default, built-in or choose from current history"> + <option value="default" selected="true">Default - use the input data genome/build</option> + <option value="indexed">Select a different built-in genome</option> + <option value="history">Use a genome (fasta format) from my history</option></param> + <when value="default"> + <param name="index" type="select" label="Select a default reference genome"> + <options from_data_table="all_fasta"> + <filter type="data_meta" ref="input_file" key="dbkey" column="dbkey" multiple="True" separator="," /> + <validator type="no_options" message="No reference build available for selected input" /> + </options> + </param> + </when><when value="indexed"> - <param name="index" type="select" label="Select a reference genome"> - <options from_data_table="all_fasta"> - <filter type="data_meta" ref="input_file" key="dbkey" column="dbkey" multiple="True" separator=","/> - <validator type="no_options" message="No reference sequences are available for the build associated with the selected input data"/> + <param name="index" type="select" label="Select a built-in reference genome" > + <options from_data_table="all_fasta"></options></param></when> @@ -35,7 +44,6 @@ <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome from history" /></when></conditional> - <param name="sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false"/><param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" /><param name="adaptors" value="" type="text" area="true" label="Adapter sequences - one per line if multiple" size="5x120" /> @@ -191,8 +199,10 @@ Written by and copyright Ross Lazarus, ross.lazarus at gmail etc, September 2010 -All rgenetics artifacts are available licensed under the LGPL +All rgenetics artefacts are available licensed under the LGPL_ Other dependencies are licensed at the author's discretion - please see each individual package for details + + .. _LGPL: http://www.gnu.org/copyleft/lesser.html </help></tool> --- a/tools/picard/rgPicardFixMate.xml Fri May 06 16:02:25 2011 -0400 +++ b/tools/picard/rgPicardFixMate.xml Sat May 07 11:56:12 2011 -0400 @@ -1,5 +1,5 @@ <tool name="Paired Read Mate Fixer:" id="rgPicFixMate" version="0.01"> - <description>(Picard)</description> + <description>for paired data</description><command interpreter="python"> picard_wrapper.py -i "$input_file" -o "$out_file" --tmpdir "${__new_file_path__}" -n "$out_prefix" --newformat "$newformat" -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/FixMateInformation.jar" --sortorder "$sortOrder" @@ -82,7 +82,7 @@ **From the Picard documentation** -.. csv-table:: GC Bias Doc +.. csv-table:: Fixmate :header-rows: 1 @@ -106,7 +106,11 @@ All the Picard tools are freely available and are documented at http://picard.sourceforge.net/command-line-overview.shtml#CollectAlignmentS… -Here, you can apply Picard tools through Galaxy which might be easier than through the native Picard command line interface. +Written by and copyright Ross Lazarus, ross.lazarus at gmail etc, September 2010 +Code cleaned up and the ugliest hacks repaired by Raphael Lullis. +Kelly Vincent wrote the first version of picard_wrapper.py that now incorporates that code. + +It takes a village of programmers to wrap a picard tool ----- @@ -116,14 +120,10 @@ This Galaxy tool is a component of the rgenetics toolkit. -Written by and copyright Ross Lazarus, ross.lazarus at gmail etc, September 2010 -Code cleaned up and the ugliest hacks repaired by Raphael Lullis. -Kelly Vincent wrote the first version of picard_wrapper.py that now incorporates that code. - -It takes a village of programmers to wrap a picard tool - -All rgenetics artifacts are available licensed under the LGPL +All rgenetics artefacts are available licensed under the LGPL_ Other dependencies are licensed at the author's discretion - please see each individual package for details + + .. _LGPL: http://www.gnu.org/copyleft/lesser.html </help></tool> --- a/tools/picard/rgPicardGCBiasMetrics.xml Fri May 06 16:02:25 2011 -0400 +++ b/tools/picard/rgPicardGCBiasMetrics.xml Sat May 07 11:56:12 2011 -0400 @@ -17,18 +17,24 @@ help="If the select list is empty, you need to upload or import some aligned short read data from a shared library"/><param name="out_prefix" value="Short Read GC Bias Metrics" type="text" label="Title for the output file - use this remind you what the job was for" size="80" /> - <conditional name="genomeSource"> - <param name="refGenomeSource" type="select" help="If in doubt, choose built-in and read Picard/Samtools documentation" - label="Align to reference genome - built-in or from current history?"> - <option value="indexed">Align to input data 'dbkey' reference genome</option> - <option value="history">Use a genome (fasta format) from my history</option> + <conditional name="genomeSource"> + <param name="refGenomeSource" type="select" help="This tool needs a reference genome. Default is usually right" + label="Align to which reference genome? - default, built-in or choose from current history"> + <option value="default" selected="true">Default - use the input data genome build</option> + <option value="indexed">Select a different built-in genome </option> + <option value="history">Use a genome (fasta format) from my history </option></param> + <when value="default"> + <param name="index" type="select" label="Select a default reference genome"> + <options from_data_table="all_fasta"> + <filter type="data_meta" ref="input_file" key="dbkey" column="dbkey" multiple="True" separator=","/> + <validator type="no_options" message="No reference build available for the selected input data" /> + </options> + </param> + </when><when value="indexed"> - <param name="index" type="select" label="Select a reference genome"> - <options from_data_table="all_fasta"> - <filter type="data_meta" ref="input_file" key="dbkey" column="dbkey" multiple="True" separator=","/> - <validator type="no_options" message="No reference sequences are available for the build associated with the selected input data"/> - </options> + <param name="index" type="select" label="Select a built-in reference genome"> + <options from_data_table="all_fasta"/></param></when><when value="history"> @@ -168,9 +174,10 @@ This Galaxy tool is a component of the rgenetics toolkit. Written by and copyright Ross Lazarus, ross.lazarus at gmail etc, September 2010 - -All rgenetics artifacts are available licensed under the LGPL +All rgenetics artefacts are available licensed under the LGPL_ Other dependencies are licensed at the author's discretion - please see each individual package for details + + .. _LGPL: http://www.gnu.org/copyleft/lesser.html </help></tool> --- a/tools/picard/rgPicardHsMetrics.xml Fri May 06 16:02:25 2011 -0400 +++ b/tools/picard/rgPicardHsMetrics.xml Sat May 07 11:56:12 2011 -0400 @@ -1,10 +1,10 @@ <tool name="Sam/bam Hybrid Selection Metrics:" id="PicardHsMetrics" version="0.01"> - <description>(Picard)</description> + <description>For (eg exome) targetted data</description><command interpreter="python"> - rgPicardHsMetrics.py -i $input_file -d $html_file.files_path -o $html_file - -b $bait_bed -t $target_bed -n "$out_prefix" --tmpdir "${__new_file_path__}" - -j ${GALAXY_DATA_INDEX_DIR}/shared/jars/CalculateHsMetrics.jar -y $input_file.ext + picard_wrapper.py -i "$input_file" -d "$html_file.files_path" -t "$html_file" --datatype "$input_file.ext" + --baitbed "$bait_bed" --targetbed "$target_bed" -n "$out_prefix" --tmpdir "${__new_file_path__}" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/CalculateHsMetrics.jar" -x "$maxheap" </command><requirements><requirement type="package">picard</requirement></requirements> @@ -13,6 +13,13 @@ <param name="out_prefix" value="Picard HS Metrics" type="text" label="Title for the output file - to remind you what the job was for" size="80" /><param name="bait_bed" type="data" format="interval" label="Bait intervals: Sequences for bait in the design - ucsc BED" size="80" /><param name="target_bed" type="data" format="interval" label="Target intervals: Sequences for targets in the design - ucsc BED" size="80" /> + <param name="maxheap" type="select" + help="If in doubt, try the default. If it fails with a complaint about java heap size, try increasing it please - larger jobs will require your own hardware." + label="Java heap size"> + <option value="4G" selected = "true">4GB default </option> + <option value="8G" >8GB use if 4GB fails</option> + <option value="16G">16GB - try this if 8GB fails</option> + </param></inputs><outputs><data format="html" name="html_file" label="${out_prefix}.html" /> @@ -23,6 +30,7 @@ <param name="input_file" value="picard_input_summary_alignment_stats.sam" ftype="sam" /><param name="bait_bed" value="picard_input_bait.bed" /><param name="target_bed" value="picard_input_bait.bed" /> + <param name="maxheap" value="8G" /><output name="html_file" file="picard_output_hs_transposed_summary_alignment_stats.html" ftype="html" lines_diff="212"/></test></tests> @@ -140,10 +148,10 @@ This is part of the rgenetics toolkit. Written by Ross Lazarus 2010 - -Licensed under the LGPL -All rgenetics artifacts are available licensed under the LGPL +All rgenetics artefacts are available licensed under the LGPL_ Other dependencies are licensed at the author's discretion - please see each individual package for details + + .. _LGPL: http://www.gnu.org/copyleft/lesser.html </help></tool> --- a/tools/picard/rgPicardInsertSize.xml Fri May 06 16:02:25 2011 -0400 +++ b/tools/picard/rgPicardInsertSize.xml Sat May 07 11:56:12 2011 -0400 @@ -1,5 +1,5 @@ <tool name="Insertion size metrics:" id="rgPicInsertSize" version="0.01"> - <description>(Picard)</description> + <description>for PAIRED data</description><command interpreter="python"> picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --taillimit "$tailLimit" --histwidth "$histWidth" --minpct "$minPct" --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/picard/rgPicardLibComplexity.xml Sat May 07 11:56:12 2011 -0400 @@ -0,0 +1,143 @@ +<tool name="Estimate Library Complexity:" id="rgEstLibComp" version="0.01"> + <description>(Picard)</description> + <command interpreter="python"> + picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --minid "$minIDbases" + --maxdiff "$maxDiff" --minmeanq "$minMeanQ" --readregex "$readRegex" --optdupdist "$optDupeDist" + -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/EstimateLibraryComplexity.jar" -d "$html_file.files_path" -t "$html_file" + </command> + <inputs> + <param format="bam,sam" name="input_file" type="data" label="Input: sam or bam format short read data in your current history" + help="If the select list is empty, you need to upload or import some aligned short read data from a shared library"/> + <param name="out_prefix" value="Library Complexity" type="text" + label="Title for the output file - use this remind you what the job was for" size="80" /> + <param name="minIDbases" value="5" type="integer" label="Minimum identical bases at starts of reads for grouping" size="5" + help="Total_reads / 4^max_id_bases reads will be compared at a time. Lower numbers = more accurate results and exponentially more time/ram" /> + <param name="maxDiff" value="0.03" type="float" + label="Maximum difference rate for identical reads" size="5" + help="The maximum rate of differences between two reads to call them identical" /> + <param name="minMeanQ" value="20" type="integer" + label="Minimum percentage" size="5" + help="The minimum mean quality of bases in a read pair. Lower average quality reads filtered out from all calculations" /> + <param name="readRegex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" type="text" size="120" + label="Regular expression that can be used to parse read names in the incoming SAM file" + help="Names are parsed to extract: tile/region, x coordinate and y coordinate, to estimate optical duplication rate" > + <sanitizer> + <valid initial="string.printable"> + <remove value="'"/> + </valid> + <mapping initial="none"> + <add source="'" target="__sq__"/> + </mapping> + </sanitizer> + </param> + <param name="optDupeDist" value="100" type="text" + label="The maximum offset between two duplicte clusters in order to consider them optical duplicates." size="5" + help="e.g. 5-10 pixels. Later Illumina software versions multiply pixel values by 10, in which case 50-100" /> + + </inputs> + <outputs> + <data format="html" name="html_file" label="${out_prefix}_lib_complexity.html"/> + </outputs> + <tests> + <test> + <param name="input_file" value="picard_input_tiny.sam" /> + <param name="out_prefix" value="Library Complexity" /> + <param name="minIDbases" value="5" /> + <param name="maxDiff" value="0.03" /> + <param name="minMeanQ" value="20" /> + <param name="readRegex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" /> + <param name="optDupeDist" value="100" /> + <output name="html_file" file="picard_output_estlibcomplexity_tinysam.html" ftype="html" lines_diff="25" /> + </test> + </tests> + <help> + +.. class:: infomark + +**Purpose** + + EstimateLibraryComplexity + Attempts to estimate library complexity from sequence alone. + Does so by sorting all reads by the first N bases (5 by default) of each read and then + comparing reads with the first N bases identical to each other for duplicates. Reads are considered to be + duplicates if they match each other with no gaps and an overall mismatch rate less than or equal to MAX_DIFF_RATE (0.03 by default). + + Reads of poor quality are filtered out so as to provide a more accurate estimate. + The filtering removes reads with any no-calls in the first N bases or with a mean base quality lower than + MIN_MEAN_QUALITY across either the first or second read. + + The algorithm attempts to detect optical duplicates separately from PCR duplicates and excludes these in the + calculation of library size. Also, since there is no alignment to screen out technical reads one + further filter is applied on the data. After examining all reads a histogram is built of + [#reads in duplicate set -> #of duplicate sets]; + all bins that contain exactly one duplicate set are then removed from the histogram as outliers before library size is estimated. + +**Why you might want to use this tool** + + This tool provides a Galaxy interface to one of the Picard tools. + If you need to estimate library complexity from sequences, the Picard tool may help. + + +**Note on the Regular Expression** + + (from the Picard docs) + This tool requires a valid regular expression to parse out the read names in the incoming SAM or BAM file. + These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. + The regular expression should contain three capture groups for the three variables, in order. + Default value: [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. + + +----- + +.. class:: infomark + +**From the Picard documentation** + +.. csv-table:: Estimate complexity docs + :header-rows: 1 + + Option Description + "INPUT=File","One or more files to combine and estimate library complexity from. Reads can be mapped or unmapped. This option may be specified 0 or more times." + "OUTPUT=File","Output file to writes per-library metrics to. Required." + "MIN_IDENTICAL_BASES=Integer","The minimum number of bases at the starts of reads that must be identical for reads to be grouped together for duplicate detection. In effect total_reads / 4^max_id_bases reads will be compared at a time, so lower numbers will produce more accurate results but consume exponentially more memory and CPU. Default value: 5." + "MAX_DIFF_RATE=Double","The maximum rate of differences between two reads to call them identical. Default value: 0.03. " + "MIN_MEAN_QUALITY=Integer","The minimum mean quality of the bases in a read pair for the read to be analyzed. Reads with lower average quality are filtered out and not considered in any calculations. Default value: 20." + "READ_NAME_REGEX=String","Regular expression that can be used to parse read names in the incoming SAM file. Read names are parsed to extract three variables: tile/region, x coordinate and y coordinate. These values are used to estimate the rate of optical duplication in order to give a more accurate estimated library size. The regular expression should contain three capture groups for the three variables, in order. Default value: [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. This option can be set to 'null' to clear the default value." + "OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer","The maximum offset between two duplicte clusters in order to consider them optical duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) unless using later versions of the Illumina pipeline that multiply pixel values by 10, in which case 50-100 is more normal. Default value: 100" + "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false. This option can be set to 'null' to clear the default value. " + + +----- + +.. class:: infomark + +**Attributions** + +Picard is supported through the SamTools project. +This tool wraps Picard and is supported through the galaxy-bugs mailing list +Please help us by completing the report form that appears automatically +if a tool fails unexpectedly when you run it in Galaxy. + +All the Picard tools are freely available and are documented +at http://picard.sourceforge.net/command-line-overview.shtml#CollectInsertSize… + +----- + +.. class:: infomark + +**Copyright** + +This Galaxy tool is a component of the rgenetics toolkit. + +Written by and copyright Ross Lazarus, ross.lazarus at gmail etc, September 2010 +Code cleaned up and the ugliest hacks repaired by Raphael Lullis + +All rgenetics artefacts are available licensed under the LGPL_ +Other dependencies are licensed at the author's discretion - please see each individual package for details + + .. _LGPL: http://www.gnu.org/copyleft/lesser.html + + </help> +</tool> + + http://bitbucket.org/galaxy/galaxy-central/changeset/3cf3d54e5b28/ changeset: r5511:3cf3d54e5b28 user: fubar date: 2011-05-07 19:58:35 summary: add test input for hsmetrics affected #: 1 file (376 bytes) --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_input_bait.bed Sat May 07 13:58:35 2011 -0400 @@ -0,0 +1,8 @@ +chr1 1 300 - CCDS635.1_cds_0_0_chr1_67052401_r +chr2 1 300 - CCDS635.1_cds_1_0_chr1_67060632_r +chr3 1 300 - CCDS635.1_cds_2_0_chr1_67065091_r +chr4 1 300 - CCDS635.1_cds_3_0_chr1_67066083_r +chr5 1 300 - CCDS635.1_cds_4_0_chr1_67071856_r +chr6 1 300 - CCDS635.1_cds_5_0_chr1_67072262_r +chr7 1 300 - CCDS635.1_cds_6_0_chr1_67073897_r +chr8 1 300 - CCDS635.1_cds_7_0_chr1_67075981_r 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: kanwei: trackster: Greatly improve LineTrack performance as it was fetching an unoptimal amount of data, decreasing performance by orders of magnitude
by Bitbucket 06 May '11

06 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/43e581afb8a5/ changeset: r5509:43e581afb8a5 user: kanwei date: 2011-05-06 22:02:25 summary: trackster: Greatly improve LineTrack performance as it was fetching an unoptimal amount of data, decreasing performance by orders of magnitude affected #: 1 file (333 bytes) --- a/lib/galaxy/visualization/tracks/data_providers.py Fri May 06 15:47:01 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Fri May 06 16:02:25 2011 -0400 @@ -329,7 +329,11 @@ start = int(start) end = int(end) - num_points = 2000 + # The first zoom level for BBI files is 640. If too much is requested, it will look at each block instead + # of summaries. The calculation done is: zoom <> (end-start)/num_points/2. + # Thus, the optimal number of points is (end-start)/num_points/2 = 640 + # num_points = (end-start) / 1280 + num_points = (end-start) / 1280 if (end - start) < num_points: num_points = end - start 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: jgoecks: Make Cufflinks wrapper compatible with v1.0.0; new options are not yet implemented.
by Bitbucket 06 May '11

06 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/ce6de0047fb8/ changeset: r5508:ce6de0047fb8 user: jgoecks date: 2011-05-06 21:47:01 summary: Make Cufflinks wrapper compatible with v1.0.0; new options are not yet implemented. affected #: 9 files (330 bytes) --- a/test-data/cufflinks_in.sam Fri May 06 14:32:55 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,183 +0,0 @@ -test_mRNA_3_187_51 99 test_chromosome 53 255 75M = 163 0 TACTATTTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_4_191_5d 163 test_chromosome 54 255 75M = 167 0 ACTATCTGACGAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTACCATTACGCGGATGACGACTAGGACTACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 -test_mRNA_5_197_46 97 test_chromosome 55 255 75M = 173 0 CTATCTGACTAGACTCGAGGCGCTTGCGTCTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_6_182_59 99 test_chromosome 56 255 75M = 158 0 TATCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCAGTACGGGGATGACGACTAGGACTACGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_8_155_9 163 test_chromosome 58 255 75M = 131 0 TGTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_8_197_1 99 test_chromosome 58 255 75M = 173 0 TCTGACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGACACTACGGGGATGGCGACTAGGACTACGGACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_9_179_52 163 test_chromosome 59 255 75M = 155 0 CTGACTAGACTGGAGGCGCTCGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_11_190_1a 99 test_chromosome 61 255 75M = 166 0 GACTAGACTGGAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 -test_mRNA_16_194_10 163 test_chromosome 66 255 75M = 170 0 GACTGGATGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTCGGACTACGGACGGACTTAAAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 -test_mRNA_21_208_24 163 test_chromosome 71 255 75M = 184 0 GAGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 -test_mRNA_22_173_62 99 test_chromosome 72 255 75M = 149 0 AGGCGCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 -test_mRNA_23_186_42 163 test_chromosome 73 255 75M = 162 0 GGCGCTTGTGACTGAGCTAGGACGTGCCACTACGGGGATGAAGACTAGGACTACGGACGGACTTAGAGCGTCAGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_26_189_30 163 test_chromosome 76 255 75M = 165 0 GCTTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 -test_mRNA_28_188_11 99 test_chromosome 78 255 75M = 164 0 TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGAACGGACTTAGAGCGTCAGATGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_28_206_1f 73 test_chromosome 78 255 75M * 0 0 TTGCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGACGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_30_231_3c 161 test_chromosome 80 255 75M = 207 0 GCGACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 -test_mRNA_33_223_4e 73 test_chromosome 83 255 75M * 0 0 ACTGAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 -test_mRNA_36_146_27 163 test_chromosome 86 255 75M = 122 0 GCGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACAGACGGACTTAGAGCGTCAGATGCAGCGACTGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_36_218_12 99 test_chromosome 86 255 75M = 194 0 GAGCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGCCTTAGAGCGTCAGATGCAGCGACTGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_38_199_29 99 test_chromosome 88 255 75M = 175 0 GCTAGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 -test_mRNA_39_219_5c 99 test_chromosome 89 255 75M = 195 0 CTAGGACGTCCCACTATGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGGCTGGACTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 -test_mRNA_41_236_55 97 test_chromosome 91 255 75M = 212 0 AGGACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_42_209_25 99 test_chromosome 92 255 75M = 185 0 GGACGTGCCACTACGTGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_44_193_3f 99 test_chromosome 94 255 75M = 169 0 ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGTCTATTTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_44_197_35 99 test_chromosome 94 255 75M = 173 0 ACGTGCAACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_44_225_1e 163 test_chromosome 94 255 75M = 201 0 ACGTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCGGGTGCAGCGACTGGACTATTTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_46_195_17 137 test_chromosome 96 255 75M * 0 0 GTGCCACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 -test_mRNA_46_232_2f 99 test_chromosome 96 255 75M = 208 0 GTGCCACTACGGGGATGACGACTAGGACTACGGCCGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_48_207_39 73 test_chromosome 98 255 75M * 0 0 GCCCCTACGGGGATGACGACTAGGACTACGGACGGATTTAGACCGTCAGATGCAGCGACTGGACTATTTAGGACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 -test_mRNA_48_249_20 161 test_chromosome 98 255 75M = 225 0 GCCACTACGGGGATGACGACTAGGACGACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_50_224_2d 163 test_chromosome 100 255 75M = 200 0 CACTACGAGGATGACGTCTAGGACTACGGACGGACTTAGAGCGTCAGACGCAGCGACTGGACTATTTAGGACGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 -test_mRNA_51_194_47 163 test_chromosome 101 255 75M = 170 0 ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 -test_mRNA_51_194_49 99 test_chromosome 101 255 75M = 170 0 ACTACGGGGATGACGACTAGGCCTACGGATGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_51_237_a 99 test_chromosome 101 255 75M = 213 0 ACTACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 -test_mRNA_51_248_14 97 test_chromosome 101 255 75M = 224 0 ACTACGGGGATGACGACGAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGAACTTTTTAGGACGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 -test_mRNA_52_261_1b 97 test_chromosome 102 255 75M = 237 0 CTACGGGAATGACGACTAGGGCTACGGAGGGACTTACAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 -test_mRNA_53_212_19 99 test_chromosome 103 255 75M = 188 0 TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGAATATTTAGGACGATCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_53_272_5a 161 test_chromosome 103 255 75M = 248 0 TACGGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 -test_mRNA_56_183_56 99 test_chromosome 106 255 75M = 159 0 GGGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTGGGACGATCGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_57_231_8 99 test_chromosome 107 255 75M = 207 0 GGGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCACCGACTGGACTATTTAGGACGATCGGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_58_218_16 163 test_chromosome 108 255 75M = 194 0 GGATGACGACTAGGACTACGGACGGACTTAGAACGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_58_220_3d 163 test_chromosome 108 255 75M = 196 0 GGATGACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 -test_mRNA_58_234_7 163 test_chromosome 108 255 75M = 210 0 GGATGACGCCTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_63_229_4c 163 test_chromosome 113 255 75M = 205 0 ACGACTAGGACTACGGACGGACTTAGAGCGTCAGATGCAGGGACTGGACTATTTAGGACGATCGGACTGAGGAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_65_238_2e 99 test_chromosome 115 255 75M = 214 0 GACTAGGACTACGGACGGACTTAGAGCGTCAGAAGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_69_229_23 163 test_chromosome 119 255 75M = 205 0 AGGACTACGGACGGACTTATAGGGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_36_146_27 83 test_chromosome 122 255 75M = 86 0 ACTACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_72_258_4 163 test_chromosome 122 255 75M = 234 0 ACTACGGACGGACTTAGAGCGTCAGATGCAGCAACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_73_240_34 99 test_chromosome 123 255 75M = 216 0 CTACGGACGGACTTAGAGCGTCAGATGCAGCGAATGGACTATTTAGGACGCTCGGACTGAGGAGGGCAGTAGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_73_259_5e 99 test_chromosome 123 255 75M = 235 0 CTACGGACGGACTTAGAGCGTCAGATGCTGCGACTGGACTATTTGGGACGATCGGACTGAGGAGGGCAGTAGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_75_204_54 73 test_chromosome 125 255 75M * 0 0 ACGGACGGACTTCGAGCCTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_75_235_21 73 test_chromosome 125 255 75M * 0 0 ACGGACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGCACGATCGGACTGAGGAGGGCAGTAGAACGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 -test_mRNA_75_277_3b 97 test_chromosome 125 255 75M = 353 0 ACGGACGGACTTAAAGCTTCAGATGCAGCGACAGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 -test_mRNA_77_256_2c 73 test_chromosome 127 255 75M * 0 0 GGACGGACTTAGAGCATCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_78_276_4b 97 test_chromosome 128 255 75M = 352 0 GACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGGCGCTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_79_256_31 137 test_chromosome 129 255 75M * 0 0 ACGGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 -test_mRNA_81_228_3a 163 test_chromosome 131 255 75M = 204 0 GGACTGAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGTAGTAGGACGCTACGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_81_245_4d 163 test_chromosome 131 255 75M = 221 0 GGACTTAGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGATGAGGGCAGTAGGACGCTACGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_8_155_9 83 test_chromosome 131 255 75M = 58 0 GGACTTCGAGCGTCAGATGCAGCGACTGTACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_82_255_2 137 test_chromosome 132 255 75M * 0 0 GACTTAGAGCGTCAGATGCAGCGACTGGACTTTTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_82_271_58 99 test_chromosome 132 255 75M = 247 0 GACTTAGAGCGTCAGTTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_85_268_53 99 test_chromosome 135 255 75M = 244 0 TTAGTGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_87_250_57 163 test_chromosome 137 255 75M = 226 0 AGAGCGTCAGATGCAGAGACTGGACTATTTAGGACGATCGGACTGAGGAGTGCAGTAGGACGCTACGTATTTGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_87_279_5f 161 test_chromosome 137 255 75M = 355 0 AGAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACCGAGGAGGGCAGTAGGACGCTACGTATTTGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_88_257_50 137 test_chromosome 138 255 75M * 0 0 GAGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 -test_mRNA_89_230_b 163 test_chromosome 139 255 75M = 206 0 AGCGTCAGGTGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_89_245_15 99 test_chromosome 139 255 75M = 221 0 AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 -test_mRNA_89_267_32 163 test_chromosome 139 255 75M = 243 0 AGCGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGAGTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_91_256_41 73 test_chromosome 141 255 75M * 0 0 CGTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 -test_mRNA_92_250_44 99 test_chromosome 142 255 75M = 226 0 GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 -test_mRNA_92_266_43 99 test_chromosome 142 255 75M = 242 0 GTCAGATGCAGCGACTGGACTATTTAGGACGATCGGACTCAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_96_238_3 163 test_chromosome 146 255 75M = 214 0 GATGCAGCGACTGGACTATTTAGGACGATCGGACGGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 -test_mRNA_97_275_26 97 test_chromosome 147 255 75M = 351 0 ATGCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_22_173_62 147 test_chromosome 149 255 75M = 72 0 GCAGCGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_103_284_2a 161 test_chromosome 153 255 75M = 360 0 CGACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_104_278_3e 161 test_chromosome 154 255 75M = 354 0 GACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTTTTTGGCGCGCGGCCCTACGGCTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_105_266_13 163 test_chromosome 155 255 75M = 242 0 ACTGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_105_276_c 161 test_chromosome 155 255 75M = 352 0 ACTGGACTATTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_9_179_52 83 test_chromosome 155 255 75M = 59 0 ACTGGACCATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_106_253_45 137 test_chromosome 156 255 75M * 0 0 CTGGACTATTTAGGTCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_107_286_5 161 test_chromosome 157 255 75M = 362 0 TGGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGCATTTGGCGCGCGGCCCTACGGCTGAGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_6_182_59 147 test_chromosome 158 255 75M = 56 0 GGACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_56_183_56 147 test_chromosome 159 255 75M = 106 0 GACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_110_267_22 163 test_chromosome 160 255 75M = 243 0 ACTAGTTAGGGCGATCGGACTGAGGAGGGCAGTAGGACGCTACGTAGTTGGCGCGCGGCCCTACGACTGAGCGTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:5 -test_mRNA_110_271_28 99 test_chromosome 160 255 75M = 247 0 ACTATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_111_297_61 161 test_chromosome 161 255 75M = 373 0 CTATTTAGGACGATCGGACTGGGGAGGGCAGTAGGACGCTACGGATTTGGCGCGCGGCCCTACGGCTGAGCGTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 -test_mRNA_23_186_42 83 test_chromosome 162 255 75M = 73 0 TATTTAGGACGATCGGACGGAGGAGGGCAGAAGGACGCTACGTATTTGGCGCGCGGCCCTACGACTGAGCGTCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 -test_mRNA_3_187_51 147 test_chromosome 163 255 75M = 53 0 ATTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_114_277_5b 161 test_chromosome 164 255 75M = 353 0 TTTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_28_188_11 147 test_chromosome 164 255 75M = 78 0 TTTAGGACGATCGGACTGAGGAAGGCAGTAGGACGCTTCGTATTTGGCGCGAGGCCCTACGGCTGAGCGTCGAGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 -test_mRNA_26_189_30 83 test_chromosome 165 255 75M = 76 0 TTAGGACGATCGGACTGAGGAGGGCAGTAGGACGGTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_33_189_4a 89 test_chromosome 165 255 75M * 0 0 TTAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACCTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGGGCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 -test_mRNA_116_271_2b 163 test_chromosome 166 255 75M = 247 0 TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_116_295_63 161 test_chromosome 166 255 75M = 371 0 TAGGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_11_190_1a 147 test_chromosome 166 255 75M = 61 0 TAGGTCGATGGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGTGGCCCTACGGCTGAGCGTCGAGCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 -test_mRNA_4_191_5d 83 test_chromosome 167 255 75M = 54 0 AGGACGATCGGACTGAGTAGGGCAGTAGGACACTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 -test_mRNA_118_297_f 161 test_chromosome 168 255 75M = 373 0 GGACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_44_193_3f 147 test_chromosome 169 255 75M = 94 0 GACGATCGGACTGGGGAGAGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 -test_mRNA_16_194_10 83 test_chromosome 170 255 75M = 66 0 ACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_51_194_47 83 test_chromosome 170 255 75M = 101 0 ACGATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_51_194_49 147 test_chromosome 170 255 75M = 101 0 ACGTTCGGACTGAGGAGGGCAGTAGGACGCCACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 -test_mRNA_122_299_6 161 test_chromosome 172 255 75M = 375 0 GATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_44_197_35 147 test_chromosome 173 255 75M = 94 0 ATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGATCGTCGAGCTTGCGATAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 -test_mRNA_5_197_46 145 test_chromosome 173 255 75M = 55 0 ATCGGACGGAGGAGGGCAGTAGGACGCTACGTATTTGGCGGGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 -test_mRNA_8_197_1 147 test_chromosome 173 255 75M = 58 0 ATCGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_125_280_48 97 test_chromosome 175 255 75M = 356 0 CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGAAACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 -test_mRNA_125_293_60 161 test_chromosome 175 255 75M = 369 0 CGGACTGAGGAGGGCAGTAGGACGCTATGTATTTGGCGCGCGGCCCTACGGCTGAGCTTCGAGGTTGCGATACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 -test_mRNA_38_199_29 147 test_chromosome 175 255 75M = 88 0 CGGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_126_282_18 161 test_chromosome 176 255 75M = 358 0 GGACTGAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 -test_mRNA_131_260_33 99 test_chromosome 181 255 70M100N5M = 236 0 GAGGAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NS:i:0 -test_mRNA_21_208_24 83 test_chromosome 184 255 67M100N8M = 71 0 GAGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGCCTGAGCGTCGAGCTTGCGATACGCCACTATTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:0 -test_mRNA_42_209_25 147 test_chromosome 185 255 66M100N9M = 92 0 AGGGCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NS:i:0 -test_mRNA_53_212_19 147 test_chromosome 188 255 63M100N12M = 103 0 GCAGTAGGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTTCTTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:1 -test_mRNA_36_218_12 147 test_chromosome 194 255 57M100N18M = 86 0 GGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NS:i:0 -test_mRNA_58_218_16 83 test_chromosome 194 255 57M100N18M = 108 0 GGACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NS:i:0 -test_mRNA_145_300_37 163 test_chromosome 195 255 56M100N19M = 376 0 GACGCTACGTATTTGGCGCGGGGCCCTATGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTAGTATATT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:5 XS:A:+ NS:i:2 -test_mRNA_39_219_5c 147 test_chromosome 195 255 56M100N19M = 89 0 GACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCCAGCTTGCGATACGCCACTATTACTTTATTATCTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:0 -test_mRNA_58_220_3d 83 test_chromosome 196 255 55M100N20M = 108 0 ACGCTACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGGTTGCGATACGCCACTATTACTTTATTATCTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NS:i:1 -test_mRNA_50_224_2d 83 test_chromosome 200 255 51M100N24M = 100 0 TACGTATTTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:0 -test_mRNA_44_225_1e 83 test_chromosome 201 255 50M100N25M = 94 0 ACGTATATGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:0 -test_mRNA_81_228_3a 83 test_chromosome 204 255 47M100N28M = 131 0 TATTTGGCGCGCGGCCCTATGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGTAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NS:i:0 -test_mRNA_63_229_4c 83 test_chromosome 205 255 46M100N29M = 113 0 ATTTGGCGCGCGGCCCTACGGCTGAGTGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:1 -test_mRNA_69_229_23 83 test_chromosome 205 255 46M100N29M = 119 0 CTTTGGCGCGCGGCCCTACGGCTGAGCGTCTAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NS:i:1 -test_mRNA_89_230_b 83 test_chromosome 206 255 45M100N30M = 139 0 TCTGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTAACTCACTCGGACGTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NS:i:0 -test_mRNA_30_231_3c 81 test_chromosome 207 255 44M100N31M = 80 0 TTGGCGCGCGGCCCTACGGCTAAGCGTCGAGCTTGCGATACGCCACTATTACTTTAATATCTTACTCGCACGTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NS:i:0 -test_mRNA_57_231_8 147 test_chromosome 207 255 44M100N31M = 107 0 TTGGCGCGCGGCCCTAGGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:0 -test_mRNA_46_232_2f 147 test_chromosome 208 255 43M100N32M = 96 0 TGGCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NS:i:0 -test_mRNA_58_234_7 83 test_chromosome 210 255 41M100N34M = 108 0 GCGCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTAGTTTATTATCTGACTCGGACGTAGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NS:i:1 -test_mRNA_41_236_55 145 test_chromosome 212 255 39M100N36M = 91 0 GCGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NS:i:0 -test_mRNA_51_237_a 147 test_chromosome 213 255 38M100N37M = 101 0 CGCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NS:i:0 -test_mRNA_65_238_2e 147 test_chromosome 214 255 37M100N38M = 115 0 GCGGCCCTACGGCTGCGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:0 -test_mRNA_96_238_3 83 test_chromosome 214 255 37M100N38M = 146 0 GCGGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCTACTAGTACTTTATTATCTTACGCGGACGTAGACGGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NS:i:2 -test_mRNA_73_240_34 147 test_chromosome 216 255 35M100N40M = 123 0 GGCCCTACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTTCTCGGACGTAGACGGATCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:0 -test_mRNA_81_245_4d 83 test_chromosome 221 255 30M100N45M = 131 0 TACGGCTGAGCGTCGAGGTTGCGATACGCCACTATTACTTTATAATCTTACTCGGACGTAGACGGATCGGCAACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:1 -test_mRNA_89_245_15 147 test_chromosome 221 255 30M100N45M = 139 0 TACGGCTGAGCGTCGAGCTTGCGATACGCCACTATTTCTCTATTATCTTACTCGGACGTAGACGGATCGGCAACG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:2 -test_mRNA_172_294_4f 99 test_chromosome 222 255 29M100N46M = 370 0 ACGGATGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTCCTCGGACGTAGACGGATCGCCAACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NS:i:1 -test_mRNA_51_248_14 145 test_chromosome 224 255 27M100N48M = 101 0 GGCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGAACGGCAACGGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NS:i:0 -test_mRNA_48_249_20 81 test_chromosome 225 255 26M100N49M = 98 0 GCTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTACTATCTTACTCGGACGGAGACGGATCGGCAACGGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NS:i:0 -test_mRNA_87_250_57 83 test_chromosome 226 255 25M100N50M = 137 0 ATGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NS:i:0 -test_mRNA_92_250_44 147 test_chromosome 226 255 25M100N50M = 142 0 CTGAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGGTACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:0 -test_mRNA_128_252_36 153 test_chromosome 228 255 23M100N52M * 0 0 GAGCGTCGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGGAACGGGACTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NS:i:0 -test_mRNA_72_258_4 83 test_chromosome 234 255 17M100N50M100N8M = 122 0 CGAGCTTGCGATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATGGGCAACGGGACTTTTTCTAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NS:i:1 -test_mRNA_73_259_5e 147 test_chromosome 235 255 16M100N50M100N9M = 123 0 GAGCTTGCGATACGCCACTATTACTGTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NS:i:0 -test_mRNA_131_260_33 147 test_chromosome 236 255 15M100N50M100N10M = 181 0 AGCTTGTGATACGCCACTATTACTTTATTATCTTACTCGGACGTAAACGGATCGGCCACGGGACTTTTTTTACTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NS:i:3 -test_mRNA_52_261_1b 145 test_chromosome 237 255 14M100N50M100N11M = 102 0 GCTTGCGATACGCCACTATTACTTAATTATCTTACTCGGACGTAGAAGGATCGGCAACGGGACTTTTTCTACTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:1 -test_mRNA_105_266_13 83 test_chromosome 242 255 9M100N50M100N16M = 155 0 CGATCCGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NS:i:1 -test_mRNA_92_266_43 147 test_chromosome 242 255 9M100N50M100N16M = 142 0 CGATACGCCACTATTACTTTCTTATCTTACTCGGACGTAGACGGAGCGGCAACGGGACTTTTTCTACTTGAGACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NS:i:2 -test_mRNA_110_267_22 83 test_chromosome 243 255 8M100N50M100N17M = 160 0 GATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NS:i:0 -test_mRNA_89_267_32 83 test_chromosome 243 255 8M100N50M100N17M = 139 0 GATACGGCACTATTACTTTATTATCTTTCTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:1 -test_mRNA_111_268_d 89 test_chromosome 244 255 7M100N50M100N18M * 0 0 ATACGCCACTATTATTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NS:i:1 -test_mRNA_85_268_53 147 test_chromosome 244 255 7M100N50M100N18M = 135 0 ATACGCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGTCAACGGGACTTTTTCTACTTGAGACTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NS:i:0 -test_mRNA_110_271_28 147 test_chromosome 247 255 4M100N50M100N21M = 160 0 CGCCACTATTACTTTATTATCTTACTCGGACGAAGACGGATCGGCAACGGGGCTTTTTCTACTTGAGACTGGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:1 -test_mRNA_116_271_2b 83 test_chromosome 247 255 4M100N50M100N21M = 166 0 CGCCACTATTACTTTATTATCTTACTCGGACGTAGACAGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NS:i:0 -test_mRNA_82_271_58 147 test_chromosome 247 255 4M100N50M100N21M = 132 0 CGCCACTATTACTTTATTATCTTACTCGGACGTAGACGCATCGGCAACGGGACTTTTTCTACTTGAGACTGGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NS:i:0 -test_mRNA_53_272_5a 81 test_chromosome 248 255 3M100N50M100N22M = 103 0 GCCACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGACACTGGGATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NS:i:1 -test_mRNA_104_274_1c 89 test_chromosome 350 255 51M100N24M * 0 0 CACTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:0 -test_mRNA_85_275_38 153 test_chromosome 351 255 50M100N25M * 0 0 ACTCTTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTACTACTTGAGACTGGGATCGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:0 -test_mRNA_97_275_26 145 test_chromosome 351 255 50M100N25M = 147 0 ACTATTACTTTATTATCTTAGTCGGACGTAGACGGATCGGAAACGGGACTCTTTCTACTTGAGACTGGGATCGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NS:i:0 -test_mRNA_105_276_c 81 test_chromosome 352 255 49M100N26M = 155 0 CTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGGCTTTTTCTACTTGAGACTGGGATCGAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:0 -test_mRNA_78_276_4b 145 test_chromosome 352 255 49M100N26M = 128 0 CTATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTAGGATCGAGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:0 -test_mRNA_114_277_5b 81 test_chromosome 353 255 48M100N27M = 164 0 TATTACTTTATTATCTTACTCGGAGGTAGACGGAACGGCAACGGGACTTTTTCTGCTTGAGACTGGGATCGAGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:4 XS:A:+ NS:i:0 -test_mRNA_75_277_3b 145 test_chromosome 353 255 48M100N27M = 125 0 TATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACCTGAGACTGGGATCGAGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:0 -test_mRNA_104_278_3e 17 test_chromosome 354 255 47M100N28M = 154 0 ATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGAATCGAGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NS:i:0 -test_mRNA_104_278_3e 81 test_chromosome 354 255 47M100N28M = 154 0 ATTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGAATCGAGGCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NS:i:0 -test_mRNA_87_279_5f 81 test_chromosome 355 255 46M100N29M = 137 0 TTACTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NS:i:0 -test_mRNA_125_280_48 145 test_chromosome 356 255 45M100N30M = 175 0 TACTTTATTATCTTACTCTGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGAGCGAGGCGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:0 -test_mRNA_126_282_18 81 test_chromosome 358 255 43M100N32M = 176 0 CTTTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NS:i:0 -test_mRNA_103_284_2a 81 test_chromosome 360 255 41M100N34M = 153 0 TTATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NS:i:0 -test_mRNA_107_286_5 81 test_chromosome 362 255 39M100N36M = 157 0 ATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NS:i:0 -test_mRNA_151_286_e 153 test_chromosome 362 255 39M100N36M * 0 0 ATTATCTTACTCGGACGTAGACGGATCGGCAACGGGACTTTATCTACTTGAGACTGGGATCGAGGCGGACTTTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NS:i:1 -test_mRNA_150_290_0 89 test_chromosome 366 255 35M100N40M * 0 0 TCTTACTCGGACGTAGACGGATCGCCAACGGGACTTTTTCTACTTGAGACTGAGACCGAGGCGGACTTTTTAGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NS:i:0 -test_mRNA_94_291_40 153 test_chromosome 367 255 34M100N41M * 0 0 CTTCCTGGGACGTAGACGGATCGGCAACGCGACATTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTGGGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:5 XS:A:+ NS:i:2 -test_mRNA_125_293_60 81 test_chromosome 369 255 32M100N43M = 175 0 TACTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NS:i:0 -test_mRNA_172_294_4f 147 test_chromosome 370 255 31M100N44M = 222 0 ACTCGGACGTAGACGGGTCGGCAGCGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACGTTTTAGGACGGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NS:i:0 -test_mRNA_116_295_63 81 test_chromosome 371 255 30M100N45M = 166 0 CTCGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NS:i:0 -test_mRNA_111_297_61 17 test_chromosome 373 255 28M100N47M = 161 0 CGGACGTAGACGGATCCGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NS:i:0 -test_mRNA_111_297_61 81 test_chromosome 373 255 28M100N47M = 161 0 CGGACGTAGACGGATCCGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NS:i:0 -test_mRNA_118_297_f 17 test_chromosome 373 255 28M100N47M = 168 0 CGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:0 -test_mRNA_118_297_f 81 test_chromosome 373 255 28M100N47M = 168 0 CGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:0 XS:A:+ NS:i:0 -test_mRNA_151_297_1d 153 test_chromosome 373 255 28M100N47M * 0 0 CGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACATTTTAGGACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NS:i:0 -test_mRNA_151_297_1d 25 test_chromosome 373 255 28M100N47M * 0 0 CGGACGTAGACGGATCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACATTTTAGGACGGGACT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:3 XS:A:+ NS:i:0 -test_mRNA_122_299_6 81 test_chromosome 375 255 26M100N49M = 172 0 GACGTAGACGGAGCGGCAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:2 XS:A:+ NS:i:0 -test_mRNA_145_300_37 83 test_chromosome 376 255 25M100N50M = 195 0 ACGTAGACGGATCGGAAACGGGACTTTTTCTACTTGAGACTGGGATCGAGGCGGACTTTTTAGGACGGGACTTGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 XS:A:+ NS:i:0 --- a/test-data/cufflinks_out1.gtf Fri May 06 14:32:55 2011 -0400 +++ b/test-data/cufflinks_out1.gtf Fri May 06 15:47:01 2011 -0400 @@ -1,4 +1,4 @@ -test_chromosome Cufflinks transcript 53 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "4464285.7142857295"; frac "1.000000"; conf_lo "4460059.943012"; conf_hi "4468511.485559"; cov "61.272321"; -test_chromosome Cufflinks exon 53 250 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "4464285.7142857295"; frac "1.000000"; conf_lo "4460059.943012"; conf_hi "4468511.485559"; cov "61.272321"; -test_chromosome Cufflinks exon 351 400 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "2"; FPKM "4464285.7142857295"; frac "1.000000"; conf_lo "4460059.943012"; conf_hi "4468511.485559"; cov "61.272321"; -test_chromosome Cufflinks exon 501 550 1000 + . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "3"; FPKM "4464285.7142857295"; frac "1.000000"; conf_lo "4460059.943012"; conf_hi "4468511.485559"; cov "61.272321"; +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"; --- a/test-data/cufflinks_out2.expr Fri May 06 14:32:55 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -trans_id bundle_id chr left right FPKM FMI frac FPKM_conf_lo FPKM_conf_hi coverage length effective_length status -CUFF.1.1 3 test_chromosome 52 550 4.46429e+06 1 1 4.46006e+06 4.46851e+06 61.2723 298 224 OK --- a/test-data/cufflinks_out3.expr Fri May 06 14:32:55 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,2 +0,0 @@ -gene_id bundle_id chr left right FPKM FPKM_conf_lo FPKM_conf_hi status -CUFF.1 3 test_chromosome 52 550 4.46429e+06 4.46006e+06 4.46851e+06 OK --- a/tools/ngs_rna/cufflinks_wrapper.py Fri May 06 14:32:55 2011 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.py Fri May 06 15:47:01 2011 -0400 @@ -32,7 +32,6 @@ parser.add_option( '-m', '--inner-mean-dist', dest='inner_mean_dist', help='This is the expected (mean) inner distance between mate pairs. \ For, example, for paired end runs with fragments selected at 300bp, \ where each end is 50bp, you should set -r to be 200. The default is 45bp.') - parser.add_option( '-Q', '--min-mapqual', dest='min_mapqual', help='Instructs Cufflinks to ignore alignments with a SAM mapping quality lower than this number. The default is 0.' ) parser.add_option( '-G', '--GTF', dest='GTF', help='Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript.' ) # Normalization options. @@ -43,7 +42,7 @@ parser.add_option( '--max-mle-iterations', dest='max_mle_iterations', help='Sets the number of iterations allowed during maximum likelihood estimation of abundances. Default: 5000' ) # Bias correction options. - parser.add_option( '-r', dest='do_bias_correction', action="store_true", help='Providing Cufflinks with a multifasta file via this option instructs it to run our new bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates.') + parser.add_option( '-b', dest='do_bias_correction', action="store_true", help='Providing Cufflinks with a multifasta file via this option instructs it to run our new bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates.') parser.add_option( '', '--dbkey', dest='dbkey', help='The build of the reference dataset' ) parser.add_option( '', '--index_dir', dest='index_dir', help='GALAXY_DATA_INDEX_DIR' ) parser.add_option( '', '--ref_file', dest='ref_file', help='The reference dataset from the history' ) @@ -54,7 +53,7 @@ try: tmp = tempfile.NamedTemporaryFile().name tmp_stdout = open( tmp, 'wb' ) - proc = subprocess.Popen( args='cufflinks 2>&1', shell=True, stdout=tmp_stdout ) + proc = subprocess.Popen( args='cufflinks --no-update-check 2>&1', shell=True, stdout=tmp_stdout ) tmp_stdout.close() returncode = proc.wait() stdout = None @@ -85,7 +84,7 @@ # Build command. # Base; always use quiet mode to avoid problems with storing log output. - cmd = "cufflinks -q" + cmd = "cufflinks -q --no-update-check" # Add options. if options.inner_dist_std_dev: @@ -100,8 +99,6 @@ cmd += ( " -p %i" % int ( options.num_threads ) ) if options.inner_mean_dist: cmd += ( " -m %i" % int ( options.inner_mean_dist ) ) - if options.min_mapqual: - cmd += ( " -Q %i" % int ( options.min_mapqual ) ) if options.GTF: cmd += ( " -G %s" % options.GTF ) if options.num_importance_samples: @@ -111,7 +108,7 @@ if options.do_normalization: cmd += ( " -N" ) if options.do_bias_correction: - cmd += ( " -r %s" % seq_path ) + cmd += ( " -b %s" % seq_path ) # Debugging. print cmd --- a/tools/ngs_rna/cufflinks_wrapper.xml Fri May 06 14:32:55 2011 -0400 +++ b/tools/ngs_rna/cufflinks_wrapper.xml Fri May 06 15:47:01 2011 -0400 @@ -10,7 +10,6 @@ -I $max_intron_len -F $min_isoform_fraction -j $pre_mrna_fraction - -Q $min_map_quality ## Include reference annotation? #if $reference_annotation.use_ref == "Yes": @@ -30,7 +29,7 @@ ## Bias correction? #if $bias_correction.do_bias_correction == "Yes": - -r + -b #if $bias_correction.seq_source.index_source == "history": --ref_file=$bias_correction.seq_source.ref_file #else: @@ -47,7 +46,6 @@ <param name="max_intron_len" type="integer" value="300000" min="1" max="600000" label="Max Intron Length" help=""/><param name="min_isoform_fraction" type="float" value="0.05" min="0" max="1" label="Min Isoform Fraction" help=""/><param name="pre_mrna_fraction" type="float" value="0.05" min="0" max="1" label="Pre MRNA Fraction" help=""/> - <param name="min_map_quality" type="integer" value="0" min="0" max="255" label="Min SAM Map Quality" help=""/><param name="do_normalization" type="select" label="Perform quartile normalization" help="Removes top 25% of genes from FPKM denominator to improve accuracy of differential expression calls for low abundance transcripts."><option value="No">No</option><option value="Yes">Yes</option> @@ -59,7 +57,7 @@ </param><when value="No"></when><when value="Yes"> - <param format="gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/> + <param format="gff3,gtf" name="reference_annotation_file" type="data" label="Reference Annotation" help="Make sure your annotation file is in GTF format and that Galaxy knows that your file is GTF--not GFF."/></when></conditional><conditional name="bias_correction"> @@ -95,8 +93,8 @@ </inputs><outputs> - <data format="tabular" name="genes_expression" label="${tool.name} on ${on_string}: gene expression" from_work_dir="genes.expr"/> - <data format="tabular" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression" from_work_dir="transcripts.expr"/> + <data format="tabular" name="genes_expression" label="${tool.name} on ${on_string}: gene expression" from_work_dir="genes.fpkm_tracking"/> + <data format="tabular" name="transcripts_expression" label="${tool.name} on ${on_string}: transcript expression" from_work_dir="isoforms.fpkm_tracking"/><data format="gtf" name="assembled_isoforms" label="${tool.name} on ${on_string}: assembled transcripts" from_work_dir="transcripts.gtf"/></outputs> @@ -106,7 +104,7 @@ --><test><param name="sPaired" value="No"/> - <param name="input" value="cufflinks_in.sam"/> + <param name="input" value="cufflinks_in.bam"/><param name="max_intron_len" value="300000"/><param name="min_isoform_fraction" value="0.05"/><param name="pre_mrna_fraction" value="0.05"/> @@ -114,8 +112,8 @@ <param name="use_ref" value="No"/><param name="do_normalization" value="No" /><param name="do_bias_correction" value="No"/> - <output name="genes_expression" format="tabular" file="cufflinks_out3.expr"/> - <output name="transcripts_expression" format="tabular" file="cufflinks_out2.expr"/> + <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"/></test></tests> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: kanwei: trackster: Indicator when drag-reordering tracks. Fix Y-axis label being too high
by Bitbucket 06 May '11

06 May '11

1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/c119abcbcdac/ changeset: r5507:c119abcbcdac user: kanwei date: 2011-05-06 20:32:55 summary: trackster: Indicator when drag-reordering tracks. Fix Y-axis label being too high affected #: 1 file (228 bytes) --- a/static/scripts/trackster.js Fri May 06 13:44:21 2011 -0400 +++ b/static/scripts/trackster.js Fri May 06 14:32:55 2011 -0400 @@ -146,13 +146,20 @@ // to handle the end specially since we don't have // insert at index if ( i === children.length ) { - if ( this !== children.get( i - 1 ) ) { - parent.append( this ); + if ( this !== children.get(i - 1) ) { + parent.append(this); } } - else if ( this !== children.get( i ) ) { - $(this).insertBefore( children.get( i ) ); + else if ( this !== children.get(i) ) { + $(this).insertBefore( children.get(i) ); } + }).bind("dragstart", function() { + $(this).css({ + "border-top": "1px solid blue", + "border-bottom": "1px solid blue" + }); + }).bind("dragend", function() { + $(this).css("border", "0px"); }); }; exports.sortable = sortable; @@ -2428,7 +2435,7 @@ this.container_div.find(".yaxislabel").remove(); var max_label = $("<div />").addClass('yaxislabel'); max_label.text( result.max ); - max_label.css({ position: "absolute", top: "22px", left: "10px", color: this.prefs.label_color }); + max_label.css({ position: "absolute", top: "24px", left: "10px", color: this.prefs.label_color }); max_label.prependTo(this.container_div); // Create canvas var canvas = this.view.canvas_manager.new_canvas(); 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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