commit/galaxy-central: 4 new changesets
4 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/2748be87612d/ changeset: r5559:2748be87612d user: fubar date: 2011-05-13 21:23:32 summary: Reordersam fails silently if contig names do not match so added an html log where this can be seen easily. Updated insertsize test affected #: 4 files (1.2 KB) --- a/test-data/picard_output_insertsize_tinysam.html Fri May 13 10:02:28 2011 -0400 +++ b/test-data/picard_output_insertsize_tinysam.html Fri May 13 15:23:32 2011 -0400 @@ -12,7 +12,7 @@ </head><body><div class="document"> -Galaxy tool CollectInsertSizeMetrics run at 12/05/2011 14:33:49</b><br/><table cellpadding="10"><tr><td> +Galaxy tool CollectInsertSizeMetrics run at 13/05/2011 15:20:46</b><br/><table cellpadding="10"><tr><td><a href="InsertSizeHist.pdf"><img src="InsertSizeHist.jpg" title="Click image preview for a print quality PDF version" hspace="10" align="middle"></a></tr></td></table><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table> @@ -26,46 +26,27 @@ <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 colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=InsertSizeHist.pdf TAIL_LIMIT=10000 MINIMUM_PCT=0.01 INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1092.dat OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/1028/dataset_1093_files/CollectInsertSizeMetrics.metrics.txt VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true STOP_AFTER=0 TMP_DIR=/tmp/rerla 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 colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Thu May 12 14:33:48 EDT 2011</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS net.sf.picard.analysis.InsertSizeMetrics</td></tr><tr class="d0"><td>MEDIAN_INSERT_SIZE</td><td>96 </td></tr> -<tr class="d1"><td>MIN_INSERT_SIZE</td><td>96 </td></tr> -<tr class="d0"><td>MAX_INSERT_SIZE</td><td>96 </td></tr> -<tr class="d1"><td>MEAN_INSERT_SIZE</td><td>96 </td></tr> -<tr class="d0"><td>STANDARD_DEVIATION</td><td>? </td></tr> -<tr class="d1"><td>READ_PAIRS</td><td>1 </td></tr> -<tr class="d0"><td>PAIR_ORIENTATION</td><td>FR </td></tr> -<tr class="d1"><td>WIDTH_OF_10_PERCENT</td><td>1 </td></tr> -<tr class="d0"><td>WIDTH_OF_20_PERCENT</td><td>1 </td></tr> -<tr class="d1"><td>WIDTH_OF_30_PERCENT</td><td>1 </td></tr> -<tr class="d0"><td>WIDTH_OF_40_PERCENT</td><td>1 </td></tr> -<tr class="d1"><td>WIDTH_OF_50_PERCENT</td><td>1 </td></tr> -<tr class="d0"><td>WIDTH_OF_60_PERCENT</td><td>1 </td></tr> -<tr class="d1"><td>WIDTH_OF_70_PERCENT</td><td>1 </td></tr> -<tr class="d0"><td>WIDTH_OF_80_PERCENT</td><td>1 </td></tr> -<tr class="d1"><td>WIDTH_OF_90_PERCENT</td><td>1 </td></tr> -<tr class="d0"><td>WIDTH_OF_99_PERCENT -</td><td>1 - </td></tr> -<tr class="d0"><td colspan="2">## HISTOGRAM java.lang.Integer</td></tr><tr class="d0"><td colspan="2">insert_size fr_count rf_count</td></tr> -<tr class="d1"><td colspan="2">96 1 0</td></tr> -<tr class="d0"><td colspan="2">201 0 1</td></tr> +<tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=InsertSizeHist.pdf TAIL_LIMIT=10000 MINIMUM_PCT=0.01 INPUT=/dev/shm/tmpHpwBHW/database/files/000/dataset_1.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/2/dataset_2_files/CollectInsertSizeMetrics.metrics.txt VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true STOP_AFTER=0 TMP_DIR=/tmp/rerla 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 colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Fri May 13 15:20:45 EDT 2011</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS net.sf.picard.analysis.InsertSizeMetrics</td></tr><tr class="d1"><td colspan="2">## HISTOGRAM java.lang.Integer</td></tr><tr class="d0"><td colspan="2">MEDIAN_INSERT_SIZE MIN_INSERT_SIZE MAX_INSERT_SIZE MEAN_INSERT_SIZE STANDARD_DEVIATION READ_PAIRS PAIR_ORIENTATION WIDTH_OF_10_PERCENT WIDTH_OF_20_PERCENT WIDTH_OF_30_PERCENT WIDTH_OF_40_PERCENT WIDTH_OF_50_PERCENT WIDTH_OF_60_PERCENT WIDTH_OF_70_PERCENT WIDTH_OF_80_PERCENT WIDTH_OF_90_PERCENT WIDTH_OF_99_PERCENT</td></tr> +<tr class="d1"><td colspan="2">96 96 96 96 ? 1 FR 1 1 1 1 1 1 1 1 1 1</td></tr> +<tr class="d0"><td colspan="2">201 201 201 201 ? 1 RF 1 1 1 1 1 1 1 1 1 1</td></tr> +<tr class="d1"><td colspan="2">insert_size fr_count rf_count</td></tr> +<tr class="d0"><td colspan="2">96 1 0</td></tr> +<tr class="d1"><td colspan="2">201 0 1</td></tr></table><b>Picard Tool Run Log</b><hr/> -<pre>Thu, 12 May 2011 14:33:48 INFO - ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/CollectInsertSizeMetrics.jar VALIDATION_STRINGENCY=LENIENT I=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1092.dat O=/udd/rerla/galaxy-central/database/job_working_directory/1028/dataset_1093_files/CollectInsertSizeMetrics.metrics.txt HISTOGRAM_FILE=InsertSizeHist.pdf TAIL_LIMIT=10000 MINIMUM_PCT=0.01 returned status 0 and stderr: -[Thu May 12 14:33:48 EDT 2011] net.sf.picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=InsertSizeHist.pdf TAIL_LIMIT=10000 MINIMUM_PCT=0.01 INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1092.dat OUTPUT=/udd/rerla/galaxy-central/database/job_working_directory/1028/dataset_1093_files/CollectInsertSizeMetrics.metrics.txt VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true STOP_AFTER=0 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -WARNING 2011-05-12 14:33:48 SinglePassSamProgram File reports sort order 'queryname', assuming it's coordinate sorted anyway. -INFO 2011-05-12 14:33:48 ProcessExecutor [1] "FR = red" "RF = blue" -INFO 2011-05-12 14:33:48 ProcessExecutor null device -INFO 2011-05-12 14:33:48 ProcessExecutor 1 -[Thu May 12 14:33:48 EDT 2011] net.sf.picard.analysis.CollectInsertSizeMetrics done. +<pre>INFO:root:## executing java -Xmx2g -jar /udd/rerla/rgalaxy/tool-data/shared/jars/CollectInsertSizeMetrics.jar VALIDATION_STRINGENCY=LENIENT I=/dev/shm/tmpHpwBHW/database/files/000/dataset_1.dat O=/udd/rerla/rgalaxy/database/job_working_directory/2/dataset_2_files/CollectInsertSizeMetrics.metrics.txt HISTOGRAM_FILE=InsertSizeHist.pdf TAIL_LIMIT=10000 MINIMUM_PCT=0.01 returned status 0 and stderr: +[Fri May 13 15:20:45 EDT 2011] net.sf.picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=InsertSizeHist.pdf TAIL_LIMIT=10000 MINIMUM_PCT=0.01 INPUT=/dev/shm/tmpHpwBHW/database/files/000/dataset_1.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/2/dataset_2_files/CollectInsertSizeMetrics.metrics.txt VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true STOP_AFTER=0 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +WARNING 2011-05-13 15:20:45 SinglePassSamProgram File reports sort order 'queryname', assuming it's coordinate sorted anyway. +INFO 2011-05-13 15:20:46 ProcessExecutor [1] "FR = red" "RF = blue" +INFO 2011-05-13 15:20:46 ProcessExecutor null device +INFO 2011-05-13 15:20:46 ProcessExecutor 1 +[Fri May 13 15:20:46 EDT 2011] net.sf.picard.analysis.CollectInsertSizeMetrics done. Runtime.totalMemory()=9109504 -Thu, 12 May 2011 14:33:49 INFO - ## executing mogrify -format jpg -resize x400 /udd/rerla/galaxy-central/database/job_working_directory/1028/dataset_1093_files/InsertSizeHist.pdf returned status 0 and nothing on stderr +INFO:root:## executing mogrify -format jpg -resize x400 /udd/rerla/rgalaxy/database/job_working_directory/2/dataset_2_files/InsertSizeHist.pdf returned status 0 and nothing on stderr -Thu, 12 May 2011 14:33:49 INFO - ## executing mogrify -format jpg -resize x400 /udd/rerla/galaxy-central/database/job_working_directory/1028/dataset_1093_files/InsertSizeHist.pdf returned status 0 and nothing on stderr +INFO:root:## executing mogrify -format jpg -resize x400 /udd/rerla/rgalaxy/database/job_working_directory/2/dataset_2_files/InsertSizeHist.pdf returned status 0 and nothing on stderr </pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html> --- a/tools/picard/picard_ReorderSam.xml Fri May 13 10:02:28 2011 -0400 +++ b/tools/picard/picard_ReorderSam.xml Fri May 13 15:23:32 2011 -0400 @@ -1,9 +1,8 @@ -<tool name="Reorder SAM:" id="picard_ReorderSam" version="0.01"> +<tool name="Reorder SAM:" id="picard_ReorderSam" version="0.02"><requirements><requirement type="package">picard</requirement></requirements><description>(Picard)</description><command interpreter="python"> - picard_wrapper.py - --input=$inputFile + picard_wrapper.py -d "$html_file.files_path" -t "$html_file" --input=$inputFile #if $source.indexSource == "built-in" --ref="${ filter( lambda x: str( x[0] ) == str( $source.ref ), $__app__.tool_data_tables[ 'picard_indexes' ].get_fields() )[0][-1] }" #else @@ -15,11 +14,7 @@ --allow-inc-dict-concord=$allowIncDictConcord --allow-contig-len-discord=$allowContigLenDiscord --output-format=$outputFormat - #if str( $outputFormat ) == "sam" - --output=$outFileSam - #else if str( $outputFormat ) == "bam" - --output=$outFileBam - #end if + --output="$out_file" -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/ReorderSam.jar" --picard-cmd="ReorderSam" </command> @@ -47,12 +42,12 @@ <param name="allowContigLenDiscord" type="boolean" checked="False" truevalue="true" falsevalue="false" label="Allow contig length discordance?" help="This is dangerous--don't check it unless you know exactly what you're doing!" /><param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output bam instead of sam" help="Uncheck for sam output" /></inputs> - <outputs> - <data name="outFileSam" format="sam" label="${tool.name} on ${on_string}: reordered sam"> - <filter>outputFormat is False</filter> - </data> - <data name="outFileBam" format="bam" label="${tool.name} on ${on_string}: reordered bam"> - <filter>outputFormat is True</filter> + <outputs> + <data format="html" name="html_file" label="ReorderBam_on_${on_string}.html" /> + <data format="bam" name="out_file" label="ReorderBam_on_${on_string}.${outputFormat}"> + <change_format> + <when input="outputFormat" value="sam" format="sam" /> + </change_format></data></outputs><tests> --- a/tools/picard/picard_wrapper.py Fri May 13 10:02:28 2011 -0400 +++ b/tools/picard/picard_wrapper.py Fri May 13 15:23:32 2011 -0400 @@ -50,7 +50,7 @@ assert opts <> None, 'PicardBase needs opts at init' self.opts = opts if self.opts.outdir == None: - self.opts.outdir = self.opts.tmpdir # fixmate has no html file eg + self.opts.outdir = os.getcwd() # fixmate has no html file eg so use temp dir assert self.opts.outdir <> None,'## PicardBase needs a temp directory if no output directory passed in' self.picname = self.baseName(opts.jar) if self.picname.startswith('picard'): @@ -78,10 +78,7 @@ def setLogging(self,logfname="picard_wrapper.log"): """setup a logger """ - today=timenow() logging.basicConfig(level=logging.INFO, - format='%(asctime)s %(levelname)s\n %(message)s', - datefmt='%a, %d %b %Y %H:%M:%S', filename=logfname, filemode='a') @@ -145,6 +142,7 @@ runme.append('-jar %s' % jar) runme += cl s,stdout = self.runCL(cl=runme, output_dir=self.opts.outdir) + print '##s=',s,'\n##stdout=',stdout return stdout def samToBam(self,infile=None,outdir=None): @@ -211,27 +209,39 @@ dat.append(srow) # want lists if row.startswith('## HISTOGRAM'): thist = True - if row.strip() == '' or i == lastr: # last line or blank means write a segment - if len(heads) > 0: - hres = ['<tr class="d%d"><td colspan="2">%s</td></tr>' % (i % 2,x) for i,x in enumerate(heads)] - res += hres - heads = [] - if len(dat) > 0: - if transpose and not thist: - tdat = map(None,*dat) # transpose an arbitrary list of lists - tdat = ['<tr class="d%d"><td>%s</td><td>%s </td></tr>\n' % ((i+len(heads)) % 2,x[0],x[1]) for i,x in enumerate(tdat) if i < maxrows] - missing = len(tdat) - maxrows - if missing > 0: - tdat.append('<tr><td colspan="2">...WARNING: %d rows deleted..see raw file %s for entire output</td></tr>' % (missing,os.path.basename(picout))) - else: - if thist or not transpose: - dat = ['\t'.join(x).strip() for x in dat] # back to strings :( - tdat = ['<tr class="d%d"><td colspan="2">%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(self.metricsOut))) - res += tdat - dat = [] + if len(heads) > 0: + hres = ['<tr class="d%d"><td colspan="2">%s</td></tr>' % (i % 2,x) for i,x in enumerate(heads)] + res += hres + heads = [] + if len(dat) > 0: + dropRows = len(dat) - maxrows + n = 0 + if dropRows > 0: + n = int(maxrows/2) + if transpose and not thist: + tdat = map(None,*dat) # transpose an arbitrary list of lists + if dropRows > 0: + dat = tdat[:n] + dat.append(('<b>...%d rows not shown - see log...</b>','')) + dat += tdat[-n:] + else: + dat = tdat + tdat = ['<tr class="d%d"><td>%s</td><td>%s </td></tr>\n' % ((i+len(heads)) % 2,x[0],x[1]) for i,x in enumerate(dat)] + if dropRows > 0: + tdat.append('<tr><td colspan="2">## WARNING: %d rows deleted..see raw file %s for entire output</td></tr>' % (dropRows,os.path.basename(picout))) + else: + if dropRows > 0: + tdat = dat[:n] + tdat.append(('<b>...%d rows not shown - see log...</b>' % dropRows,'')) + tdat += dat[-n:] + else: + tdat = dat + dat = ['\t'.join(x).strip() for x in tdat] # back to strings :( + tdat = ['<tr class="d%d"><td colspan="2">%s</td></tr>\n' % ((i+len(heads)) % 2,x) for i,x in enumerate(dat)] + if dropRows > 0: + tdat.append('<tr><td>## WARNING: %d rows deleted..see raw file %s for entire output</td></tr>' % (dropRows,os.path.basename(self.metricsOut))) + res += tdat + dat = [] res.append('</table>\n') return res @@ -273,11 +283,15 @@ res.append('<b>Picard Tool Run Log</b><hr/>\n') rlog = ['<pre>',] if llen > maxloglines: - rlog += l[:maxloglines] - rlog.append('\n<b>## WARNING - %d log lines truncated - %s contains entire output' % (llen - maxloglines,self.log_filename)) + n = min(50,int(maxloglines/2)) + rlog += l[:n] + rlog.append('------------ ## %d rows deleted ## --------------\n' % (llen-maxloglines)) + rlog += l[-n:] else: rlog += l rlog.append('</pre>') + if llen > maxloglines: + rlog.append('\n<b>## WARNING - %d log lines truncated - <a href="%s">%s</a> contains entire output</b>' % (llen - maxloglines,self.log_filename,self.log_filename)) res += rlog else: res.append("### Odd, Picard left no log file %s - must have really barfed badly?\n" % self.log_filename) --- a/tools/picard/rgPicardInsertSize.xml Fri May 13 10:02:28 2011 -0400 +++ b/tools/picard/rgPicardInsertSize.xml Fri May 13 15:23:32 2011 -0400 @@ -1,11 +1,11 @@ -<tool name="Insertion size metrics:" id="rgPicInsertSize" version="0.01"> +<tool name="Insertion size metrics:" id="PicardInsertSize" version="0.02"><description>for PAIRED data</description> + <requirements><requirement type="package">picard</requirement></requirements><command interpreter="python"> picard_wrapper.py -i "$input_file" -n "$out_prefix" --tmpdir "${__new_file_path__}" --taillimit "$tailLimit" --histwidth "$histWidth" --minpct "$minPct" -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/CollectInsertSizeMetrics.jar" -d "$html_file.files_path" -t "$html_file" </command> - <requirements><requirement type="package">picard</requirement></requirements><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"/> http://bitbucket.org/galaxy/galaxy-central/changeset/a7832bbcd110/ changeset: r5560:a7832bbcd110 user: fubar date: 2011-05-13 22:54:31 summary: Picard reorder test fix and parameter changes affected #: 3 files (1.1 KB) --- a/test-data/picard_RS_output3.sam Fri May 13 15:23:32 2011 -0400 +++ b/test-data/picard_RS_output3.sam Fri May 13 16:54:31 2011 -0400 @@ -1,26 +1,26 @@ @HD VN:1.0 SO:unsorted -@SQ SN:phiX1 LN:1120 UR:picard_RS_input4.fasta AS:phiX_buildBlah1.1 M5:40156fecb557ec9a4e0e7d0d5379d346 SP:phiX174 -@SQ SN:phiX2 LN:1190 UR:picard_RS_input4.fasta AS:phiX_buildBlah1.1 M5:3ecdb3921cbd184296cefdc675595fc1 SP:phiX174 -@SQ SN:phiX3 LN:1330 UR:picard_RS_input4.fasta AS:phiX_buildBlah1.1 M5:60435b7625ee8862e4af3e839b195198 SP:phiX174 -@SQ SN:phiX4 LN:910 UR:picard_RS_input4.fasta AS:phiX_buildBlah1.1 M5:ae8509d7b91ed64a44dd718513b1fd06 SP:phiX174 -@SQ SN:phiX5 LN:828 UR:picard_RS_input4.fasta AS:phiX_buildBlah1.1 M5:459c70115963cbce5021cac2bc9dfbd1 SP:phiX174 +@SQ SN:phiX1 LN:1120 UR:dataset_3.dat AS:phiX_buildBlah1.1 M5:40156fecb557ec9a4e0e7d0d5379d346 SP:phiX174 +@SQ SN:phiX2 LN:1190 UR:dataset_3.dat AS:phiX_buildBlah1.1 M5:3ecdb3921cbd184296cefdc675595fc1 SP:phiX174 +@SQ SN:phiX3 LN:1330 UR:dataset_3.dat AS:phiX_buildBlah1.1 M5:60435b7625ee8862e4af3e839b195198 SP:phiX174 +@SQ SN:phiX4 LN:910 UR:dataset_3.dat AS:phiX_buildBlah1.1 M5:ae8509d7b91ed64a44dd718513b1fd06 SP:phiX174 +@SQ SN:phiX5 LN:828 UR:dataset_3.dat AS:phiX_buildBlah1.1 M5:459c70115963cbce5021cac2bc9dfbd1 SP:phiX174 @PG ID:Bowtie VN:0.12.7 CL:"bowtie -q -p 4 -S --phred33-quals /tmp/tmp1E6jpl/tmpDg42o9 dataset_437.dat" -HWI-EAS91_1_30788AAXX:1:1:1570:620/1 4 * 0 0 * * 0 0 GAGTAACAAAGTAAAGTTTGGACCGTTTTTGTCTCGTGCTCGTCGCTGCG IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII XM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1572:270/1 0 phiX3 1208 255 50M * 0 0 TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1572:324/1 4 * 0 0 * * 0 0 AAGGTGCTTAAATTCGTGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII XM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1761:343/1 0 phiX1 5 255 50M * 0 0 TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII XA:i:0 MD:Z:50 NM:i:0 HWI-EAS91_1_30788AAXX:1:1:1578:331/1 0 phiX1 209 255 50M * 0 0 TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1647:512/1 0 phiX1 401 255 50M * 0 0 TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1599:330/1 0 phiX1 803 255 50M * 0 0 AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII XA:i:0 MD:Z:30G19 NM:i:1 +HWI-EAS91_1_30788AAXX:1:1:1746:351/1 0 phiX2 98 255 50M * 0 0 CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 HWI-EAS91_1_30788AAXX:1:1:1582:633/1 0 phiX2 397 255 50M * 0 0 CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 HWI-EAS91_1_30788AAXX:1:1:1598:534/1 0 phiX2 597 255 50M * 0 0 GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1599:330/1 0 phiX1 803 255 50M * 0 0 AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII XA:i:0 MD:Z:30G19 NM:i:1 +HWI-EAS91_1_30788AAXX:1:1:1749:466/1 0 phiX2 1081 255 50M * 0 0 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1763:587/1 0 phiX3 191 255 50M * 0 0 AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 HWI-EAS91_1_30788AAXX:1:1:1616:363/1 0 phiX3 408 255 50M * 0 0 TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1768:715/1 0 phiX3 808 255 50M * 0 0 ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1572:270/1 0 phiX3 1208 255 50M * 0 0 TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1785:1272/1 0 phiX4 178 255 50M * 0 0 TATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCT III""""""IIIIIIIII""FI"IIII""II+ICI"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1673:514/1 0 phiX4 378 255 50M * 0 0 ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1634:330/1 0 phiX4 778 255 50M * 0 0 GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1570:620/1 4 * 0 0 * * 0 0 GAGTAACAAAGTAAAGTTTGGACCGTTTTTGTCTCGTGCTCGTCGCTGCG IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII XM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1572:324/1 4 * 0 0 * * 0 0 AAGGTGCTTAAATTCGTGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII XM:i:0 +HWI-EAS91_1_30788AAXX:1:1:1652:270/1 4 * 0 0 * * 0 0 AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGACTTTGCATTGTTTAATTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII XM:i:0 HWI-EAS91_1_30788AAXX:1:1:1629:446/1 4 * 0 0 * * 0 0 AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1634:330/1 0 phiX4 778 255 50M * 0 0 GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1647:512/1 0 phiX1 401 255 50M * 0 0 TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1652:270/1 4 * 0 0 * * 0 0 AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGACTTTGCATTGTTTAATTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII XM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1673:514/1 0 phiX4 378 255 50M * 0 0 ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1746:351/1 0 phiX2 98 255 50M * 0 0 CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1749:466/1 0 phiX2 1081 255 50M * 0 0 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1761:343/1 0 phiX1 5 255 50M * 0 0 TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1763:587/1 0 phiX3 191 255 50M * 0 0 AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1768:715/1 0 phiX3 808 255 50M * 0 0 ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1785:1272/1 0 phiX4 178 255 50M * 0 0 TATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCT III""""""IIIIIIIII""FI"IIII""II+ICI"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 --- a/tools/picard/picard_ReorderSam.xml Fri May 13 15:23:32 2011 -0400 +++ b/tools/picard/picard_ReorderSam.xml Fri May 13 16:54:31 2011 -0400 @@ -6,14 +6,14 @@ #if $source.indexSource == "built-in" --ref="${ filter( lambda x: str( x[0] ) == str( $source.ref ), $__app__.tool_data_tables[ 'picard_indexes' ].get_fields() )[0][-1] }" #else - --ref-file=$refFile + --ref-file=$source.refFile --species-name=$source.speciesName --build-name=$source.buildName --trunc-names=$source.truncateSeqNames #end if --allow-inc-dict-concord=$allowIncDictConcord --allow-contig-len-discord=$allowContigLenDiscord - --output-format=$outputFormat + --newformat=$outputFormat --output="$out_file" -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/ReorderSam.jar" --picard-cmd="ReorderSam" --- a/tools/picard/picard_wrapper.py Fri May 13 15:23:32 2011 -0400 +++ b/tools/picard/picard_wrapper.py Fri May 13 16:54:31 2011 -0400 @@ -142,7 +142,6 @@ runme.append('-jar %s' % jar) runme += cl s,stdout = self.runCL(cl=runme, output_dir=self.opts.outdir) - print '##s=',s,'\n##stdout=',stdout return stdout def samToBam(self,infile=None,outdir=None): @@ -214,32 +213,12 @@ res += hres heads = [] if len(dat) > 0: - dropRows = len(dat) - maxrows - n = 0 - if dropRows > 0: - n = int(maxrows/2) if transpose and not thist: tdat = map(None,*dat) # transpose an arbitrary list of lists - if dropRows > 0: - dat = tdat[:n] - dat.append(('<b>...%d rows not shown - see log...</b>','')) - dat += tdat[-n:] - else: - dat = tdat - tdat = ['<tr class="d%d"><td>%s</td><td>%s </td></tr>\n' % ((i+len(heads)) % 2,x[0],x[1]) for i,x in enumerate(dat)] - if dropRows > 0: - tdat.append('<tr><td colspan="2">## WARNING: %d rows deleted..see raw file %s for entire output</td></tr>' % (dropRows,os.path.basename(picout))) + tdat = ['<tr class="d%d"><td>%s</td><td>%s </td></tr>\n' % ((i+len(heads)) % 2,x[0],x[1]) for i,x in enumerate(tdat)] else: - if dropRows > 0: - tdat = dat[:n] - tdat.append(('<b>...%d rows not shown - see log...</b>' % dropRows,'')) - tdat += dat[-n:] - else: - tdat = dat - dat = ['\t'.join(x).strip() for x in tdat] # back to strings :( - tdat = ['<tr class="d%d"><td colspan="2">%s</td></tr>\n' % ((i+len(heads)) % 2,x) for i,x in enumerate(dat)] - if dropRows > 0: - tdat.append('<tr><td>## WARNING: %d rows deleted..see raw file %s for entire output</td></tr>' % (dropRows,os.path.basename(self.metricsOut))) + tdat = ['\t'.join(x).strip() for x in dat] # back to strings :( + tdat = ['<tr class="d%d"><td colspan="2">%s</td></tr>\n' % ((i+len(heads)) % 2,x) for i,x in enumerate(tdat)] res += tdat dat = [] res.append('</table>\n') @@ -654,10 +633,11 @@ haveTempout = True elif pic.picname == 'ReorderSam': + tmp_fd, tempout = tempfile.mkstemp( dir=opts.tmpdir,prefix='ReOrderTempOut') # input cl.append('INPUT=%s' % opts.input) # output - cl.append('OUTPUT=%s' % opts.output) + cl.append('OUTPUT=%s' % tempout) # reference cl.append('REFERENCE=%s' % ref_file_name) # incomplete dict concordance @@ -667,6 +647,7 @@ if opts.allow_contig_len_discord == 'true': cl.append('ALLOW_CONTIG_LENGTH_DISCORDANCE=true') pic.runPic(opts.jar, cl) + haveTempout = True elif pic.picname == 'ReplaceSamHeader': tmp_fd, tempout = tempfile.mkstemp( dir=opts.tmpdir,prefix='RSHTempOut') http://bitbucket.org/galaxy/galaxy-central/changeset/ec0cc878d423/ changeset: r5561:ec0cc878d423 user: fubar date: 2011-05-13 23:12:19 summary: finally have picard reorder tests working affected #: 2 files (3.7 KB) --- a/test-data/picard_RS_output2.sam Fri May 13 16:54:31 2011 -0400 +++ b/test-data/picard_RS_output2.sam Fri May 13 17:12:19 2011 -0400 @@ -1,22 +0,0 @@ -@HD VN:1.0 SO:unsorted -@SQ SN:phiX174 LN:5386 UR:file:/afs/bx.psu.edu/user/kpvincent/working/phiX.fa M5:f479307bca04825e98008f37e4f6251a -@PG ID:Bowtie VN:0.12.7 CL:"bowtie -q -p 4 -S --phred33-quals /genome/phiX/bowtie_index/phiX dataset_437.dat" -HWI-EAS91_1_30788AAXX:1:1:1761:343/1 0 phiX174 5 255 50M * 0 0 TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1647:512/1 0 phiX174 401 255 50M * 0 0 TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1578:331/1 0 phiX174 209 255 50M * 0 0 TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1746:351/1 0 phiX174 1218 255 50M * 0 0 CTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1582:633/1 0 phiX174 1517 255 50M * 0 0 CCGCTTCCTCCTGAGACTGAGCTTTCTCGCCAAATGACGACTTCTACCAC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1599:330/1 0 phiX174 803 255 50M * 0 0 AGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAGTGATGTAATGTC IIIIIII""IIIIIIIIIIIIIIIIIII<III@II"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1598:534/1 0 phiX174 1717 255 50M * 0 0 GCGCTCTAATCTCTGGGCATCTGGCTATGATGTTGATGGAACTGACCAAA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1749:466/1 0 phiX174 2201 255 50M * 0 0 TTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTTATCGCAATCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1570:620/1 4 * 0 0 * * 0 0 GAGTAACAAAGTAAAGTTTGGACCGTTTTTGTCTCGTGCTCGTCGCTGCG IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII XM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1629:446/1 0 phiX174 2301 255 50M * 0 0 AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1763:587/1 0 phiX174 2501 255 50M * 0 0 AAGCTACATCGTCAACGTTATATTTTGATAGTTTGACGGTTAATGCTGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1616:363/1 0 phiX174 2718 255 50M * 0 0 TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1572:270/1 0 phiX174 3518 255 50M * 0 0 TGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1768:715/1 0 phiX174 3118 255 50M * 0 0 ACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTGGTGCTATGGCTAAAGCT IIIIIII""IIIIIIIIIIIIIDIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1785:1272/1 0 phiX174 3818 255 50M * 0 0 TATTTTTCATGGTATTGATAAAGCTGTTGCCGATACTTGGAACAATTTCT III""""""IIIIIIIII""FI"IIII""II+ICI"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1673:514/1 0 phiX174 4018 255 50M * 0 0 ATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTATTGAGGCT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIII1"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1652:270/1 4 * 0 0 * * 0 0 AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGACTTTGCATTGTTTAATTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII XM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1572:324/1 4 * 0 0 * * 0 0 AAGGTGCTTAAATTCGTGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII XM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1634:330/1 0 phiX174 4418 255 50M * 0 0 GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 --- a/test-data/picard_RS_output3.sam Fri May 13 16:54:31 2011 -0400 +++ b/test-data/picard_RS_output3.sam Fri May 13 17:12:19 2011 -0400 @@ -1,9 +1,9 @@ @HD VN:1.0 SO:unsorted -@SQ SN:phiX1 LN:1120 UR:dataset_3.dat AS:phiX_buildBlah1.1 M5:40156fecb557ec9a4e0e7d0d5379d346 SP:phiX174 -@SQ SN:phiX2 LN:1190 UR:dataset_3.dat AS:phiX_buildBlah1.1 M5:3ecdb3921cbd184296cefdc675595fc1 SP:phiX174 -@SQ SN:phiX3 LN:1330 UR:dataset_3.dat AS:phiX_buildBlah1.1 M5:60435b7625ee8862e4af3e839b195198 SP:phiX174 -@SQ SN:phiX4 LN:910 UR:dataset_3.dat AS:phiX_buildBlah1.1 M5:ae8509d7b91ed64a44dd718513b1fd06 SP:phiX174 -@SQ SN:phiX5 LN:828 UR:dataset_3.dat AS:phiX_buildBlah1.1 M5:459c70115963cbce5021cac2bc9dfbd1 SP:phiX174 +@SQ SN:phiX1 LN:1120 UR:dataset_5.dat AS:phiX_buildBlah1.1 M5:40156fecb557ec9a4e0e7d0d5379d346 SP:phiX174 +@SQ SN:phiX2 LN:1190 UR:dataset_5.dat AS:phiX_buildBlah1.1 M5:3ecdb3921cbd184296cefdc675595fc1 SP:phiX174 +@SQ SN:phiX3 LN:1330 UR:dataset_5.dat AS:phiX_buildBlah1.1 M5:60435b7625ee8862e4af3e839b195198 SP:phiX174 +@SQ SN:phiX4 LN:910 UR:dataset_5.dat AS:phiX_buildBlah1.1 M5:ae8509d7b91ed64a44dd718513b1fd06 SP:phiX174 +@SQ SN:phiX5 LN:828 UR:dataset_5.dat AS:phiX_buildBlah1.1 M5:459c70115963cbce5021cac2bc9dfbd1 SP:phiX174 @PG ID:Bowtie VN:0.12.7 CL:"bowtie -q -p 4 -S --phred33-quals /tmp/tmp1E6jpl/tmpDg42o9 dataset_437.dat" HWI-EAS91_1_30788AAXX:1:1:1761:343/1 0 phiX1 5 255 50M * 0 0 TTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGA IIIIIII""IIIIIIIIIII?I0IIIIHIIIGIIIII0II?I""IIIIII XA:i:0 MD:Z:50 NM:i:0 HWI-EAS91_1_30788AAXX:1:1:1578:331/1 0 phiX1 209 255 50M * 0 0 TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 http://bitbucket.org/galaxy/galaxy-central/changeset/a4a9c884b805/ changeset: r5562:a4a9c884b805 user: fubar date: 2011-05-13 23:12:44 summary: branch merge affected #: 2 files (67 bytes) --- a/lib/galaxy/visualization/tracks/data_providers.py Fri May 13 17:12:19 2011 -0400 +++ b/lib/galaxy/visualization/tracks/data_providers.py Fri May 13 17:12:44 2011 -0400 @@ -332,10 +332,11 @@ # 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 num_points = (end-start) / 1280 - if (end - start) < num_points: + if num_points < 1: num_points = end - start + num_points = max(num_points, 10) data = bbi.query(chrom, start, end, num_points) f.close() --- a/static/scripts/trackster.js Fri May 13 17:12:19 2011 -0400 +++ b/static/scripts/trackster.js Fri May 13 17:12:44 2011 -0400 @@ -181,6 +181,7 @@ // Other constants. DENSITY = 200, + RESOLUTION = 5, FEATURE_LEVELS = 10, DEFAULT_DATA_QUERY_WAIT = 5000, // Maximum number of chromosomes that are selectable at any one time. @@ -762,7 +763,7 @@ this.high = Math.ceil(high); // 10^log10(range / DENSITY) Close approximation for browser window, assuming DENSITY = window width - this.resolution = Math.pow( 10, Math.ceil( Math.log( (this.high - this.low) / DENSITY ) / Math.LN10 ) ); + this.resolution = Math.pow( RESOLUTION, Math.ceil( Math.log( (this.high - this.low) / DENSITY ) / Math.log(RESOLUTION) ) ); this.zoom_res = Math.pow( FEATURE_LEVELS, Math.max(0,Math.ceil( Math.log( this.resolution, FEATURE_LEVELS ) / Math.log(FEATURE_LEVELS) ))); // Overview 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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