| Previous changeset 4:ab1f60c26526 (2014-02-21) Next changeset 6:4ff1e04010e6 (2015-01-15) |
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Commit message:
Uploaded |
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modified:
picard_AddOrReplaceReadGroups.xml picard_FastqToSam.xml picard_ReorderSam.xml picard_ReplaceSamHeader.xml picard_SamToFastq.xml tool_dependencies.xml |
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added:
picard_AddCommentsToBam.xml picard_BedToIntervalList.xml picard_CleanSam.xml picard_CollectAlignmentSummaryMetrics.xml picard_CollectBaseDistributionByCycle.xml picard_CollectGcBiasMetrics.xml picard_CollectInsertSizeMetrics.xml picard_CollectRnaSeqMetrics.xml picard_CollectWgsMetrics.xml picard_DownsampleSam.xml picard_EstimateLibraryComplexity.xml picard_FilterSamReads.xml picard_FixMateInformation.xml picard_MarkDuplicates.xml picard_MarkDuplicatesWithMateCigar.xml picard_MeanQualityByCycle.xml picard_MergeBamAlignment.xml picard_MergeSamFiles.xml picard_NormalizeFasta.xml picard_QualityScoreDistribution.xml picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml picard_RevertSam.xml picard_SortSam.xml picard_ValidateSamFile.xml picard_macros.xml test-data/picard_ARRG.bam test-data/picard_ARRG_test1.bam test-data/picard_AddCommentsToBam.bam test-data/picard_AddCommentsToBam_test1.bam test-data/picard_BedToIntervalList.bed test-data/picard_BedToIntervalList_ref.fa test-data/picard_BedToIntervalList_test1.pif test-data/picard_CASM.bam test-data/picard_CASM_ref.fa test-data/picard_CASM_test1.tab test-data/picard_CleanSam.bam test-data/picard_CleanSam_test1.bam test-data/picard_CollectBaseDistributionByCycle.bam test-data/picard_CollectBaseDistributionByCycle_ref.fa test-data/picard_CollectBaseDistributionByCycle_test1.tab test-data/picard_CollectGcBiasMetrics.bam test-data/picard_CollectGcBiasMetrics_ref.fa test-data/picard_CollectGcBiasMetrics_test1.tab test-data/picard_CollectInsertSizeMetrics.bam test-data/picard_CollectInsertSizeMetrics_ref.fa test-data/picard_CollectInsertSizeMetrics_test1.tab test-data/picard_CollectRnaSeqMetrics.bam test-data/picard_CollectRnaSeqMetrics.refFlat test-data/picard_CollectRnaSeqMetrics.refFlat~ test-data/picard_CollectRnaSeqMetrics_ref.fa test-data/picard_CollectRnaSeqMetrics_test1.tab test-data/picard_CollectWgsMetrics.bam test-data/picard_CollectWgsMetrics_ref.fa test-data/picard_CollectWgsMetrics_test1.tab test-data/picard_DownsampleSam.bam test-data/picard_DownsampleSam_test1.bam test-data/picard_EstimateLibraryComplexity.bam test-data/picard_EstimateLibraryComplexity_test1.tab test-data/picard_FastqToSam_read1.fq test-data/picard_FastqToSam_read2.fq test-data/picard_FastqToSam_test1.bam test-data/picard_FilterSamReads.bam test-data/picard_FilterSamReads_exclude_reads_test2.bam test-data/picard_FilterSamReads_include_reads_test1.bam test-data/picard_FilterSamReads_read_list_file.tab test-data/picard_FixMateInformation.bam test-data/picard_FixMateInformation_test1.bam test-data/picard_MarkDuplicates.bam test-data/picard_MarkDuplicatesWithMateCigar.bam test-data/picard_MarkDuplicatesWithMateCigar_test1.bam test-data/picard_MarkDuplicates_test1.bam test-data/picard_MeanQualityByCycle.bam test-data/picard_MeanQualityByCycle_ref.fa test-data/picard_MeanQualityByCycle_test1.tab test-data/picard_MergeBamAlignment_aligned.bam test-data/picard_MergeBamAlignment_ref.fa test-data/picard_MergeBamAlignment_test1.bam test-data/picard_MergeBamAlignment_unaligned.bam test-data/picard_MergeSamFiles_input1.bam test-data/picard_MergeSamFiles_input2.bam test-data/picard_MergeSamFiles_input3.bam test-data/picard_MergeSamFiles_test1.bam test-data/picard_NormalizeFasta_ref.fa test-data/picard_NormalizeFasta_test1.fa test-data/picard_QualityScoreDistribution.bam test-data/picard_QualityScoreDistribution_ref.fa test-data/picard_QualityScoreDistribution_test1.tab test-data/picard_ReorderSam.bam test-data/picard_ReorderSam_ref.fa test-data/picard_ReorderSam_test1.bam test-data/picard_ReplaceSamHeader.bam test-data/picard_ReplaceSamHeader_header.bam test-data/picard_ReplaceSamHeader_test1.bam test-data/picard_RevertOriginalBaseQualitiesAndAddMateCigar.bam test-data/picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam test-data/picard_RevertSam.bam test-data/picard_RevertSam_test1.bam test-data/picard_SamToFastq.bam test-data/picard_SamToFastq_test1.fq test-data/picard_SortSam.bam test-data/picard_SortSam_test1.bam test-data/picard_ValidateSamFile.bam test-data/picard_ValidateSamFile_ref.fa test-data/picard_ValidateSamFile_test1.txt |
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removed:
picard_BamIndexStats.xml picard_SamToFastq_wrapper.py picard_wrapper.py rgPicardASMetrics.xml rgPicardFixMate.xml rgPicardGCBiasMetrics.xml rgPicardHsMetrics.xml rgPicardInsertSize.xml rgPicardLibComplexity.xml rgPicardMarkDups.xml test-data/bfast_out1.sam test-data/bwa_wrapper_in2.fastqsanger test-data/bwa_wrapper_in3.fastqsanger test-data/bwa_wrapper_out3.sam test-data/phiX.fasta test-data/picard_ARRG_input1.bam test-data/picard_ARRG_input1.sam test-data/picard_ARRG_input2.sam test-data/picard_ARRG_output1.sam test-data/picard_ARRG_output2.bam test-data/picard_ARRG_output2.sam test-data/picard_ARRG_output3.bam test-data/picard_ARRG_output3.bam.bai test-data/picard_ARRG_output3.sam test-data/picard_BIS_input1.bam test-data/picard_BIS_input1.sam test-data/picard_BIS_output1.txt test-data/picard_BIS_output2.txt test-data/picard_MD_output1.txt test-data/picard_MD_output2.bam test-data/picard_MD_output3.txt test-data/picard_MD_output4.sam test-data/picard_RSH_input1.bam test-data/picard_RSH_input1.sam test-data/picard_RSH_output1.sam test-data/picard_RSH_output2.bam test-data/picard_RSH_output2.sam test-data/picard_RS_input1.bam test-data/picard_RS_input2.sam test-data/picard_RS_input3.bam test-data/picard_RS_input3.sam test-data/picard_RS_input4.fasta test-data/picard_RS_output1.bam test-data/picard_RS_output2.sam test-data/picard_RS_output3.sam test-data/picard_fastq_to_sam_out1.bam test-data/picard_fastq_to_sam_out1.bam.bai test-data/picard_fastq_to_sam_out2.bam test-data/picard_fastq_to_sam_out2.bam.bai test-data/picard_input_bait.bed test-data/picard_input_coordinate_sorted.bam test-data/picard_input_hg18.trimmed.fasta test-data/picard_input_sorted_pair.bam test-data/picard_input_sorted_pair.sam test-data/picard_input_summary_alignment_stats.sam test-data/picard_input_tiny.sam test-data/picard_input_tiny_coord.bam test-data/picard_input_tiny_coord.sam test-data/picard_output_AsMetrics_indexed_hg18_sorted_pair.html test-data/picard_output_GcBias_uploaded_hg18_summary_alignment_stats.html test-data/picard_output_alignment_summary_metrics.html test-data/picard_output_collect_AS_sorted_pair.txt test-data/picard_output_estlibcomplexity_tinysam.html test-data/picard_output_fixmate_sorted_pair.bam test-data/picard_output_fixmate_sorted_pair.sam test-data/picard_output_fixmate_tiny.bam test-data/picard_output_gc_summary_alignment_stats.pdf test-data/picard_output_gc_summary_alignment_stats.txt test-data/picard_output_hs_transposed_summary_alignment_stats.html test-data/picard_output_insertsize_tinysam.html test-data/picard_output_markdups_remdupes.bam test-data/picard_output_markdups_sortedpairsam.bam test-data/picard_output_markdups_sortedpairsam.html test-data/picard_output_markdups_sortedpairsam.sam test-data/picard_output_validate_tiny_sam.html test-data/picard_summary_alignment_stats.sam test-data/random_phiX_1.fastqsanger |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_AddCommentsToBam.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_AddCommentsToBam.xml Tue Dec 16 19:03:21 2014 -0500 |
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| @@ -0,0 +1,79 @@ +<tool name="AddCommentsToBam" id="picard_AddCommentsToBam" version="1.126.0"> + <description>add comments to BAM dataset</description> + <requirements><requirement type="package" version="1.126.0">picard</requirement></requirements> + + <macros> + <import>picard_macros.xml</import> + </macros> + + <command> + @java_options@ + java -jar \$JAVA_JAR_PATH/picard.jar + AddCommentsToBam + INPUT="${inputFile}" + OUTPUT="${outFile}" + #for $element in $comments: + COMMENT="${element.comment}" + #end for + QUIET=true + VERBOSITY=ERROR + VALIDATION_STRINGENCY=${validation_stringency} + </command> + + <inputs> + <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" /> + <repeat name="comments" title="Comment" min="1" help="You can provide multiple comments"> + <param name="comment" type="text" size="50" label="Add this comment to BAM dataset" help="COMMENT"/> + </repeat> + + <expand macro="VS" /> + + </inputs> + + <outputs> + <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM with comments"/> + </outputs> + + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + + <tests> + <test> + <param name="inputFile" value="picard_AddCommentsToBam.bam" /> + <param name="comment" value="test1" /> + <param name="validation_stringency" value="LENIENT" /> + <output name="outFile" file="picard_AddCommentsToBam_test1.bam" ftype="bam" /> + </test> + </tests> + <help> + +.. class:: infomark + +**Purpose** + +Adds one or more comments (@CO) to the header of a specified BAM dataset. + +@dataset_collections@ + +@description@ + + COMMENT=String + C=String Comments to add to the BAM file This option may be specified 0 or more times. + +@more_info@ + </help> +</tool> + + + + + + + + + + + + + |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_AddOrReplaceReadGroups.xml --- a/picard_AddOrReplaceReadGroups.xml Fri Feb 21 12:07:49 2014 -0500 +++ b/picard_AddOrReplaceReadGroups.xml Tue Dec 16 19:03:21 2014 -0500 |
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| b'@@ -1,96 +1,81 @@\n-<tool name="Add or Replace Groups" id="picard_ARRG" version="1.56.0">\n- <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>\n- <command interpreter="python">\n- picard_wrapper.py\n- --input="${inputFile}"\n- --rg-lb="${rglb}"\n- --rg-pl="${rgpl}"\n- --rg-pu="${rgpu}"\n- --rg-sm="${rgsm}"\n- --rg-id="${rgid}"\n- --rg-opts="${readGroupOpts.rgOpts}"\n- #if $readGroupOpts.rgOpts == "full"\n- --rg-cn="${readGroupOpts.rgcn}"\n- --rg-ds="${readGroupOpts.rgds}"\n+<tool name="AddOrReplaceReadGroups" id="picard_AddOrReplaceReadGroups" version="1.126.0">\n+ <description>add or replaces read group information</description>\n+ <requirements>\n+ <requirement type="package" version="1.126.0">picard</requirement>\n+ </requirements>\n+ \n+ <macros>\n+ <import>picard_macros.xml</import>\n+ </macros>\n+ \n+ <command>\n+ @java_options@\n+ java -jar \\$JAVA_JAR_PATH/picard.jar\n+ AddOrReplaceReadGroups\n+ INPUT="${inputFile}"\n+ RGLB="${rglb}"\n+ RGPL="${rgpl}"\n+ RGPU="${rgpu}"\n+ RGSM="${rgsm}"\n+ RGID="${rgid}"\n+ \n+ #if str( $rgcn):\n+ RGCN="${rgcn}"\n #end if\n- --output-format="${outputFormat}"\n- --output="${outFile}"\n- -j "\\$JAVA_JAR_PATH/AddOrReplaceReadGroups.jar"\n- --tmpdir "${__new_file_path__}" \n+ \n+ #if str( $rgds):\n+ RGDS="${rgds}"\n+ #end if\n+ \n+ #if str( $rgpi):\n+ RGPI="${rgpi}"\n+ #end if\n+\n+ #if str( $rgdt):\n+ RGDT="${rgdt}"\n+ #end if\n+ \n+ VALIDATION_STRINGENCY="${validation_stringency}"\n+ QUIET=true\n+ VERBOSITY=ERROR\n+ OUTPUT="${outFile}"\n+ \n </command>\n+ \n <inputs>\n- <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to add or replace read groups in"\n- help="If empty, upload or import a SAM/BAM dataset." />\n- <param name="rgid" value="1" type="text" label="Read group ID (ID tag)" help="The most important read group tag. Galaxy will use a value of \'1\' if nothing provided." />\n- <param name="rgsm" value="" type="text" label="Read group sample name (SM tag)" />\n- <param name="rglb" value="" type="text" label="Read group library (LB tag)" />\n- <param name="rgpl" value="" type="text" label="Read group platform (PL tag)" help="illumina, solid, 454, pacbio, helicos" />\n- <param name="rgpu" value="" type="text" label="Read group platform unit" help="like run barcode, etc." />\n- <conditional name="readGroupOpts">\n- <param name="rgOpts" type="select" label="Specify additional (optional) arguments" help="Allows you to set RGCN and RGDS.">\n- <option value="preSet">Use pre-set defaults</option>\n- <option value="full">Set optional arguments</option>\n- </param>\n- <when value="preSet" />\n- <when value="full">\n- <param name="rgcn" value="" type="text" label="Read group sequencing center name" help="Leave set to <null> for default (none)" />\n- <param name="rgds" value="" type="text" label="Read group description" help="Leave set to <null> for default (none)" />\n- </when>\n- </conditional>\n- <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output bam instead of sam" help="Uncheck for sam output" />\n+ <param format="bam,sam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />\n+ <param name="rgid" value="A" type="text" label="Read Group ID" help="RGID; Required" />\n+ <param name="rgsm" value="sample-a" type="text" label="Read Group Sample name" help="RGSM; Required" />\n+ <param name="rglb" value="tumor-a" type="text" label="Read Group library" help="RGLB; Required" />\n+ <param name="rgpl" value="Illumina" type="text" label="Read Group Platform" help="RGPL; Required; e.g., Illumina, 454, IonTorrent, etc" />\n+ <'..b" PI:400\n- \n- Mom's data:\n- @RG ID:FLOWCELL1.LANE5 PL:illumina LB:LIB-MOM-1 SM:MOM PI:200\n- @RG ID:FLOWCELL1.LANE6 PL:illumina LB:LIB-MOM-1 SM:MOM PI:200\n- @RG ID:FLOWCELL1.LANE7 PL:illumina LB:LIB-MOM-2 SM:MOM PI:400\n- @RG ID:FLOWCELL1.LANE8 PL:illumina LB:LIB-MOM-2 SM:MOM PI:400\n- \n- Kid's data:\n- @RG ID:FLOWCELL2.LANE1 PL:illumina LB:LIB-KID-1 SM:KID PI:200\n- @RG ID:FLOWCELL2.LANE2 PL:illumina LB:LIB-KID-1 SM:KID PI:200\n- @RG ID:FLOWCELL2.LANE3 PL:illumina LB:LIB-KID-2 SM:KID PI:400\n- @RG ID:FLOWCELL2.LANE4 PL:illumina LB:LIB-KID-2 SM:KID PI:400\n+ OUTPUT=File\n+ O=File Output file (bam or sam). Required. \n \n-Note the hierarchical relationship between read groups (unique for each lane) to libraries (sequenced on two lanes) and samples (across four lanes, two lanes for each library).\n-\n-**Picard documentation**\n+ SORT_ORDER=SortOrder\n+ SO=SortOrder Optional sort order to output in. If not supplied OUTPUT is in the same order as INPUT. \n+ Default value: null. Possible values: {unsorted, queryname, coordinate} \n \n-This is a Galaxy wrapper for AddOrReplaceReadGroups, a part of the external package Picard-tools_.\n-\n- .. _Picard-tools: http://www.google.com/search?q=picard+samtools\n+ RGID=String\n+ ID=String Read Group ID Default value: 1. This option can be set to 'null' to clear the default \n+ value. \n \n-------\n-\n-.. class:: infomark\n-\n-**Inputs, outputs, and parameters**\n-\n-Either a sam file or a bam file must be supplied. If a bam file is used, it must\n-be coordinate-sorted. Galaxy currently coordinate-sorts all bam files.\n-\n-The output file is either bam (the default) or sam, according to user selection,\n-and contains the same information as the input file except for the appropraite\n-additional (or modified) read group tags. Bam is recommended since it is smaller.\n-\n-From the Picard documentation.\n-\n-AddOrReplaceReadGroups REQUIRED parameters::\n-\n- Option (Type) Description\n+ RGLB=String\n+ LB=String Read Group Library Required. \n \n- RGLB=String Read Group Library\n- RGPL=String Read Group platform (e.g. illumina, solid)\n- RGPU=String Read Group platform unit (eg. run barcode)\n- RGSM=String Read Group sample name\n- RGID=String Read Group ID; Default value: null (empty)\n+ RGPL=String\n+ PL=String Read Group platform (e.g. illumina, solid) Required. \n \n-AddOrReplaceReadGroups OPTIONAL parameters::\n+ RGPU=String\n+ PU=String Read Group platform unit (eg. run barcode) Required. \n \n- Option (Type) Description\n- \n- RGCN=String Read Group sequencing center name; Default value: null (empty)\n- RGDS=String Read Group description Default value: null (empty)\n+ RGSM=String\n+ SM=String Read Group sample name Required. \n \n-One parameter that Picard's AddOrReplaceReadGroups offers that is automatically\n-set by Galaxy is the SORT_ORDER, which is set to coordinate.\n+ RGCN=String\n+ CN=String Read Group sequencing center name Default value: null. \n \n-.. class:: warningmark\n-\n-**Warning on SAM/BAM quality**\n+ RGDS=String\n+ DS=String Read Group description Default value: null. \n \n-Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**\n-flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears\n-to be the only way to deal with SAM/BAM that cannot be parsed.\n+ RGDT=Iso8601Date\n+ DT=Iso8601Date Read Group run date Default value: null. \n \n+ RGPI=Integer\n+ PI=Integer Read Group predicted insert size Default value: null. \n \n-\n+@more_info@\n </help>\n </tool>\n \n@@ -203,3 +145,4 @@\n \n \n \n+\n" |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_BamIndexStats.xml --- a/picard_BamIndexStats.xml Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,118 +0,0 @@ -<tool name="BAM Index Statistics" id="picard_BamIndexStats" version="1.56.0"> - <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> - <command interpreter="python"> - picard_wrapper.py - --input "${input_file}" - --bai-file "${input_file.metadata.bam_index}" - -t "${htmlfile}" - -d "${htmlfile.files_path}" - -j "\$JAVA_JAR_PATH/BamIndexStats.jar" - --tmpdir "${__new_file_path__}" - </command> - <inputs> - <param format="bam" name="input_file" type="data" label="BAM dataset to generate statistics for" - help="If empty, upload or import a BAM dataset" /> - </inputs> - <outputs> - <data format="html" name="htmlfile" label="${tool.name}_on_${on_string}.html" /> - </outputs> - <tests> - <test> - <!-- Command - java -jar BamIndexStats.jar I=test-data/picard_input_tiny_coord.bam > picard_BIS_output1.txt - picard_input_tiny_coord.bam can be created from picard_input_tiny_coord.sam - --> - <param name="input_file" value="picard_input_tiny_coord.bam" ftype="bam" /> - <output name="htmlfile" file="picard_BIS_output1.txt" ftype="html" compare="contains" lines_diff="12"/> - </test> - <test> - <!-- Command - java -jar BamIndexStats.jar I=test-data/picard_BIS_input1.bam > picard_BIS_output2.txt - picard_BIS_input1.bam can be created from picard_BIS_input1.sam - --> - <param name="input_file" value="picard_BIS_input1.bam" ftype="bam" /> - <output name="htmlfile" file="picard_BIS_output2.txt" ftype="html" compare="contains" lines_diff="12" /> - </test> - </tests> - <help> - -.. class:: infomark - -**Purpose** - -Generate Bam Index Stats for a provided BAM file. - -**Picard documentation** - -This is a Galaxy wrapper for BamIndexStats, a part of the external package Picard-tools_. - - .. _Picard-tools: http://www.google.com/search?q=picard+samtools - ------- - -.. class:: infomark - -**Inputs and outputs** - -The only input is the BAM file you wish to obtain statistics for, which is required. -Note that it must be coordinate-sorted. Galaxy currently coordinate-sorts all BAM files. - -This tool outputs an HTML file that contains links to the actual metrics results, as well -as a log file with info on the exact command run. - -.. class:: warningmark - -**Warning on SAM/BAM quality** - -Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT** -flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears -to be the only way to deal with SAM/BAM that cannot be parsed. - ------- - -**Example** - -Given a BAM file created from the following:: - - @HD VN:1.0 SO:coordinate - @SQ SN:chr1 LN:101 - @SQ SN:chr7 LN:404 - @SQ SN:chr8 LN:202 - @SQ SN:chr10 LN:303 - @SQ SN:chr14 LN:505 - @RG ID:0 SM:Hi,Mom! - @RG ID:1 SM:samplesample DS:ClearDescription - @PG ID:1 PN:Hey! VN:2.0 - @CO Just a generic comment to make the header longer - read1 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))II'I*/)-I*-)I.-)I)I),/-II..)./.,.).*II,I.II-)III0*IIIIIIII/32/,01460II/6/*0*/2/283//36868/I RG:Z:0 - read2 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))II'I*/)-I*-)I.-)I)I),/-II..)./.,.).*II,I.II-)III0*IIIIIIII/32/,01460II/6/*0*/2/283//36868/I RG:Z:0 - read3 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))II'I*/)-I*-)I.-)I)I),/-II..)./.,.).*II,I.II-)III0*IIIIIIII/32/,01460II/6/*0*/2/283//36868/I RG:Z:0 - read4 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))II'I*/)-I*-)I.-)I)I),/-II..)./.,.).*II,I.II-)III0*IIIIIIII/32/,01460II/6/*0*/2/283//36868/I RG:Z:0 - read5 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))II'I*/)-I*-)I.-)I)I),/-II..)./.,.).*II,I.II-)III0*IIIIIIII/32/,01460II/6/*0*/2/283//36868/I RG:Z:0 - read6 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA I/15445666651/566666553+2/14/I/555512+3/)-'/-I-'*+))*''13+3)'//++''/'))/3+I*5++)I'2+I+/*I-II*)I-./1'1 RG:Z:0 - read7 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA I/15445666651/566666553+2/14/I/555512+3/)-'/-I-'*+))*''13+3)'//++''/'))/3+I*5++)I'2+I+/*I-II*)I-./1'1 RG:Z:0 - read8 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA I/15445666651/566666553+2/14/I/555512+3/)-'/-I-'*+))*''13+3)'//++''/'))/3+I*5++)I'2+I+/*I-II*)I-./1'1 RG:Z:0 - -The following metrics file will be produced:: - - chr1 length= 101 Aligned= 0 Unaligned= 0 - chr7 length= 404 Aligned= 7 Unaligned= 0 - chr8 length= 202 Aligned= 0 Unaligned= 0 - chr10 length= 303 Aligned= 0 Unaligned= 0 - chr14 length= 505 Aligned= 0 Unaligned= 0 - NoCoordinateCount= 1 - - </help> -</tool> - - - - - - - - - - - - |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_BedToIntervalList.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_BedToIntervalList.xml Tue Dec 16 19:03:21 2014 -0500 |
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| @@ -0,0 +1,117 @@ +<tool name="BedToIntervalList" id="picard_BedToIntervalList" version="1.126.0"> + <description>convert coordinate data into picard interval list format</description> + <requirements><requirement type="package" version="1.126.0">picard</requirement></requirements> + + <macros> + <import>picard_macros.xml</import> + </macros> + + <command> + @java_options@ + + #set $picard_dict = "localref.dict" + #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension + + ln -s "${reference_source.ref_file}" "${ref_fasta}" && + + #if str( $reference_source.reference_source_selector ) == "history": + + java -jar \$JAVA_JAR_PATH/picard.jar CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}" + QUIET=true + VERBOSITY=ERROR + + && + + #else: + + #set $ref_fasta = str( $reference_source.ref_file.fields.path ) ## getting path of reference fasta file (must end with .fa) + #set $picard_dict=$ref_fasta[:-2]+"dict" ## replacing .fa with .dict + + #end if + + java -jar \$JAVA_JAR_PATH/picard.jar + BedToIntervalList + INPUT="${inputFile}" + OUTPUT="${outFile}" + + SEQUENCE_DICTIONARY="${picard_dict}" + QUIET=true + VERBOSITY=ERROR + + </command> + + <inputs> + + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Load picard dictionary file from"> + <option value="cached">Local cache</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list"> + <options from_data_table="picard_indexes"> + <filter type="sort_by" column="2" /> + <validator type="no_options" message="No indexes are available" /> + </options> + <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" /> + </when> + </conditional> + + <param format="bed" name="inputFile" type="data" label="Select coordinate dataset or dataset collection" help="This can be a bed or interval dataset" /> + + </inputs> + <outputs> + <data name="outFile" format="picard_interval_list" label="${tool.name} on ${on_string}: Picard interval list"> + </data> + </outputs> + <tests> + <test> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="picard_BedToIntervalList_ref.fa" ftype="fasta" /> + <param name="inputFile" value="picard_BedToIntervalList.bed" ftype="bed"/> + <output name="outFile" file="picard_BedToIntervalList_test1.pif" ftype="picard_interval_list" lines_diff="2" /> + </test> + </tests> + + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + + <help> + +.. class:: infomark + +**Purpose** + +Convert coordinate data (such as BED or Galaxy Interval) into Picard Interval Format. + +@dataset_collections@ + +@description@ + + SEQUENCE_DICTIONARY=File + SD=File The sequence dictionary. You can either use dictionary pre-cached + on this instance of Galaxy, or create one on teh fly from a FASTA + file uploaded to history (right pane of the interface). + + +@more_info@ + </help> +</tool> + + + + + + + + + + + + + |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_CleanSam.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_CleanSam.xml Tue Dec 16 19:03:21 2014 -0500 |
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| @@ -0,0 +1,63 @@ +<tool id="picard_CleanSam" name="CleanSam" version="1.126.0"> + + <description>perform SAM/BAM grooming</description> + + <requirements> + <requirement type="package" version="1.126.0">picard</requirement> + </requirements> + + <macros> + <import>picard_macros.xml</import> + </macros> + + <command> + @java_options@ + java -jar \$JAVA_JAR_PATH/picard.jar + CleanSam + INPUT="${inputFile}" + OUTPUT="${outFile}" + QUIET=true + VERBOSITY=ERROR + VALIDATION_STRINGENCY=${validation_stringency} + </command> + + <inputs> + <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> + + <expand macro="VS" /> + + </inputs> + + <outputs> + <data name="outFile" format="bam" label="${tool.name} on ${on_string}: cleaned BAM dataset"> + </data> + </outputs> + + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + + <tests> + <test> + <param name="inputFile" ftype="bam" value="picard_CleanSam.bam" /> + <output name="outFile" file="picard_CleanSam_test1.bam" ftype="bam" /> + </test> + </tests> + + <help> + +.. class:: infomark + +**Purpose** + +Read SAM/BAM and perform various fix-ups. Currently, the only fix-ups are: + + 1. to soft-clip an alignment that hangs off the end of its reference sequence. + 2. to set MAPQ to 0 if a read is unmapped. + +@dataset_collections@ + +@more_info@ + + </help> +</tool> \ No newline at end of file |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_CollectAlignmentSummaryMetrics.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_CollectAlignmentSummaryMetrics.xml Tue Dec 16 19:03:21 2014 -0500 |
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| @@ -0,0 +1,137 @@ +<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="1.126.0"> + <description>writes a file containing summary alignment metrics</description> + <requirements> + <requirement type="package" version="1.126.0">picard</requirement> + </requirements> + + <macros> + <import>picard_macros.xml</import> + </macros> + + <command> + @java_options@ + ##set up input files + + #set $reference_fasta_filename = "localref.fa" + + #if str( $reference_source.reference_source_selector ) == "history": + ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && + #else: + #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) + #end if + + java -jar \$JAVA_JAR_PATH/picard.jar + CollectAlignmentSummaryMetrics + INPUT="${inputFile}" + OUTPUT="${outFile}" + MAX_INSERT_SIZE=${maxinsert} + #for $sequence in $adapters: + ADAPTER_SEQUENCE="${sequence.adapter}" + #end for + METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}" + IS_BISULFITE_SEQUENCED="${bisulphite}" + + REFERENCE_SEQUENCE="${reference_fasta_filename}" + + ASSUME_SORTED="${assume_sorted}" + + VALIDATION_STRINGENCY="${validation_stringency}" + QUIET=true + VERBOSITY=ERROR + + </command> + <inputs> + <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Load reference genome from"> + <option value="cached">Local cache</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> + <options from_data_table="all_fasta"> + </options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> + </when> + </conditional> + <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL"> + <option value="ALL_READS" selected="True">All reads</option> + <option value="SAMPLE">Sample</option> + <option value="LIBRARY">Library</option> + <option value="READ_GROUP">Read group</option> + </param> + <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> + <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" help="IS_BISULFITE_SEQUENCED"/> + <repeat name="adapters" title="Adapter" min="0" help="You can provide multiple adaptor sequences"> + <param name="adapter" type="text" size="50" label="Use this adaptor sequence" help="ADAPTER_SEQUENCE"/> + </repeat> + <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric" size="20" help="MAX_INSERT_SIZE"/> + + <expand macro="VS" /> + + </inputs> + + <outputs> + <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary stats"/> + </outputs> + + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + + + <tests> + <test> + <param name="bisulphite" value="false" /> + <param name="sorted" value="true" /> + <param name="adaptors" value="" /> + <param name="maxinsert" value="100000" /> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="picard_CASM_ref.fa" /> + <param name="inputFile" value="picard_CASM.bam" ftype="bam" /> + <output name="outFile" file="picard_CASM_test1.tab" ftype="tabular" lines_diff="4"/> + </test> + </tests> + + <help> + +.. class:: infomark + +**Purpose** + +Reads a SAM or BAM file and writes a file containing summary alignment metrics. + +@dataset_collections@ + +@description@ + + MAX_INSERT_SIZE=Integer Paired end reads above this insert size will be considered chimeric along with + inter-chromosomal pairs. Default value: 100000. + + ADAPTER_SEQUENCE=String List of adapter sequences to use when processing the alignment metrics This option may + be specified 0 or more times. + + METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel + LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE, + LIBRARY, READ_GROUP} This option may be specified 0 or more times. + + IS_BISULFITE_SEQUENCED=Boolean + BS=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. + + + REFERENCE_SEQUENCE=File + R=File Reference sequence fasta Default value: null. + + ASSUME_SORTED=Boolean + AS=Boolean If true (default), then the sort order in the header file will be ignored. + +@more_info@ + + </help> +</tool> + + |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_CollectBaseDistributionByCycle.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_CollectBaseDistributionByCycle.xml Tue Dec 16 19:03:21 2014 -0500 |
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| @@ -0,0 +1,116 @@ +<tool name="CollectBaseDistributionByCycle" id="picard_CollectBaseDistributionByCycle" version="1.126.0"> + <description>charts the nucleotide distribution per cycle in a SAM or BAM dataset</description> + <requirements> + <requirement type="package" version="1.126.0">picard</requirement> + </requirements> + + <macros> + <import>picard_macros.xml</import> + </macros> + + <command> + @java_options@ + ##set up input files + + #set $reference_fasta_filename = "localref.fa" + + #if str( $reference_source.reference_source_selector ) == "history": + ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && + #else: + #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) + #end if + + java -jar \$JAVA_JAR_PATH/picard.jar + CollectBaseDistributionByCycle + INPUT="${inputFile}" + OUTPUT="${outFile}" + CHART_OUTPUT="${pdfFile}" + ALIGNED_READS_ONLY="${aligned_reads_only}" + PF_READS_ONLY="${pf_reads_only}" + REFERENCE_SEQUENCE="${reference_fasta_filename}" + ASSUME_SORTED="${assume_sorted}" + + VALIDATION_STRINGENCY="${validation_stringency}" + QUIET=true + VERBOSITY=ERROR + + </command> + <inputs> + <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Load reference genome from"> + <option value="cached">Local cache</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> + <options from_data_table="all_fasta"> + </options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> + </when> + </conditional> + <param name="aligned_reads_only" type="boolean" label="Calculate the base distribution over aligned reads only" checked="true" truevalue="true" falsevalue="false" help="ALIGNED_READS_ONLY"/> + <param name="pf_reads_only" type="boolean" label="Calculate the base distribution over PF (passing filtering) reads only" checked="true" truevalue="true" falsevalue="false" help="PF_READS_ONLY"/> + <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> + + <expand macro="VS" /> + + </inputs> + + <outputs> + <data format="tabular" name="outFile"/> + <data format="pdf" name="pdfFile"/> + </outputs> + + <tests> + <test> + <param name="aligned_reads_only" value="true" /> + <param name="pf_reads_only" value="true" /> + <param name="assume_sorted" value="true" /> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="picard_CollectBaseDistributionByCycle_ref.fa" /> + <param name="inputFile" value="picard_CollectBaseDistributionByCycle.bam" ftype="bam" /> + <output name="outFile" file="picard_CollectBaseDistributionByCycle_test1.tab" ftype="tabular" lines_diff="4"/> + </test> + </tests> + + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + + <help> + +.. class:: infomark + +**Purpose** + +Program to chart the nucleotide distribution per cycle in a SAM or BAM file. + +@dataset_collections@ + +@description@ + + ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value: + false. This option can be set to 'null' to clear the default value. Possible values: + {true, false} + + PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false. + This option can be set to 'null' to clear the default value. Possible values: {true, + false} + + REFERENCE_SEQUENCE=File + R=File Reference sequence fasta Default value: null. + + ASSUME_SORTED=Boolean + AS=Boolean If true (default), then the sort order in the header file will be ignored. Default + +@more_info@ + + </help> +</tool> + + |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_CollectGcBiasMetrics.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_CollectGcBiasMetrics.xml Tue Dec 16 19:03:21 2014 -0500 |
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| @@ -0,0 +1,117 @@ +<tool name="CollectGcBiasMetrics" id="picard_CollectGcBiasMetrics" version="1.126.0"> + <description>charts the GC bias metrics</description> + <requirements> + <requirement type="package" version="1.126.0">picard</requirement> + </requirements> + + <macros> + <import>picard_macros.xml</import> + </macros> + + <command> + @java_options@ + ##set up input files + + #set $reference_fasta_filename = "localref.fa" + + #if str( $reference_source.reference_source_selector ) == "history": + ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && + #else: + #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) + #end if + + java -jar \$JAVA_JAR_PATH/picard.jar + CollectGcBiasMetrics + INPUT="${inputFile}" + OUTPUT="${outFile}" + CHART_OUTPUT="${pdfFile}" + SUMMARY_OUTPUT="${summaryFile}" + WINDOW_SIZE="${window_size}" + MINIMUM_GENOME_FRACTION="${minimum_genome_fraction}" + IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}" + REFERENCE_SEQUENCE="${reference_fasta_filename}" + ASSUME_SORTED="${assume_sorted}" + + VALIDATION_STRINGENCY="${validation_stringency}" + QUIET=true + VERBOSITY=ERROR + + </command> + <inputs> + <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Load reference genome from"> + <option value="cached">Local cache</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> + <options from_data_table="all_fasta"> + </options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> + </when> + </conditional> + <param name="window_size" type="integer" value="100" label="The size of windows on the genome that are used to bin reads" help="WINDOW_SIZE; default=100"/> + <param name="minimum_genome_fraction" type="float" value="0.00005" label="For summary metrics, exclude GC windows that include less than this fraction of the genome" help="MINIMUM_GENOME_FRACTION; default=0.0005"/> + <param name="is_bisulfite_sequenced" type="boolean" label="Calculate the base distribution over PF (passing filtering) reads only" checked="true" truevalue="true" falsevalue="false" help="PF_READS_ONLY"/> + <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> + + <expand macro="VS" /> + + </inputs> + + <outputs> + <data format="tabular" name="summaryFile" label="${tool.name} on ${on_string}: Summary stats"/> + <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/> + <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/> + </outputs> + + <tests> + <test> + <param name="window_size" value="100" /> + <param name="minimum_genome_fraction" value="0.00005" /> + <param name="assume_sorted" value="true" /> + <param name="is_bisulfite_sequenced" value="true" /> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="picard_CollectGcBiasMetrics_ref.fa" /> + <param name="inputFile" value="picard_CollectGcBiasMetrics.bam" ftype="bam" /> + <output name="outFile" file="picard_CollectGcBiasMetrics_test1.tab" ftype="tabular" lines_diff="4"/> + </test> + </tests> + + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + + <help> + +.. class:: infomark + +**Purpose** + +Program to chart the nucleotide distribution per cycle in a SAM or BAM file. + +@dataset_collections@ + +@description@ + + ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value: + false. Possible values: {true, false} + + PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false. + This option can be set to 'null' to clear the default value. Possible values: {true, + false} + + ASSUME_SORTED=Boolean + AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True + +@more_info@ + + </help> +</tool> + + |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_CollectInsertSizeMetrics.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_CollectInsertSizeMetrics.xml Tue Dec 16 19:03:21 2014 -0500 |
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| @@ -0,0 +1,141 @@ +<tool name="CollectInsertSizeMetrics" id="picard_CollectInsertSizeMetrics" version="1.126.0"> + <description>plots distribution of insert sizes</description> + <requirements> + <requirement type="package" version="1.126.0">picard</requirement> + </requirements> + + <macros> + <import>picard_macros.xml</import> + </macros> + + <command> + @java_options@ + ##set up input files + + #set $reference_fasta_filename = "localref.fa" + + #if str( $reference_source.reference_source_selector ) == "history": + ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && + #else: + #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) + #end if + + java -jar \$JAVA_JAR_PATH/picard.jar + CollectInsertSizeMetrics + INPUT="${inputFile}" + OUTPUT="${outFile}" + HISTOGRAM_FILE="${histFile}" + DEVIATIONS="${deviations}" + + #if str( $hist_width ): + HISTOGRAM_WIDTH="${hist_width}" + #end if + + MINIMUM_PCT="${min_pct}" + REFERENCE_SEQUENCE="${reference_fasta_filename}" + ASSUME_SORTED="${assume_sorted}" + METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}" + + VALIDATION_STRINGENCY="${validation_stringency}" + QUIET=true + VERBOSITY=ERROR + + </command> + <inputs> + <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Load reference genome from"> + <option value="cached">Local cache</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> + <options from_data_table="all_fasta"> + </options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> + </when> + </conditional> + <param name="deviations" type="float" value="10.0" label="Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION" help="DEVIATIONS; This option is offered because insert size data typically includes enough anomalous values from chimeras and other artifacts to make the mean and SD grossly misleading regarding the real distribution. default=10.0"/> + <param name="hist_width" type="integer" optional="True" label="Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail" help="HISTOGRAM_WIDTH; optional"/> + <param name="min_pct" type="float" value="0.05" label="When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads" help="MINIMUM_PCT; (Range: 0 to 1). default=0.05. "/> + <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> + <param name="metric_accumulation_level" type="select" label="The level(s) at which to accumulate metrics" multiple="true" help="METRIC_ACCUMULATION_LEVEL"> + <option value="ALL_READS" selected="True">All reads</option> + <option value="SAMPLE">Sample</option> + <option value="LIBRARY">Library</option> + <option value="READ_GROUP">Read group</option> + </param> + + <expand macro="VS" /> + + </inputs> + + <outputs> + <data format="tabular" name="outFile"/> + <data format="pdf" name="histFile"/> + </outputs> + + <tests> + <test> + <param name="metric_accumulation_level" value="ALL_READS"/> + <param name="deviations" value="10.0" /> + <param name="hist_width" value="500" /> + <param name="min_pct" value="0.05" /> + <param name="assume_sorted" value="true" /> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="picard_CollectInsertSizeMetrics_ref.fa" /> + <param name="inputFile" value="picard_CollectInsertSizeMetrics.bam" ftype="bam" /> + <output name="outFile" file="picard_CollectInsertSizeMetrics_test1.tab" ftype="tabular" lines_diff="4"/> + </test> + </tests> + + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + + <help> + +.. class:: infomark + +**Purpose** + +Reads a SAM or BAM dataset and writes a file containing metrics about the statistical distribution of insert size (excluding duplicates) and generates a Histogram plot. + +@dataset_collections@ + +@description@ + + + DEVIATIONS=Double Generate mean, sd and plots by trimming the data down to MEDIAN + + DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION. This is done because insert size data typically + includes enough anomalous values from chimeras and other artifacts to make the mean and + sd grossly misleading regarding the real distribution. Default value: 10.0. + + HISTOGRAM_WIDTH=Integer + W=Integer Explicitly sets the Histogram width, overriding automatic truncation of Histogram tail. + Also, when calculating mean and standard deviation, only bins <= Histogram_WIDTH will be + included. Default value: not set. + + MINIMUM_PCT=Float + M=Float When generating the Histogram, discard any data categories (out of FR, TANDEM, RF) that + have fewer than this percentage of overall reads. (Range: 0 to 1). Default value: 0.05. + + METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel + LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE, + LIBRARY, READ_GROUP} This option may be specified 0 or more times. + + ASSUME_SORTED=Boolean + AS=Boolean If true (default), then the sort order in the header file will be ignored. Default + value: true. This option can be set to 'null' to clear the default value. Possible + values: {true, false} + +@more_info@ + + </help> +</tool> + + |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_CollectRnaSeqMetrics.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_CollectRnaSeqMetrics.xml Tue Dec 16 19:03:21 2014 -0500 |
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| b'@@ -0,0 +1,204 @@\n+<tool name="CollectRnaSeqMetrics" id="picard_CollectRnaSeqMetrics" version="1.126.0">\n+<description> collect metrics about the alignment of RNA to various functional classes of loci in the genome</description>\n+<requirements>\n+ <requirement type="package" version="1.126.0">picard</requirement>\n+</requirements>\n+\n+<macros>\n+ <import>picard_macros.xml</import>\n+</macros>\n+ \n+\n+ <command>\n+ \n+ ## Set up input files\n+ \n+ ## Reference sequences\n+\n+ #set $reference_fasta_filename = "localref.fa"\n+ \n+ #if str( $reference_source.reference_source_selector ) == "history":\n+ ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&\n+ #else:\n+ #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )\n+ #end if\n+ \n+ ## refFlat data\n+ ## The awk line below converts a file obtained from UCSC as specified in the tool help to refFlat format\n+ \n+ grep -v \'^#\' ${refFlat} | awk \'{print $11"\\t"$1"\\t"$2"\\t"$3"\\t"$4"\\t"$5"\\t"$6"\\t"$7"\\t"$8"\\t"$9"\\t"$10}\' > refFlat.tab &&\n+ \n+ ## Start picard command\n+ \n+ @java_options@\n+ java -jar \\$JAVA_JAR_PATH/picard.jar\n+ CollectRnaSeqMetrics\n+ REF_FLAT=refFlat.tab\n+ \n+ #if str( $ribosomal_intervals ) != "None":\n+\t RIBOSOMAL_INTERVALS="${ribosomal_intervals}"\n+ #end if\n+ \n+ STRAND_SPECIFICITY="${strand_specificity}"\n+ MINIMUM_LENGTH="${minimum_length}"\n+ CHART_OUTPUT="${pdfFile}"\n+\n+ #for $sequence_to_ignore in $ignore_list:\n+\t IGNORE_SEQUENCE="${sequence_to_ignore.sequence}"\n+ #end for\n+ \n+ RRNA_FRAGMENT_PERCENTAGE="${rrna_fragment_percentage}"\n+ METRIC_ACCUMULATION_LEVEL="${metric_accumulation_level}"\n+ INPUT="${inputFile}"\n+ OUTPUT="${outFile}"\n+ REFERENCE_SEQUENCE="${reference_fasta_filename}"\n+ ASSUME_SORTED="${assume_sorted}"\n+ \n+ QUIET=true\n+ VERBOSITY=ERROR\n+ VALIDATION_STRINGENCY=${validation_stringency}\n+ \n+ </command>\n+ \n+ <inputs>\n+ <param format="sam,bam" type="data" name="inputFile" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />\n+ <conditional name="reference_source">\n+\t <param name="reference_source_selector" type="select" label="Load reference genome from">\n+\t <option value="cached">Local cache</option>\n+\t <option value="history">History</option>\n+\t </param>\n+\t <when value="cached">\n+\t <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE">\n+\t <options from_data_table="all_fasta"></options>\n+\t <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>\n+\t </param>\n+\t </when>\n+\t <when value="history">\n+\t <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" />\n+\t </when>\n+ </conditional> \n+ <param format="tabular" name="refFlat" type="data" label="Gene annotations in refFlat form" help="See "Obtaining gene annotations in refFlat format" below for help" />\n+ <param name="ribosomal_intervals" format="picard_interval_list" type="data" optional="True" label="Location of rRNA sequences in genome, in interval_list format" help="RIBOSOMAL_INTERVALS; If not specified no bases will be identified as being ribosomal. The list of intervals can be geberated from BED or Interval datasets using Galaxy BedToIntervalList tool"/>\n+ <param name="strand_specificity" type="select" label="What is the RNA-seq library strand specificity" help="STRAND_SPECIFICITY; For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND if the reads are expected to be on the transcription strand.">\n+\t <option value="NONE" select="True">None</op'..b'param name="strand_specificity" value="NONE" />\n+ <param name="rrna_fragment_percentage" value="0.8" />\n+ <output name="outFile" file="picard_CollectRnaSeqMetrics_test1.tab" ftype="tabular" lines_diff="4"/>\n+ </test>\n+\n+ </tests>\n+ <help>\n+\n+.. class:: infomark\n+\n+**Purpose**\n+\n+Collects metrics about the alignment of RNA to various functional classes of loci in the genome: coding, intronic, UTR, intergenic, ribosomal.\n+\n+@dataset_collections@\n+\n+-----\n+\n+.. class:: warningmark\n+\n+**Obtaining gene annotations in refFlat format**\n+\n+This tool requires gene annotations in refFlat_ format. These data can be obtained from UCSC table browser directly through Galaxy by following these steps:\n+\n+ 1. Click on **Get Data** in the upper part of left pane of Galaxy interface\n+ 2. Click on **UCSC Main** link\n+ 3. Set your genome and dataset of interest. It **must** be the same genome build against which you have mapped the reads contained in the BAM file you are analyzing\n+ 4. In the **output format** field choose **selected fields from primary and related tables**\n+ 5. Click **get output** button\n+ 6. In the first table presented at the top of the page select (using checkboxes) first 11 fields:\n+ name\n+ chrom\n+ strand\n+ txStart\n+ txEnd\n+ cdsStart\n+ cdsEnd\n+ exonCount\n+ exonStarts\n+ exonEnds\n+ proteinId\n+ 7. Click **done with selection**\n+ 8. Click **Send query to Galaxy**\n+ 9. A new dataset will appear in the current Galaxy history\n+ 10. Use this dataset as the input for **Gene annotations in refFlat form** dropdown of this tool\n+ \n+.. _refFlat: http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat\n+\n+@description@\n+\n+ REF_FLAT=File Gene annotations in refFlat form. Format described here: \n+ http://genome.ucsc.edu/goldenPath/gbdDescriptionsOld.html#RefFlat Required. \n+\n+ RIBOSOMAL_INTERVALS=File Location of rRNA sequences in genome, in interval_list format. If not specified no bases \n+ will be identified as being ribosomal. Format described here: \n+ http://picard.sourceforge.net/javadoc/net/sf/picard/util/IntervalList.html and can be\n+\t\t\t\t generated from BED datasetes using Galaxy\'s wrapper for picard_BedToIntervalList tool\n+\n+ STRAND_SPECIFICITY=StrandSpecificity\n+ STRAND=StrandSpecificity For strand-specific library prep. For unpaired reads, use FIRST_READ_TRANSCRIPTION_STRAND \n+ if the reads are expected to be on the transcription strand. Required. Possible values: \n+ {NONE, FIRST_READ_TRANSCRIPTION_STRAND, SECOND_READ_TRANSCRIPTION_STRAND} \n+\n+ MINIMUM_LENGTH=Integer When calculating coverage based values (e.g. CV of coverage) only use transcripts of this \n+ length or greater. Default value: 500.\n+\n+ IGNORE_SEQUENCE=String If a read maps to a sequence specified with this option, all the bases in the read are \n+ counted as ignored bases. \n+\n+ RRNA_FRAGMENT_PERCENTAGE=Double\n+ This percentage of the length of a fragment must overlap one of the ribosomal intervals \n+ for a read or read pair by this must in order to be considered rRNA. Default value: 0.8. \n+\n+ METRIC_ACCUMULATION_LEVEL=MetricAccumulationLevel\n+ LEVEL=MetricAccumulationLevel The level(s) at which to accumulate metrics. Possible values: {ALL_READS, SAMPLE, \n+ LIBRARY, READ_GROUP} This option may be specified 0 or more times.\n+\t\t\t\t \n+ ASSUME_SORTED=Boolean\n+ AS=Boolean If true (default), then the sort order in the header file will be ignored. Default \n+ value: true. Possible values: {true, false} \n+\n+@more_info@\n+\n+ </help>\n+</tool>\n' |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_CollectWgsMetrics.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_CollectWgsMetrics.xml Tue Dec 16 19:03:21 2014 -0500 |
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| @@ -0,0 +1,111 @@ +<tool name="CollectWgsMetrics" id="picard_CollectWgsMetrics" version="1.126.0"> + <description>compute metrics for evaluating of whole genome sequencing experiments</description> + <requirements> + <requirement type="package" version="1.126.0">picard</requirement> + </requirements> + + <macros> + <import>picard_macros.xml</import> + </macros> + + <command> + @java_options@ + ##set up input files + + #set $reference_fasta_filename = "localref.fa" + + #if str( $reference_source.reference_source_selector ) == "history": + ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && + #else: + #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) + #end if + + java -jar \$JAVA_JAR_PATH/picard.jar + CollectWgsMetrics + INPUT="${inputFile}" + OUTPUT="${outFile}" + REFERENCE_SEQUENCE="${reference_fasta_filename}" + MINIMUM_MAPPING_QUALITY="${minimum_mapping_quality}" + MINIMUM_BASE_QUALITY="${minimum_base_quality}" + COVERAGE_CAP="${coverage_cap}" + + VALIDATION_STRINGENCY="${validation_stringency}" + QUIET=true + VERBOSITY=ERROR + + </command> + <inputs> + <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Load reference genome from"> + <option value="cached">Local cache</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> + <options from_data_table="all_fasta"> + </options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> + </when> + </conditional> + <param name="minimum_mapping_quality" type="integer" value="20" label="Minimum mapping quality for a read to contribute coverage" help="MINIMUM_MAPPING_QUALITY; default=20"/> + <param name="minimum_base_quality" type="integer" value="20" label="Minimum base quality for a base to contribute coverage" help="MINIMUM_BASE_QUALITY; default=20"/> + <param name="coverage_cap" type="integer" value="250" label="Treat bases with coverage exceeding this value as if they had coverage at this value" help="COVERAGE_CAP; default=250"/> + + + <expand macro="VS" /> + + </inputs> + + <outputs> + <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/> + </outputs> + + <tests> + <test> + <param name="reference_source_selector" value="history" /> + <param name="minimum_mapping_quality" value="20" /> + <param name="minimum_base_quality" value="20" /> + <param name="coverage_cap" value="250" /> + <param name="ref_file" value="picard_CollectWgsMetrics_ref.fa" /> + <param name="inputFile" value="picard_CollectWgsMetrics.bam" ftype="bam" /> + <output name="outFile" file="picard_CollectWgsMetrics_test1.tab" ftype="tabular" lines_diff="4"/> + </test> + </tests> + + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + + <help> + +.. class:: infomark + +**Purpose** + +Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments. + +@dataset_collections@ + +@description@ + + MINIMUM_MAPPING_QUALITY=Integer + MQ=Integer Minimum mapping quality for a read to contribute coverage. Default value: 20. + + MINIMUM_BASE_QUALITY=Integer + Q=Integer Minimum base quality for a base to contribute coverage. Default value: 20. + + COVERAGE_CAP=Integer + CAP=Integer Treat bases with coverage exceeding this value as if they had coverage at this value. + Default value: 250. + +@more_info@ + + </help> +</tool> + + |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_DownsampleSam.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_DownsampleSam.xml Tue Dec 16 19:03:21 2014 -0500 |
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| @@ -0,0 +1,79 @@ +<tool name="Downsample SAM/BAM" id="picard_DownsampleSam" version="1.126.0"> + <description>Downsample a file to retain a subset of the reads</description> + <requirements> + <requirement type="package" version="1.126.0">picard</requirement> + </requirements> + + <macros> + <import>picard_macros.xml</import> + </macros> + + <command> + @java_options@ + java -jar + \$JAVA_JAR_PATH/picard.jar + DownsampleSam + INPUT="${inputFile}" + OUTPUT="${outFile}" + PROBABILITY=${probability} + RANDOM_SEED=${seed} + QUIET=true + VERBOSITY=ERROR + VALIDATION_STRINGENCY=${validation_stringency} + </command> + <inputs> + <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM or BAM dataset" /> + <param name="probability" type="float" size="4" min="0.0" max="1.0" label="Probability (between 0 and 1) that any given read will be kept" help="PROBABILITY; specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" /> + <param name="seed" type="integer" size="5" label="Random seed value" help="RANDOM_SEED; default=1" value="1" /> + + <expand macro="VS" /> + + </inputs> + + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + + <outputs> + <data name="outFile" format="bam" label="${tool.name} on ${on_string}: downsampled BAM"/> + </outputs> + + <tests> + <test> + <param name="inputFile" value="picard_DownsampleSam.bam" ftype="bam" /> + <param name="probability" value="0.1" /> + <param name="seed" value="1024" /> + <param name="validation_stringency" value="LENIENT" /> + <output name="outFile" file="picard_DownsampleSam_test1.bam" ftype="bam"/> + </test> + </tests> + <help> + +.. class:: infomark + +**Purpose** + +Randomly down-sample a SAM or BAM file to retain a random subset of the reads. Mate-pairs are either both kept or both discarded. Reads marked as not primary alignments are all discarded. Each read is given a probability P of being retained - results with the exact same input in the same order and with the same value for RANDOM_SEED will produce the same results. + +@dataset_collections@ + +@description@ + + INPUT=File + I=File The input SAM or BAM file to downsample. Required. + + OUTPUT=File + O=File The output, downsampled, SAM or BAM file to write. Required. + + RANDOM_SEED=Long + R=Long Random seed to use if reproducibilty is desired. Setting to null will cause multiple + invocations to produce different results. + + PROBABILITY=Double + P=Double The probability of keeping any individual read, between 0 and 1. + + + +@more_info@ + </help> +</tool> |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_EstimateLibraryComplexity.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_EstimateLibraryComplexity.xml Tue Dec 16 19:03:21 2014 -0500 |
| [ |
| b'@@ -0,0 +1,135 @@\n+<tool name="EstimateLibraryComplexity" id="picard_EstimateLibraryComplexity" version="1.126.0">\n+ <description>assess sequence library complexity from read sequences</description>\n+ <requirements>\n+ <requirement type="package" version="1.126.0">picard</requirement>\n+ </requirements>\n+ \n+ <macros>\n+ <import>picard_macros.xml</import>\n+ </macros>\n+ \n+ <command>\n+ @java_options@\n+ \n+ java -jar \\$JAVA_JAR_PATH/picard.jar\n+ EstimateLibraryComplexity\n+ \n+ INPUT="${inputFile}"\n+ OUTPUT="${outFile}"\n+ \n+ MIN_IDENTICAL_BASES="${min_identical_bases}"\n+ MAX_DIFF_RATE="${max_diff_rate}"\n+ MIN_MEAN_QUALITY="${min_mean_quality}"\n+ MAX_GROUP_RATIO="${max_group_ratio}"\n+ READ_NAME_REGEX="${read_name_regex}"\n+ OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}"\n+ \n+ VALIDATION_STRINGENCY="${validation_stringency}"\n+ QUIET=true\n+ VERBOSITY=ERROR\n+ \n+ </command>\n+ <inputs>\n+ <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset" />\n+ <param name="min_identical_bases" type="integer" value="5" label="The minimum number of bases at the starts of reads that must be identical for reads to be grouped together for duplicate detection" help="MIN_IDENTICAL_BASES; 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=5"/>\n+ <param name="max_diff_rate" type="float" value="0.03" label="The maximum rate of differences between two reads to call them identical" help="MAX_DIFF_RATE; default=0.03"/>\n+ <param name="min_mean_quality" type="integer" min="0" max="93" value="20" label="The minimum mean quality of the bases in a read pair for the read to be analyzed" help="MIN_MEAN_QUALITY; Reads with lower average quality are filtered out and not considered in any calculations; default=20"/>\n+ <param name="max_group_ratio" type="integer" value="500" label="Do not process self-similar groups that are this many times over the mean expected group size" help="MAX_GROUP_RATIO; I.e. if the input contains 10m read pairs and MIN_IDENTICAL_BASES is set to 5, then the mean expected group size would be approximately 10 reads; default-500"/>\n+\n+ <param name="read_name_regex" type="text" size="40" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*." label="Regular expression that can be used to parse read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; 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. See help below for more info; default=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.">\n+ <sanitizer>\n+ <valid initial="string.printable">\n+ </valid>\n+ </sanitizer>\n+ </param>\n+ <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/>\n+\n+ <expand macro="VS" />\n+ \n+ </inputs> \n+ \n+ <outputs>\n+ <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Library complexity report"/>\n+ </outputs>\n+ \n+ <tests>\n+ <test>\n+ <param name="inputFile" value="picard_EstimateLibraryComplexity.bam" ftype="bam"/>\n+ <param name="min_identical_bases" value="5"/>\n+ <param name="max_diff_rate" value="0.03"/>\n+ <param name="min_mean_quality" value="20"/>\n+ <param name="read_name_regex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."/>\n+ <param name="optical_duplicate_pixel_distance" value="100"/>\n+ <param name="max_group_ratio" value="500"/>\n+ <param name="validation_stringency'..b'll mismatch rate less than or equal to MAX_DIFF_RATE (0.03 by default).\n+\n+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+N bases or with a mean base quality lower than MIN_MEAN_QUALITY across either the first or second read.\n+\n+Unpaired reads are ignored in this computation.\n+The algorithm attempts to detect optical duplicates separately from PCR duplicates and excludes these in the calculation of library size.\n+\n+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\n+is built of [#reads in duplicate set -> #of duplicate sets]; all bins that contain exactly one duplicate set are then removed from the Histogram\n+as outliers before library size is estimated.\n+\n+@dataset_collections@\n+\n+@description@\n+\n+ MIN_IDENTICAL_BASES=Integer The minimum number of bases at the starts of reads that must be identical for reads to be \n+ grouped together for duplicate detection. In effect total_reads / 4^max_id_bases reads \n+ will be compared at a time, so lower numbers will produce more accurate results but \n+ consume exponentially more memory and CPU. Default value: 5. \n+ \n+ MAX_DIFF_RATE=Double The maximum rate of differences between two reads to call them identical. Default value: \n+ 0.03.\n+ \n+ MIN_MEAN_QUALITY=Integer The minimum mean quality of the bases in a read pair for the read to be analyzed. Reads \n+ with lower average quality are filtered out and not considered in any calculations. \n+ Default value: 20.\n+ \n+ MAX_GROUP_RATIO=Integer Do not process self-similar groups that are this many times over the mean expected group \n+ size. I.e. if the input contains 10m read pairs and MIN_IDENTICAL_BASES is set to 5, then \n+ the mean expected group size would be approximately 10 reads. Default value: 500.\n+ \n+ READ_NAME_REGEX=String Regular expression that can be used to parse read names in the incoming SAM file. Read \n+ names are parsed to extract three variables: tile/region, x coordinate and y coordinate. \n+ These values are used to estimate the rate of optical duplication in order to give a more \n+ accurate estimated library size. Set this option to null to disable optical duplicate \n+ detection. The regular expression should contain three capture groups for the three \n+ variables, in order. It must match the entire read name. Note that if the default regex \n+ is specified, a regex match is not actually done, but instead the read name is split on \n+ colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be \n+ tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements \n+ are assumed to be tile, x and y values. Default value: \n+ [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.\n+ \n+ OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer \n+ The maximum offset between two duplicte clusters in order to consider them optical \n+ duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) \n+ unless using later versions of the Illumina pipeline that multiply pixel values by 10, in \n+ which case 50-100 is more normal. Default value: 100.\n+ \n+\n+@more_info@\n+\n+ </help>\n+</tool>\n+\n+\n' |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_FastqToSam.xml --- a/picard_FastqToSam.xml Fri Feb 21 12:07:49 2014 -0500 +++ b/picard_FastqToSam.xml Tue Dec 16 19:03:21 2014 -0500 |
| [ |
| b'@@ -1,145 +1,230 @@\n-<tool id="picard_FastqToSam" name="FASTQ to BAM" version="1.56.0">\n- <description>creates an unaligned BAM file</description>\n- <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>\n- <!-- Dan Blankenberg -->\n- <command>java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC\n- -jar "\\$JAVA_JAR_PATH/FastqToSam.jar"\n- FASTQ="${input_fastq1}"\n- #if str( $input_fastq2) != "None":\n- FASTQ2="${input_fastq2}"\n+<tool name="FastqToSam" id="picard_FastqToSam" version="1.126.0">\n+ <description>convert Fastq data into unaligned BAM</description>\n+ <requirements>\n+ <requirement type="package" version="1.126.0">picard</requirement>\n+ </requirements>\n+ \n+ <macros>\n+ <import>picard_macros.xml</import>\n+ </macros>\n+ \n+ <command>\n+ @java_options@\n+ \n+ java -jar \\$JAVA_JAR_PATH/picard.jar\n+ FastqToSam\n+ \n+ #if str( $input_type.input_type_selector ) == "se":\n+ FASTQ="${input_type.fastq}"\n+ #elif str( $input_type.input_type_selector ) == "pe":\n+ FASTQ="${input_type.fastq}"\n+ FASTQ2="${input_type.fastq2}"\n+ #else\n+ FASTQ="${input_type.fastq.forward}"\n+ FASTQ2="${input_type.fastq.reverse}"\n #end if\n- QUALITY_FORMAT="${ dict( fastqsanger=\'Standard\', fastqcssanger=\'Standard\', fastqillumina=\'Illumina\', fastqsolexa=\'Solexa\' )[ $input_fastq1.ext ] }" ##Solexa, Illumina, Standard\n- OUTPUT="${output_bam}"\n+ \n+ QUALITY_FORMAT="${quality_format}"\n+ OUTPUT="${outFile}"\n READ_GROUP_NAME="${read_group_name}"\n- SAMPLE_NAME="${sample_name}" \n- #if $param_type.param_type_selector == "advanced":\n- #if str( $param_type.library_name ) != "":\n- LIBRARY_NAME="${param_type.library_name}" \n- #end if\n- #if str( $param_type.platform_unit ) != "":\n- PLATFORM_UNIT="${param_type.platform_unit}"\n- #end if\n- #if str( $param_type.platform ) != "":\n- PLATFORM="${param_type.platform}"\n- #end if \n- #if str( $param_type.sequencing_center ) != "":\n- SEQUENCING_CENTER="${param_type.sequencing_center}"\n- #end if \n- #if str( $param_type.predicted_insert_size ) != "":\n- PREDICTED_INSERT_SIZE="${param_type.predicted_insert_size}"\n- #end if \n- #if str( $param_type.description.value ) != "":\n- DESCRIPTION="${param_type.description}"\n- #end if \n- #if str( $param_type.run_date ) != "":\n- RUN_DATE="${param_type.run_date}"\n- #end if\n- #if str( $param_type.min_q ) != "":\n- MIN_Q="${param_type.min_q}"\n- #end if\n- #if str( $param_type.max_q ) != "":\n- MAX_Q="${param_type.max_q}"\n- #end if\n- SORT_ORDER="${param_type.sort_order}"\n- #else:\n- SORT_ORDER=coordinate ##unsorted, queryname, coordinate; always use coordinate\n+ SAMPLE_NAME="${sample_name}"\n+ \n+ #if str( $library_name ):\n+ LIBRARY_NAME="${library_name}"\n+ #end if\n+ \n+ #if str( $platform_unit ):\n+ PLATFORM_UNIT="${platform_unit}"\n+ #end if\n+ \n+ #if str( $platform ):\n+ PLATFORM="${platform}"\n+ #end if\n+ \n+ #if str( $sequencing_center ):\n+ SEQUENCING_CENTER="${sequencing_center}"\n+ #end if\n+ \n+ #if str( $predicted_insert_size ):\n+ PREDICTED_INSERT_SIZE="${predicted_insert_size}"\n #end if\n- 2>&1 \n- || echo "Error running Picard FastqToSAM" >&2\n+ \n+ #if str( $comment ):\n+ COMMENT="${comment}"\n+ #end if\n+ \n+ #if str( $description ):\n+ DESCRIPTION="${description}"\n+ #end if\n+ \n+ #if str( $run_date ):\n+ RUN_DATE="${run_date}"\n+ #end if\n+ \n+ MIN_Q="${min_q}"\n+ MAX_Q="${max_q}"\n+ STRIP_UNPAIRED_MATE_NUMBER="${strip_unpairied_mate_number}"\n+ ALLOW_AND_IGNORE_EMPTY_LINES="${allow_and_ignore_empty_lines}"\n+ \n+ SORT_ORDER=coordinate\n+ VALIDATION_STRINGENCY="${validation_stringency}"\n+ '..b'stqQualityFormat\n+ V=FastqQualityFormat A value describing how the quality values are encoded in the fastq. Either Solexa for \n+ pre-pipeline 1.3 style scores (solexa scaling + 66), Illumina for pipeline 1.3 and above \n+ (phred scaling + 64) or Standard for phred scaled scores with a character shift of 33. \n+ If this value is not specified, the quality format will be detected automatically. \n+ Default value: null. Possible values: {Solexa, Illumina, Standard} \n \n-------\n+ READ_GROUP_NAME=String\n+ RG=String Read group name Default value: A. \n+ \n+ SAMPLE_NAME=String\n+ SM=String Sample name to insert into the read group header Required. \n+ \n+ LIBRARY_NAME=String\n+ LB=String The library name to place into the LB attribute in the read group header.\n+ \n+ PLATFORM_UNIT=String\n+ PU=String The platform unit (often run_barcode.lane) to insert into the read group header.\n+ \n+ PLATFORM=String\n+ PL=String The platform type (e.g. illumina, solid) to insert into the read group header.\n+ \n+ SEQUENCING_CENTER=String\n+ CN=String The sequencing center from which the data originated.\n+ \n+ PREDICTED_INSERT_SIZE=Integer\n+ PI=Integer Predicted median insert size, to insert into the read group header.\n+ \n+ COMMENT=String\n+ CO=String Comment to include in the merged output file\'s header. \n+ \n+ DESCRIPTION=String\n+ DS=String Inserted into the read group header. \n+ \n+ RUN_DATE=Iso8601Date\n+ DT=Iso8601Date Date the run was produced, to insert into the read group header. \n+ \n+ MIN_Q=Integer Minimum quality allowed in the input fastq. An exception will be thrown if a quality is \n+ less than this value. Default value: 0.\n+ \n+ MAX_Q=Integer Maximum quality allowed in the input fastq. An exception will be thrown if a quality is \n+ greater than this value. Default value: 93.\n+ \n+ STRIP_UNPAIRED_MATE_NUMBER=Boolean\n+ If true and this is an unpaired fastq any occurance of \'/1\' will be removed from the end \n+ of a read name. Default value: false. Possible values: {true, false} \n+ \n+ ALLOW_AND_IGNORE_EMPTY_LINES=Boolean\n+ Allow (and ignore) empty lines Default value: false. Possible values: {true, false} \n+ \n \n-Please cite the website "http://picard.sourceforge.net".\n+@more_info@\n \n-------\n+ </help>\n+</tool>\n \n \n-**Input formats**\n-\n-FastqToSam accepts FASTQ input files. If using paired-end data, you should select two FASTQ files.\n-\n-------\n-\n-**Outputs**\n-\n-The output is in BAM format, see http://samtools.sourceforge.net for more details.\n-\n--------\n-\n-**FastqToSam settings**\n-\n-This is list of FastqToSam options::\n-\n- READ_GROUP_NAME=String\tRead group name Default value: A. This option can be set to \'null\' to clear the default value.\n- SAMPLE_NAME=String\tSample name to insert into the read group header Required.\n- LIBRARY_NAME=String\tThe library name to place into the LB attribute in the read group header Default value: null.\n- PLATFORM_UNIT=String\tThe platform unit (often run_barcode.lane) to insert into the read group header Default value: null.\n- PLATFORM=String\tThe platform type (e.g. illumina, solid) to insert into the read group header Default value: null.\n- SEQUENCING_CENTER=String\tThe sequencing center from which the data originated Default value: null.\n- PREDICTED_INSERT_SIZE=Integer\tPredicted median insert size, to insert into the read group header Default value: null.\n- DESCRIPTION=String\tInserted into the read group header Default value: null. \n- </help>\n-</tool>\n' |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_FilterSamReads.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_FilterSamReads.xml Tue Dec 16 19:03:21 2014 -0500 |
| [ |
| @@ -0,0 +1,134 @@ +<tool name="FilterSamReads" id="picard_FilterSamReads" version="1.126.0"> + <description>include or exclude aligned and unaligned reads and read lists</description> + <requirements> + <requirement type="package" version="1.126.0">picard</requirement> + </requirements> + + <macros> + <import>picard_macros.xml</import> + </macros> + + <command> + @java_options@ + + ##Sam Sorting is performed here because FilterSamReads requires input to be in query-sorted order + + java -jar \$JAVA_JAR_PATH/picard.jar + SortSam + INPUT="${inputFile}" + OUTPUT=query_sorted_bam.bam + SORT_ORDER=queryname + VALIDATION_STRINGENCY=LENIENT + QUIET=true + VERBOSITY=ERROR + + && + + java -jar \$JAVA_JAR_PATH/picard.jar + FilterSamReads + INPUT=query_sorted_bam.bam + FILTER="${filter_type.filter}" + + #if ( str( $filter_type.filter ) == "includeReadList" or str( $filter_type.filter ) == "excludeReadList" ): + READ_LIST_FILE="${filter_type.read_list_file}" + #end if + + OUTPUT="${outFile}" + SORT_ORDER=coordinate + VALIDATION_STRINGENCY="${validation_stringency}" + QUIET=true + VERBOSITY=ERROR + + </command> + <inputs> + <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> + <conditional name="filter_type"> + <param name="filter" type="select" label="Select filtering type" help="FILTER; see Help for deatiled info"> + <option value="includeAligned">Include aligned</option> + <option value="excludeAligned">Exclude aligned</option> + <option value="includeReadList">Include read list</option> + <option value="excludeReadList">Exclude read list</option> + </param> + <when value="includeAligned"/> <!-- do nothing --> + <when value="excludeAligned"/> <!-- do nothing --> + <when value="includeReadList"> + <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be INCLUDED in the output" help="READ_LIST_FILE"/> + </when> + <when value="excludeReadList"> + <param name="read_list_file" type="data" format="tabular" label="Dataset containing read names that will be EXCLUDED in the output" help="READ_LIST_FILE"/> + </when> + </conditional> + + <expand macro="VS" /> + + </inputs> + + <outputs> + <data format="bam" name="outFile" label="${tool.name} on ${on_string}: filtered BAM"/> + </outputs> + + <tests> + <test> + <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/> + <param name="filter" value="includeReadList"/> + <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/> + <param name="validation_stringency" value="LENIENT"/> + <output name="outFile" file="picard_FilterSamReads_include_reads_test1.bam" ftype="bam" lines_diff="2"/> + </test> + <test> + <param name="inputFile" value="picard_FilterSamReads.bam" ftype="bam"/> + <param name="filter" value="excludeReadList"/> + <param name="read_list_file" value="picard_FilterSamReads_read_list_file.tab" ftype="tabular"/> + <param name="validation_stringency" value="LENIENT"/> + <output name="outFile" file="picard_FilterSamReads_exclude_reads_test2.bam" ftype="bam" lines_diff="2"/> + </test> + </tests> + + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + + <help> + +**Purpose** + +Computes a number of metrics that are useful for evaluating coverage and performance of whole genome sequencing experiments. + +------ + +.. class:: warningmark + +**Warning on using this tool on BWA-MEM output** + +This tool will likely fail on BAM datasets generated by BWA MEM as it generates partial read alignemnts. + +@dataset_collections@ + +@description@ + + FILTER=Filter Filter. Required. Possible values: + includeAligned [OUTPUT SAM/BAM will contain aligned + reads only. (Note that *both* first and + second of paired reads must be aligned to be included + in the OUTPUT SAM or BAM)], + + excludeAligned [OUTPUT SAM/BAM will contain un-mapped reads only. + (Note that *both* first and second of pair must be aligned to be + excluded from the OUTPUT SAM or BAM)] + + includeReadList [OUTPUT SAM/BAM will contain reads + that are supplied in the READ_LIST_FILE file] + + excludeReadList [OUTPUT bam will contain + reads that are *not* supplied in the READ_LIST_FILE file]} + + READ_LIST_FILE=File + RLF=File Read List File containing reads that will be included or excluded from the OUTPUT SAM or + BAM file. Default value: null. + +@more_info@ + + </help> +</tool> + + |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_FixMateInformation.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_FixMateInformation.xml Tue Dec 16 19:03:21 2014 -0500 |
| b |
| @@ -0,0 +1,85 @@ +<tool name="FixMateInformation" id="picard_FixMateInformation" version="1.126.0"> + <description>ensure that all mate-pair information is in sync between each read and it's mate pair</description> + <requirements> + <requirement type="package" version="1.126.0">picard</requirement> + </requirements> + + <macros> + <import>picard_macros.xml</import> + </macros> + + <command> + @java_options@ + + java -jar \$JAVA_JAR_PATH/picard.jar + FixMateInformation + INPUT="${inputFile}" + OUTPUT="${outFile}" + ASSUME_SORTED=${assume_sorted} + ADD_MATE_CIGAR=${add_mate_cigar} + + SORT_ORDER=coordinate + VALIDATION_STRINGENCY="${validation_stringency}" + QUIET=true + VERBOSITY=ERROR + + </command> + <inputs> + <param name="inputFile" multiple="True" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> + <param name="add_mate_cigar" type="boolean" checked="true" truevalue="True" falsevalue="False" label="Adds the mate CIGAR tag (MC) if true, does not if false" help="ADD_MATE_CIGAR; default=True"/> + <param name="assume_sorted" type="boolean" truevalue="True" falsevalue="False" label="Assume that the input file is QUERYNAME sorted" help="ASSUME_SORTED; default=False"/> + + <expand macro="VS" /> + + </inputs> + + <outputs> + <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM with fixed mates"/> + </outputs> + + <tests> + <test> + <param name="inputFile" value="picard_FixMateInformation.bam" ftype="bam"/> + <param name="add_mate_cigar" value="True"/> + <param name="assume_sorted" value="False"/> + <param name="validation_stringency" value="LENIENT"/> + <output name="outFile" file="picard_FixMateInformation_test1.bam" ftype="bam" lines_diff="2"/> + </test> + </tests> + + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + + <help> + +**Purpose** + +Ensure that all mate-pair information is in sync between each read and it's mate pair. Reads marked with the secondary alignment flag are written to the output file unchanged. + +------ + +.. class:: warningmark + +**Warning on using ASSUME_SORTED option** + +Datasets imported into Galaxy are automatically coordinate sorted. So use this option (set it to True) only if you are sure that this is necessary. If you are not sure - a good rule of thumb +is to assume that the BAM you are working with is coordinate sorted. + +@dataset_collections@ + +@description@ + + ASSUME_SORTED=Boolean + AS=Boolean If true, assume that the input file is queryname sorted, even if the header says + otherwise. Default value: false. + + ADD_MATE_CIGAR=Boolean + MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Default value: true. + +@more_info@ + + </help> +</tool> + + |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_MarkDuplicates.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_MarkDuplicates.xml Tue Dec 16 19:03:21 2014 -0500 |
| [ |
| @@ -0,0 +1,130 @@ +<tool name="MarkDuplicates" id="picard_MarkDuplicates" version="1.126.0"> + <description>examine aligned records in BAM datasets to locate duplicate molecules</description> + <requirements> + <requirement type="package" version="1.126.0">picard</requirement> + </requirements> + + <macros> + <import>picard_macros.xml</import> + </macros> + + <command> + @java_options@ + + java -jar \$JAVA_JAR_PATH/picard.jar + MarkDuplicates + + INPUT="${inputFile}" + OUTPUT="${outFile}" + + METRICS_FILE="${metrics_file}" + #for $element in $comments: + COMMENT="${element.comment}" + #end for + REMOVE_DUPLICATES="${remove_duplicates}" + ASSUME_SORTED="${assume_sorted}" + + DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}" + + READ_NAME_REGEX="${read_name_regex}" + OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}" + + VALIDATION_STRINGENCY="${validation_stringency}" + QUIET=true + VERBOSITY=ERROR + + </command> + <inputs> + <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> + <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments"> + <param name="comment" type="text" size="50" label="Add this comment to BAM dataset"/> + </repeat> + <param name="remove_duplicates" type="boolean" label="If true do not write duplicates to the output file instead of writing them with appropriate flags set" help="REMOVE_DUPLICATES; default=False"/> + <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED; default=True"/> + + <param name="duplicate_scoring_strategy" type="select" label="The scoring strategy for choosing the non-duplicate among candidates" help="DUPLICATE_SCORING_STRATEGY; default=SUM_OF_BASE_QUALITIES"> + <option value="SUM_OF_BASE_QUALITIES">SUM_OF_BASE_QUALITIES</option> + <option value="TOTAL_MAPPED_REFERENCE_LENGTH">TOTAL_MAPPED_REFERENCE_LENGTH</option> + </param> + + + <param name="read_name_regex" type="text" size="40" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*." label="Regular expression that can be used to parse read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; 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. See help below for more info; default=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."> + <sanitizer> + <valid initial="string.printable"> + </valid> + </sanitizer> + </param> + <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/> + + <expand macro="VS" /> + + </inputs> + + <outputs> + <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: MarkDuplicate metrics"/> + <data format="bam" name="outFile" label="${tool.name} on ${on_string}: MarkDuplicates BAM output"/> + </outputs> + + <tests> + <test> + <param name="inputFile" value="picard_MarkDuplicates.bam" ftype="bam"/> + <param name="comment" value="test-run"/> + <param name="assume_sorted" value="True"/> + <param name="remove_duplicates" value="True"/> + <param name="read_name_regex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*."/> + <param name="optical_duplicate_pixel_distance" value="100"/> + <param name="duplicate_scoring_strategy" value="SUM_OF_BASE_QUALITIES"/> + <param name="validation_stringency" value="LENIENT"/> + <output name="outFile" file="picard_MarkDuplicates_test1.bam" ftype="bam" lines_diff="2"/> + </test> + </tests> + + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + + <help> + +**Purpose** + +Examines aligned records in the supplied SAM or BAM dataset to locate duplicate molecules. All records are then written to the output file with the duplicate records flagged. + +@dataset_collections@ + +@description@ + + COMMENT=String + CO=String Comment(s) to include in the output file's header. This option may be specified 0 or + more times. + + REMOVE_DUPLICATES=Boolean If true do not write duplicates to the output file instead of writing them with + appropriate flags set. Default value: false. + + 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. Set this option to null to disable optical duplicate + detection. The regular expression should contain three capture groups for the three + variables, in order. It must match the entire read name. Note that if the default regex + is specified, a regex match is not actually done, but instead the read name is split on + colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be + tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements + are assumed to be tile, x and y values. Default value: + [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. + + DUPLICATE_SCORING_STRATEGY=ScoringStrategy + DS=ScoringStrategy The scoring strategy for choosing the non-duplicate among candidates. Default value: + SUM_OF_BASE_QUALITIES. Possible values: {SUM_OF_BASE_QUALITIES, TOTAL_MAPPED_REFERENCE_LENGTH} + + 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. + +@more_info@ + + </help> +</tool> + + |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_MarkDuplicatesWithMateCigar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_MarkDuplicatesWithMateCigar.xml Tue Dec 16 19:03:21 2014 -0500 |
| [ |
| b'@@ -0,0 +1,165 @@\n+<tool name="MarkDuplicatesWithMateCigar" id="picard_MarkDuplicatesWithMateCigar" version="1.126.0">\n+ <description>examine aligned records in BAM datasets to locate duplicate molecules</description>\n+ <requirements>\n+ <requirement type="package" version="1.126.0">picard</requirement>\n+ </requirements>\n+ \n+ <macros>\n+ <import>picard_macros.xml</import>\n+ </macros>\n+ \n+ <command>\n+ @java_options@\n+ \n+ java -jar \\$JAVA_JAR_PATH/picard.jar\n+ MarkDuplicatesWithMateCigar\n+ \n+ INPUT="${inputFile}"\n+ OUTPUT="${outFile}"\n+ \n+ METRICS_FILE="${metrics_file}"\n+ #for $element in $comments:\n+ COMMENT="${element.comment}"\n+ #end for\n+ \n+ MINIMUM_DISTANCE="${minimum_distance}"\n+ SKIP_PAIRS_WITH_NO_MATE_CIGAR="${skip_pairs_with_no_mate_cigar}"\n+ \n+ \n+ REMOVE_DUPLICATES="${remove_duplicates}"\n+ ASSUME_SORTED="${assume_sorted}"\n+ \n+ DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}"\n+ \n+ READ_NAME_REGEX="${read_name_regex}"\n+ OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}"\n+ \n+ \n+ BLOCK_SIZE=100000\n+ VALIDATION_STRINGENCY="${validation_stringency}"\n+ QUIET=true\n+ VERBOSITY=ERROR\n+ \n+ </command>\n+ <inputs>\n+ <param format="bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>\n+ <param name="comment" type="text" size="50" label="Add this comment to BAM dataset"/>\n+ \n+ <param name="minimum_distance" type="integer" value="-1" label="The minimum distance to buffer records to account for clipping on the 5\' end of the records" help="MINIMUM_DISTANCE; Set this number to -1 to use twice the first read\'s read length (or 100, whichever is smaller); default=-1"/>\n+ <param name="skip_pairs_with_no_mate_cigar" type="boolean" checked="true" truevalue="true" falsevalue="false" label="Skip record pairs with no mate cigar and include them in the output" help="SKIP_PAIRS_WITH_NO_MATE_CIGAR; default=True"/>\n+ <param name="remove_duplicates" type="boolean" label="If true do not write duplicates to the output file instead of writing them with appropriate flags set" help="REMOVE_DUPLICATES; default=False"/>\n+ <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED; default=True"/>\n+\n+ <param name="duplicate_scoring_strategy" type="select" label="The scoring strategy for choosing the non-duplicate among candidates" help="DUPLICATE_SCORING_STRATEGY; default=TOTAL_MAPPED_REFERENCE_LENGTH">\n+ <option value="TOTAL_MAPPED_REFERENCE_LENGTH" select="True">TOTAL_MAPPED_REFERENCE_LENGTH</option>\n+ <option value="SUM_OF_BASE_QUALITIES">SUM_OF_BASE_QUALITIES</option>\n+ </param>\n+\n+\n+ <param name="read_name_regex" type="text" size="40" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*." label="Regular expression that can be used to parse read names in the incoming SAM/BAM dataset" help="READ_NAME_REGEX; 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. See help below for more info; default=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.">\n+ <sanitizer>\n+ <valid initial="string.printable">\n+ </valid>\n+ </sanitizer>\n+ </param>\n+ <param name="optical_duplicate_pixel_distance" type="integer" value="100" min="0" max="500" label="The maximum offset between two duplicte clusters in order to consider them optical duplicates" help="OPTICAL_DUPLICATE_PIXEL_DISTANCE; default=100"/>\n+\n+ <expand macro="VS" />\n+ \n+ </inputs> \n+ \n+ <outputs>\n+ <data format="txt" name="metrics_file" label="${tool.name} on ${on_string}: MarkDuplicate metrics"/>\n+ <data format="bam" name="outFile" label="${tool.nam'..b" duplicate records flagged.\n+\n+------\n+\n+.. class:: warningmark\n+\n+On the difference between **MarkDuplicates** and **picard_MarkDuplicatesWithMateCigar**\n+\n+From Samtools Announce MailingList_:\n+\n+This tool can replace MarkDuplicates if the input SAM/BAM has Mate CIGAR (MC) optional tags pre-computed\n+(see the tools RevertOriginalBaseQualitiesAndAddMateCigar and FixMateInformation). This allows the new tool\n+to perform a streaming duplicate marking routine (i.e. a single-pass). This tool cannot be used with\n+alignments that have large gaps or reference skips, which happens frequently in RNA-seq data.\n+\n+.. _MailingList: http://sourceforge.net/p/samtools/mailman/message/32910359/\n+\n+@dataset_collections@\n+\n+@description@\n+\n+ MINIMUM_DISTANCE=Integer The minimum distance to buffer records to account for clipping on the 5' end of the \n+ records.Set this number to -1 to use twice the first read's read length (or 100, \n+ whichever is smaller). Default value: -1. This option can be set to 'null' to clear the \n+ default value. \n+ \n+ SKIP_PAIRS_WITH_NO_MATE_CIGAR=Boolean\n+ Skip record pairs with no mate cigar and include them in the output. Default value: \n+ true. This option can be set to 'null' to clear the default value. Possible values: \n+ {true, false} \n+\n+ COMMENT=String \n+ CO=String Comment(s) to include in the output file's header. This option may be specified 0 or \n+ more times. \n+\n+ REMOVE_DUPLICATES=Boolean If true do not write duplicates to the output file instead of writing them with \n+ appropriate flags set. Default value: false. \n+ \n+ READ_NAME_REGEX=String Regular expression that can be used to parse read names in the incoming SAM file. Read \n+ names are parsed to extract three variables: tile/region, x coordinate and y coordinate. \n+ These values are used to estimate the rate of optical duplication in order to give a more \n+ accurate estimated library size. Set this option to null to disable optical duplicate \n+ detection. The regular expression should contain three capture groups for the three \n+ variables, in order. It must match the entire read name. Note that if the default regex \n+ is specified, a regex match is not actually done, but instead the read name is split on \n+ colon character. For 5 element names, the 3rd, 4th and 5th elements are assumed to be \n+ tile, x and y values. For 7 element names (CASAVA 1.8), the 5th, 6th, and 7th elements \n+ are assumed to be tile, x and y values. Default value: \n+ [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*.\n+ \n+ DUPLICATE_SCORING_STRATEGY=ScoringStrategy\n+ DS=ScoringStrategy The scoring strategy for choosing the non-duplicate among candidates. Default value: \n+ TOTAL_MAPPED_REFERENCE_LENGTH. Possible values: {SUM_OF_BASE_QUALITIES, TOTAL_MAPPED_REFERENCE_LENGTH} \n+ \n+ OPTICAL_DUPLICATE_PIXEL_DISTANCE=Integer\n+ The maximum offset between two duplicte clusters in order to consider them optical \n+ duplicates. This should usually be set to some fairly small number (e.g. 5-10 pixels) \n+ unless using later versions of the Illumina pipeline that multiply pixel values by 10, in \n+ which case 50-100 is more normal. Default value: 100. \n+\n+@more_info@\n+\n+ </help>\n+</tool>\n+\n+\n" |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_MeanQualityByCycle.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_MeanQualityByCycle.xml Tue Dec 16 19:03:21 2014 -0500 |
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| @@ -0,0 +1,113 @@ +<tool name="MeanQualityByCycle" id="picard_MeanQualityByCycle" version="1.126.0"> + <description>chart distribution of base qualities</description> + <requirements> + <requirement type="package" version="1.126.0">picard</requirement> + </requirements> + + <macros> + <import>picard_macros.xml</import> + </macros> + + <command> + @java_options@ + ##set up input files + + #set $reference_fasta_filename = "localref.fa" + + #if str( $reference_source.reference_source_selector ) == "history": + ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && + #else: + #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) + #end if + + java -jar \$JAVA_JAR_PATH/picard.jar + MeanQualityByCycle + INPUT="${inputFile}" + OUTPUT="${outFile}" + CHART_OUTPUT="${pdfFile}" + REFERENCE_SEQUENCE="${reference_fasta_filename}" + ALIGNED_READS_ONLY="${aligned_reads_only}" + PF_READS_ONLY="${pf_reads_only}" + + ASSUME_SORTED="${assume_sorted}" + + VALIDATION_STRINGENCY="${validation_stringency}" + QUIET=true + VERBOSITY=ERROR + + </command> + <inputs> + <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Load reference genome from"> + <option value="cached">Local cache</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> + <options from_data_table="all_fasta"> + </options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> + </when> + </conditional> + <param name="aligned_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true, calculate mean quality over aligned reads only" help="ALIGNED_READS_ONLY; default=False"/> + <param name="pf_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true calculate mean quality over reads passing quality filter" help="PF_READS_ONLY; default=False"/> + <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED"/> + + <expand macro="VS" /> + + </inputs> + + <outputs> + <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/> + <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/> + </outputs> + + <tests> + <test> + <param name="assume_sorted" value="true" /> + <param name="aligned_reads_only" value="false" /> + <param name="pf_reads_only" value="false" /> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="picard_MeanQualityByCycle_ref.fa" /> + <param name="inputFile" value="picard_MeanQualityByCycle.bam" ftype="bam" /> + <output name="outFile" file="picard_MeanQualityByCycle_test1.tab" ftype="tabular" lines_diff="4"/> + </test> + </tests> + + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + + <help> + +.. class:: infomark + +**Purpose** + +Program to chart the distribution of base qualities by cycle within reads supplied in a SAM or BAM dataset. + +@dataset_collections@ + +@description@ + + ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value: + false. Possible values: {true, false} + + PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false. + This option can be set to 'null' to clear the default value. Possible values: {true, + false} + + ASSUME_SORTED=Boolean + AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True + +@more_info@ + + </help> +</tool> + + |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_MergeBamAlignment.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_MergeBamAlignment.xml Tue Dec 16 19:03:21 2014 -0500 |
| b |
| b'@@ -0,0 +1,329 @@\n+<tool name="MergeBamAlignment" id="picard_MergeBamAlignment" version="1.126.0">\n+ <description>merge alignment data with additional info stored in an unmapped BAM dataset</description>\n+ <requirements><requirement type="package" version="1.126.0">picard</requirement></requirements>\n+ \n+ <macros>\n+ <import>picard_macros.xml</import>\n+ </macros>\n+ \n+ <command>\n+ @java_options@\n+ #set $picard_dict = "localref.dict"\n+ #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension\n+ \n+ ln -s "${reference_source.ref_file}" "${ref_fasta}" &&\n+ \n+ #if str( $reference_source.reference_source_selector ) == "history":\n+ \n+ java -jar \\$JAVA_JAR_PATH/picard.jar CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"\n+ QUIET=true\n+ VERBOSITY=ERROR\n+ \n+ &&\n+ \n+ #else:\n+ \n+ #set $ref_fasta = str( $reference_source.ref_file.fields.path )\n+ \n+ #end if\n+ \n+ java -jar \\$JAVA_JAR_PATH/picard.jar\n+ MergeBamAlignment\n+ UNMAPPED_BAM="${unmapped_bam}"\n+ \n+ PAIRED_RUN=true ##This argument is ignored and will be removed. Required. Possible values: {true, false}\n+ \n+ #if str( $aligned_or_read1_and_read2.aligned_or_read1_and_read2_selector ) == "paired_one_file":\n+ #for $dataset in $aligned_or_read1_and_read2.aligned_bams:\n+ ALIGNED_BAM="${dataset.aligned_bam}"\n+ #end for\n+ #elif str( $aligned_or_read1_and_read2.aligned_or_read1_and_read2_selector ) == "paired_two_files":\n+ #for $dataset in $aligned_or_read1_and_read2.read1_aligned_bams:\n+ READ1_ALIGNED_BAM="${dataset.read1_aligned_bam}"\n+ #end for\n+ #for $dataset in $aligned_or_read1_and_read2.read2_aligned_bams:\n+ READ2_ALIGNED_BAM="${dataset.read1_aligned_bam}"\n+ #end for\n+ #else\n+ #for $dataset in $aligned_or_read1_and_read2.read1_aligned_bams:\n+ READ1_ALIGNED_BAM="${dataset.read1_aligned_bam}"\n+ #end for\n+ #end if\n+ \n+ OUTPUT="${outFile}"\n+ REFERENCE_SEQUENCE="${ref_fasta}"\n+ \n+ CLIP_ADAPTERS="${clip_adapters}"\n+ IS_BISULFITE_SEQUENCE="${is_bisulfite_sequence}"\n+ ALIGNED_READS_ONLY="${aligned_reads_only}"\n+ MAX_INSERTIONS_OR_DELETIONS="${max_insertions_or_deletions}"\n+ \n+ #for $attribute in $attributes_to_retain:\n+ ATTRIBUTES_TO_RETAIN="${$attribute.attribute}"\n+ #end for\n+ \n+ #for $attribute in $attributes_to_remove:\n+ ATTRIBUTES_TO_REMOVE="${$attribute.attribute}"\n+ #end for\n+ \n+ READ1_TRIM="${read1_trim}"\n+ READ2_TRIM="${read2_trim}"\n+ \n+ #if str( $orientations ) != "None":\n+ #for $orientation in str( $orientations ).split(\',\'): ## See trello card https://trello.com/c/9nW02Zhd\n+ EXPECTED_ORIENTATIONS="${orientation}"\n+ #end for\n+ #end if\n+ \n+ ALIGNER_PROPER_PAIR_FLAGS="${aligner_proper_pair_flags}" \n+ PRIMARY_ALIGNMENT_STRATEGY="${primary_alignment_strategy}"\n+ CLIP_OVERLAPPING_READS="${clip_overlapping_reads}"\n+ INCLUDE_SECONDARY_ALIGNMENTS="${include_secondary_alignments}"\n+ ADD_MATE_CIGAR="${add_mate_cigar}"\n+ \n+ VALIDATION_STRINGENCY="${validation_stringency}"\n+\n+ SORT_ORDER=coordinate\n+ QUIET=true\n+ VERBOSITY=ERROR\n+ \n+ </command>\n+ \n+ <inputs>\n+ \n+ <conditional name="reference_source">\n+ <param name="reference_source_selector" type="select" label="Load reference genome from">\n+ <option value="cached">Local cache</option>\n+ <option value="history">History</option>\n+ </param>\n+ <when value="cached">\n+ <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">\n+ <options from_data_table="picard_indexes">\n+ <filter type="sort_by" column="2" />\n+ <validator type="no_opt'..b" the alignment data when merging. This option may be specified 0 or more times. \n+ \n+ ATTRIBUTES_TO_REMOVE=String Attributes from the alignment record that should be removed when merging. This overrides \n+ ATTRIBUTES_TO_RETAIN if they share common tags. This option may be specified 0 or more \n+ times. \n+ \n+ READ1_TRIM=Integer\n+ R1_TRIM=Integer The number of bases trimmed from the beginning of read 1 prior to alignment Default \n+ value: 0. \n+ \n+ READ2_TRIM=Integer\n+ R2_TRIM=Integer The number of bases trimmed from the beginning of read 2 prior to alignment Default \n+ value: 0. \n+ \n+ EXPECTED_ORIENTATIONS=PairOrientation\n+ ORIENTATIONS=PairOrientation The expected orientation of proper read pairs. Replaces JUMP_SIZE Possible values: {FR, \n+ RF, TANDEM} This option may be specified 0 or more times. Cannot be used in conjuction \n+ with option(s) JUMP_SIZE (JUMP)\n+ \n+ ALIGNER_PROPER_PAIR_FLAGS=Boolean\n+ Use the aligner's idea of what a proper pair is rather than computing in this program. \n+ Default value: false. Possible values: {true, false} \n+ \n+ SORT_ORDER=SortOrder\n+ SO=SortOrder The order in which the merged reads should be output. Default value: coordinate.\n+ Possible values: {unsorted, queryname, coordinate} \n+ \n+ PRIMARY_ALIGNMENT_STRATEGY=PrimaryAlignmentStrategy\n+ Strategy for selecting primary alignment when the aligner has provided more than one \n+ alignment for a pair or fragment, and none are marked as primary, more than one is marked \n+ as primary, or the primary alignment is filtered out for some reason. BestMapq expects \n+ that multiple alignments will be correlated with HI tag, and prefers the pair of \n+ alignments with the largest MAPQ, in the absence of a primary selected by the aligner. \n+ EarliestFragment prefers the alignment which maps the earliest base in the read. Note \n+ that EarliestFragment may not be used for paired reads. BestEndMapq is appropriate for \n+ cases in which the aligner is not pair-aware, and does not output the HI tag. It simply \n+ picks the alignment for each end with the highest MAPQ, and makes those alignments \n+ primary, regardless of whether the two alignments make sense together.MostDistant is also \n+ for a non-pair-aware aligner, and picks the alignment pair with the largest insert size. \n+ If all alignments would be chimeric, it picks the alignments for each end with the best \n+ MAPQ. For all algorithms, ties are resolved arbitrarily. Default value: BestMapq.\n+ Possible values: {BestMapq, EarliestFragment, BestEndMapq, MostDistant} \n+ \n+ CLIP_OVERLAPPING_READS=BooleanFor paired reads, soft clip the 3' end of each read if necessary so that it does not \n+ extend past the 5' end of its mate. Default value: true. Possible values: {true, false} \n+ \n+ INCLUDE_SECONDARY_ALIGNMENTS=Boolean\n+ If false, do not write secondary alignments to output. Default value: true.\n+ Possible values: {true, false} \n+ \n+ ADD_MATE_CIGAR=Boolean\n+ MC=Boolean Adds the mate CIGAR tag (MC) if true, does not if false. Possible values: {true, false} \n+\n+\n+\n+\n+@more_info@\n+ </help>\n+</tool>\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n+\n" |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_MergeSamFiles.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_MergeSamFiles.xml Tue Dec 16 19:03:21 2014 -0500 |
| b |
| @@ -0,0 +1,96 @@ +<tool name="MergeSamFiles" id="picard_MergeSamFiles" version="1.126.0"> + <description>merges multiple SAM/BAM datasets into one</description> + <requirements> + <requirement type="package" version="1.126.0">picard</requirement> + </requirements> + + <macros> + <import>picard_macros.xml</import> + </macros> + + <command> + @java_options@ + + java -jar \$JAVA_JAR_PATH/picard.jar + MergeSamFiles + + #for $element in $inputFile: + INPUT="${element}" + #end for + + OUTPUT="${outFile}" + MERGE_SEQUENCE_DICTIONARIES="${merge_sequence_dictionaries}" + + ASSUME_SORTED="${assume_sorted}" + #for $element in $comments: + COMMENT="${element.comment}" + #end for + + USE_THREADING=true + SORT_ORDER=coordinate + VALIDATION_STRINGENCY="${validation_stringency}" + QUIET=true + VERBOSITY=ERROR + + </command> + <inputs> + <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> + <param name="merge_sequence_dictionaries" type="boolean" label="Merge the sequence dictionaries of the datasets being merged" help="MERGE_SEQUENCE_DICTIONARIES; default=False"/> + <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" help="ASSUME_SORTED; default=False"/> + + <repeat name="comments" title="Comment" min="0" help="You can provide multiple comments"> + <param name="comment" type="text" size="50" label="Add this comment to BAM dataset" help="COMMENT"/> + </repeat> + + <expand macro="VS" /> + + </inputs> + + <outputs> + <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Merged BAM dataset"/> + </outputs> + + <tests> + <test> + <param name="inputFile" value="picard_MergeSamFiles_input1.bam,picard_MergeSamFiles_input2.bam,picard_MergeSamFiles_input3.bam" ftype="bam"/> + <param name="assume_sorted" value="False"/> + <param name="merge_sequence_dictionaries" value="False"/> + <param name="validation_stringency" value="LENIENT"/> + <output name="outFile" file="picard_MergeSamFiles_test1.bam" ftype="bam" lines_diff="2"/> + </test> + </tests> + + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + + <help> + +**Purpose** + +Merges multiple SAM/BAM datasets into one. + +@dataset_collections@ + +@description@ + + ASSUME_SORTED=Boolean + AS=Boolean If true, assume that the input files are in the same sort order as the requested output + sort order, even if their headers say otherwise. Default value: false. This option can + be set to 'null' to clear the default value. Possible values: {true, false} + + MERGE_SEQUENCE_DICTIONARIES=Boolean + MSD=Boolean Merge the sequence dictionaries Default value: false. This option can be set to 'null' + to clear the default value. Possible values: {true, false} + + COMMENT=String + CO=String Comment(s) to include in the merged output file's header. This option may be specified 0 + or more times. + + +@more_info@ + + </help> +</tool> + + |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_NormalizeFasta.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_NormalizeFasta.xml Tue Dec 16 19:03:21 2014 -0500 |
| b |
| @@ -0,0 +1,74 @@ +<tool name="NormalizeFasta" id="picard_NormalizeFasta" version="1.126.0"> + <description>normalize fasta datasets</description> + <requirements> + <requirement type="package" version="1.126.0">picard</requirement> + </requirements> + + <macros> + <import>picard_macros.xml</import> + </macros> + + <command> + @java_options@ + + + ## Two lines below are due to the fact that picard likes fasta files to have extension .fa + #set $fasta_file="local_fasta.fa" + ln -s "${inputFile}" "${fasta_file}" && + + java -jar \$JAVA_JAR_PATH/picard.jar + NormalizeFasta + + INPUT="${fasta_file}" + OUTPUT="${outFile}" + LINE_LENGTH="${line_length}" + TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}" + + QUIET=true + VERBOSITY=ERROR + + </command> + <inputs> + <param format="fasta" name="inputFile" type="data" label="FASTA dataset or dataset collection" help="If empty, upload or import a FASTA dataset" /> + <param name="line_length" type="integer" value="100" min="1" max="200" label="The line length to be used for the output fasta file" help="LINE_LENGTH; default=100"/> + <param name="truncate_sequence_names_at_whitespaces" type="boolean" label="Truncate sequence names at first whitespace" help="TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE; default=False"/> + </inputs> + + <outputs> + <data format="fasta" name="outFile" label="${tool.name} on ${on_string}: Normalized FASTA dataset"/> + </outputs> + + <tests> + <test> + <param name="inputFile" value="picard_NormalizeFasta_ref.fa" ftype="fasta"/> + <param name="line_length" value="40"/> + <param name="truncate_sequence_names_at_whitespaces" value="False"/> + <output name="outFile" file="picard_NormalizeFasta_test1.fa" ftype="fasta"/> + </test> + </tests> + + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + + <help> + +**Purpose** + +Takes any dataset that conforms to the fasta format and normalizes it so that all lines of sequence except the last line per named sequence are of the same length. + +@dataset_collections@ + +@description@ + + LINE_LENGTH=Integer The line length to be used for the output fasta file. Default value: 100. + + TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE=Boolean + Truncate sequence names at first whitespace. Default value: false. Possible values: {true, false} + +@more_info@ + + </help> +</tool> + + |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_QualityScoreDistribution.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_QualityScoreDistribution.xml Tue Dec 16 19:03:21 2014 -0500 |
| b |
| @@ -0,0 +1,118 @@ +<tool name="QualityScoreDistribution" id="picard_QualityScoreDistribution" version="1.126.0"> + <description>chart quality score distribution</description> + <requirements> + <requirement type="package" version="1.126.0">picard</requirement> + </requirements> + + <macros> + <import>picard_macros.xml</import> + </macros> + + <command> + @java_options@ + ##set up input files + + #set $reference_fasta_filename = "localref.fa" + + #if str( $reference_source.reference_source_selector ) == "history": + ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" && + #else: + #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path ) + #end if + + java -jar \$JAVA_JAR_PATH/picard.jar + QualityScoreDistribution + INPUT="${inputFile}" + OUTPUT="${outFile}" + CHART_OUTPUT="${pdfFile}" + REFERENCE_SEQUENCE="${reference_fasta_filename}" + ALIGNED_READS_ONLY="${aligned_reads_only}" + PF_READS_ONLY="${pf_reads_only}" + INCLUDE_NO_CALLS="${include_no_calls}" + + ASSUME_SORTED="${assume_sorted}" + + VALIDATION_STRINGENCY="${validation_stringency}" + QUIET=true + VERBOSITY=ERROR + + </command> + <inputs> + <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> + <conditional name="reference_source"> + <param name="reference_source_selector" type="select" label="Load reference genome from"> + <option value="cached">Local cache</option> + <option value="history">History</option> + </param> + <when value="cached"> + <param name="ref_file" type="select" label="Using reference genome" help="REFERENCE_SEQUENCE"> + <options from_data_table="all_fasta"> + </options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/> + </param> + </when> + <when value="history"> + <param name="ref_file" type="data" format="fasta" label="Use the folloing dataset as the reference sequence" help="REFERENCE_SEQUENCE; You can upload a FASTA sequence to the history and use it as reference" /> + </when> + </conditional> + <param name="aligned_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true, calculate mean quality over aligned reads only" help="ALIGNED_READS_ONLY; default=False"/> + <param name="pf_reads_only" type="boolean" truevalue="true" falsevalue="false" label="If set to true calculate mean quality over reads passing quality filter" help="PF_READS_ONLY; default=False"/> + <param name="include_no_calls" type="boolean" label="If set to true, include quality for no-call bases in the distribution" help="INCLUDE_NO_CALLS; default=False"/> + <param name="assume_sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false" help="ASSUME_SORTED; default=True"/> + + <expand macro="VS" /> + + </inputs> + + <outputs> + <data format="tabular" name="outFile" label="${tool.name} on ${on_string}: Summary data"/> + <data format="pdf" name="pdfFile" label="${tool.name} on ${on_string}: Chart PDF"/> + </outputs> + + <tests> + <test> + <param name="assume_sorted" value="true" /> + <param name="aligned_reads_only" value="false" /> + <param name="pf_reads_only" value="false" /> + <param name="include_no_calls" value="false" /> + <param name="reference_source_selector" value="history" /> + <param name="ref_file" value="picard_QualityScoreDistribution_ref.fa" /> + <param name="inputFile" value="picard_QualityScoreDistribution.bam" ftype="bam" /> + <output name="outFile" file="picard_QualityScoreDistribution_test1.tab" ftype="tabular" lines_diff="4"/> + </test> + </tests> + + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + + <help> + +.. class:: infomark + +**Purpose** + +Program to chart quality score distributions in a SAM or BAM dataset. + +@dataset_collections@ + +@description@ + + ALIGNED_READS_ONLY=Boolean If set to true, calculate the base distribution over aligned reads only. Default value: + false. Possible values: {true, false} + + PF_READS_ONLY=Boolean If set to true calculate the base distribution over PF reads only. Default value: false. + Possible values: {true, false} + + INCLUDE_NO_CALLS=Boolean If set to true, include quality for no-call bases in the distribution. Default value: + false. Possible values: {true, false} + + ASSUME_SORTED=Boolean + AS=Boolean If true (default), then the sort order in the header file will be ignored. Default: True + +@more_info@ + + </help> +</tool> + + |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_ReorderSam.xml --- a/picard_ReorderSam.xml Fri Feb 21 12:07:49 2014 -0500 +++ b/picard_ReorderSam.xml Tue Dec 16 19:03:21 2014 -0500 |
| b |
| b'@@ -1,155 +1,120 @@\n-<tool name="Reorder SAM/BAM" id="picard_ReorderSam" version="1.56.0">\n- <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>\n- <command interpreter="python">\n- picard_wrapper.py\n- --input="${inputFile}"\n- #if $source.indexSource == "built-in"\n- --ref="${source.ref.fields.path}"\n- #else\n- --ref-file="${refFile}"\n- --species-name="${source.speciesName}"\n- --build-name="${source.buildName}"\n- --trunc-names="${source.truncateSeqNames}"\n- #end if\n- --allow-inc-dict-concord="${allowIncDictConcord}"\n- --allow-contig-len-discord="${allowContigLenDiscord}"\n- --output-format="${outputFormat}"\n- --output="${outFile}"\n- --tmpdir "${__new_file_path__}" \n- -j "\\$JAVA_JAR_PATH/ReorderSam.jar"\n+<tool name="ReorderSam" id="picard_ReorderSam" version="1.126.0">\n+ <description>reorder reads to match ordering in reference sequences</description>\n+ <requirements><requirement type="package" version="1.126.0">picard</requirement></requirements>\n+ \n+ <macros>\n+ <import>picard_macros.xml</import>\n+ </macros>\n+ \n+ <command>\n+ @java_options@\n+ #set $picard_dict = "localref.dict"\n+ #set $ref_fasta = "localref.fa" ## This is done because picards "likes" .fa extension\n+ \n+ ln -s "${reference_source.ref_file}" "${ref_fasta}" &&\n+ \n+ #if str( $reference_source.reference_source_selector ) == "history":\n+ \n+ java -jar \\$JAVA_JAR_PATH/picard.jar CreateSequenceDictionary REFERENCE="${ref_fasta}" OUTPUT="${picard_dict}"\n+ QUIET=true\n+ VERBOSITY=ERROR\n+ \n+ &&\n+ \n+ #else:\n+ \n+ #set $ref_fasta = str( $reference_source.ref_file.fields.path )\n+ \n+ #end if\n+ \n+ java -jar \\$JAVA_JAR_PATH/picard.jar\n+ ReorderSam\n+ INPUT="${inputFile}"\n+ OUTPUT="${outFile}"\n+ REFERENCE="${ref_fasta}"\n+ ALLOW_INCOMPLETE_DICT_CONCORDANCE="${allow_incomplete_dict_concordance}"\n+ ALLOW_CONTIG_LENGTH_DISCORDANCE="${allow_contig_length_discordance}"\n+ \n+ VALIDATION_STRINGENCY="${validation_stringency}"\n+ QUIET=true\n+ VERBOSITY=ERROR\n+ \n </command>\n+ \n <inputs>\n- <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to be reordered"\n- help="If empty, upload or import a SAM/BAM dataset." />\n- <conditional name="source">\n- <param name="indexSource" type="select" label="Select Reference Genome" help="This tool will re-order SAM/BAM in the same order as reference selected below.">\n- <option value="built-in">Locally cached</option>\n+ \n+ <conditional name="reference_source">\n+ <param name="reference_source_selector" type="select" label="Load reference genome from">\n+ <option value="cached">Local cache</option>\n <option value="history">History</option>\n </param>\n- <when value="built-in">\n- <param name="ref" type="select" label="Select a reference genome">\n- <options from_data_table="picard_indexes" />\n+ <when value="cached">\n+ <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">\n+ <options from_data_table="picard_indexes">\n+ <filter type="sort_by" column="2" />\n+ <validator type="no_options" message="No indexes are available" />\n+ </options>\n+ <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>\n </param>\n </when>\n- <when value="history">\n- <param name="refFile" type="data" format="fasta" metadata_name="dbkey" label="Using reference file" />\n- <param name="speciesName" type="text" value="" label="Species name" />\n- <param name="buildName" type="text" value="" label="Build name" />\n- <param name="truncateSeqNames" type="boolean" checked="Fa'..b'"True" />\n+ <param name="reference_source_selector" value="history" />\n+ <param name="ref_file" value="picard_ReorderSam_ref.fa" ftype="fasta" />\n+ <param name="inputFile" value="picard_ReorderSam.bam" ftype="bam"/>\n+ <param name="allow_incomplete_dict_concordance" value="false"/>\n+ <param name="allow_contig_length_discordance" value="false"/>\n+ <output name="outFile" file="picard_ReorderSam_test1.bam" ftype="bam" lines_diff="2"/>\n </test>\n </tests>\n+ \n+ <stdio>\n+ <exit_code range="1:" level="fatal"/>\n+ </stdio>\n+ \n <help>\n \n .. class:: infomark\n \n **Purpose**\n \n-Reorder SAM/BAM to match contig ordering in a particular reference file. Note that this is\n-not the same as sorting as done by the SortSam tool, which sorts by either coordinate\n-values or query name. The ordering in ReorderSam is based on exact name matching of\n-contigs/chromosomes. Reads that are mapped to a contig that is not in the new reference file are\n-not included in the output.\n-\n-**Picard documentation**\n-\n-This is a Galaxy wrapper for ReorderSam, a part of the external package Picard-tools_.\n-\n- .. _Picard-tools: http://www.google.com/search?q=picard+samtools\n-\n-------\n-\n-.. class:: infomark \n+ReorderSam reorders reads in a SAM/BAM file to match the contig ordering in a provided reference file, as determined by exact name matching of contigs. Reads mapped to contigs absent in the new reference are dropped.\n \n-**Inputs, outputs, and parameters**\n-\n-For the file that needs to be reordered, either a sam file or a bam file must be supplied.\n-If a bam file is used, it must be coordinate-sorted. A reference file is also required,\n-so either a fasta file should be supplied or a built-in reference can be selected.\n+@dataset_collections@\n \n-The output contains the same reads as the input file but the reads have been rearranged so\n-they appear in the same order as the provided reference file. The tool will output either\n-bam (the default) or sam, according to user selection. Bam is recommended since it is smaller.\n-\n-The only extra parameters that can be set are flags for allowing incomplete dict concordance\n-and allowing contig length discordance. If incomplete dict concordance is allowed, only a\n-partial overlap of the bam contigs with the new reference sequence contigs is required. By\n-default it is off, requiring a corresponding contig in the new reference for each read contig.\n-If contig length discordance is allowed, contig names that are the same between a read and the\n-new reference contig are allowed even if they have different lengths. This is usually not a\n-good idea, unless you know exactly what you\'re doing. It\'s off by default.\n+----\n \n .. class:: warningmark\n \n-**Warning on SAM/BAM quality**\n+Not to be confused with **SortSam**.\n+\n+@description@\n \n-Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**\n-flag when it runs Picard, which allows reads to be discarded if they\'re empty or don\'t map. This appears\n-to be the only way to deal with SAM/BAM that cannot be parsed.\n+ ALLOW_INCOMPLETE_DICT_CONCORDANCE=Boolean\n+ S=Boolean If true, then allows only a partial overlap of the BAM contigs with the new reference \n+ sequence contigs. By default, this tool requires a corresponding contig in the new \n+ reference for each read contig Default value: false. Possible values: {true, false} \n+ \n+ ALLOW_CONTIG_LENGTH_DISCORDANCE=Boolean\n+ U=Boolean If true, then permits mapping from a read contig to a new reference contig with the same \n+ name but a different length. Highly dangerous, only use if you know what you are doing. \n+ Default value: false. Possible values: {true, false} \n \n-\n+@more_info@\n </help>\n </tool>\n \n@@ -164,3 +129,4 @@\n \n \n \n+\n' |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_ReplaceSamHeader.xml --- a/picard_ReplaceSamHeader.xml Fri Feb 21 12:07:49 2014 -0500 +++ b/picard_ReplaceSamHeader.xml Tue Dec 16 19:03:21 2014 -0500 |
| b |
| @@ -1,115 +1,67 @@ -<tool name="Replace SAM/BAM Header" id="picard_ReplaceSamHeader" version="1.56.0"> - <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> - <command interpreter="python"> - picard_wrapper.py - --input "${inputFile}" - -o "${outFile}" - --header-file "${headerFile}" - --output-format "${outputFormat}" - -j "\$JAVA_JAR_PATH/ReplaceSamHeader.jar" - --tmpdir "${__new_file_path__}" +<tool name="ReplaceSamHeader" id="picard_ReplaceSamHeader" version="1.126.0"> + <description>replace header in a SAM/BAM dataset</description> + <requirements> + <requirement type="package" version="1.126.0">picard</requirement> + </requirements> + + <macros> + <import>picard_macros.xml</import> + </macros> + + <command> + @java_options@ + + + ## Two lines below are due to the fact that picard likes fasta files to have extension .fa + #set $fasta_file="local_fasta.fa" + ln -s "${inputFile}" "${fasta_file}" && + + java -jar \$JAVA_JAR_PATH/picard.jar + ReplaceSamHeader + + INPUT="${inputFile}" + HEADER="${header}" + OUTPUT="${outFile}" + + QUIET=true + VERBOSITY=ERROR + </command> <inputs> - <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to replace header in (TARGET)" - help="If empty, upload or import a SAM/BAM dataset." /> - <param format="bam,sam" name="headerFile" type="data" label="SAM/BAM to reader header from (SOURCE)" - help="If empty, upload or import a SAM/BAM dataset." /> - <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" /> - </inputs> + <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection (header recepient dataset)" help="If empty, upload or import a SAM/BAM dataset"/> + <param name="header" type="data" format="sam,bam" label="SAM/BAM dataset from which Header will be read (header source dataset)" help="HEADER; If empty, upload or import a SAM/BAM dataset"/> + </inputs> + <outputs> - <data name="outFile" format="bam" label="${tool.name} on ${on_string}: ${outputFormat} with replaced header"> - <change_format> - <when input="outputFormat" value="sam" format="sam" /> - </change_format> - </data> + <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM file with replaced header"/> </outputs> + <tests> <test> - <!-- Command: - java -jar ReplaceSamHeader.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_input_tiny_coord.bam HEADER=test-data/picard_RSH_input1.bam O=picard_RSH_output1.sam - picard_RSH_input1.bam can be made from picard_RSH_input1.sam - --> - <param name="inputFile" value="picard_input_tiny_coord.bam" ftype="bam" /> - <param name="headerFile" value="picard_RSH_input1.bam" ftype="bam" /> - <param name="outputFormat" value="False" /> - <output name="outFile" file="picard_RSH_output1.sam" ftype="sam" /> - </test> - <test> - <!-- Command: - java -jar ReplaceSamHeader.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_input_tiny_coord.sam HEADER=test-data/picard_RSH_input1.bam O=picard_RSH_output2.sam - picard_RSH_input1.bam can be made from picard_RSH_input1.sam - --> - <param name="inputFile" value="picard_input_tiny_coord.sam" ftype="sam" /> - <param name="headerFile" value="picard_RSH_input1.bam" ftype="bam" /> - <param name="outputFormat" value="False" /> - <output name="outFile" file="picard_RSH_output2.sam" ftype="sam" /> - </test> - <test> - <!-- Command: - java -jar ReplaceSamHeader.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_input_tiny_coord.sam HEADER=test-data/picard_RSH_input1.sam O=picard_RSH_output2.bam - --> - <param name="inputFile" value="picard_input_tiny_coord.sam" ftype="sam" /> - <param name="headerFile" value="picard_RSH_input1.sam" ftype="sam" /> - <param name="outputFormat" value="True" /> - <output name="outFile" file="picard_RSH_output2.bam" ftype="bam" /> + <param name="inputFile" value="picard_ReplaceSamHeader.bam" ftype="bam"/> + <param name="header" value="picard_ReplaceSamHeader_header.bam" ftype="bam"/> + <output name="outFile" file="picard_ReplaceSamHeader_test1.bam" ftype="bam"/> </test> </tests> + + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + <help> - -.. class:: infomark - **Purpose** -Replace Sam Header with the header from another sam file. The tool does not do any -significant validation, so it's up to the user to make sure that the elements in -the header are relevant and that the new header has all the required things. - -Replace the SAMFileHeader in a SAM file with the given header. Validation is -minimal. It is up to the user to ensure that all the elements referred to in the -SAMRecords are present in the new header. Sort order of the two input files must -be the same. - -**Picard documentation** - -This is a Galaxy wrapper for ReplaceSamHeader, a part of the external package Picard-tools_. - - .. _Picard-tools: http://www.google.com/search?q=picard+samtools - ------- - -.. class:: infomark +Replace the SAMFileHeader in a SAM/BAM dataset with the given header. Validation is minimal. It is up to the user to ensure that all the elements referred to in the SAMRecords are present in the new header. Sort order of the two input datasets must be the same. +@dataset_collections@ -**Inputs and outputs** - -Either a sam file or a bam file is required as the file whose header will be replaced. -The header file is also required and can also be either sam or bam (it does not have -to be the same type as the other file). In both cases, if a bam file is used, it must -be coordinate-sorted. Galaxy currently coordinate-sorts all bam files. - -The tool will output either bam (the default) or sam. Bam is recommended since it is smaller. +@description@ -.. class:: warningmark - -**Warning on SAM/BAM quality** + HEADER=File SAM file from which SAMFileHeader will be read. Required. -Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT** -flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears -to be the only way to deal with SAM/BAM that cannot be parsed. - - +@more_info@ </help> </tool> - - - - - - - - - - |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_RevertOriginalBaseQualitiesAndAddMateCigar.xml Tue Dec 16 19:03:21 2014 -0500 |
| b |
| @@ -0,0 +1,79 @@ +<tool name="RevertOriginalBaseQualitiesAndAddMateCigar" id="picard_RevertOriginalBaseQualitiesAndAddMateCigar" version="1.126.0"> + <description>revert the original base qualities and add the mate cigar tag</description> + <requirements> + <requirement type="package" version="1.126.0">picard</requirement> + </requirements> + + <macros> + <import>picard_macros.xml</import> + </macros> + + <command> + @java_options@ + + java -jar \$JAVA_JAR_PATH/picard.jar + RevertOriginalBaseQualitiesAndAddMateCigar + + INPUT="${inputFile}" + OUTPUT="${outFile}" + + RESTORE_ORIGINAL_QUALITIES="${restore_original_qualities}" + MAX_RECORDS_TO_EXAMINE="${max_records_to_examine}" + + SORT_ORDER=coordinate + VALIDATION_STRINGENCY="${validation_stringency}" + QUIET=true + VERBOSITY=ERROR + + </command> + <inputs> + <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> + <param name="restore_original_qualities" type="boolean" checked="True" label="Restore original qualities from the OQ field to the QUAL field if available" help="RESTORE_ORIGINAL_QUALITIES; default=True"/> + <param name="max_records_to_examine" type="integer" value="10000" min="0" label="The maximum number of records to examine to determine if we can exit early and not output, given that there are a no original base qualities (if we are to restore) and mate cigars exist. Set to 0 to never skip the dataset" help="MAX_RECORDS_TO_EXAMINE; default=10,000"/> + + <expand macro="VS" /> + + </inputs> + + <outputs> + <data format="bam" name="outFile" label="${tool.name} on ${on_string}: Reverted BAM dataset"/> + </outputs> + + <tests> + <test> + <param name="inputFile" value="picard_RevertOriginalBaseQualitiesAndAddMateCigar.bam" ftype="bam"/> + <param name="restore_original_qualities" value="True"/> + <param name="max_records_to_examine" value="10000"/> + <param name="validation_stringency" value="LENIENT"/> + <output name="outFile" file="picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam" ftype="bam" lines_diff="2"/> + </test> + </tests> + + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + + <help> + +**Purpose** + +Reverts the original base qualities and adds the mate cigar tag to SAM or BAMs. + +@dataset_collections@ + +@description@ + + RESTORE_ORIGINAL_QUALITIES=Boolean + OQ=Boolean True to restore original qualities from the OQ field to the QUAL field if available. + Default value: true. Possible values: {true, false} + + MAX_RECORDS_TO_EXAMINE=IntegerThe maximum number of records to examine to determine if we can exit early and not + output, given that there are a no original base qualities (if we are to restore) and mate + cigars exist. Set to 0 to never skip the file. Default value: 10000. + +@more_info@ + + </help> +</tool> + + |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_RevertSam.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_RevertSam.xml Tue Dec 16 19:03:21 2014 -0500 |
| b |
| b'@@ -0,0 +1,140 @@\n+<tool name="RevertSam" id="picard_RevertSam" version="1.126.0">\n+ <description>revert SAM/BAM datasets to a previous state</description>\n+ <requirements>\n+ <requirement type="package" version="1.126.0">picard</requirement>\n+ </requirements>\n+ \n+ <macros>\n+ <import>picard_macros.xml</import>\n+ </macros>\n+ \n+ <command>\n+ @java_options@\n+ \n+ java -jar \\$JAVA_JAR_PATH/picard.jar\n+ RevertSam\n+ \n+ INPUT="${inputFile}"\n+ OUTPUT="${outFile}"\n+ \n+ RESTORE_ORIGINAL_QUALITIES="${restore_original_qualities}"\n+ REMOVE_DUPLICATE_INFORMATION="${remove_duplicate_information}"\n+ REMOVE_ALIGNMENT_INFORMATION="${remove_alignment_information}"\n+ \n+ #for $attribute_to_clear in $attributes_to_clear:\n+ ATTRIBUTE_TO_CLEAR="${attribute_to_clear.attribute}"\n+ #end for\n+ \n+ SANITIZE="${sanitize}"\n+ MAX_DISCARD_FRACTION="${max_discard_fraction}"\n+ SAMPLE_ALIAS="${sample_alias}"\n+ LIBRARY_NAME="${library_name}"\n+ \n+ SORT_ORDER="${sort_order}"\n+ VALIDATION_STRINGENCY="${validation_stringency}"\n+ QUIET=true\n+ VERBOSITY=ERROR\n+ \n+ </command>\n+ <inputs>\n+ <param format="sam,bam" name="inputFile" type="data" multiple="True" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/>\n+ <param name="restore_original_qualities" type="boolean" checked="True" label="Restore original qualities from the OQ field to the QUAL field if available" help="RESTORE_ORIGINAL_QUALITIES; default=True"/>\n+ <param name="remove_duplicate_information" type="boolean" checked="True" label="Remove duplicate read flags from all reads" help="REMOVE_DUPLICATE_INFORMATION; Note that if this is true and REMOVE_ALIGNMENT_INFORMATION is set to False, the output may have the unusual but sometimes desirable trait of having unmapped reads that are marked as duplicates; default=True"/>\n+ <param name="remove_alignment_information" type="boolean" checked="True" label="Remove all alignment information from the file" help="REMOVE_ALIGNMENT_INFORMATION; default=True"/>\n+ <repeat name="attributes_to_clear" title="Clear attribute" min="0" help="You can provide multiple attributes">\n+ <param name="attribute" type="text" size="10" label="When removing alignment information, specify optional tags to remove (e.g., XM)" help="ATTRIBUTE_TO_CLEAR"/>\n+ </repeat>\n+ <param name="sanitize" type="boolean" label="Discard reads in order to produce a consistent output BAM" help="SANITIZE; WARNING: This option is potentially destructive. Reads discarded include (but are not limited to) paired reads with missing mates, duplicated records, records with mismatches in length of bases and qualities. This option can only be enabled if the output sort order is queryname and will always cause sorting to occur; default=False"/>\n+ <param name="max_discard_fraction" value="0.01" type="float" min="0.0" max="1.0" label="If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to sanitization then the program will exit with an Exception instead of exiting cleanly" help="MAX_DISCARD_FRACTION; default=0.01"/>\n+ <param name="sample_alias" type="text" size="40" value="null" label="The sample alias to use in the reverted output file. This will override the existing sample alias in the file and is used only if all the read groups in the input file have the same sample alias" help="SAMPLE_ALIAS; default=Null"/>\n+ <param name="library_name" type="text" size="40" value="null" label="The library name to use in the reverted output file. This will override the existing sample alias in the file and is used only if all the read groups in the input file have the same sample alias" help="LIBRARY_NAME; default=Null"/>\n+ <param name="sort_order" type="select" label="The sort order to create the reverted output file with" help="SORT_ORDER; Picard default=queryname; Galaxy default=coordinate">\n+ <option value="coordinate" selecte'..b'nputFile" value="picard_RevertSam.bam" ftype="bam"/>\n+ <param name="restore_original_qualities" value="True"/>\n+ <param name="remove_duplicate_information" value="True"/>\n+ <param name="remove_alignment_information" value="True"/>\n+ <param name="attribute" value="XM"/>\n+ <param name="sanitize" value="False"/>\n+ <param name="max_discard_fraction" value="0.01"/>\n+ <param name="sample_alias" value="null"/>\n+ <param name="library_name" value="null"/>\n+ <param name="sort_order" value="coordinate"/>\n+ <param name="validation_stringency" value="LENIENT"/>\n+ <output name="outFile" file="picard_RevertSam_test1.bam" ftype="bam" lines_diff="2"/>\n+ </test>\n+ </tests>\n+ \n+ <stdio>\n+ <exit_code range="1:" level="fatal"/>\n+ </stdio>\n+ \n+ <help>\n+\n+**Purpose**\n+\n+Reverts SAM or BAM files to a previous state by removing certain types of information and/or substituting in the original quality scores when available.\n+\n+@dataset_collections@\n+\n+@description@\n+\n+ SORT_ORDER=SortOrder \n+ SO=SortOrder The sort order to create the reverted output file with. Default value: queryname.\n+ Possible values: {unsorted, queryname, coordinate} \n+ \n+ RESTORE_ORIGINAL_QUALITIES=Boolean\n+ OQ=Boolean True to restore original qualities from the OQ field to the QUAL field if available. \n+ Default value: true. Possible values: {true, false} \n+ \n+ REMOVE_DUPLICATE_INFORMATION=Boolean\n+ Remove duplicate read flags from all reads. Note that if this is true and \n+ REMOVE_ALIGNMENT_INFORMATION==false, the output may have the unusual but sometimes \n+ desirable trait of having unmapped reads that are marked as duplicates. Default value: \n+ true. Possible values: {true, false} \n+ \n+ REMOVE_ALIGNMENT_INFORMATION=Boolean\n+ Remove all alignment information from the file. Default value: true. TPossible values: {true, false} \n+ \n+ ATTRIBUTE_TO_CLEAR=String When removing alignment information, the set of optional tags to remove. This option may \n+ be specified 0 or more times. \n+ \n+ SANITIZE=Boolean WARNING: This option is potentially destructive. If enabled will discard reads in order \n+ to produce a consistent output BAM. Reads discarded include (but are not limited to) \n+ paired reads with missing mates, duplicated records, records with mismatches in length of \n+ bases and qualities. This option can only be enabled if the output sort order is \n+ queryname and will always cause sorting to occur. Possible values: {true, false} \n+ \n+ MAX_DISCARD_FRACTION=Double If SANITIZE=true and higher than MAX_DISCARD_FRACTION reads are discarded due to \n+ sanitization thenthe program will exit with an Exception instead of exiting cleanly. \n+ Output BAM will still be valid. Default value: 0.01. \n+ \n+ SAMPLE_ALIAS=String\n+ ALIAS=String The sample alias to use in the reverted output file. This will override the existing \n+ sample alias in the file and is used only if all the read groups in the input file have \n+ the same sample alias Default value: null. \n+ \n+ LIBRARY_NAME=String\n+ LIB=String The library name to use in the reverted output file. This will override the existing \n+ sample alias in the file and is used only if all the read groups in the input file have \n+ the same sample alias Default value: null. \n+ \n+@more_info@\n+\n+ </help>\n+</tool>\n+\n+\n' |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_SamToFastq.xml --- a/picard_SamToFastq.xml Fri Feb 21 12:07:49 2014 -0500 +++ b/picard_SamToFastq.xml Tue Dec 16 19:03:21 2014 -0500 |
| b |
| b'@@ -1,189 +1,200 @@\n-<tool id="picard_SamToFastq" name="SAM to FASTQ" version="1.56.1" force_history_refresh="True">\n- <description>creates a FASTQ file</description>\n- <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>\n- <!-- Dan Blankenberg -->\n- <command interpreter="python">picard_SamToFastq_wrapper.py\n- -p \'\n- java -XX:DefaultMaxRAMFraction=1 -XX:+UseParallelGC\n- -jar "\\$JAVA_JAR_PATH/SamToFastq.jar"\n- INPUT="${input_sam}"\n- VALIDATION_STRINGENCY="LENIENT"\n+<tool name="SamToFastq" id="picard_SamToFastq" version="1.126.0">\n+ <description>extract reads and qualities from SAM/BAM dataset and convert to fastq</description>\n+ <requirements>\n+ <requirement type="package" version="1.126.0">picard</requirement>\n+ </requirements>\n+ \n+ <macros>\n+ <import>picard_macros.xml</import>\n+ </macros>\n+ \n+ <command>\n+ \n+ echo "BAM" > $report && ## This is necessary for output dataset detection (see output tags below)\n+ \n+ @java_options@\n+ \n+ java -jar \\$JAVA_JAR_PATH/picard.jar\n+ SamToFastq\n+ \n+ INPUT="${inputFile}"\n+ \n+ #if str( $output_per_rg ) == "true":\n+ OUTPUT_PER_RG=true\n+ OUTPUT_DIR=.\n+ #elif str( $output_per_rg ) == "false" and str( $interleave ) == "false":\n+ FASTQ=READ1.fastq\n+ SECOND_END_FASTQ=READ2.fastq\n+ UNPAIRED_FASTQ=UNPAIRED_READS.fastq\n+ #elif str( $output_per_rg ) == "false" and str( $interleave ) == "true":\n+ FASTQ=INTERLEAVED.fastq\n+ #end if\n+ \n RE_REVERSE="${re_reverse}"\n+ INTERLEAVE="${interleave}"\n INCLUDE_NON_PF_READS="${include_non_pf_reads}"\n- #if str( $clipping_attribute ):\n- CLIPPING_ATTRIBUTE="${clipping_attribute}"\n- #end if\n- #if str( $clipping_action ):\n- CLIPPING_ACTION="${clipping_action}"\n+ CLIPPING_ATTRIBUTE="${clipping_attribute}"\n+ CLIPPING_ACTION="${clipping_action}"\n+ READ1_TRIM="${read1_trim}"\n+ \n+ #if int($read1_max_bases_to_write) > -1:\n+ READ1_MAX_BASES_TO_WRITE="${read1_max_bases_to_write}"\n #end if\n- #if str( $read1_trim ):\n- READ1_TRIM="${read1_trim}"\n+ \n+ READ2_TRIM="${read2_trim}"\n+ \n+ #if int($read2_max_bases_to_write) > -1:\n+ READ2_MAX_BASES_TO_WRITE="${read2_max_bases_to_write}"\n #end if\n- #if str( $read1_max_bases_to_write ):\n- READ1_MAX_BASES_TO_WRITE="${read1_max_bases_to_write}"\n- #end if\n+ \n INCLUDE_NON_PRIMARY_ALIGNMENTS="${include_non_primary_alignments}"\n \n- #if str( $output_per_read_group_selector ) == \'per_sam_file\':\n- ##OUTPUT_PER_RG=false\n- FASTQ="${output_fastq1}"\n- \n- #if str( $single_paired_end_type.single_paired_end_type_selector ) == \'paired\':\n- SECOND_END_FASTQ="${output_fastq2}"\n- #if str( $single_paired_end_type.read2_trim ): \n- READ2_TRIM="${single_paired_end_type.read2_trim}"\n- #end if\n- #if str( $single_paired_end_type.read2_max_bases_to_write ):\n- READ2_MAX_BASES_TO_WRITE="${single_paired_end_type.read2_max_bases_to_write}"\n- #end if\n- #end if\n- \'\n- #else:\n- OUTPUT_PER_RG=true\n- #if str( $single_paired_end_type.single_paired_end_type_selector ) == \'paired\':\n- \' \n- --read_group_file_2 "${output_fastq2}"\n- --file_id_2 "${output_fastq2.id}"\n- -p \'\n- #if str( $single_paired_end_type.read2_trim ): \n- READ2_TRIM="${single_paired_end_type.read2_trim}"\n- #end if\n- #if str( $single_paired_end_type.read2_max_bases_to_write ):\n- READ2_MAX_BASES_TO_WRITE="${single_paired_end_type.read2_max_bases_to_write}"\n- #end if\n- #end if\n- \'\n- --read_group_file_1 "${output_fastq1}"\n- --new_files_path "${__new_file_path__}"\n- --file_id_1 "${output_fastq1.id}"\n- #end if\n+ \n+ VALIDATION_STRINGENCY="${validation_strin'..b"ible values: {true, false}\n- CLIPPING_ATTRIBUTE=String\tThe attribute that stores the position at which the SAM record should be clipped Default value: null.\n- CLIPPING_ACTION=String\tThe action that should be taken with clipped reads: 'X' means the reads and qualities should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in the clipped region; and any integer means that the base qualities should be set to that value in the clipped region. Default value: null.\n- READ1_TRIM=Integer\tThe number of bases to trim from the beginning of read 1. Default value: 0. This option can be set to 'null' to clear the default value.\n- READ1_MAX_BASES_TO_WRITE=Integer\tThe maximum number of bases to write from read 1 after trimming. If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written. Default value: null.\n- READ2_TRIM=Integer\tThe number of bases to trim from the beginning of read 2. Default value: 0. This option can be set to 'null' to clear the default value.\n- READ2_MAX_BASES_TO_WRITE=Integer\tThe maximum number of bases to write from read 2 after trimming. If there are fewer than this many bases left after trimming, all will be written. If this value is null then all bases left after trimming will be written. Default value: null.\n- INCLUDE_NON_PRIMARY_ALIGNMENTS=Boolean\tIf true, include non-primary alignments in the output. Support of non-primary alignments in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and there are paired reads with non-primary alignments. Default value: false. This option can be set to 'null' to clear the default value. Possible values: {true, false} \n-\n+ CLIPPING_ATTRIBUTE=String\n+ CLIP_ATTR=String The attribute that stores the position at which the SAM record should be clipped Default \n+ value: null. \n+ \n+ CLIPPING_ACTION=String\n+ CLIP_ACT=String The action that should be taken with clipped reads: 'X' means the reads and qualities \n+ should be trimmed at the clipped position; 'N' means the bases should be changed to Ns in \n+ the clipped region; and any integer means that the base qualities should be set to that \n+ value in the clipped region. Default value: null. \n+ \n+ READ1_TRIM=Integer\n+ R1_TRIM=Integer The number of bases to trim from the beginning of read 1. Default value: 0. \n+ \n+ READ1_MAX_BASES_TO_WRITE=Integer\n+ R1_MAX_BASES=Integer The maximum number of bases to write from read 1 after trimming. If there are fewer than \n+ this many bases left after trimming, all will be written. If this value is null then all \n+ bases left after trimming will be written. Default value: null. \n+ \n+ READ2_TRIM=Integer\n+ R2_TRIM=Integer The number of bases to trim from the beginning of read 2. Default value: 0. \n+ \n+ READ2_MAX_BASES_TO_WRITE=Integer\n+ R2_MAX_BASES=Integer The maximum number of bases to write from read 2 after trimming. If there are fewer than \n+ this many bases left after trimming, all will be written. If this value is null then all \n+ bases left after trimming will be written. Default value: null. \n+ \n+ INCLUDE_NON_PRIMARY_ALIGNMENTS=Boolean\n+ If true, include non-primary alignments in the output. Support of non-primary alignments \n+ in SamToFastq is not comprehensive, so there may be exceptions if this is set to true and \n+ there are paired reads with non-primary alignments. Default value: false.\n+ Possible values: {true, false} \n+ \n+@more_info@\n \n </help>\n </tool>\n+\n+\n" |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_SamToFastq_wrapper.py --- a/picard_SamToFastq_wrapper.py Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,93 +0,0 @@ -#!/usr/bin/env python -#Dan Blankenberg - -""" -A wrapper script for running the Picard SamToFastq command. Allows parsing read groups into separate files. -""" - -import sys, optparse, os, tempfile, subprocess, shutil - -CHUNK_SIZE = 2**20 #1mb - - -def cleanup_before_exit( tmp_dir ): - if tmp_dir and os.path.exists( tmp_dir ): - shutil.rmtree( tmp_dir ) - -def open_file_from_option( filename, mode = 'rb' ): - if filename: - return open( filename, mode = mode ) - return None - -def __main__(): - #Parse Command Line - parser = optparse.OptionParser() - parser.add_option( '-p', '--pass_through', dest='pass_through_options', action='append', type="string", help='These options are passed through directly to PICARD, without any modification.' ) - parser.add_option( '-1', '--read_group_file_1', dest='read_group_file_1', action='store', type="string", default=None, help='Read Group 1 output file, when using multiple readgroups' ) - parser.add_option( '-2', '--read_group_file_2', dest='read_group_file_2', action='store', type="string", default=None, help='Read Group 2 output file, when using multiple readgroups and paired end' ) - parser.add_option( '', '--stdout', dest='stdout', action='store', type="string", default=None, help='If specified, the output of stdout will be written to this file.' ) - parser.add_option( '', '--stderr', dest='stderr', action='store', type="string", default=None, help='If specified, the output of stderr will be written to this file.' ) - parser.add_option( '-n', '--new_files_path', dest='new_files_path', action='store', type="string", default=None, help='new_files_path') - parser.add_option( '-i', '--file_id_1', dest='file_id_1', action='store', type="string", default=None, help='file_id_1') - parser.add_option( '-f', '--file_id_2', dest='file_id_2', action='store', type="string", default=None, help='file_id_2') - (options, args) = parser.parse_args() - - tmp_dir = tempfile.mkdtemp( prefix='tmp-picard-' ) - if options.pass_through_options: - cmd = ' '.join( options.pass_through_options ) - else: - cmd = '' - if options.new_files_path is not None: - print 'Creating FASTQ files by Read Group' - assert None not in [ options.read_group_file_1, options.new_files_path, options.file_id_1 ], 'When using read group aware, you need to specify --read_group_file_1, --read_group_file_2 (when paired end), --new_files_path, and --file_id' - cmd = '%s OUTPUT_DIR="%s"' % ( cmd, tmp_dir) - #set up stdout and stderr output options - stdout = open_file_from_option( options.stdout, mode = 'wb' ) - if stdout is None: - stdout = sys.stdout - stderr = open_file_from_option( options.stderr, mode = 'wb' ) - #if no stderr file is specified, we'll use our own - if stderr is None: - stderr = tempfile.NamedTemporaryFile( prefix="picard-stderr-", dir=tmp_dir ) - - proc = subprocess.Popen( args=cmd, stdout=stdout, stderr=stderr, shell=True, cwd=tmp_dir ) - return_code = proc.wait() - - if return_code: - stderr_target = sys.stderr - else: - stderr_target = sys.stdout - stderr.flush() - stderr.seek(0) - while True: - chunk = stderr.read( CHUNK_SIZE ) - if chunk: - stderr_target.write( chunk ) - else: - break - stderr.close() - #if rg aware, put files where they belong - if options.new_files_path is not None: - fastq_1_name = options.read_group_file_1 - fastq_2_name = options.read_group_file_2 - file_id_1 = options.file_id_1 - file_id_2 = options.file_id_2 - if file_id_2 is None: - file_id_2 = file_id_1 - for filename in sorted( os.listdir( tmp_dir ) ): - if filename.endswith( '_1.fastq' ): - if fastq_1_name: - shutil.move( os.path.join( tmp_dir, filename ), fastq_1_name ) - fastq_1_name = None - else: - shutil.move( os.path.join( tmp_dir, filename ), os.path.join( options.new_files_path, 'primary_%s_%s - 1_visible_fastqsanger' % ( file_id_1, filename[:-len( '_1.fastq' )] ) ) ) - elif filename.endswith( '_2.fastq' ): - if fastq_2_name: - shutil.move( os.path.join( tmp_dir, filename ), fastq_2_name ) - fastq_2_name = None - else: - shutil.move( os.path.join( tmp_dir, filename ), os.path.join( options.new_files_path, 'primary_%s_%s - 2_visible_fastqsanger' % ( file_id_2, filename[:-len( '_2.fastq' )] ) ) ) - - cleanup_before_exit( tmp_dir ) - -if __name__=="__main__": __main__() |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_SortSam.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_SortSam.xml Tue Dec 16 19:03:21 2014 -0500 |
| b |
| @@ -0,0 +1,70 @@ +<tool id="picard_SortSam" name="SortSam" version="1.126.0"> + + <description>sort SAM/BAM dataset</description> + + <requirements> + <requirement type="package" version="1.126.0">picard</requirement> + </requirements> + + <macros> + <import>picard_macros.xml</import> + </macros> + + <command> + @java_options@ + java -jar \$JAVA_JAR_PATH/picard.jar + SortSam + INPUT="${inputFile}" + OUTPUT="${outFile}" + SORT_ORDER="${sort_order}" + QUIET=true + VERBOSITY=ERROR + VALIDATION_STRINGENCY=${validation_stringency} + </command> + + <inputs> + <param name="inputFile" type="data" format="sam,bam" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset"/> + <param name="sort_order" type="select" display="radio" label="Sort order" help="SORT_ORDER; default=coordinate"> + <option value="coordinate" selected="True">Coordinate</option> + <option value="queryname">Queryname</option> + <option value="unsorted">Unsorted</option> + </param> + <expand macro="VS" /> + </inputs> + + <outputs> + <data name="outFile" format="bam" label="${tool.name} on ${on_string}: BAM sorted in ${sort_order} order"> + </data> + </outputs> + + <stdio> + <exit_code range="1:" level="fatal"/> + </stdio> + + <tests> + <test> + <param name="inputFile" ftype="bam" value="picard_SortSam.bam" /> + <param name="sort_order" value="queryname"/> + <output name="outFile" file="picard_SortSam_test1.bam" ftype="bam" lines_diff="2"/> + </test> + </tests> + + <help> + +.. class:: infomark + +**Purpose** + +Sorts the input SAM or BAM. + +@dataset_collections@ + +@description@ + + SORT_ORDER=SortOrder + SO=SortOrder Sort order of output file Required. Possible values: {unsorted, queryname, coordinate} + + @more_info@ + + </help> +</tool> \ No newline at end of file |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_ValidateSamFile.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_ValidateSamFile.xml Tue Dec 16 19:03:21 2014 -0500 |
| [ |
| b'@@ -0,0 +1,230 @@\n+<tool name="ValidateSamFile" id="picard_ValidateSamFile" version="1.122.0">\n+ <description>assess validity of SAM/BAM dataset</description>\n+ <requirements>\n+ <requirement type="package" version="1.122.0">picard</requirement>\n+ </requirements>\n+ \n+ <macros>\n+ <import>picard_macros.xml</import>\n+ </macros>\n+ \n+ <command>\n+ \n+ ##set the maximum number of open file to hard maximum or 4096 if on a mac (mac gives \'unlimited\' as output of `ulimit -Hn` command\n+ \n+ [ `ulimit -Hn` = unlimited ] && ulimit -Sn 4096 || ulimit -Sn `ulimit -Hn`\n+ \n+ &&\n+ \n+ ##set up input files\n+\n+ #set $reference_fasta_filename = "localref.fa"\n+ \n+ #if str( $reference_source.reference_source_selector ) == "history":\n+ ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&\n+ #else:\n+ #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )\n+ #end if\n+ \n+ @java_options@\n+ \n+ java -jar \\$JAVA_JAR_PATH/picard.jar\n+ ValidateSamFile\n+ \n+ INPUT="${inputFile}"\n+ OUTPUT="${outFile}"\n+ MODE="${mode}"\n+ \n+ #if str( $ignore ) != "None":\n+ #for $element in str( $ignore ).split(\',\'): ## See trello card https://trello.com/c/9nW02Zhd\n+ IGNORE="${element}"\n+ #end for\n+ #end if\n+ \n+ MAX_OUTPUT="${max_output}"\n+ REFERENCE_SEQUENCE="${reference_fasta_filename}"\n+ IGNORE_WARNINGS="${ignore_warnings}"\n+ IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}"\n+ MAX_OPEN_TEMP_FILES=`ulimit -Sn`\n+ \n+ VERBOSITY=ERROR\n+ QUIET=true\n+ \n+ </command>\n+ <inputs>\n+ <param format="sam,bam" name="inputFile" type="data" label="SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset." />\n+ <conditional name="reference_source">\n+ <param name="reference_source_selector" type="select" label="Load reference genome from">\n+ <option value="cached">Local cache</option>\n+ <option value="history">History</option>\n+ </param>\n+ <when value="cached">\n+ <param name="ref_file" type="select" label="Use dictionary from the list" help="Select genome from the list">\n+ <options from_data_table="picard_indexes">\n+ <filter type="sort_by" column="2" />\n+ <validator type="no_options" message="No indexes are available" />\n+ </options>\n+ <validator type="no_options" message="A built-in dictionary is not available for the build associated with the selected input file"/>\n+ </param>\n+ </when>\n+ <when value="history"> \n+ <param name="ref_file" type="data" format="fasta" label="Use the following dataset to create dictionary" help="You can upload a FASTA sequence to the history from which Picard will automatically generate dictionary using CreateSequenceDictionary command" />\n+ </when>\n+ </conditional>\n+ \n+ <param name="mode" type="select" label="Select output mode" help="MODE">\n+ <option value="VERBOSE">Verbose</option>\n+ <option value="SUMMARY">Summary</option>\n+ </param>\n+ <param name="ignore" type="select" multiple="true" display="checkboxes" label="Select validation error types to ignore" help="IGNORE">\n+ <option value="INVALID_QUALITY_FORMAT">INVALID_QUALITY_FORMAT</option>\n+ <option value="INVALID_FLAG_PROPER_PAIR">INVALID_FLAG_PROPER_PAIR</option>\n+ <option value="INVALID_FLAG_MATE_UNMAPPED"/>\n+ <option value="MISMATCH_FLAG_MATE_UNMAPPED"/>\n+ <option value="INVALID_FLAG_MATE_NEG_STRAND"/>\n+ <option value="MISMATCH_FLAG_MATE_NEG_STRAND"/>\n+ <option value="INVALID_FLAG_FIRST_OF_PAIR"/>\n+ <option value="INVALID_FLAG_SECOND_OF_PAIR"/>\n+ <option value="PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND"/>\n+ <option value="INVALID_FLAG_NOT_PRIM_ALIGNMENT"/>\n+ <option value="INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT"/>\n+ <option value="INVALID_FLAG_READ_UNMAPPED"/>\n+ '..b"s@\n+\n+@description@\n+\n+ MODE=Mode\n+ M=Mode Mode of output Default value: VERBOSE. This option can be set to 'null' to clear the \n+ default value. Possible values: {VERBOSE, SUMMARY} \n+ \n+ IGNORE=Type List of validation error types to ignore. Possible values: {INVALID_QUALITY_FORMAT, \n+ INVALID_FLAG_PROPER_PAIR, INVALID_FLAG_MATE_UNMAPPED, MISMATCH_FLAG_MATE_UNMAPPED, \n+ INVALID_FLAG_MATE_NEG_STRAND, MISMATCH_FLAG_MATE_NEG_STRAND, INVALID_FLAG_FIRST_OF_PAIR, \n+ INVALID_FLAG_SECOND_OF_PAIR, PAIRED_READ_NOT_MARKED_AS_FIRST_OR_SECOND, \n+ INVALID_FLAG_NOT_PRIM_ALIGNMENT, INVALID_FLAG_SUPPLEMENTARY_ALIGNMENT, \n+ INVALID_FLAG_READ_UNMAPPED, INVALID_INSERT_SIZE, INVALID_MAPPING_QUALITY, INVALID_CIGAR, \n+ ADJACENT_INDEL_IN_CIGAR, INVALID_MATE_REF_INDEX, MISMATCH_MATE_REF_INDEX, \n+ INVALID_REFERENCE_INDEX, INVALID_ALIGNMENT_START, MISMATCH_MATE_ALIGNMENT_START, \n+ MATE_FIELD_MISMATCH, INVALID_TAG_NM, MISSING_TAG_NM, MISSING_HEADER, \n+ MISSING_SEQUENCE_DICTIONARY, MISSING_READ_GROUP, RECORD_OUT_OF_ORDER, \n+ READ_GROUP_NOT_FOUND, RECORD_MISSING_READ_GROUP, INVALID_INDEXING_BIN, \n+ MISSING_VERSION_NUMBER, INVALID_VERSION_NUMBER, TRUNCATED_FILE, \n+ MISMATCH_READ_LENGTH_AND_QUALS_LENGTH, EMPTY_READ, CIGAR_MAPS_OFF_REFERENCE, \n+ MISMATCH_READ_LENGTH_AND_E2_LENGTH, MISMATCH_READ_LENGTH_AND_U2_LENGTH, \n+ E2_BASE_EQUALS_PRIMARY_BASE, BAM_FILE_MISSING_TERMINATOR_BLOCK, UNRECOGNIZED_HEADER_TYPE, \n+ POORLY_FORMATTED_HEADER_TAG, HEADER_TAG_MULTIPLY_DEFINED, \n+ HEADER_RECORD_MISSING_REQUIRED_TAG, INVALID_DATE_STRING, TAG_VALUE_TOO_LARGE, \n+ INVALID_INDEX_FILE_POINTER, INVALID_PREDICTED_MEDIAN_INSERT_SIZE, \n+ DUPLICATE_READ_GROUP_ID, MISSING_PLATFORM_VALUE, INVALID_PLATFORM_VALUE, \n+ DUPLICATE_PROGRAM_GROUP_ID, MATE_NOT_FOUND, MATES_ARE_SAME_END, \n+ MISMATCH_MATE_CIGAR_STRING, MATE_CIGAR_STRING_INVALID_PRESENCE} This option may be \n+ specified 0 or more times. \n+ \n+ MAX_OUTPUT=Integer\n+ MO=Integer The maximum number of lines output in verbose mode Default value: 100. This option can \n+ be set to 'null' to clear the default value. \n+ \n+ REFERENCE_SEQUENCE=File\n+ R=File Reference sequence file, the NM tag check will be skipped if this is missing Default \n+ value: null. \n+ \n+ IGNORE_WARNINGS=Boolean If true, only report errors and ignore warnings. Default value: false. This option can \n+ be set to 'null' to clear the default value. Possible values: {true, false} \n+ \n+ VALIDATE_INDEX=Boolean If true and input is a BAM file with an index file, also validates the index. Default \n+ value: true. This option can be set to 'null' to clear the default value. Possible \n+ values: {true, false} \n+ \n+ IS_BISULFITE_SEQUENCED=Boolean\n+ BISULFITE=Boolean Whether the SAM or BAM file consists of bisulfite sequenced reads. If so, C->T is not \n+ counted as an error in computing the value of the NM tag. Default value: false. This \n+ option can be set to 'null' to clear the default value. Possible values: {true, false} \n+ \n+@more_info@\n+\n+ </help>\n+</tool>\n+\n+\n" |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/picard_macros.xml Tue Dec 16 19:03:21 2014 -0500 |
| b |
| @@ -0,0 +1,85 @@ +<macros> + <xml name="VS"> + <param name="validation_stringency" type="select" label="Select validation stringency" help=" Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded."> + <option value="LENIENT" selected="True">Lenient</option> + <option value="SILENT">Silent</option> + <option value="STRICT">Strict</option> + </param> + </xml> + + <token name="@java_options@"> + _JAVA_OPTIONS=\${_JAVA_OPTIONS:-'-Xmx2048m -Xms256m'} && + export _JAVA_OPTIONS && + </token> + + <token name="@more_info@"> +------ + +**Additional information** + +Additional information about Picard tools is available from Picard web site at http://broadinstitute.github.io/picard/. + </token> + + + <token name="@description@"> +------ + +**Inputs, outputs, and parameters** + +Either a SAM file or a BAM file must be supplied. Galaxy automatically coordinate-sorts all uploaded BAM files. + +From Picard documentation( http://broadinstitute.github.io/picard/):: + + </token> + <token name="@RG@"> +------- + +**Read Groups are Important!** + +Setting read groups correctly from the start will simplify your life greatly because you can merge multiple BAM files into one significantly reducing the number of analysis steps. Below we provide an explanation of read groups fields taken from GATK FAQ webpage: + +.. csv-table:: + :header-rows: 1 + + Tag,Importance,Definition,Meaning + "ID","Required","Read group identifier. Each @RG line must have a unique ID. The value of ID is used in the RG tags of alignment records. Must be unique among all read groups in header section. Read group IDs may be modified when merging SAM files in order to handle collisions.","Ideally, this should be a globally unique identify across all sequencing data in the world, such as the Illumina flowcell + lane name and number. Will be referenced by each read with the RG:Z field, allowing tools to determine the read group information associated with each read, including the sample from which the read came. Also, a read group is effectively treated as a separate run of the NGS instrument in tools like base quality score recalibration (a GATK component) -- all reads within a read group are assumed to come from the same instrument run and to therefore share the same error model." + "SM","Sample. Use pool name where a pool is being sequenced.","Required. As important as ID.","The name of the sample sequenced in this read group. GATK tools treat all read groups with the same SM value as containing sequencing data for the same sample. Therefore it's critical that the SM field be correctly specified, especially when using multi-sample tools like the Unified Genotyper (a GATK component)." + "PL","Platform/technology used to produce the read. Valid values: ILLUMINA, SOLID, LS454, HELICOS and PACBIO.","Important. Not currently used in the GATK, but was in the past, and may return. The only way to known the sequencing technology used to generate the sequencing data","It's a good idea to use this field." + "LB","DNA preparation library identify","Essential for MarkDuplicates","MarkDuplicates uses the LB field to determine which read groups might contain molecular duplicates, in case the same DNA library was sequenced on multiple lanes." + +**Example of Read Group usage** + +Support we have a trio of samples: MOM, DAD, and KID. Each has two DNA libraries prepared, one with 400 bp inserts and another with 200 bp inserts. Each of these libraries is run on two lanes of an illumina hiseq, requiring 3 x 2 x 2 = 12 lanes of data. When the data come off the sequencer, we would create 12 BAM files, with the following @RG fields in the header:: + + Dad's data: + @RG ID:FLOWCELL1.LANE1 PL:illumina LB:LIB-DAD-1 SM:DAD PI:200 + @RG ID:FLOWCELL1.LANE2 PL:illumina LB:LIB-DAD-1 SM:DAD PI:200 + @RG ID:FLOWCELL1.LANE3 PL:illumina LB:LIB-DAD-2 SM:DAD PI:400 + @RG ID:FLOWCELL1.LANE4 PL:illumina LB:LIB-DAD-2 SM:DAD PI:400 + + Mom's data: + @RG ID:FLOWCELL1.LANE5 PL:illumina LB:LIB-MOM-1 SM:MOM PI:200 + @RG ID:FLOWCELL1.LANE6 PL:illumina LB:LIB-MOM-1 SM:MOM PI:200 + @RG ID:FLOWCELL1.LANE7 PL:illumina LB:LIB-MOM-2 SM:MOM PI:400 + @RG ID:FLOWCELL1.LANE8 PL:illumina LB:LIB-MOM-2 SM:MOM PI:400 + + Kid's data: + @RG ID:FLOWCELL2.LANE1 PL:illumina LB:LIB-KID-1 SM:KID PI:200 + @RG ID:FLOWCELL2.LANE2 PL:illumina LB:LIB-KID-1 SM:KID PI:200 + @RG ID:FLOWCELL2.LANE3 PL:illumina LB:LIB-KID-2 SM:KID PI:400 + @RG ID:FLOWCELL2.LANE4 PL:illumina LB:LIB-KID-2 SM:KID PI:400 + +Note the hierarchical relationship between read groups (unique for each lane) to libraries (sequenced on two lanes) and samples (across four lanes, two lanes for each library). + </token> + <token name="@dataset_collections@"> +------ + +**Dataset collections - processing large numbers of datasets at once** + +This will be added shortly + + + </token> + + +</macros> |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e picard_wrapper.py --- a/picard_wrapper.py Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| b'@@ -1,776 +0,0 @@\n-#!/usr/bin/env python\n-"""\n-Originally written by Kelly Vincent\n-pretty output and additional picard wrappers by Ross Lazarus for rgenetics\n-Runs all available wrapped Picard tools.\n-usage: picard_wrapper.py [options]\n-code Ross wrote licensed under the LGPL\n-see http://www.gnu.org/copyleft/lesser.html\n-"""\n-\n-import optparse, os, sys, subprocess, tempfile, shutil, time, logging\n-\n-galhtmlprefix = """<?xml version="1.0" encoding="utf-8" ?>\n-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">\n-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">\n-<head>\n-<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />\n-<meta name="generator" content="Galaxy %s tool output - see http://getgalaxy.org/" />\n-<title></title>\n-<link rel="stylesheet" href="/static/style/base.css" type="text/css" />\n-</head>\n-<body>\n-<div class="document">\n-"""\n-galhtmlattr = """Galaxy tool %s run at %s</b><br/>"""\n-galhtmlpostfix = """</div></body></html>\\n"""\n-\n-\n-def stop_err( msg ):\n- sys.stderr.write( \'%s\\n\' % msg )\n- sys.exit()\n- \n-\n-def timenow():\n- """return current time as a string\n- """\n- return time.strftime(\'%d/%m/%Y %H:%M:%S\', time.localtime(time.time()))\n-\n-\n-class PicardBase():\n- """\n- simple base class with some utilities for Picard\n- adapted and merged with Kelly Vincent\'s code april 2011 Ross\n- lots of changes...\n- """\n- \n- def __init__(self, opts=None,arg0=None):\n- """ common stuff needed at init for a picard tool\n- """\n- assert opts <> None, \'PicardBase needs opts at init\'\n- self.opts = opts\n- if self.opts.outdir == None:\n- self.opts.outdir = os.getcwd() # fixmate has no html file eg so use temp dir\n- assert self.opts.outdir <> None,\'## PicardBase needs a temp directory if no output directory passed in\'\n- self.picname = self.baseName(opts.jar)\n- if self.picname.startswith(\'picard\'):\n- self.picname = opts.picard_cmd # special case for some tools like replaceheader?\n- self.progname = self.baseName(arg0)\n- self.version = \'0.002\'\n- self.delme = [] # list of files to destroy\n- self.title = opts.title\n- self.inputfile = opts.input\n- try:\n- os.makedirs(opts.outdir)\n- except:\n- pass\n- try:\n- os.makedirs(opts.tmpdir)\n- except:\n- pass\n- self.log_filename = os.path.join(self.opts.outdir,\'%s.log\' % self.picname)\n- self.metricsOut = os.path.join(opts.outdir,\'%s.metrics.txt\' % self.picname)\n- self.setLogging(logfname=self.log_filename)\n- \n- def baseName(self,name=None):\n- return os.path.splitext(os.path.basename(name))[0]\n-\n- def setLogging(self,logfname="picard_wrapper.log"):\n- """setup a logger\n- """\n- logging.basicConfig(level=logging.INFO,\n- filename=logfname,\n- filemode=\'a\')\n-\n-\n- def readLarge(self,fname=None):\n- """ read a potentially huge file.\n- """\n- try:\n- # get stderr, allowing for case where it\'s very large\n- tmp = open( fname, \'rb\' )\n- s = \'\'\n- buffsize = 1048576\n- try:\n- while True:\n- more = tmp.read( buffsize )\n- if len(more) > 0:\n- s += more\n- else:\n- break\n- except OverflowError:\n- pass\n- tmp.close()\n- except Exception, e:\n- stop_err( \'Read Large Exception : %s\' % str( e ) ) \n- return s\n- \n- def runCL(self,cl=None,output_dir=None):\n- """ construct and run a command line\n- we have galaxy\'s temp path as opt.temp_dir so don\'t really need isolation\n- sometimes stdout is needed as the output - ugly hacks to deal with potentially v'..b'ORDANCE=true\')\n- # contig length discordance\n- if opts.allow_contig_len_discord == \'true\':\n- cl.append(\'ALLOW_CONTIG_LENGTH_DISCORDANCE=true\')\n- stdouts,rval = pic.runPic(opts.jar, cl)\n- haveTempout = True\n-\n- elif pic.picname == \'ReplaceSamHeader\':\n- cl.append(\'INPUT=%s\' % opts.input)\n- cl.append(\'OUTPUT=%s\' % tempout)\n- cl.append(\'HEADER=%s\' % opts.header_file)\n- stdouts,rval = pic.runPic(opts.jar, cl)\n- haveTempout = True\n-\n- elif pic.picname == \'CalculateHsMetrics\':\n- maxloglines = 100\n- baitfname = os.path.join(opts.outdir,\'rgPicardHsMetrics.bait\')\n- targetfname = os.path.join(opts.outdir,\'rgPicardHsMetrics.target\')\n- baitf = pic.makePicInterval(opts.baitbed,baitfname)\n- if opts.targetbed == opts.baitbed: # same file sometimes\n- targetf = baitf\n- else:\n- targetf = pic.makePicInterval(opts.targetbed,targetfname) \n- cl.append(\'BAIT_INTERVALS=%s\' % baitf)\n- cl.append(\'TARGET_INTERVALS=%s\' % targetf)\n- cl.append(\'INPUT=%s\' % os.path.abspath(opts.input))\n- cl.append(\'OUTPUT=%s\' % pic.metricsOut)\n- cl.append(\'TMP_DIR=%s\' % opts.tmpdir)\n- stdouts,rval = pic.runPic(opts.jar,cl)\n- \n- elif pic.picname == \'ValidateSamFile\':\n- import pysam\n- doTranspose = False\n- sortedfile = os.path.join(opts.outdir,\'rgValidate.sorted\')\n- stf = open(pic.log_filename,\'w\')\n- tlog = None\n- if opts.datatype == \'sam\': # need to work with a bam \n- tlog,tempbam,rval = pic.samToBam(opts.input,opts.outdir)\n- try:\n- tlog = pic.sortSam(tempbam,sortedfile,opts.outdir)\n- except:\n- print \'## exception on sorting sam file %s\' % opts.input\n- else: # is already bam\n- try:\n- tlog = pic.sortSam(opts.input,sortedfile,opts.outdir)\n- except: # bug - [bam_sort_core] not being ignored - TODO fixme\n- print \'## exception on sorting bam file %s\' % opts.input\n- if tlog:\n- print \'##tlog=\',tlog\n- stf.write(tlog)\n- stf.write(\'\\n\')\n- sortedfile = \'%s.bam\' % sortedfile # samtools does that \n- cl.append(\'O=%s\' % pic.metricsOut)\n- cl.append(\'TMP_DIR=%s\' % opts.tmpdir)\n- cl.append(\'I=%s\' % sortedfile)\n- opts.maxerrors = \'99999999\'\n- cl.append(\'MAX_OUTPUT=%s\' % opts.maxerrors)\n- if opts.ignoreflags[0] <> \'None\': # picard error values to ignore\n- igs = [\'IGNORE=%s\' % x for x in opts.ignoreflags if x <> \'None\']\n- cl.append(\' \'.join(igs))\n- if opts.bisulphite.lower() <> \'false\':\n- cl.append(\'IS_BISULFITE_SEQUENCED=true\')\n- if opts.ref <> None or opts.ref_file <> None:\n- cl.append(\'R=%s\' % ref_file_name)\n- stdouts,rval = pic.runPic(opts.jar,cl)\n- if opts.datatype == \'sam\':\n- pic.delme.append(tempbam)\n- newsam = opts.output\n- outformat = \'bam\'\n- pe = open(pic.metricsOut,\'r\').readlines()\n- pic.cleanSam(insam=sortedfile, newsam=newsam, picardErrors=pe,outformat=outformat)\n- pic.delme.append(sortedfile) # not wanted\n- stf.close()\n- pic.cleanup()\n- else:\n- print >> sys.stderr,\'picard.py got an unknown tool name - %s\' % pic.picname\n- sys.exit(1)\n- if haveTempout:\n- # Some Picard tools produced a potentially intermediate bam file. \n- # Either just move to final location or create sam\n- if os.path.exists(tempout):\n- shutil.move(tempout, os.path.abspath(opts.output))\n- if opts.htmlout <> None or doFix: # return a pretty html page\n- pic.fixPicardOutputs(transpose=doTranspose,maxloglines=maxloglines)\n- if rval <> 0:\n- print >> sys.stderr, \'## exit code=%d; stdout=%s\' % (rval,stdouts)\n- # signal failure\n-if __name__=="__main__": __main__()\n-\n' |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e rgPicardASMetrics.xml --- a/rgPicardASMetrics.xml Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,162 +0,0 @@\n-<tool name="SAM/BAM Alignment Summary Metrics" id="PicardASMetrics" version="1.56.0">\n- <command interpreter="python">\n- picard_wrapper.py -i "${input_file}" -d "${html_file.files_path}" -t "${html_file}"\n- --assumesorted "${sorted}" -b "${bisulphite}" --adaptors "${adaptors}" --maxinsert "${maxinsert}" -n "${out_prefix}" --datatype "${input_file.ext}"\n- -j \\$JAVA_JAR_PATH/CollectAlignmentSummaryMetrics.jar --tmpdir "${__new_file_path__}" \n-#if $genomeSource.refGenomeSource == "history":\n- --ref-file "${genomeSource.ownFile}"\n-#else\n- --ref "${genomeSource.index.fields.path}"\n-#end if\n- </command>\n- <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>\n- <inputs>\n- <param format="sam,bam" name="input_file" type="data" label="SAM/BAM dataset to generate statistics for"\n- help="If empty, upload or import a SAM/BAM dataset."/>\n- <param name="out_prefix" value="Picard Alignment Summary Metrics" type="text"\n- label="Title for the output file" help="Use this remind you what the job was for." size="80" />\n-\n- <conditional name="genomeSource">\n- \n- <param name="refGenomeSource" type="select" label="Select Reference Genome">\n- <option value="default" selected="true">Use the assigned data genome/build</option>\n- <option value="indexed">Select a different built-in genome</option>\n- <option value="history">Use a genome (fasta format) from my history</option>\n- </param>\n- <when value="default">\n- <param name="index" type="select" label="Check the assigned reference genome" help="Galaxy thinks that the reads in you dataset were aligned against this reference. If this is not correct, use the \'Select a build-in reference genome\' option of the \'Select Reference Genome\' dropdown to select approprtiate Reference.">\n- <options from_data_table="all_fasta">\n- <filter type="data_meta" ref="input_file" key="dbkey" column="1" multiple="True" separator="," />\n- <validator type="no_options" message="No reference build available for selected input" /> \n- </options>\n- </param>\n- </when>\n- <when value="indexed">\n- <param name="index" type="select" label="Select a built-in reference genome" help="This list contains genomes cached at this Galaxy instance. If your genome of interest is not present here request it by using \'Help\' link at the top of Galaxy interface or use the \'Use a genome (fasta format) from my history\' option of the \'Select Reference Genome\' dropdown.">\n- <options from_data_table="all_fasta">\n- </options>\n- </param>\n- </when>\n- <when value="history">\n- <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome from history" help="This option works best for relatively small genomes. If you are working with large human-sized genomes, send request to Galaxy team for adding your reference to this Galaxy instance by using \'Help\' link at the top of Galaxy interface."/>\n- </when>\n- </conditional>\n- <param name="sorted" type="boolean" label="Assume the input file is already sorted" checked="true" truevalue="true" falsevalue="false"/>\n- <param name="bisulphite" type="boolean" label="Input file contains Bisulphite sequenced reads" checked="false" falsevalue="false" truevalue="true" />\n- <param name="adaptors" value="" type="text" area="true" label="Adapter sequences" help="One per line if multiple" size="5x120" />\n- <param name="maxinsert" value="100000" type="integer" label="Larger paired end reads and inter-chromosomal pairs considered chimeric " size="20" />\n- </inputs>\n- <outputs>\n- <data format="html" name="html_file" label="${out_prefix}.html" />\n- </outputs>\n- <tests>\n- <test>\n- <param name="out_prefix" value="AsMetrics" />\n- <param name="bisulphite" value="false" />\n- <param name="sorted" value="true" />\n- '..b' with inter-chromosomal pairs. Default value: 100000."\n- "ADAPTER_SEQUENCE=String","This option may be specified 0 or more times. "\n- "IS_BISULFITE_SEQUENCED=Boolean","Whether the SAM or BAM file consists of bisulfite sequenced reads. Default value: false. "\n- "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created."\n-\n-The output produced by the tool has the following columns::\n-\n- 1. CATEGORY: One of either UNPAIRED (for a fragment run), FIRST_OF_PAIR when metrics are for only the first read in a paired run, SECOND_OF_PAIR when the metrics are for only the second read in a paired run or PAIR when the metrics are aggregeted for both first and second reads in a pair.\n- 2. TOTAL_READS: The total number of reads including all PF and non-PF reads. When CATEGORY equals PAIR this value will be 2x the number of clusters.\n- 3. PF_READS: The number of PF reads where PF is defined as passing Illumina\'s filter.\n- 4. PCT_PF_READS: The percentage of reads that are PF (PF_READS / TOTAL_READS)\n- 5. PF_NOISE_READS: The number of PF reads that are marked as noise reads. A noise read is one which is composed entirey of A bases and/or N bases. These reads are marked as they are usually artifactual and are of no use in downstream analysis.\n- 6. PF_READS_ALIGNED: The number of PF reads that were aligned to the reference sequence. This includes reads that aligned with low quality (i.e. their alignments are ambiguous).\n- 7. PCT_PF_READS_ALIGNED: The percentage of PF reads that aligned to the reference sequence. PF_READS_ALIGNED / PF_READS\n- 8. PF_HQ_ALIGNED_READS: The number of PF reads that were aligned to the reference sequence with a mapping quality of Q20 or higher signifying that the aligner estimates a 1/100 (or smaller) chance that the alignment is wrong.\n- 9. PF_HQ_ALIGNED_BASES: The number of bases aligned to the reference sequence in reads that were mapped at high quality. Will usually approximate PF_HQ_ALIGNED_READS * READ_LENGTH but may differ when either mixed read lengths are present or many reads are aligned with gaps.\n- 10. PF_HQ_ALIGNED_Q20_BASES: The subest of PF_HQ_ALIGNED_BASES where the base call quality was Q20 or higher.\n- 11. PF_HQ_MEDIAN_MISMATCHES: The median number of mismatches versus the reference sequence in reads that were aligned to the reference at high quality (i.e. PF_HQ_ALIGNED READS).\n- 12. PF_HQ_ERROR_RATE: The percentage of bases that mismatch the reference in PF HQ aligned reads.\n- 13. MEAN_READ_LENGTH: The mean read length of the set of reads examined. When looking at the data for a single lane with equal length reads this number is just the read length. When looking at data for merged lanes with differing read lengths this is the mean read length of all reads.\n- 14. READS_ALIGNED_IN_PAIRS: The number of aligned reads who\'s mate pair was also aligned to the reference.\n- 15. PCT_READS_ALIGNED_IN_PAIRS: The percentage of reads who\'s mate pair was also aligned to the reference. READS_ALIGNED_IN_PAIRS / PF_READS_ALIGNED\n- 16. BAD_CYCLES: The number of instrument cycles in which 80% or more of base calls were no-calls.\n- 17. STRAND_BALANCE: The number of PF reads aligned to the positive strand of the genome divided by the number of PF reads aligned to the genome.\n- 18. PCT_CHIMERAS: The percentage of reads that map outside of a maximum insert size (usually 100kb) or that have the two ends mapping to different chromosomes.\n- 19. PCT_ADAPTER: The percentage of PF reads that are unaligned and match to a known adapter sequence right from the start of the read.\n-\n-.. class:: warningmark\n-\n-**Warning on SAM/BAM quality**\n-\n-Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**\n-flag when it runs Picard, which allows reads to be discarded if they\'re empty or don\'t map. This appears\n-to be the only way to deal with SAM/BAM that cannot be parsed.\n-\n-\n- </help>\n-</tool>\n-\n' |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e rgPicardFixMate.xml --- a/rgPicardFixMate.xml Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,107 +0,0 @@ -<tool name="Paired Read Mate Fixer" id="rgPicFixMate" version="1.56.0"> - <description>for paired data</description> - <command interpreter="python"> - picard_wrapper.py -i "${input_file}" -o "${out_file}" --tmpdir "${__new_file_path__}" -n "${out_prefix}" - --output-format "${outputFormat}" -j "\$JAVA_JAR_PATH/FixMateInformation.jar" --sortorder "${sortOrder}" - </command> - <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> - <inputs> - <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to fix" - help="If empty, upload or import a SAM/BAM dataset."/> - <param name="sortOrder" type="select" help="If in doubt, leave as default and read Picard/Samtools documentation" - label="Sort order"> - <option value="coordinate" selected ="true">Coordinate sort</option> - <option value="queryname">Query name sort</option> - <option value="unsorted">Unsorted - docs not clear if this means unchanged or not</option> - </param> - <param name="out_prefix" value="Fix Mate" type="text" - label="Title for the output file" help="Use this remind you what the job was for." size="80" /> - <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 format="bam" name="out_file" label="${tool.name} on ${on_string}: ${outputFormat} with fixed mates"> - <change_format> - <when input="outputFormat" value="sam" format="sam" /> - </change_format> - </data> - </outputs> - <tests> - <test> - <param name="input_file" value="picard_input_sorted_pair.sam" /> - <param name="sortOrder" value="coordinate" /> - <param name="outputFormat" value="True" /> - <param name="out_prefix" value="Test FixMate" /> - <output name="out_file" file="picard_output_fixmate_sorted_pair.bam" ftype="bam" /> - </test> - <test> - <param name="input_file" value="picard_input_sorted_pair.sam" /> - <param name="sortOrder" value="coordinate" /> - <param name="outputFormat" value="False" /> - <param name="out_prefix" value="Test FixMate" /> - <output name="out_file" file="picard_output_fixmate_sorted_pair.sam" ftype="sam" /> - </test> - </tests> - <help> - - -.. class:: infomark - -**Purpose** - -Ensure that all mate-pair information is in sync between each read and it's mate pair. - -**Picard documentation** - -This is a Galaxy wrapper for FixMateInformation, a part of the external package Picard-tools_. - - .. _Picard-tools: http://www.google.com/search?q=picard+samtools - -.. class:: warningmark - -**Useful for paired data only** - -Likely won't do anything helpful for single end sequence data -Currently, Galaxy doesn't distinguish paired from single ended SAM/BAM so make sure -the data you choose are valid (paired end) SAM or BAM data - unless you trust this -tool not to harm your data. - ------ - -.. class:: infomark - -**Syntax** - -- **Input** - a paired read sam/bam format aligned short read data in your current history -- **Sort order** - can be used to adjust the ordering of reads -- **Title** - the title to use for all output files from this job - use it for high level metadata -- **Output Format** - either SAM or compressed as BAM - ------ - -.. class:: infomark - -**Inputs, outputs, and parameters** - -.. csv-table:: - - :header-rows: 1 - - Option,Description - "INPUT=File","The input file to fix. This option may be specified 0 or more times." - "OUTPUT=File","The output file to write to" - "SORT_ORDER=SortOrder","Optional sort order if the OUTPUT file should be sorted differently than the INPUT file. Default value: null. Possible values: {unsorted, queryname, coordinate}" - "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false" - -.. class:: warningmark - -**Warning on SAM/BAM quality** - -Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT** -flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears -to be the only way to deal with SAM/BAM that cannot be parsed. - - - </help> -</tool> - - |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e rgPicardGCBiasMetrics.xml --- a/rgPicardGCBiasMetrics.xml Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,150 +0,0 @@\n-<tool name="SAM/BAM GC Bias Metrics" id="PicardGCBiasMetrics" version="1.56.0">\n- <command interpreter="python">\n- picard_wrapper.py -i "${input_file}" -d "${html_file.files_path}" -t "${html_file}"\n- --windowsize "${windowsize}" --mingenomefrac "${mingenomefrac}" -n "${out_prefix}" --tmpdir "${__new_file_path__}"\n- -j "\\$JAVA_JAR_PATH/CollectGcBiasMetrics.jar"\n-#if $genomeSource.refGenomeSource == "history":\n- --ref-file "${genomeSource.ownFile}"\n-#else:\n- --ref "${genomeSource.index.fields.path}"\n-#end if\n- </command>\n- <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>\n- <inputs>\n- <param format="sam,bam" name="input_file" type="data" label="SAM/BAM dataset to generateGC bias metrics"\n- help="If empty, upload or import a SAM/BAM dataset."/>\n- <param name="out_prefix" value="Short Read GC Bias Metrics" type="text"\n- label="Title for the output file" help="Use this remind you what the job was for." size="80" />\n- <conditional name="genomeSource"> \n- <param name="refGenomeSource" type="select" label="Select Reference Genome">\n- <option value="default" selected="true">Use the assigned data genome/build</option>\n- <option value="indexed">Select a different built-in genome</option>\n- <option value="history">Use a genome (fasta format) from my history</option>\n- </param>\n- <when value="default">\n- <param name="index" type="select" label="Check the assigned reference genome" help="Galaxy thinks that the reads in you dataset were aligned against this reference. If this is not correct, use the \'Select a build-in reference genome\' option of the \'Select Reference Genome\' dropdown to select approprtiate Reference.">\n- <options from_data_table="all_fasta">\n- <filter type="data_meta" ref="input_file" key="dbkey" column="1" multiple="True" separator=","/>\n- <validator type="no_options" message="No reference build available for the selected input data" />\n- </options>\n- </param>\n- </when>\n- <when value="indexed">\n- <param name="index" type="select" label="Select a built-in reference genome" help="This list contains genomes cached at this Galaxy instance. If your genome of interest is not present here request it by using \'Help\' link at the top of Galaxy interface or use the \'Use a genome (fasta format) from my history\' option of the \'Select Reference Genome\' dropdown.">\n- <options from_data_table="all_fasta"/>\n- </param>\n- </when>\n- <when value="history">\n- <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select a reference genome from history" help="This option works best for relatively small genomes. If you are working with large human-sized genomes, send request to Galaxy team for adding your reference to this Galaxy instance by using \'Help\' link at the top of Galaxy interface."/>\n- </when>\n- </conditional>\n- <param name="windowsize" type="integer" label="GC minimum window size" value="100"\n- help="The size of windows on the genome that are used to bin reads. Default value: 100."/>\n- <param name="mingenomefrac" value="0.00001" type="float" label="Minimum Genome Fraction"\n- help="For summary metrics, exclude GC windows that include less than this fraction of the genome. Default value: 1.0E-5." />\n- <!--\n- \n- Users can be enabled to set Java heap size by uncommenting this option and adding \'-x "$maxheap"\' to the <command> tag.\n- If commented out the heapsize defaults to the value specified within picard_wrapper.py\n- \n- <param name="maxheap" type="select" help="If in doubt, choose 8G and read Picard documentation please"\n- label="Java heap size">\n- <option value="1G">1GB: very small data</option>\n- <option value="2G" selected="true">2GB</option>\n- <option value="4G">4GB for larger datasets </option>\n- <option value="8G" >8GB use if '..b'yntax**\n-\n-- **Input** - SAM/BAM format aligned short read data in your current history\n-- **Title** - the title to use for all output files from this job - use it for high level metadata\n-- **Reference Genome** - Galaxy (and Picard) needs to know which genomic reference was used to generate alignemnts within the input SAM/BAM dataset. Here you have three choices:\n-\n- - *Assigned data genome/build* - a genome specified for this dataset. If you your SAM/BAM dataset has an assigned reference genome it will be displayed below this dropdown. If it does not -> use one of the following two options.\n- - *Select a different built-in genome* - this option will list all reference genomes presently cached at this instance of Galaxy.\n- - *Select a reference genome from history* - alternatively you can upload your own version of reference genome into your history and use it with this option. This is however not advisable with large human-sized genomes. If your genome is large contact Galaxy team using "Help" link at the top of the interface and provide exact details on where we can download sequences you would like to use as the refenece. We will then install them as a part of locally cached genomic references.\n- \n-- **Window Size** see Picard documentation http://picard.sourceforge.net/command-line-overview.shtml#CollectGCBiasMetrics\n-- **Minimum Genome Fraction** See Picard documentation at http://picard.sourceforge.net/command-line-overview.shtml#CollectGCBiasMetrics\n-\n------\n-\n-.. class:: infomark\n-\n-**Inputs, outputs, and parameters**\n-\n-The Picard documentation (reformatted for Galaxy) says:\n-\n-.. csv-table::\n- :header-rows: 1\n-\n- Option,Description\n- "REFERENCE_SEQUENCE=File","The reference sequence fasta file. Required."\n- "INPUT=File","The BAM or SAM file containing aligned reads. Required."\n- "OUTPUT=File","The text file to write the metrics table to. Required."\n- "CHART_OUTPUT=File","The PDF file to render the chart to. Required."\n- "SUMMARY_OUTPUT=File","The text file to write summary metrics to. Default value: null."\n- "WINDOW_SIZE=Integer","The size of windows on the genome that are used to bin reads. Default value: 100."\n- "MINIMUM_GENOME_FRACTION=Double","For summary metrics, exclude GC windows that include less than this fraction of the genome. Default value: 1.0E-5."\n- "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false."\n-\n-The output produced by the tool has the following columns::\n-\n- 1. GC: The G+C content of the reference sequence represented by this bin. Values are from 0% to 100%\n- 2. WINDOWS: The number of windows on the reference genome that have this G+C content.\n- 3. READ_STARTS: The number of reads who\'s start position is at the start of a window of this GC.\n- 4. MEAN_BASE_QUALITY: The mean quality (determined via the error rate) of all bases of all reads that are assigned to windows of this GC.\n- 5. NORMALIZED_COVERAGE: The ration of "coverage" in this GC bin vs. the mean coverage of all GC bins. A number of 1 represents mean coverage, a number less than one represents lower than mean coverage (e.g. 0.5 means half as much coverage as average) while a number greater than one represents higher than mean coverage (e.g. 3.1 means this GC bin has 3.1 times more reads per window than average).\n- 6. ERROR_BAR_WIDTH: The radius of error bars in this bin based on the number of observations made. For example if the normalized coverage is 0.75 and the error bar width is 0.1 then the error bars would be drawn from 0.65 to 0.85.\n-\n-.. class:: warningmark\n-\n-**Warning on SAM/BAM quality**\n-\n-Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**\n-flag when it runs Picard, which allows reads to be discarded if they\'re empty or don\'t map. This appears\n-to be the only way to deal with SAM/BAM that cannot be parsed.\n-\n- </help>\n-</tool>\n' |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e rgPicardHsMetrics.xml --- a/rgPicardHsMetrics.xml Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,156 +0,0 @@\n-<tool name="SAM/BAM Hybrid Selection Metrics" id="PicardHsMetrics" version="1.56.0">\n- <description>for targeted resequencing data</description>\n- <command interpreter="python">\n-\n- picard_wrapper.py -i "${input_file}" -d "${html_file.files_path}" -t "${html_file}" --datatype "${input_file.ext}"\n- --baitbed "${bait_bed}" --targetbed "${target_bed}" -n "${out_prefix}" --tmpdir "${__new_file_path__}"\n- -j "\\$JAVA_JAR_PATH/CalculateHsMetrics.jar"\n-\n- </command>\n- <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>\n- <inputs>\n- <param format="sam,bam" name="input_file" type="data" label="SAM/BAM dataset to generate statistics for" />\n- <param name="out_prefix" value="Picard HS Metrics" type="text" label="Title for the output file" help="Use to remind you what the job was for." size="80" />\n- <param name="bait_bed" type="data" format="bed,interval" label="Bait intervals: Sequences for bait in the design" help="Note specific format requirements below!" size="80" />\n- <param name="target_bed" type="data" format="bed,interval" label="Target intervals: Sequences for targets in the design" help="Note specific format requirements below!" size="80" />\n- <!--\n- \n- Users can be enabled to set Java heap size by uncommenting this option and adding \'-x "$maxheap"\' to the <command> tag.\n- If commented out the heapsize defaults to the value specified within picard_wrapper.py\n- \n- <param name="maxheap" type="select" \n- help="If in doubt, try the default. If it fails with a complaint about java heap size, try increasing it please - larger jobs will require your own hardware."\n- label="Java heap size">\n- <option value="4G" selected = "true">4GB default </option>\n- <option value="8G" >8GB use if 4GB fails</option>\n- <option value="16G">16GB - try this if 8GB fails</option>\n- </param>\n- \n- -->\n- </inputs>\n- <outputs>\n- <data format="html" name="html_file" label="${out_prefix}.html" />\n- </outputs>\n- <tests>\n- <test>\n- <!-- Uncomment this if maxheap parameter is enabled\n- <param name="maxheap" value="8G" />\n- -->\n- <param name="out_prefix" value="HSMetrics" />\n- <param name="input_file" value="picard_input_summary_alignment_stats.sam" ftype="sam" />\n- <param name="bait_bed" value="picard_input_bait.bed" />\n- <param name="target_bed" value="picard_input_bait.bed" />\n- <output name="html_file" file="picard_output_hs_transposed_summary_alignment_stats.html" ftype="html" lines_diff="212"/>\n- </test>\n- </tests>\n- <help>\n-\n-.. class:: infomark\n-\n-**Summary**\n-\n-Calculates a set of Hybrid Selection specific metrics from an aligned SAM or BAM file.\n-\n-.. class:: warnmark\n-\n-**WARNING about bait and target files**\n-\n-Picard is very fussy about the bait and target file format. If these are not exactly right, it will fail with an error something like:\n-\n-Exception in thread "main" net.sf.picard.PicardException: Invalid interval record contains 6 fields: chr1 45787123 45787316 CASO_22G_25063 1000 +\n-\n-If you see an error like that from this tool, please do NOT report it to any of the Galaxy mailing lists as it is not a bug! \n-It means you must reformat your bait and target files. Galaxy cannot do that for you automatically unfortunately.\n-\n-The required definition is described in the documentation at http://www.broadinstitute.org/gsa/wiki/index.php/Built-in_command-line_arguments\n-and the sample provided looks like this:\n-\n-chr1 1104841 1104940 + target_1\n-chr1 1105283 1105599 + target_2\n-chr1 1105712 1105860 + target_3\n-chr1 1105960 1106119 + target_4\n-\n-So your bait and target files MUST have 5 columns with chr, start, end, strand and name tab delimited and in exactly that order.\n-Note that the Picard mandated sam header described in the documentation linked above is automagically added by the tool in Galaxy.\n-\n-.. '..b'arget terrirtoy / bait territory. 1 == perfectly efficient, 0.5 = half of baited bases are not target.\n- 6. TOTAL_READS: The total number of reads in the SAM or BAM file examine.\n- 7. PF_READS: The number of reads that pass the vendor\'s filter.\n- 8. PF_UNIQUE_READS: The number of PF reads that are not marked as duplicates.\n- 9. PCT_PF_READS: PF reads / total reads. The percent of reads passing filter.\n- 10. PCT_PF_UQ_READS: PF Unique Reads / Total Reads.\n- 11. PF_UQ_READS_ALIGNED: The number of PF unique reads that are aligned with mapping score > 0 to the reference genome.\n- 12. PCT_PF_UQ_READS_ALIGNED: PF Reads Aligned / PF Reads.\n- 13. PF_UQ_BASES_ALIGNED: The number of bases in the PF aligned reads that are mapped to a reference base. Accounts for clipping and gaps.\n- 14. ON_BAIT_BASES: The number of PF aligned bases that mapped to a baited region of the genome.\n- 15. NEAR_BAIT_BASES: The number of PF aligned bases that mapped to within a fixed interval of a baited region, but not on a baited region.\n- 16. OFF_BAIT_BASES: The number of PF aligned bases that mapped to neither on or near a bait.\n- 17. ON_TARGET_BASES: The number of PF aligned bases that mapped to a targetted region of the genome.\n- 18. PCT_SELECTED_BASES: On+Near Bait Bases / PF Bases Aligned.\n- 19. PCT_OFF_BAIT: The percentage of aligned PF bases that mapped neither on or near a bait.\n- 20. ON_BAIT_VS_SELECTED: The percentage of on+near bait bases that are on as opposed to near.\n- 21. MEAN_BAIT_COVERAGE: The mean coverage of all baits in the experiment.\n- 22. MEAN_TARGET_COVERAGE: The mean coverage of targets that recieved at least coverage depth = 2 at one base.\n- 23. PCT_USABLE_BASES_ON_BAIT: The number of aligned, de-duped, on-bait bases out of the PF bases available.\n- 24. PCT_USABLE_BASES_ON_TARGET: The number of aligned, de-duped, on-target bases out of the PF bases available.\n- 25. FOLD_ENRICHMENT: The fold by which the baited region has been amplified above genomic background.\n- 26. ZERO_CVG_TARGETS_PCT: The number of targets that did not reach coverage=2 over any base.\n- 27. FOLD_80_BASE_PENALTY: The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets.\n- 28. PCT_TARGET_BASES_2X: The percentage of ALL target bases acheiving 2X or greater coverage.\n- 29. PCT_TARGET_BASES_10X: The percentage of ALL target bases acheiving 10X or greater coverage.\n- 30. PCT_TARGET_BASES_20X: The percentage of ALL target bases acheiving 20X or greater coverage.\n- 31. PCT_TARGET_BASES_30X: The percentage of ALL target bases acheiving 30X or greater coverage.\n- 32. HS_LIBRARY_SIZE: The estimated number of unique molecules in the selected part of the library.\n- 33. HS_PENALTY_10X: The "hybrid selection penalty" incurred to get 80% of target bases to 10X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 10X coverage I need to sequence until PF_ALIGNED_BASES = 10^6 * 10 * HS_PENALTY_10X.\n- 34. HS_PENALTY_20X: The "hybrid selection penalty" incurred to get 80% of target bases to 20X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 20X coverage I need to sequence until PF_ALIGNED_BASES = 10^6 * 20 * HS_PENALTY_20X.\n- 35. HS_PENALTY_30X: The "hybrid selection penalty" incurred to get 80% of target bases to 10X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 30X coverage I need to sequence until PF_ALIGNED_BASES = 10^6 * 30 * HS_PENALTY_30X.\n-\n-.. class:: warningmark\n-\n-**Warning on SAM/BAM quality**\n-\n-Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**\n-flag when it runs Picard, which allows reads to be discarded if they\'re empty or don\'t map. This appears to be the only way to deal with SAM/BAM that cannot be parsed.\n-\n-\n- </help>\n-</tool>\n' |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e rgPicardInsertSize.xml --- a/rgPicardInsertSize.xml Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,97 +0,0 @@ -<tool name="Insertion size metrics" id="PicardInsertSize" version="1.56.0"> - <description>for PAIRED data</description> - <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> - <command interpreter="python"> - picard_wrapper.py -i "${input_file}" -n "${out_prefix}" --tmpdir "${__new_file_path__}" --deviations "${deviations}" - --histwidth "${histWidth}" --minpct "${minPct}" --malevel "${malevel}" - -j "\$JAVA_JAR_PATH/CollectInsertSizeMetrics.jar" -d "${html_file.files_path}" -t "${html_file}" - </command> - <inputs> - <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to generate statistics for" - help="If empty, upload or import a SAM/BAM dataset."/> - <param name="out_prefix" value="Insertion size metrics" type="text" - label="Title for the output file" help="Use this remind you what the job was for" size="120" /> - <param name="deviations" value="10.0" type="float" - label="Deviations" size="5" - help="See Picard documentation: Generate mean, sd and plots by trimming the data down to MEDIAN + DEVIATIONS*MEDIAN_ABSOLUTE_DEVIATION" /> - <param name="histWidth" value="0" type="integer" - label="Histogram width" size="5" - help="Explicitly sets the histogram width option - leave 0 to ignore" /> - <param name="minPct" value="0.05" type="float" - label="Minimum percentage" size="5" - help="Discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads" /> - <param name="malevel" value="0" type="select" multiple="true" label="Metric Accumulation Level" - help="Level(s) at which metrics will be accumulated"> - <option value="ALL_READS" selected="true">All reads (default)</option> - <option value="SAMPLE" default="true">Sample</option> - <option value="LIBRARY" default="true">Library</option> - <option value="READ_GROUP" default="true">Read group</option> - </param> - </inputs> - <outputs> - <data format="html" name="html_file" label="InsertSize_${out_prefix}.html"/> - </outputs> - <tests> - <test> - <param name="input_file" value="picard_input_tiny.sam" /> - <param name="out_prefix" value="Insertion size metrics" /> - <param name="deviations" value="10.0" /> - <param name="histWidth" value="0" /> - <param name="minPct" value="0.01" /> - <param name="malevel" value="ALL_READS" /> - <output name="html_file" file="picard_output_insertsize_tinysam.html" ftype="html" compare="contains" lines_diff="40" /> - </test> - </tests> - <help> - - -.. class:: infomark - -**Purpose** - -Reads a SAM or BAM file and describes the distribution -of insert size (excluding duplicates) with metrics and a histogram plot. - -**Picard documentation** - -This is a Galaxy wrapper for CollectInsertSizeMetrics, a part of the external package Picard-tools_. - - .. _Picard-tools: http://www.google.com/search?q=picard+samtools - -.. class:: warningmark - -**Useful for paired data only** - -This tool works for paired data only and can be expected to fail for single end data. - ------ - -.. class:: infomark - -**Inputs, outputs, and parameters** - -Picard documentation says (reformatted for Galaxy): - -.. csv-table:: - :header-rows: 1 - - Option,Description - "INPUT=File","SAM or BAM file Required." - "OUTPUT=File","File to write insert size metrics to Required." - "HISTOGRAM_FILE=File","File to write insert size histogram chart to Required." - "TAIL_LIMIT=Integer","When calculating mean and stdev stop when the bins in the tail of the distribution contain fewer than mode/TAIL_LIMIT items. This also limits how much data goes into each data category of the histogram." - "HISTOGRAM_WIDTH=Integer","Explicitly sets the histogram width, overriding the TAIL_LIMIT option. Also, when calculating mean and stdev, only bins LE HISTOGRAM_WIDTH will be included. " - "MINIMUM_PCT=Float","When generating the histogram, discard any data categories (out of FR, TANDEM, RF) that have fewer than this percentage of overall reads. (Range: 0 to 1) Default value: 0.01." - "STOP_AFTER=Integer","Stop after processing N reads, mainly for debugging. Default value: 0." - "CREATE_MD5_FILE=Boolean","Whether to create an MD5 digest for any BAM files created. Default value: false." - -.. class:: warningmark - -**Warning on SAM/BAM quality** - -Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT** -flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears -to be the only way to deal with SAM/BAM that cannot be parsed. - - </help> -</tool> |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e rgPicardLibComplexity.xml --- a/rgPicardLibComplexity.xml Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,123 +0,0 @@ -<tool name="Estimate Library Complexity" id="rgEstLibComp" version="1.56.0"> - <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> - <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 "\$JAVA_JAR_PATH/EstimateLibraryComplexity.jar" -d "${html_file.files_path}" -t "${html_file}" - </command> - <inputs> - <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset" - help="If empty, upload or import a SAM/BAM dataset."/> - <param name="out_prefix" value="Library Complexity" type="text" - label="Title for the output file" help="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/memory." /> - <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="30" /> - </test> - </tests> - <help> - -.. class:: infomark - -**Purpose** - -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. - -**Picard documentation** - -This is a Galaxy wrapper for EstimateLibraryComplexity, a part of the external package Picard-tools_. - - .. _Picard-tools: http://www.google.com/search?q=picard+samtools - ------ - -.. class:: infomark - -**Inputs, outputs, and parameters** - -Picard documentation says (reformatted for Galaxy): - -.. csv-table:: - :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:: warningmark - -**Warning on SAM/BAM quality** - -Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT** -flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears -to be the only way to deal with SAM/BAM that cannot be parsed. - -.. class:: infomark - -**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]+).*. - - - </help> -</tool> - - |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e rgPicardMarkDups.xml --- a/rgPicardMarkDups.xml Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,130 +0,0 @@ -<tool name="Mark Duplicate reads" id="rgPicardMarkDups" version="1.56.0"> - <command interpreter="python"> - picard_wrapper.py -i "${input_file}" -n "${out_prefix}" --tmpdir "${__new_file_path__}" -o "${out_file}" - --remdups "${remDups}" --assumesorted "${assumeSorted}" --readregex "${readRegex}" --optdupdist "${optDupeDist}" - -j "\$JAVA_JAR_PATH/MarkDuplicates.jar" -d "${html_file.files_path}" -t "${html_file}" -e "${input_file.ext}" - </command> - <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements> - <inputs> - <param format="bam,sam" name="input_file" type="data" label="SAM/BAM dataset to mark duplicates in" - help="If empty, upload or import a SAM/BAM dataset."/> - <param name="out_prefix" value="Dupes Marked" type="text" - label="Title for the output file" help="Use this remind you what the job was for" size="80" /> - <param name="remDups" value="false" type="boolean" label="Remove duplicates from output file" - truevalue="true" falsevalue="false" checked="yes" - help="If true do not write duplicates to the output file instead of writing them with appropriate flags set." /> - <param name="assumeSorted" value="true" type="boolean" label="Assume reads are already ordered" - truevalue="true" falsevalue="false" checked="yes" - help="If true assume input data are already sorted (most Galaxy SAM/BAM should be)." /> - <param name="readRegex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" type="text" size="80" - 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="integer" - label="The maximum offset between two duplicate 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." > - <validator type="in_range" message="Minimum optical dupe distance must be positive" min="0" /> - </param> - - </inputs> - <outputs> - <data format="bam" name="out_file" label="MarkDups_${out_prefix}.bam"/> - <data format="html" name="html_file" label="MarkDups_${out_prefix}.html"/> - </outputs> - <tests> - <test> - <param name="input_file" value="picard_input_tiny_coord.bam" ftype="bam" /> - <param name="out_prefix" value="Dupes Marked" /> - <param name="remDups" value="false" /> - <param name="assumeSorted" value="true" /> - <param name="readRegex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" /> - <param name="optDupeDist" value="100" /> - <output name="out_file" file="picard_output_markdups_sortedpairsam.bam" ftype="bam" compare="diff" /> - <output name="html_file" file="picard_output_markdups_sortedpairsam.html" ftype="html" lines_diff="75" /> - </test> - <test> - <param name="input_file" value="picard_input_tiny_coord.sam" ftype="sam" /> - <param name="out_prefix" value="Dupes Marked" /> - <param name="remDups" value="true" /> - <param name="assumeSorted" value="true" /> - <param name="readRegex" value="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" /> - <param name="optDupeDist" value="100" /> - <output name="out_file" file="picard_output_markdups_remdupes.bam" ftype="bam" compare="diff" /> - <output name="html_file" file="picard_output_markdups_sortedpairsam.html" ftype="html" lines_diff="75" /> - </test> - </tests> - - <help> - -.. class:: infomark - -**Purpose** - -Marks all duplicate reads in a provided SAM or BAM file and either removes them or flags them. - -**Picard documentation** - -This is a Galaxy wrapper for MarkDuplicates, a part of the external package Picard-tools_. - - .. _Picard-tools: http://www.google.com/search?q=picard+samtools - ------ - -.. class:: infomark - -**Inputs, outputs, and parameters** - -Picard documentation says (reformatted for Galaxy): - -.. csv-table:: Mark Duplicates docs - :header-rows: 1 - - Option,Description - "INPUT=File","The input SAM or BAM file to analyze. Must be coordinate sorted. Required." - "OUTPUT=File","The output file to right marked records to Required." - "METRICS_FILE=File","File to write duplication metrics to Required." - "REMOVE_DUPLICATES=Boolean","If true do not write duplicates to the output file instead of writing them with appropriate flags set. Default value: false." - "ASSUME_SORTED=Boolean","If true, assume that the input file is coordinate sorted, even if the header says otherwise. Default value: false." - "MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=Integer","This option is obsolete. ReadEnds will always be spilled to disk. Default value: 50000." - "MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=Integer","Maximum number of file handles to keep open when spilling read ends to disk." - "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. " - "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" - -.. class:: warningmark - -**Warning on SAM/BAM quality** - -Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT** -flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears -to be the only way to deal with SAM/BAM that cannot be parsed. -.. class:: infomark - -**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]+). - -Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules. All records are then written to the output file with the duplicate records flagged unless the remove duplicates option is selected. In some cases you may want to do this, but please only do this if you really understand what you are doing. - - </help> -</tool> - - - - - - - - - - - - |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/bfast_out1.sam --- a/test-data/bfast_out1.sam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,23 +0,0 @@ -@HD VN:0.1.2 SO:unsorted GO:none -@SQ SN:phiX174 LN:5386 -@PG ID:bfast VN:0.6.4d -random_phiX_region_0 0 phiX174 553 255 50M * 0 0 TTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_1 0 phiX174 3693 255 50M * 0 0 GTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_2 0 phiX174 375 255 50M * 0 0 AATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_3 0 phiX174 3168 255 50M * 0 0 GGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_4 0 phiX174 5254 255 50M * 0 0 ACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGAC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_5 0 phiX174 5066 255 50M * 0 0 AGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_6 0 phiX174 1226 255 50M * 0 0 CACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_7 0 phiX174 1096 255 50M * 0 0 AACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCG ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_8 0 phiX174 535 255 50M * 0 0 CTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_9 0 phiX174 3669 255 50M * 0 0 CAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_10 0 phiX174 4887 255 50M * 0 0 TACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_11 0 phiX174 1849 255 50M * 0 0 TATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_12 0 phiX174 4145 255 50M * 0 0 AGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_13 0 phiX174 1853 255 50M * 0 0 TTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_14 0 phiX174 2800 255 50M * 0 0 CCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGC ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2300 NM:i:1 NH:i:1 IH:i:1 HI:i:1 MD:Z:11T38 XA:i:0 -random_phiX_region_15 0 phiX174 1910 255 50M * 0 0 AACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_16 0 phiX174 3366 255 50M * 0 0 GCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_17 0 phiX174 2165 255 50M * 0 0 CATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAG ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_18 0 phiX174 2051 255 50M * 0 0 TGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 -random_phiX_region_19 0 phiX174 5099 255 50M * 0 0 GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACT ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ PG:Z:bfast AS:i:2500 NM:i:0 NH:i:1 IH:i:1 HI:i:1 MD:Z:50 XA:i:0 |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/bwa_wrapper_in2.fastqsanger --- a/test-data/bwa_wrapper_in2.fastqsanger Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,120 +0,0 @@ -@seq1/1 -GGACTCAGATAGTAATCC -+ -II#IIIIIII$5+.(9II -@seq2/1 -ATTCGACCTATCCTTGCG -+ -IIIIIIIIIIIIIIIIII -@seq3/1 -GTAACAAAGTTTGGATTG -+ -IIIIIIIIIIIIIIIIII -@seq4/1 -AGCCGCTCGTCTTTTATG -+ -IIIIIIIIIIIIIIIIII -@seq5/1 -CAGTTATATGGCTTTTGG -+ -IIIIIIIIIIIIIIIIII -@seq6/1 -AGGCGCTCGTCTTGGTAT -+ -IIIIIIIIIIIIIIIIII -@seq7/1 -TGTAGGTGGTCAACCAAT -+ -IIIIIIIIIIIIIIIIII -@seq8/1 -ACACCCGTCCTTTACGTC -+ -IIIIIIIIIIIIIIIIII -@seq9/1 -GCCGCTATTCAGGTTGTT -+ -IIIIIIIIIIIIIIIIII -@seq10/1 -ATTCTTTCTTTTCGTATC -+ -IIIIIIIIIIIIIIIIII -@seq11/1 -GCATTTCTACTCCTTCTC -+ -II#IIIIIII$5+.(9II -@seq12/1 -CGCGCTTCGATAAAAATG -+ -IIIIIIIIIIIIIIIIII -@seq13/1 -ATTTCTACTCTTTCTCAT -+ -IIIIIIIIIIIIIIIIII -@seq14/1 -CCCTTTTGAATGTCACGC -+ -IIIIIIIIIIIIIIIIII -@seq15/1 -CCAACTTACCAAGGTGGG -+ -IIIIIIIIIIIIIIIIII -@seq16/1 -TCAGGGTATTAAAAGAGA -+ -IIIIIIIIIIIIIIIIII -@seq17/1 -GTGATGTGCTTGCTACCG -+ -IIIIIIIIIIIIIIIIII -@seq18/1 -TCAATCCCCCATGCTTGG -+ -IIIIIIIIIIIIIIIIII -@seq19/1 -TTCCTGCGCTTAATGCTT -+ -IIIIIIIIIIIIIIIIII -@seq20/1 -CTTATTACCATTTCAACT -+ -IIIIIIIIIIIIIIIIII -@seq21/1 -CTGATACCAATAAAACCC -+ -II#IIIIIII$5+.(9II -@seq22/1 -AATCAAACTTACCAAGGG -+ -IIIIIIIIIIIIIIIIII -@seq23/1 -TGTGCTTCCCCAACTTGA -+ -IIIIIIIIIIIIIIIIII -@seq24/1 -TTTCTCAATCCCCAATGC -+ -IIIIIIIIIIIIIIIIII -@seq25/1 -TTGCTACTGACCGCTCTT -+ -IIIIIIIIIIIIIIIIII -@seq26/1 -CCGCGTGAAATTTCTATG -+ -IIIIIIIIIIIIIIIIII -@seq27/1 -CGCTAATCAAGTTGTTTC -+ -IIIIIIIIIIIIIIIIII -@seq28/1 -AAAGAGATTATTTGTCGG -+ -IIIIIIIIIIIIIIIIII -@seq29/1 -CAAATTAATGCGCGCTTC -+ -IIIIIIIIIIIIIIIIII -@seq30/1 -ATCCCCTATGCTTGGCTT -+ -IIIIIIIIIIIIIIIIII |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/bwa_wrapper_in3.fastqsanger --- a/test-data/bwa_wrapper_in3.fastqsanger Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,120 +0,0 @@ -@seq1/2 -ACGCTCCTTTAAAATATC -+ -IIIII$%*$G$A31I&&B -@seq2/2 -CAGCTCGAGAAGCTCTTA -+ -IIIIIIIIIIIIIIIIII -@seq3/2 -CTACTGACCGCTCTCGTG -+ -IIIIIIIIIIIIIIIIII -@seq4/2 -TAGGTGGTCAACCATTTT -+ -IIIIIIIIIIIIIIIIII -@seq5/2 -TTTCTATGTGGCTTAATA -+ -IIIIIIIIIIIIIIIIII -@seq6/2 -GTAGGTGGTCAACAATTT -+ -IIIIIIIIIIIIIIIIII -@seq7/2 -TTTAATTGCAGGGGCTTC -+ -IIIIIIIIIIIIIIIIII -@seq8/2 -ATGCGCTCTATTCTCTGG -+ -IIIIIIIIIIIIIIIIII -@seq9/2 -TTCTGTTGGTGCTGATAT -+ -IIIIIIIIIIIIIIIIII -@seq10/2 -AGGGCGTTGAGTTCGATA -+ -IIIIIIIIIIIIIIIIII -@seq11/2 -ATCCCCAATGCTTGGCTT -+ -IIIII$%*$G$A31I&&B -@seq12/2 -GGATTGGCGTTTCCAACC -+ -IIIIIIIIIIIIIIIIII -@seq13/2 -CCCCAATCCTTGCCTTCC -+ -IIIAAIIIIIIIIIIIII -@seq14/2 -TGATATTTTGACTTTGAG -+ -IIIIIIIIIIIIIIIIII -@seq15/2 -TTACGAAACGCGACGCCG -+ -IIIIIIIIIIIIIIIIII -@seq16/2 -TTATTTTTCTCCAGCCAC -+ -IIIIIIIIIIIIIIIIII -@seq17/2 -AAACAATACTTTAGGCAT -+ -IIIIIIIIIIIIIIIIII -@seq18/2 -CCGTTCCATAAGCAGATG -+ -IIIIIIIIIIIIIIIIII -@seq19/2 -GAGCGTCCTGGTGCTGAT -+ -IIIIIIIIIIIIIIIIII -@seq20/2 -ACTCCGGTTATCGCTGGC -+ -IIIIIIIIIIIIIIIIII -@seq21/2 -TAAGCATTTGGTTCAGGG -+ -IIIII$%*$G$A31I&&B -@seq22/2 -GTTACGACGCGACGCCGT -+ -IIIIIIIIIIIIIIIIII -@seq23/2 -TTTAATAACCCTATAGAC -+ -IIIIIIIIIIIIIIIIII -@seq24/2 -CTTGGCTTCCCTAAGCAG -+ -IIIIIIIIIIIIIIIIII -@seq25/2 -CGTGCTCGTTGCTGCGTT -+ -IIIIIIIIIIIIIIIIII -@seq26/2 -AAGGATGTTTTCCGTTCT -+ -IIIIIIIIIIIIIIIIII -@seq27/2 -TGTTTGGTGCTGATATTG -+ -IIIIIIIIIIIIIIIIII -@seq28/2 -TCCAGCCACTAAAGTGAG -+ -IIIIIIIIIIIIIIIIII -@seq29/2 -GATAATGATTGGGGTATC -+ -IIIIIIIIIIIIIIIIII -@seq30/2 -ACCATAAGCAGATGGATA -+ -IIIIIIIIIIIIIIIIII |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/bwa_wrapper_out3.sam --- a/test-data/bwa_wrapper_out3.sam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,63 +0,0 @@\n-@SQ\tSN:phiX174\tLN:5386\n-@RG\tID:abcdefg\tLB:lib-mom-A\tPL:ILLUMINA\tSM:mom\tDS:descrip\tDT:2010-11-01\tPI:400\n-@PG\tID:bwa\tPN:bwa\tVN:0.5.9-r16\n-seq1\t113\tphiX174\t340\t37\t18M\t=\t322\t-18\tGGATTACTATCTGAGTCC\tII9(.+5$IIIIIII#II\tRG:Z:abcdefg\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:25\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:18\n-seq1\t177\tphiX174\t322\t25\t18M\t=\t340\t18\tGATATTTTAAAGGAGCGT\tB&&I13A$G$*%$IIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:2\tSM:i:25\tAM:i:25\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:2C8A6\n-seq2\t65\tphiX174\t141\t37\t18M\t=\t159\t18\tATTCGACCTATCCTTGCG\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:18\n-seq2\t129\tphiX174\t159\t37\t18M\t=\t141\t-18\tCAGCTCGAGAAGCTCTTA\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:18\n-seq3\t65\tphiX174\t505\t37\t18M\t=\t523\t18\tGTAACAAAGTTTGGATTG\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:18\n-seq3\t129\tphiX174\t523\t37\t18M\t=\t505\t-18\tCTACTGACCGCTCTCGTG\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:18\n-seq4\t69\tphiX174\t945\t0\t*\t=\t945\t0\tAGCCGCTCGTCTTTTATG\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\n-seq4\t137\tphiX174\t945\t23\t18M\t=\t945\t0\tTAGGTGGTCAACCATTTT\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:1\tSM:i:23\tAM:i:0\tX0:i:1\tX1:i:1\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:12A5\tXA:Z:phiX174,+945,17M1S,2;\n-seq5\t65\tphiX174\t4985\t37\t18M\t=\t5003\t18\tCAGTTATATGGCTTTTGG\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:1\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:13G4\n-seq5\t129\tphiX174\t5003\t37\t18M\t=\t4985\t-18\tTTTCTATGTGGCTTAATA\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:1\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:13A4\n-seq6\t65\tphiX174\t925\t37\t11M1D7M\t=\t944\t19\tAGGCGCTCGTCTTGGTAT\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:1\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:1\tXG:i:1\tMD:Z:11^T7\n-seq6\t129\tphiX174\t944\t37\t18M\t=\t925\t-19\tGTAGGTGGTCAACAATTT\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:18\n-seq7\t65\tphiX174\t943\t25\t18M\t=\t960\t17\tTGTAGGTGGTCAACCAAT\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:2\tSM:i:25\tAM:i:25\tX0:i:1\tX1:i:1\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:14A1T1\tXA:Z:phiX174,+943,13M1I4M,2;\n-seq7\t129\tphiX174\t960\t37\t18M\t=\t943\t-17\tTTTAATTGCAGGGGCTTC\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:25\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:18\n-seq8\t69\tphiX174\t1715\t0\t*\t=\t1715\t0\tACACCCGTCCTTTACGTC\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\n-seq8\t137\tphiX174\t1715\t37\t18M\t=\t1715\t0\tATGCGCTCTATTCTCTGG\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:1\tSM:i:37\tAM:i:0\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:10A7\n-seq9\t65\tphiX174\t2596\t37\t18M\t=\t2613\t17\tGCCGCTATTCAGGTTGTT\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:1\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:7A10\n-seq9\t129\tphiX174\t2613\t37\t18M\t=\t2596\t-17\tTTCTGTTGGTGCTGATAT\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:18\n-seq10\t65\tphiX174\t4149\t25\t18M\t=\t4168\t19\tATTCTTTCTTTTCGTATC\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:2\tSM:i:25\tAM:i:25\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:5G11G0\n-seq10\t129\tphiX174\t4168\t37\t18M\t=\t4149\t-19\tAGGGCGTTGAGTTCGATA\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:25\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:18\n-seq11\t65\tphiX174\t4072\t37\t18M\t=\t4091\t19\tGCATTTCTACTCCTTCTC\tII#IIIIIII$5+.(9II\tRG:Z:abcdefg\tXT:A:U\tNM:i:1\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:12T5\n-seq11\t129\tphiX174\t4091\t37\t18M\t=\t4072\t-19\tATCCCCAATGCTTGGCTT\tIIIII$%*$G$A31I&&B\tRG:Z:abcdefg\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:18\n-seq12\t65\tphiX174\t5349\t37\t18M\t=\t5365\t16\tCGCGCTTCGATAAAAATG\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:25\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:18\n-seq12\t129\tphiX174\t5365\t25\t18M\t=\t5349\t-16\tGGATTGGCGTTTCCAACC\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:2\tSM:i:25\tAM:i:25\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:0T9A'..b'\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:9A8\n-seq18\t133\tphiX174\t4088\t0\t*\t=\t4088\t0\tCCGTTCCATAAGCAGATG\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\n-seq19\t65\tphiX174\t3304\t37\t18M\t=\t3324\t20\tTTCCTGCGCTTAATGCTT\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:1\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:6A11\n-seq19\t129\tphiX174\t3324\t37\t18M\t=\t3304\t-20\tGAGCGTCCTGGTGCTGAT\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:1\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:6G11\n-seq20\t65\tphiX174\t1082\t37\t18M\t=\t1100\t18\tCTTATTACCATTTCAACT\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:18\n-seq20\t129\tphiX174\t1100\t37\t18M\t=\t1082\t-18\tACTCCGGTTATCGCTGGC\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:18\n-seq21\t65\tphiX174\t1344\t23\t18M\t=\t1363\t19\tCTGATACCAATAAAACCC\tII#IIIIIII$5+.(9II\tRG:Z:abcdefg\tXT:A:U\tNM:i:1\tSM:i:23\tAM:i:23\tX0:i:1\tX1:i:1\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:15T2\tXA:Z:phiX174,+1344,15M1D3M,2;\n-seq21\t129\tphiX174\t1363\t37\t18M\t=\t1344\t-19\tTAAGCATTTGGTTCAGGG\tIIIII$%*$G$A31I&&B\tRG:Z:abcdefg\tXT:A:U\tNM:i:1\tSM:i:37\tAM:i:23\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:10T7\n-seq22\t69\tphiX174\t5215\t0\t*\t=\t5215\t0\tAATCAAACTTACCAAGGG\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\n-seq22\t137\tphiX174\t5215\t37\t18M\t=\t5215\t0\tGTTACGACGCGACGCCGT\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:18\n-seq23\t65\tphiX174\t4289\t37\t18M\t=\t4308\t19\tTGTGCTTCCCCAACTTGA\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:1\tSM:i:37\tAM:i:25\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:6C11\n-seq23\t129\tphiX174\t4308\t25\t18M\t=\t4289\t-19\tTTTAATAACCCTATAGAC\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:2\tSM:i:25\tAM:i:25\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:0A8A8\n-seq24\t65\tphiX174\t4084\t37\t18M\t=\t4101\t17\tTTTCTCAATCCCCAATGC\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:18\n-seq24\t129\tphiX174\t4101\t37\t18M\t=\t4084\t-17\tCTTGGCTTCCCTAAGCAG\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:1\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:10A7\n-seq25\t65\tphiX174\t520\t37\t18M\t=\t537\t17\tTTGCTACTGACCGCTCTT\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:1\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:17C0\n-seq25\t129\tphiX174\t537\t37\t18M\t=\t520\t-17\tCGTGCTCGTTGCTGCGTT\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:1\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:9C8\n-seq26\t65\tphiX174\t1976\t37\t18M\t=\t1994\t18\tCCGCGTGAAATTTCTATG\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:18\n-seq26\t129\tphiX174\t1994\t37\t18M\t=\t1976\t-18\tAAGGATGTTTTCCGTTCT\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:18\n-seq27\t65\tphiX174\t2598\t37\t18M\t=\t2614\t16\tCGCTAATCAAGTTGTTTC\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:1\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:9G8\n-seq27\t129\tphiX174\t2614\t37\t3M1D15M\t=\t2598\t-16\tTGTTTGGTGCTGATATTG\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:2\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:1\tXG:i:1\tMD:Z:1C1^G15\n-seq28\t65\tphiX174\t2890\t25\t18M\t=\t2906\t16\tAAAGAGATTATTTGTCGG\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:2\tSM:i:25\tAM:i:25\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:16T0C0\n-seq28\t129\tphiX174\t2906\t37\t18M\t=\t2890\t-16\tTCCAGCCACTAAAGTGAG\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:1\tSM:i:37\tAM:i:25\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:10T7\n-seq29\t73\tphiX174\t5339\t37\t18M\t=\t5339\t0\tCAAATTAATGCGCGCTTC\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:1\tSM:i:37\tAM:i:0\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:6T11\n-seq29\t133\tphiX174\t5339\t0\t*\t=\t5339\t0\tGATAATGATTGGGGTATC\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\n-seq30\t65\tphiX174\t4091\t37\t18M\t=\t4108\t17\tATCCCCTATGCTTGGCTT\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:1\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:6A11\n-seq30\t129\tphiX174\t4108\t37\t18M\t=\t4091\t-17\tACCATAAGCAGATGGATA\tIIIIIIIIIIIIIIIIII\tRG:Z:abcdefg\tXT:A:U\tNM:i:1\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:0T17\n' |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/phiX.fasta --- a/test-data/phiX.fasta Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,79 +0,0 @@ ->phiX174 -GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT -GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA -ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG -TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA -GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC -TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT -TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT -CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT -TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG -TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC -GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA -CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG -TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT -AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC -CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA -TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC -TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA -CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA -GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT -GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA -ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC -TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT -TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC -ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC -CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT -GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC -CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC -TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG -TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT -TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA -AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT -TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT -ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC -GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC -TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT -TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA -TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG -TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC -CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG -AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC -CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT -TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG -CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA -AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT -GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG -GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA -TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT -CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG -TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA -GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC -CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA -TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA -AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC -TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT -CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA -TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG -TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT -CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT -TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC -ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG -TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA -ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG -GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC -CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT -GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG -GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT -ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG -CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC -CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC -GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT -CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG -CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA -TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT -TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG -TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC -AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC -TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA - |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_ARRG.bam |
| b |
| Binary file test-data/picard_ARRG.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_ARRG_input1.bam |
| b |
| Binary file test-data/picard_ARRG_input1.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_ARRG_input1.sam --- a/test-data/picard_ARRG_input1.sam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,25 +0,0 @@ -@HD VN:1.0 SO:coordinate -@SQ SN:chr1 LN:10001 -@SQ SN:chr2 LN:100001 -@SQ SN:chr3 LN:10001 -@SQ SN:chr4 LN:1001 -@RG ID:rg1 SM:s1 -@RG ID:rg2 SM:s3 -bar:record:4 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:6 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 -bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:3 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 -bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:7 77 chr1 20 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 -bar:record:8 77 chr1 30 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 -bar:record:4 141 chr1 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:5 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg2 -bar:record:6 141 chr1 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg2 -bar:record:2 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:2 141 chr2 30 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg2 -bar:record:3 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:8 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:5 141 chr3 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:9 77 chr4 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:7 141 chr4 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:9 141 chr4 60 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_ARRG_input2.sam --- a/test-data/picard_ARRG_input2.sam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,23 +0,0 @@ -@HD VN:1.0 SO:coordinate -@SQ SN:chr1 LN:10001 -@SQ SN:chr2 LN:100001 -@SQ SN:chr3 LN:10001 -@SQ SN:chr4 LN:1001 -bar:record:4 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 -bar:record:6 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 -bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 -bar:record:3 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 -bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 -bar:record:7 77 chr1 20 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 -bar:record:8 77 chr1 30 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 -bar:record:4 141 chr1 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 -bar:record:5 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 -bar:record:6 141 chr1 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 -bar:record:2 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 -bar:record:2 141 chr2 30 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 -bar:record:3 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 -bar:record:8 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 -bar:record:5 141 chr3 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 -bar:record:9 77 chr4 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 -bar:record:7 141 chr4 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 -bar:record:9 141 chr4 60 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_ARRG_output1.sam --- a/test-data/picard_ARRG_output1.sam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,24 +0,0 @@ -@HD VN:1.0 SO:coordinate -@SQ SN:chr1 LN:10001 -@SQ SN:chr2 LN:100001 -@SQ SN:chr3 LN:10001 -@SQ SN:chr4 LN:1001 -@RG ID:one PL:illumina PU:peaewe LB:lib SM:sam1 -bar:record:4 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:one -bar:record:6 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:one -bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:one -bar:record:3 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:one -bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:one -bar:record:7 77 chr1 20 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:one -bar:record:8 77 chr1 30 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:one -bar:record:4 141 chr1 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:one -bar:record:5 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:one -bar:record:6 141 chr1 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:one -bar:record:2 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:one -bar:record:2 141 chr2 30 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:one -bar:record:3 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:one -bar:record:8 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:one -bar:record:5 141 chr3 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:one -bar:record:9 77 chr4 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:one -bar:record:7 141 chr4 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:one -bar:record:9 141 chr4 60 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:one |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_ARRG_output2.bam |
| b |
| Binary file test-data/picard_ARRG_output2.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_ARRG_output2.sam --- a/test-data/picard_ARRG_output2.sam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,24 +0,0 @@ -@HD VN:1.0 SO:coordinate -@SQ SN:chr1 LN:10001 -@SQ SN:chr2 LN:100001 -@SQ SN:chr3 LN:10001 -@SQ SN:chr4 LN:1001 -@RG ID:M5 PL:IL PU:PLAT LB:LIB DS:description with spaces SM:smp CN:FamousCenter -bar:record:4 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M5 -bar:record:6 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M5 -bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M5 -bar:record:3 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M5 -bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M5 -bar:record:7 77 chr1 20 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M5 -bar:record:8 77 chr1 30 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M5 -bar:record:4 141 chr1 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M5 -bar:record:5 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M5 -bar:record:6 141 chr1 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M5 -bar:record:2 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M5 -bar:record:2 141 chr2 30 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M5 -bar:record:3 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M5 -bar:record:8 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M5 -bar:record:5 141 chr3 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M5 -bar:record:9 77 chr4 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M5 -bar:record:7 141 chr4 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M5 -bar:record:9 141 chr4 60 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M5 |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_ARRG_output3.bam |
| b |
| Binary file test-data/picard_ARRG_output3.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_ARRG_output3.bam.bai |
| b |
| Binary file test-data/picard_ARRG_output3.bam.bai has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_ARRG_output3.sam --- a/test-data/picard_ARRG_output3.sam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,24 +0,0 @@ -@HD VN:1.0 SO:coordinate -@SQ SN:chr1 LN:10001 -@SQ SN:chr2 LN:100001 -@SQ SN:chr3 LN:10001 -@SQ SN:chr4 LN:1001 -@RG ID:M6 PL:IL PU:PLAT LB:LIB SM:smp1 -bar:record:4 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M6 -bar:record:6 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M6 -bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M6 -bar:record:3 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M6 -bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M6 -bar:record:7 77 chr1 20 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M6 -bar:record:8 77 chr1 30 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M6 -bar:record:4 141 chr1 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M6 -bar:record:5 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M6 -bar:record:6 141 chr1 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M6 -bar:record:2 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M6 -bar:record:2 141 chr2 30 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M6 -bar:record:3 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M6 -bar:record:8 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M6 -bar:record:5 141 chr3 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M6 -bar:record:9 77 chr4 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:M6 -bar:record:7 141 chr4 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M6 -bar:record:9 141 chr4 60 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:M6 |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_ARRG_test1.bam |
| b |
| Binary file test-data/picard_ARRG_test1.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_AddCommentsToBam.bam |
| b |
| Binary file test-data/picard_AddCommentsToBam.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_AddCommentsToBam_test1.bam |
| b |
| Binary file test-data/picard_AddCommentsToBam_test1.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_BIS_input1.bam |
| b |
| Binary file test-data/picard_BIS_input1.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_BIS_input1.sam --- a/test-data/picard_BIS_input1.sam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,18 +0,0 @@ -@HD VN:1.0 SO:coordinate -@SQ SN:chr1 LN:101 -@SQ SN:chr7 LN:404 -@SQ SN:chr8 LN:202 -@SQ SN:chr10 LN:303 -@SQ SN:chr14 LN:505 -@RG ID:0 SM:Hi,Mom! -@RG ID:1 SM:samplesample DS:ClearDescription -@PG ID:1 PN:Hey! VN:2.0 -@CO Just a generic comment to make the header longer -both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 -read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 -both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_BIS_output1.txt --- a/test-data/picard_BIS_output1.txt Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,39 +0,0 @@ -<style type="text/css"> - tr.d0 td {background-color: oldlace; color: black;} - tr.d1 td {background-color: aliceblue; color: black;} - </style><?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"> -<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 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"> -Galaxy tool BamIndexStats run at 12/05/2011 14:18:06</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table> -<tr><td><a href="BamIndexStats.log">BamIndexStats.log</a></td></tr> -<tr><td><a href="BamIndexStats.metrics.txt">BamIndexStats.metrics.txt</a></td></tr> -</table><p/> -<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</b><hr/> -<table cellpadding="3" > -<tr class="d0"><td colspan="2">chr1 length= 101 Aligned= 0 Unaligned= 0</td></tr> -<tr class="d1"><td colspan="2">chr7 length= 404 Aligned= 7 Unaligned= 0</td></tr> -<tr class="d0"><td colspan="2">chr8 length= 202 Aligned= 0 Unaligned= 0</td></tr> -<tr class="d1"><td colspan="2">NoCoordinateCount= 1</td></tr> -</table> -<b>Picard Tool Run Log</b><hr/> -<pre>Thu, 12 May 2011 14:18:06 INFO - ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/BamIndexStats.jar VALIDATION_STRINGENCY=LENIENT INPUT=/udd/rerla/galaxy-central/database/job_working_directory/955/dataset_1015_files/tmp45bd_D.bam returned status 0 and stderr: -[Thu May 12 14:18:06 EDT 2011] net.sf.picard.sam.BamIndexStats INPUT=/udd/rerla/galaxy-central/database/job_working_directory/955/dataset_1015_files/tmp45bd_D.bam VALIDATION_STRINGENCY=LENIENT TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -[Thu May 12 14:18:06 EDT 2011] net.sf.picard.sam.BamIndexStats 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 running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html> - |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_BIS_output2.txt --- a/test-data/picard_BIS_output2.txt Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,41 +0,0 @@ -<style type="text/css"> - tr.d0 td {background-color: oldlace; color: black;} - tr.d1 td {background-color: aliceblue; color: black;} - </style><?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"> -<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 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"> -Galaxy tool BamIndexStats run at 12/05/2011 14:18:22</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table> -<tr><td><a href="BamIndexStats.log">BamIndexStats.log</a></td></tr> -<tr><td><a href="BamIndexStats.metrics.txt">BamIndexStats.metrics.txt</a></td></tr> -</table><p/> -<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</b><hr/> -<table cellpadding="3" > -<tr class="d0"><td colspan="2">chr1 length= 101 Aligned= 0 Unaligned= 0</td></tr> -<tr class="d1"><td colspan="2">chr7 length= 404 Aligned= 7 Unaligned= 0</td></tr> -<tr class="d0"><td colspan="2">chr8 length= 202 Aligned= 0 Unaligned= 0</td></tr> -<tr class="d1"><td colspan="2">chr10 length= 303 Aligned= 0 Unaligned= 0</td></tr> -<tr class="d0"><td colspan="2">chr14 length= 505 Aligned= 0 Unaligned= 0</td></tr> -<tr class="d1"><td colspan="2">NoCoordinateCount= 1</td></tr> -</table> -<b>Picard Tool Run Log</b><hr/> -<pre>Thu, 12 May 2011 14:18:22 INFO - ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/BamIndexStats.jar VALIDATION_STRINGENCY=LENIENT INPUT=/udd/rerla/galaxy-central/database/job_working_directory/957/dataset_1017_files/tmpqXGksN.bam returned status 0 and stderr: -[Thu May 12 14:18:21 EDT 2011] net.sf.picard.sam.BamIndexStats INPUT=/udd/rerla/galaxy-central/database/job_working_directory/957/dataset_1017_files/tmpqXGksN.bam VALIDATION_STRINGENCY=LENIENT TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -[Thu May 12 14:18:22 EDT 2011] net.sf.picard.sam.BamIndexStats 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 running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html> - |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_BedToIntervalList.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_BedToIntervalList.bed Tue Dec 16 19:03:21 2014 -0500 |
| b |
| @@ -0,0 +1,8 @@ +chrM 0 100 +chrM 20 500 +chrM 700 800 +chrM 1000 5000 +chrM 2000 2500 +chrM 6000 7000 +chrM 8000 8250 +chrM 10000 10010 |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_BedToIntervalList_ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_BedToIntervalList_ref.fa Tue Dec 16 19:03:21 2014 -0500 |
| b |
| b'@@ -0,0 +1,239 @@\n+>chrM\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG\n+GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC\n+CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA\n+ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC\n+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC\n+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA\n+CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC\n+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC\n+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC\n+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA\n+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA\n+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT\n+CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC\n+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC\n+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA\n+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC\n+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA\n+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA\n+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA\n+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA\n+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA\n+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC\n+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA\n+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT\n+AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG\n+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC\n+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG\n+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC\n+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC\n+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA\n+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT\n+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA\n+TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG\n+TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA\n+GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG\n+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG\n+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA\n+ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT\n+TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA\n+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC\n+CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC\n+CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG\n+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC\n+AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC\n+TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG\n+CCATAATATGATT'..b'GTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA\n+CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA\n+TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT\n+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT\n+CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA\n+TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC\n+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC\n+AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC\n+CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC\n+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA\n+AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC\n+TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC\n+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA\n+CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC\n+AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA\n+TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA\n+ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA\n+TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA\n+CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA\n+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC\n+CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC\n+CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG\n+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC\n+CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC\n+CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA\n+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA\n+CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC\n+ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC\n+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC\n+TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA\n+GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT\n+CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT\n+TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC\n+TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA\n+GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC\n+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC\n+TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC\n+CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA\n+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC\n+ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA\n+ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA\n+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG\n+TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC\n+TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC\n+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n+\n' |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_BedToIntervalList_test1.pif --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_BedToIntervalList_test1.pif Tue Dec 16 19:03:21 2014 -0500 |
| b |
| @@ -0,0 +1,8 @@ +@HD VN:1.4 SO:unsorted +@SQ SN:chrM LN:16569 UR:file:/Users/anton/galaxy-central/database/job_working_directory/000/881/localref.fa M5:c68f52674c9fb33aef52dcf399755519 +chrM 1 500 + . +chrM 701 800 + . +chrM 1001 5000 + . +chrM 6001 7000 + . +chrM 8001 8250 + . +chrM 10001 10010 + . |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_CASM.bam |
| b |
| Binary file test-data/picard_CASM.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_CASM_ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CASM_ref.fa Tue Dec 16 19:03:21 2014 -0500 |
| b |
| b'@@ -0,0 +1,239 @@\n+>gi|251831106|ref|NC_012920.1| Homo sapiens mitochondrion, complete genome\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG\n+GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC\n+CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA\n+ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC\n+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC\n+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA\n+CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC\n+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC\n+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC\n+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA\n+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA\n+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT\n+CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC\n+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC\n+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA\n+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC\n+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA\n+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA\n+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA\n+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA\n+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA\n+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC\n+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA\n+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT\n+AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG\n+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC\n+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG\n+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC\n+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC\n+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA\n+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT\n+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA\n+TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG\n+TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA\n+GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG\n+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG\n+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA\n+ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT\n+TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA\n+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC\n+CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC\n+CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG\n+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC\n+AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC\n+TCCTTTAACCTCTCCA'..b'GTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA\n+CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA\n+TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT\n+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT\n+CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA\n+TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC\n+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC\n+AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC\n+CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC\n+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA\n+AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC\n+TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC\n+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA\n+CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC\n+AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA\n+TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA\n+ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA\n+TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA\n+CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA\n+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC\n+CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC\n+CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG\n+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC\n+CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC\n+CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA\n+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA\n+CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC\n+ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC\n+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC\n+TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA\n+GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT\n+CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT\n+TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC\n+TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA\n+GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC\n+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC\n+TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC\n+CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA\n+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC\n+ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA\n+ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA\n+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG\n+TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC\n+TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC\n+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n+\n' |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_CASM_test1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CASM_test1.tab Tue Dec 16 19:03:21 2014 -0500 |
| [ |
| @@ -0,0 +1,12 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, METRIC_ACCUMULATION_LEVEL=None] IS_BISULFITE_SEQUENCED=false INPUT=/Users/anton/galaxy-central/database/files/000/dataset_616.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_639.dat REFERENCE_SEQUENCE=localref.fa ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT METRIC_ACCUMULATION_LEVEL=[ALL_READS] STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +## htsjdk.samtools.metrics.StringHeader +# Started on: Thu Oct 02 13:35:09 EDT 2014 + +## METRICS CLASS picard.analysis.AlignmentSummaryMetrics +CATEGORY TOTAL_READS PF_READS PCT_PF_READS PF_NOISE_READS PF_READS_ALIGNED PCT_PF_READS_ALIGNED PF_ALIGNED_BASES PF_HQ_ALIGNED_READS PF_HQ_ALIGNED_BASES PF_HQ_ALIGNED_Q20_BASES PF_HQ_MEDIAN_MISMATCHES PF_MISMATCH_RATE PF_HQ_ERROR_RATE PF_INDEL_RATE MEAN_READ_LENGTH READS_ALIGNED_IN_PAIRS PCT_READS_ALIGNED_IN_PAIRS BAD_CYCLES STRAND_BALANCE PCT_CHIMERAS PCT_ADAPTER SAMPLE LIBRARY READ_GROUP +FIRST_OF_PAIR 100 100 1 0 100 1 17831 100 17831 16865 1 0.008188 0.008188 0 251 99 0.99 0 0.46 0 0 +SECOND_OF_PAIR 100 100 1 0 99 0.99 17907 99 17907 16887 1 0.008879 0.008879 0 251 99 1 0 0.545455 0 0 +PAIR 200 200 1 0 199 0.995 35738 199 35738 33752 1 0.008534 0.008534 0 251 198 0.994975 0 0.502513 0 0 + + |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_CleanSam.bam |
| b |
| Binary file test-data/picard_CleanSam.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_CleanSam_test1.bam |
| b |
| Binary file test-data/picard_CleanSam_test1.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_CollectBaseDistributionByCycle.bam |
| b |
| Binary file test-data/picard_CollectBaseDistributionByCycle.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_CollectBaseDistributionByCycle_ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectBaseDistributionByCycle_ref.fa Tue Dec 16 19:03:21 2014 -0500 |
| b |
| b'@@ -0,0 +1,239 @@\n+>gi|251831106|ref|NC_012920.1| Homo sapiens mitochondrion, complete genome\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG\n+GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC\n+CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA\n+ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC\n+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC\n+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA\n+CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC\n+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC\n+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC\n+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA\n+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA\n+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT\n+CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC\n+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC\n+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA\n+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC\n+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA\n+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA\n+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA\n+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA\n+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA\n+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC\n+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA\n+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT\n+AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG\n+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC\n+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG\n+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC\n+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC\n+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA\n+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT\n+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA\n+TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG\n+TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA\n+GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG\n+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG\n+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA\n+ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT\n+TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA\n+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC\n+CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC\n+CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG\n+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC\n+AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC\n+TCCTTTAACCTCTCCA'..b'GTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA\n+CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA\n+TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT\n+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT\n+CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA\n+TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC\n+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC\n+AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC\n+CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC\n+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA\n+AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC\n+TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC\n+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA\n+CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC\n+AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA\n+TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA\n+ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA\n+TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA\n+CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA\n+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC\n+CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC\n+CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG\n+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC\n+CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC\n+CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA\n+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA\n+CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC\n+ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC\n+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC\n+TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA\n+GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT\n+CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT\n+TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC\n+TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA\n+GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC\n+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC\n+TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC\n+CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA\n+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC\n+ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA\n+ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA\n+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG\n+TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC\n+TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC\n+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n+\n' |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_CollectBaseDistributionByCycle_test1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectBaseDistributionByCycle_test1.tab Tue Dec 16 19:03:21 2014 -0500 |
| b |
| b'@@ -0,0 +1,511 @@\n+## htsjdk.samtools.metrics.StringHeader\n+# picard.analysis.CollectBaseDistributionByCycle CHART_OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_660.dat ALIGNED_READS_ONLY=true PF_READS_ONLY=true INPUT=/Users/anton/galaxy-central/database/files/000/dataset_616.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_659.dat REFERENCE_SEQUENCE=/Users/anton/temp/mt.fa ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false\n+## htsjdk.samtools.metrics.StringHeader\n+# Started on: Fri Oct 03 10:05:03 EDT 2014\n+\n+## METRICS CLASS\tpicard.analysis.BaseDistributionByCycleMetrics\n+READ_END\tCYCLE\tPCT_A\tPCT_C\tPCT_G\tPCT_T\tPCT_N\n+1\t1\t21\t22\t29\t28\t0\n+1\t2\t49\t13\t12\t26\t0\n+1\t3\t35\t22\t13\t30\t0\n+1\t4\t28\t20\t13\t39\t0\n+1\t5\t37\t20\t10\t33\t0\n+1\t6\t22\t29\t13\t36\t0\n+1\t7\t34\t16\t25\t25\t0\n+1\t8\t33\t19\t15\t33\t0\n+1\t9\t25\t28\t27\t20\t0\n+1\t10\t30\t22\t14\t34\t0\n+1\t11\t29\t26\t18\t27\t0\n+1\t12\t28\t34\t12\t26\t0\n+1\t13\t39\t25\t7\t29\t0\n+1\t14\t23\t20\t28\t29\t0\n+1\t15\t22\t21\t29\t28\t0\n+1\t16\t32\t22\t16\t30\t0\n+1\t17\t25\t19\t24\t32\t0\n+1\t18\t25\t29\t20\t26\t0\n+1\t19\t21\t32\t18\t29\t0\n+1\t20\t31\t20\t11\t38\t0\n+1\t21\t34\t23\t14\t29\t0\n+1\t22\t18\t32\t20\t30\t0\n+1\t23\t29\t20\t9\t42\t0\n+1\t24\t27\t14\t18\t41\t0\n+1\t25\t35\t25\t13\t27\t0\n+1\t26\t41\t18\t11\t30\t0\n+1\t27\t21\t19\t26\t34\t0\n+1\t28\t29\t22\t19\t30\t0\n+1\t29\t21\t27\t23\t29\t0\n+1\t30\t21\t25\t20\t34\t0\n+1\t31\t27\t27\t11\t35\t0\n+1\t32\t39\t22\t19\t20\t0\n+1\t33\t25\t25\t15\t35\t0\n+1\t34\t25\t30\t12\t33\t0\n+1\t35\t30\t29\t16\t25\t0\n+1\t36\t31\t20\t19\t30\t0\n+1\t37\t32\t28\t13\t27\t0\n+1\t38\t19\t36\t19\t26\t0\n+1\t39\t22\t36\t17\t25\t0\n+1\t40\t17\t28\t15\t40\t0\n+1\t41\t38\t22\t14\t26\t0\n+1\t42\t37\t20\t20\t23\t0\n+1\t43\t24\t26\t20\t30\t0\n+1\t44\t24\t27\t15\t34\t0\n+1\t45\t24\t24\t17\t35\t0\n+1\t46\t29\t23\t20\t28\t0\n+1\t47\t21\t31\t12\t36\t0\n+1\t48\t20\t39\t18\t23\t0\n+1\t49\t33\t28\t14\t25\t0\n+1\t50\t28\t31\t12\t29\t0\n+1\t51\t29\t30\t13\t28\t0\n+1\t52\t32\t21\t18\t29\t0\n+1\t53\t14\t42\t17\t27\t0\n+1\t54\t32\t20\t31\t17\t0\n+1\t55\t24\t21\t17\t38\t0\n+1\t56\t31\t18\t20\t31\t0\n+1\t57\t23\t36\t12\t29\t0\n+1\t58\t18\t34\t18\t30\t0\n+1\t59\t20\t31\t21\t28\t0\n+1\t60\t26\t32\t19\t23\t0\n+1\t61\t19\t33\t20\t28\t0\n+1\t62\t29\t26\t18\t27\t0\n+1\t63\t26\t32\t10\t32\t0\n+1\t64\t27\t31\t18\t24\t0\n+1\t65\t34\t21\t16\t29\t0\n+1\t66\t17\t32\t20\t31\t0\n+1\t67\t38\t23\t22\t17\t0\n+1\t68\t29\t21\t22\t28\t0\n+1\t69\t22\t24\t28\t26\t0\n+1\t70\t27\t21\t20\t32\t0\n+1\t71\t14\t27\t29\t30\t0\n+1\t72\t28\t29\t21\t22\t0\n+1\t73\t17\t32\t23\t28\t0\n+1\t74\t17\t33\t19\t31\t0\n+1\t75\t34\t24\t10\t32\t0\n+1\t76\t22\t39\t13\t26\t0\n+1\t77\t26\t18\t30\t26\t0\n+1\t78\t39\t24\t17\t20\t0\n+1\t79\t16\t22\t26\t36\t0\n+1\t80\t21\t22\t31\t26\t0\n+1\t81\t12\t32\t28\t28\t0\n+1\t82\t23\t37\t15\t25\t0\n+1\t83\t27\t17\t19\t37\t0\n+1\t84\t24\t34\t17\t25\t0\n+1\t85\t26\t22\t23\t29\t0\n+1\t86\t20\t31\t26\t23\t0\n+1\t87\t25\t26\t20\t29\t0\n+1\t88\t18\t24\t38\t20\t0\n+1\t89\t13\t26\t30\t31\t0\n+1\t90\t18\t27\t21\t34\t0\n+1\t91\t26\t35\t18\t21\t0\n+1\t92\t17\t32\t24\t27\t0\n+1\t93\t34\t15\t25\t26\t0\n+1\t94\t17\t24\t23\t36\t0\n+1\t95\t22\t25\t29\t24\t0\n+1\t96\t33\t28\t19\t20\t0\n+1\t97\t12\t32\t23\t33\t0\n+1\t98\t20\t37\t20\t23\t0\n+1\t99\t16\t38\t21\t25\t0\n+1\t100\t18\t25\t19\t38\t0\n+1\t101\t30\t20\t32\t18\t0\n+1\t102\t23\t26\t20\t31\t0\n+1\t103\t25\t17\t29\t29\t0\n+1\t104\t20\t30\t28\t22\t0\n+1\t105\t19\t20\t31\t30\t0\n+1\t106\t28\t27\t19\t26\t0\n+1\t107\t16\t26\t32\t26\t0\n+1\t108\t29\t23\t29\t19\t0\n+1\t109\t23\t34\t26\t17\t0\n+1\t110\t11\t28\t27\t34\t0\n+1\t111\t23\t32\t25\t20\t0\n+1\t112\t26\t22\t24\t28\t0\n+1\t113\t14\t34\t27\t25\t0\n+1\t114\t18\t22\t37\t23\t0\n+1\t115\t22\t26\t24\t28\t0\n+1\t116\t18\t22\t34\t26\t0\n+1\t117\t30\t23\t18\t29\t0\n+1\t118\t18\t24\t29\t29\t0\n+1\t119\t19\t38\t23\t20\t0\n+1\t120\t22\t21\t23\t34\t0\n+1\t121\t22\t37\t20\t21\t0\n+1\t122\t16\t25\t27\t32\t0\n+1\t123\t14\t39\t23\t24\t0\n+1\t124\t19\t34\t29\t18\t0\n+1\t125\t22\t24\t30\t24\t0\n+1\t126\t20\t25\t24\t31\t0\n+1\t127\t25\t22\t29\t24\t0\n+1\t128\t16\t29\t23\t32\t0\n+1\t129\t28\t27\t25\t20\t0\n+1\t130\t22\t19\t23\t36\t0\n+1\t131\t10\t35\t29\t26\t0\n+1\t132\t22\t25\t25\t28\t0\n+1\t133\t20\t26\t35\t19\t0\n+1\t134\t13\t28\t32\t27\t0\n+1\t135\t22\t20\t26\t32\t0\n+1\t136\t27\t21\t24\t28\t0\n+1\t137\t25\t25\t22\t28\t0\n+1\t138\t17\t28\t25\t30\t0\n+1\t139\t14\t35\t24\t27\t0\n+1\t140\t15\t28\t25\t32\t0\n+1\t141\t23\t39\t19\t19\t0\n+1\t142\t13\t17\t41\t29\t0\n+1\t143\t15\t23\t27\t35\t0\n+1\t144\t16\t33\t22\t29\t0\n+1\t145\t22\t28\t17\t33\t0\n+1\t146\t21\t22\t32\t25\t0\n+1\t147\t14\t31\t30\t25\t0\n+1\t148\t24\t21\t33\t22\t0\n+1\t149\t20\t18\t37\t25\t0\n+1\t150\t22\t20\t30\t28\t0\n+1\t151\t20\t26\t33\t21\t0\n+1\t152\t19\t26\t22\t33\t0\n+1\t153\t21\t25\t24\t30\t0\n+1\t154\t17\t28\t15\t40\t0\n+1\t155\t25\t19\t25\t31\t0\n+1\t156\t25\t36\t16\t23\t0\n+1\t157\t28\t23\t23\t26\t0\n+1\t158\t17\t27\t21\t35\t0\n+1\t1'..b'353535\t0\n+2\t421\t24.242424\t19.191919\t32.323232\t24.242424\t0\n+2\t422\t10.10101\t36.363636\t25.252525\t28.282828\t0\n+2\t423\t22.222222\t23.232323\t29.292929\t25.252525\t0\n+2\t424\t23.232323\t25.252525\t25.252525\t26.262626\t0\n+2\t425\t18.181818\t26.262626\t30.30303\t25.252525\t0\n+2\t426\t24.242424\t27.272727\t26.262626\t22.222222\t0\n+2\t427\t19.191919\t32.323232\t28.282828\t20.20202\t0\n+2\t428\t18.181818\t27.272727\t22.222222\t32.323232\t0\n+2\t429\t23.232323\t31.313131\t24.242424\t21.212121\t0\n+2\t430\t16.161616\t23.232323\t17.171717\t43.434343\t0\n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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_CollectGcBiasMetrics.bam |
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| Binary file test-data/picard_CollectGcBiasMetrics.bam has changed |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_CollectGcBiasMetrics_ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectGcBiasMetrics_ref.fa Tue Dec 16 19:03:21 2014 -0500 |
| b |
| b'@@ -0,0 +1,239 @@\n+>gi|251831106|ref|NC_012920.1| Homo sapiens mitochondrion, complete genome\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG\n+GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC\n+CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA\n+ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC\n+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC\n+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA\n+CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC\n+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC\n+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC\n+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA\n+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA\n+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT\n+CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC\n+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC\n+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA\n+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC\n+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA\n+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA\n+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA\n+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA\n+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA\n+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC\n+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA\n+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT\n+AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG\n+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC\n+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG\n+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC\n+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC\n+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA\n+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT\n+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA\n+TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG\n+TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA\n+GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG\n+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG\n+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA\n+ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT\n+TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA\n+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC\n+CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC\n+CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG\n+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC\n+AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC\n+TCCTTTAACCTCTCCA'..b'GTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA\n+CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA\n+TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT\n+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT\n+CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA\n+TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC\n+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC\n+AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC\n+CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC\n+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA\n+AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC\n+TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC\n+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA\n+CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC\n+AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA\n+TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA\n+ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA\n+TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA\n+CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA\n+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC\n+CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC\n+CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG\n+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC\n+CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC\n+CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA\n+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA\n+CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC\n+ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC\n+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC\n+TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA\n+GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT\n+CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT\n+TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC\n+TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA\n+GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC\n+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC\n+TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC\n+CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA\n+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC\n+ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA\n+ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA\n+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG\n+TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC\n+TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC\n+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n+\n' |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_CollectGcBiasMetrics_test1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectGcBiasMetrics_test1.tab Tue Dec 16 19:03:21 2014 -0500 |
| b |
| @@ -0,0 +1,48 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.analysis.CollectGcBiasMetrics REFERENCE_SEQUENCE=localref.fa INPUT=/Users/anton/galaxy-central/database/files/000/dataset_616.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_707.dat CHART_OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_708.dat SUMMARY_OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_706.dat WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=5.0E-5 ASSUME_SORTED=true IS_BISULFITE_SEQUENCED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +## htsjdk.samtools.metrics.StringHeader +# Started on: Sat Oct 04 11:22:58 EDT 2014 + +## METRICS CLASS picard.analysis.GcBiasDetailMetrics +GC WINDOWS READ_STARTS MEAN_BASE_QUALITY NORMALIZED_COVERAGE ERROR_BAR_WIDTH +24 2 0 0 0 0 +25 15 0 0 0 0 +26 13 0 0 0 0 +27 18 0 0 0 0 +28 50 5 21 4.843529 2.166092 +29 47 0 0 0 0 +30 63 0 0 0 0 +31 97 4 20 1.997332 0.998666 +32 167 3 23 0.870095 0.50235 +33 178 4 22 1.088434 0.544217 +34 225 8 22 1.722144 0.60887 +35 291 5 22 0.832222 0.372181 +36 391 1 21 0.123875 0.123875 +37 506 4 24 0.382888 0.191444 +38 570 0 0 0 0 +39 640 0 0 0 0 +40 729 0 0 0 0 +41 846 1 24 0.057252 0.057252 +42 1060 1 24 0.045694 0.045694 +43 1182 13 22 0.532706 0.147746 +44 1113 8 22 0.348142 0.123087 +45 1161 7 20 0.29203 0.110377 +46 1113 5 20 0.217589 0.097309 +47 1035 8 23 0.374379 0.132363 +48 956 9 23 0.455981 0.151994 +49 913 1 24 0.053051 0.053051 +50 785 5 22 0.308505 0.137968 +51 607 5 22 0.398973 0.178426 +52 436 104 22 11.553373 1.132901 +53 354 13 23 1.778697 0.493322 +54 288 0 0 0 0 +55 232 6 21 1.252637 0.511387 +56 133 0 0 0 0 +57 108 2 24 0.89695 0.634239 +58 65 0 0 0 0 +59 38 0 0 0 0 +60 29 0 0 0 0 +61 10 0 0 0 0 +62 2 0 0 0 0 + + |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_CollectInsertSizeMetrics.bam |
| b |
| Binary file test-data/picard_CollectInsertSizeMetrics.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_CollectInsertSizeMetrics_ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectInsertSizeMetrics_ref.fa Tue Dec 16 19:03:21 2014 -0500 |
| b |
| b'@@ -0,0 +1,239 @@\n+>gi|251831106|ref|NC_012920.1| Homo sapiens mitochondrion, complete genome\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG\n+GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC\n+CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA\n+ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC\n+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC\n+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA\n+CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC\n+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC\n+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC\n+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA\n+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA\n+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT\n+CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC\n+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC\n+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA\n+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC\n+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA\n+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA\n+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA\n+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA\n+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA\n+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC\n+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA\n+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT\n+AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG\n+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC\n+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG\n+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC\n+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC\n+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA\n+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT\n+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA\n+TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG\n+TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA\n+GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG\n+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG\n+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA\n+ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT\n+TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA\n+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC\n+CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC\n+CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG\n+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC\n+AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC\n+TCCTTTAACCTCTCCA'..b'GTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA\n+CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA\n+TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT\n+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT\n+CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA\n+TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC\n+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC\n+AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC\n+CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC\n+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA\n+AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC\n+TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC\n+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA\n+CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC\n+AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA\n+TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA\n+ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA\n+TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA\n+CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA\n+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC\n+CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC\n+CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG\n+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC\n+CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC\n+CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA\n+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA\n+CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC\n+ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC\n+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC\n+TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA\n+GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT\n+CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT\n+TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC\n+TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA\n+GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC\n+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC\n+TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC\n+CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA\n+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC\n+ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA\n+ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA\n+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG\n+TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC\n+TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC\n+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n+\n' |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_CollectInsertSizeMetrics_test1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectInsertSizeMetrics_test1.tab Tue Dec 16 19:03:21 2014 -0500 |
| [ |
| @@ -0,0 +1,56 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.analysis.CollectInsertSizeMetrics HISTOGRAM_FILE=/Users/anton/galaxy-central/database/files/000/dataset_699.dat DEVIATIONS=10.0 HISTOGRAM_WIDTH=500 MINIMUM_PCT=0.05 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=/Users/anton/galaxy-central/database/files/000/dataset_616.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_698.dat REFERENCE_SEQUENCE=/Users/anton/temp/mt.fa ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +## htsjdk.samtools.metrics.StringHeader +# Started on: Sat Oct 04 10:14:44 EDT 2014 + +## METRICS CLASS picard.analysis.InsertSizeMetrics +MEDIAN_INSERT_SIZE MEDIAN_ABSOLUTE_DEVIATION 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 SAMPLE LIBRARY READ_GROUP +200 28 112 251 193.969697 36.171207 99 FR 7 15 33 43 57 73 83 99 125 177 + +## HISTOGRAM java.lang.Integer +insert_size All_Reads.fr_count +112 1 +120 1 +132 2 +134 2 +138 5 +139 1 +140 1 +141 1 +151 2 +156 4 +157 1 +159 1 +161 2 +169 1 +172 1 +173 1 +177 3 +179 3 +182 3 +184 4 +185 2 +187 1 +192 1 +193 1 +194 3 +200 2 +201 5 +203 8 +205 1 +208 1 +213 4 +216 1 +222 1 +228 5 +229 2 +230 1 +231 3 +233 1 +236 2 +238 2 +241 4 +242 3 +250 2 +251 3 + |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_CollectRnaSeqMetrics.bam |
| b |
| Binary file test-data/picard_CollectRnaSeqMetrics.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_CollectRnaSeqMetrics.refFlat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectRnaSeqMetrics.refFlat Tue Dec 16 19:03:21 2014 -0500 |
| b |
| @@ -0,0 +1,21 @@ +#hg19.knownGene.name hg19.knownGene.chrom hg19.knownGene.strand hg19.knownGene.txStart hg19.knownGene.txEnd hg19.knownGene.cdsStart hg19.knownGene.cdsEnd hg19.knownGene.exonCount hg19.knownGene.exonStarts hg19.knownGene.exonEnds hg19.kgXref.kgID +uc004coq.4 chrM - 235 368 235 235 1 235, 368, uc004coq.4 +uc022bqo.2 chrM + 650 674 650 650 1 650, 674, uc022bqo.2 +uc004cor.1 chrM + 1603 1634 1603 1603 1 1603, 1634, uc004cor.1 +uc004cos.5 chrM + 1843 4264 1843 1843 1 1843, 4264, uc004cos.5 +uc022bqp.1 chrM - 5543 5566 5543 5543 1 5543, 5566, uc022bqp.1 +uc022bqq.1 chrM - 5585 5606 5585 5585 1 5585, 5606, uc022bqq.1 +uc022bqr.1 chrM - 5690 5714 5690 5690 1 5690, 5714, uc022bqr.1 +uc031tga.1 chrM + 5904 7439 5904 5904 1 5904, 7439, uc031tga.1 +uc022bqs.1 chrM - 7586 15888 7586 7586 2 7586,15503, 7982,15888, uc022bqs.1 +uc011mfi.2 chrM + 7586 9208 7586 7586 1 7586, 9208, uc011mfi.2 +uc022bqt.1 chrM - 8366 14149 8366 8366 2 8366,13449, 8472,14149, uc022bqt.1 +uc022bqu.2 chrM + 10059 10404 10059 10059 1 10059, 10404, uc022bqu.2 +uc004cov.5 chrM + 10470 12138 10470 10470 1 10470, 12138, uc004cov.5 +uc031tgb.1 chrM - 10760 14149 10760 10760 2 10760,13978, 11231,14149, uc031tgb.1 +uc004cow.2 chrM + 12207 12264 12207 12207 1 12207, 12264, uc004cow.2 +uc004cox.4 chrM + 12907 14149 12907 12907 1 12907, 14149, uc004cox.4 +uc022bqv.1 chrM - 14674 14698 14674 14674 1 14674, 14698, uc022bqv.1 +uc022bqw.1 chrM + 14856 15888 14856 14856 1 14856, 15888, uc022bqw.1 +uc022bqx.1 chrM - 15959 16024 15959 15959 1 15959, 16024, uc022bqx.1 +uc004coz.1 chrM + 15998 16571 15998 15998 1 15998, 16571, uc004coz.1 |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_CollectRnaSeqMetrics.refFlat~ --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectRnaSeqMetrics.refFlat~ Tue Dec 16 19:03:21 2014 -0500 |
| b |
| @@ -0,0 +1,21 @@ +hg19.kgXref.kgID #hg19.knownGene.name hg19.knownGene.chrom hg19.knownGene.strand hg19.knownGene.txStart hg19.knownGene.txEnd hg19.knownGene.cdsStart hg19.knownGene.cdsEnd hg19.knownGene.exonCount hg19.knownGene.exonStarts hg19.knownGene.exonEnds +uc004coq.4 uc004coq.4 chrM - 235 368 235 235 1 235, 368, +uc022bqo.2 uc022bqo.2 chrM + 650 674 650 650 1 650, 674, +uc004cor.1 uc004cor.1 chrM + 1603 1634 1603 1603 1 1603, 1634, +uc004cos.5 uc004cos.5 chrM + 1843 4264 1843 1843 1 1843, 4264, +uc022bqp.1 uc022bqp.1 chrM - 5543 5566 5543 5543 1 5543, 5566, +uc022bqq.1 uc022bqq.1 chrM - 5585 5606 5585 5585 1 5585, 5606, +uc022bqr.1 uc022bqr.1 chrM - 5690 5714 5690 5690 1 5690, 5714, +uc031tga.1 uc031tga.1 chrM + 5904 7439 5904 5904 1 5904, 7439, +uc022bqs.1 uc022bqs.1 chrM - 7586 15888 7586 7586 2 7586,15503, 7982,15888, +uc011mfi.2 uc011mfi.2 chrM + 7586 9208 7586 7586 1 7586, 9208, +uc022bqt.1 uc022bqt.1 chrM - 8366 14149 8366 8366 2 8366,13449, 8472,14149, +uc022bqu.2 uc022bqu.2 chrM + 10059 10404 10059 10059 1 10059, 10404, +uc004cov.5 uc004cov.5 chrM + 10470 12138 10470 10470 1 10470, 12138, +uc031tgb.1 uc031tgb.1 chrM - 10760 14149 10760 10760 2 10760,13978, 11231,14149, +uc004cow.2 uc004cow.2 chrM + 12207 12264 12207 12207 1 12207, 12264, +uc004cox.4 uc004cox.4 chrM + 12907 14149 12907 12907 1 12907, 14149, +uc022bqv.1 uc022bqv.1 chrM - 14674 14698 14674 14674 1 14674, 14698, +uc022bqw.1 uc022bqw.1 chrM + 14856 15888 14856 14856 1 14856, 15888, +uc022bqx.1 uc022bqx.1 chrM - 15959 16024 15959 15959 1 15959, 16024, +uc004coz.1 uc004coz.1 chrM + 15998 16571 15998 15998 1 15998, 16571, |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_CollectRnaSeqMetrics_ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectRnaSeqMetrics_ref.fa Tue Dec 16 19:03:21 2014 -0500 |
| b |
| b'@@ -0,0 +1,239 @@\n+>chrM\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG\n+GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC\n+CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA\n+ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC\n+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC\n+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA\n+CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC\n+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC\n+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC\n+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA\n+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA\n+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT\n+CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC\n+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC\n+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA\n+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC\n+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA\n+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA\n+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA\n+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA\n+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA\n+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC\n+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA\n+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT\n+AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG\n+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC\n+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG\n+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC\n+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC\n+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA\n+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT\n+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA\n+TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG\n+TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA\n+GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG\n+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG\n+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA\n+ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT\n+TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA\n+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC\n+CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC\n+CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG\n+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC\n+AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC\n+TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG\n+CCATAATATGATT'..b'GTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA\n+CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA\n+TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT\n+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT\n+CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA\n+TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC\n+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC\n+AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC\n+CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC\n+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA\n+AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC\n+TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC\n+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA\n+CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC\n+AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA\n+TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA\n+ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA\n+TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA\n+CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA\n+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC\n+CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC\n+CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG\n+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC\n+CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC\n+CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA\n+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA\n+CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC\n+ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC\n+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC\n+TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA\n+GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT\n+CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT\n+TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC\n+TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA\n+GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC\n+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC\n+TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC\n+CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA\n+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC\n+ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA\n+ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA\n+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG\n+TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC\n+TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC\n+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n+\n' |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_CollectRnaSeqMetrics_test1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectRnaSeqMetrics_test1.tab Tue Dec 16 19:03:21 2014 -0500 |
| [ |
| @@ -0,0 +1,113 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.analysis.CollectRnaSeqMetrics REF_FLAT=refFlat.tab STRAND_SPECIFICITY=NONE MINIMUM_LENGTH=500 CHART_OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_792.dat RRNA_FRAGMENT_PERCENTAGE=0.8 METRIC_ACCUMULATION_LEVEL=[ALL_READS] INPUT=/Users/anton/galaxy-central/database/files/000/dataset_773.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_793.dat REFERENCE_SEQUENCE=localref.fa ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +## htsjdk.samtools.metrics.StringHeader +# Started on: Mon Oct 06 22:24:48 EDT 2014 + +## METRICS CLASS picard.analysis.RnaSeqMetrics +PF_BASES PF_ALIGNED_BASES RIBOSOMAL_BASES CODING_BASES UTR_BASES INTRONIC_BASES INTERGENIC_BASES IGNORED_READS CORRECT_STRAND_READS INCORRECT_STRAND_READS PCT_RIBOSOMAL_BASES PCT_CODING_BASES PCT_UTR_BASES PCT_INTRONIC_BASES PCT_INTERGENIC_BASES PCT_MRNA_BASES PCT_USABLE_BASES PCT_CORRECT_STRAND_READS MEDIAN_CV_COVERAGE MEDIAN_5PRIME_BIAS MEDIAN_3PRIME_BIAS MEDIAN_5PRIME_TO_3PRIME_BIAS SAMPLE LIBRARY READ_GROUP +48870 48712 0 38786 3735 6191 0 0 0 0 0.796231 0.076675 0.127094 0.796231 0.793657 0 0.867456 0.432948 0.262822 0.657143 + +## HISTOGRAM java.lang.Integer +normalized_position All_Reads.normalized_coverage +0 0.31117 +1 0.324521 +2 0.280175 +3 0.229683 +4 0.247568 +5 0.252404 +6 0.37536 +7 0.454337 +8 0.498193 +9 0.717955 +10 0.852206 +11 0.841585 +12 0.883517 +13 0.878327 +14 0.971971 +15 0.946456 +16 1.096539 +17 1.085217 +18 1.030988 +19 1.169726 +20 1.06324 +21 1.124029 +22 1.021164 +23 1.111695 +24 1.036323 +25 0.996034 +26 1.08738 +27 1.107549 +28 0.955729 +29 0.907313 +30 1.049856 +31 1.068308 +32 1.05576 +33 1.004803 +34 1.044887 +35 1.020916 +36 0.914561 +37 0.943721 +38 0.938101 +39 0.921157 +40 1.059497 +41 1.067667 +42 1.164889 +43 1.252036 +44 1.294715 +45 1.236472 +46 1.169812 +47 1.236597 +48 1.067639 +49 1.045102 +50 0.994369 +51 0.923449 +52 0.915703 +53 0.920667 +54 0.840804 +55 0.731542 +56 0.785935 +57 0.803421 +58 0.797747 +59 0.754627 +60 0.748683 +61 0.774967 +62 0.880321 +63 0.958948 +64 1.066362 +65 1.151358 +66 1.289535 +67 1.358181 +68 1.33396 +69 1.140164 +70 1.260899 +71 1.226678 +72 1.259541 +73 1.288495 +74 1.484984 +75 1.41511 +76 1.351353 +77 1.337399 +78 1.340637 +79 1.293356 +80 1.327074 +81 1.345788 +82 1.469492 +83 1.563011 +84 1.528971 +85 1.651207 +86 1.640289 +87 1.468521 +88 1.482936 +89 1.396498 +90 1.326153 +91 1.191411 +92 1.054954 +93 0.938397 +94 0.82527 +95 0.630468 +96 0.417112 +97 0.327528 +98 0.308028 +99 0.329076 +100 0.315292 + |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_CollectWgsMetrics.bam |
| b |
| Binary file test-data/picard_CollectWgsMetrics.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_CollectWgsMetrics_ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectWgsMetrics_ref.fa Tue Dec 16 19:03:21 2014 -0500 |
| b |
| b'@@ -0,0 +1,239 @@\n+>chrM\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG\n+GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC\n+CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA\n+ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC\n+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC\n+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA\n+CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC\n+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC\n+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC\n+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA\n+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA\n+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT\n+CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC\n+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC\n+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA\n+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC\n+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA\n+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA\n+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA\n+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA\n+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA\n+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC\n+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA\n+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT\n+AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG\n+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC\n+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG\n+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC\n+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC\n+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA\n+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT\n+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA\n+TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG\n+TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA\n+GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG\n+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG\n+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA\n+ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT\n+TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA\n+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC\n+CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC\n+CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG\n+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC\n+AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC\n+TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG\n+CCATAATATGATT'..b'GTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA\n+CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA\n+TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT\n+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT\n+CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA\n+TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC\n+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC\n+AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC\n+CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC\n+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA\n+AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC\n+TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC\n+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA\n+CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC\n+AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA\n+TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA\n+ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA\n+TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA\n+CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA\n+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC\n+CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC\n+CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG\n+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC\n+CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC\n+CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA\n+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA\n+CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC\n+ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC\n+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC\n+TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA\n+GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT\n+CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT\n+TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC\n+TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA\n+GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC\n+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC\n+TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC\n+CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA\n+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC\n+ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA\n+ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA\n+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG\n+TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC\n+TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC\n+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n+\n' |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_CollectWgsMetrics_test1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_CollectWgsMetrics_test1.tab Tue Dec 16 19:03:21 2014 -0500 |
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| @@ -0,0 +1,263 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.analysis.CollectWgsMetrics INPUT=/Users/anton/galaxy-central/database/files/000/dataset_773.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_802.dat REFERENCE_SEQUENCE=localref.fa MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 COVERAGE_CAP=250 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT STOP_AFTER=-1 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +## htsjdk.samtools.metrics.StringHeader +# Started on: Tue Oct 07 15:46:29 EDT 2014 + +## METRICS CLASS picard.analysis.CollectWgsMetrics$WgsMetrics +GENOME_TERRITORY MEAN_COVERAGE SD_COVERAGE MEDIAN_COVERAGE MAD_COVERAGE PCT_EXC_MAPQ PCT_EXC_DUPE PCT_EXC_UNPAIRED PCT_EXC_BASEQ PCT_EXC_OVERLAP PCT_EXC_CAPPED PCT_EXC_TOTAL PCT_5X PCT_10X PCT_15X PCT_20X PCT_25X PCT_30X PCT_40X PCT_50X PCT_60X PCT_70X PCT_80X PCT_90X PCT_100X +16568 2.915983 3.836089 2 2 0 0 0 0 0.008069 0 0.008069 0.240464 0.055831 0.02541 0.011045 0 0 0 0 0 0 0 0 0 + +## HISTOGRAM java.lang.Integer +coverage count +0 5225 +1 3010 +2 1806 +3 1333 +4 1210 +5 1247 +6 672 +7 468 +8 361 +9 311 +10 210 +11 95 +12 78 +13 52 +14 69 +15 64 +16 29 +17 31 +18 53 +19 61 +20 65 +21 74 +22 32 +23 12 +24 0 +25 0 +26 0 +27 0 +28 0 +29 0 +30 0 +31 0 +32 0 +33 0 +34 0 +35 0 +36 0 +37 0 +38 0 +39 0 +40 0 +41 0 +42 0 +43 0 +44 0 +45 0 +46 0 +47 0 +48 0 +49 0 +50 0 +51 0 +52 0 +53 0 +54 0 +55 0 +56 0 +57 0 +58 0 +59 0 +60 0 +61 0 +62 0 +63 0 +64 0 +65 0 +66 0 +67 0 +68 0 +69 0 +70 0 +71 0 +72 0 +73 0 +74 0 +75 0 +76 0 +77 0 +78 0 +79 0 +80 0 +81 0 +82 0 +83 0 +84 0 +85 0 +86 0 +87 0 +88 0 +89 0 +90 0 +91 0 +92 0 +93 0 +94 0 +95 0 +96 0 +97 0 +98 0 +99 0 +100 0 +101 0 +102 0 +103 0 +104 0 +105 0 +106 0 +107 0 +108 0 +109 0 +110 0 +111 0 +112 0 +113 0 +114 0 +115 0 +116 0 +117 0 +118 0 +119 0 +120 0 +121 0 +122 0 +123 0 +124 0 +125 0 +126 0 +127 0 +128 0 +129 0 +130 0 +131 0 +132 0 +133 0 +134 0 +135 0 +136 0 +137 0 +138 0 +139 0 +140 0 +141 0 +142 0 +143 0 +144 0 +145 0 +146 0 +147 0 +148 0 +149 0 +150 0 +151 0 +152 0 +153 0 +154 0 +155 0 +156 0 +157 0 +158 0 +159 0 +160 0 +161 0 +162 0 +163 0 +164 0 +165 0 +166 0 +167 0 +168 0 +169 0 +170 0 +171 0 +172 0 +173 0 +174 0 +175 0 +176 0 +177 0 +178 0 +179 0 +180 0 +181 0 +182 0 +183 0 +184 0 +185 0 +186 0 +187 0 +188 0 +189 0 +190 0 +191 0 +192 0 +193 0 +194 0 +195 0 +196 0 +197 0 +198 0 +199 0 +200 0 +201 0 +202 0 +203 0 +204 0 +205 0 +206 0 +207 0 +208 0 +209 0 +210 0 +211 0 +212 0 +213 0 +214 0 +215 0 +216 0 +217 0 +218 0 +219 0 +220 0 +221 0 +222 0 +223 0 +224 0 +225 0 +226 0 +227 0 +228 0 +229 0 +230 0 +231 0 +232 0 +233 0 +234 0 +235 0 +236 0 +237 0 +238 0 +239 0 +240 0 +241 0 +242 0 +243 0 +244 0 +245 0 +246 0 +247 0 +248 0 +249 0 +250 0 + |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_DownsampleSam.bam |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_DownsampleSam_test1.bam |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_EstimateLibraryComplexity.bam |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_EstimateLibraryComplexity_test1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_EstimateLibraryComplexity_test1.tab Tue Dec 16 19:03:21 2014 -0500 |
| [ |
| @@ -0,0 +1,18 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.sam.markduplicates.EstimateLibraryComplexity INPUT=[/Users/anton/galaxy-central/database/files/000/dataset_951.dat] OUTPUT=/Users/anton/galaxy-central/database/files/001/dataset_1073.dat MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 MAX_GROUP_RATIO=500 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*. OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3472024 CREATE_INDEX=false CREATE_MD5_FILE=false +## htsjdk.samtools.metrics.StringHeader +# Started on: Fri Oct 17 13:39:31 EDT 2014 + +## METRICS CLASS picard.sam.DuplicationMetrics +LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE +Unknown 0 982 0 0 116 0 0.118126 3822 + +## HISTOGRAM java.lang.Integer +duplication_group_count Unknown +1 781 +2 65 +3 12 +4 5 +5 3 +6 1 + |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_FastqToSam_read1.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_FastqToSam_read1.fq Tue Dec 16 19:03:21 2014 -0500 |
| b |
| b'@@ -0,0 +1,4000 @@\n+@M01368:8:000000000-A3GHV:1:1101:6911:8255/1\n+ATCTGGTTCCTACTTCAGGGCCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATT\n++\n+BCCCCFFFFFFFGGGGGGGGGGGHHHHGHGHHHHHHHHHGGGGGGHHHHGHHHHHHHHHHGHHHHHHGGHGGHHHGHHHHFHHGHHHHHHHHHGHEHEFFGHHEGGCEFGGFHHHBGHHGHHHHGHFHHHGHGHGHGGCDFDDACGGGGGGGAAFFFFFFFFFBAFFFFFB;FFFFFFADDFFFFFFFFFFEFFFFFFFFFFBFFFFFFFFFFFFFFEFFFFFFFFBFEFFFFEFE;DFFFDFBFF/9BFB\n+@M01368:8:000000000-A3GHV:1:1101:14518:9998/1\n+GTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGAT\n++\n+AAAAAFFFFFFFGGGGGGGGGGHGGHHHHGHHHHHHHGCGHHHHHHHHHHHHHHHGGGGGHHHHHHHHHGHHGFHFE5BGEEHFGGGHHHHHHHHFBHHGGGGFHGHHFGHHHHGHHHHHHGEGGGGFHFHGEGHHGGCDGDGHGGGDGGHGGCGGGHGHHH/ACDG?.1FGCDCCGCA.CC@CDCHFHGFFGGGEBFGAB//CEFBFGG.:;D;;A0AFFFFFB..:@ABFF//;BFFFFFBF/9D:A//\n+@M01368:8:000000000-A3GHV:1:1101:18422:19051/1\n+GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n++\n+CCCCCFDDDDDFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHFHHHHGGGGHHHHHHHHHGHHHHHHHHHHHHGGHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHGCGGGHHHHHHHHHHHHHHHHHHHHHHGFDHGFHCFGGGGFGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;FFFFFFFFFFFFFFFFFFFFFFFFFFFFEFBFFFFFFFFFF:FFF.\n+@M01368:8:000000000-A3GHV:1:1101:25545:21098/1\n+ATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATAAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGGCTTATTTAAGGGGAACGGGTGGGG\n++\n+33AA?DFD5BDFGGGFEBDGEGHEGHGEGHCEGGHHCHGHHFFHHGFGAGE53FF2FAFFGDE5FFFE5GFBFGAEE1GHHHGHHHEHE3FGHF@GEGEGGHHGG3FAGFFDE?EEE3GFEGFGFGGCG?GHHHFHGGGC@DHFFHD/A<C@EGFDCGGGHFHHHEGFGHBFHG0:CEHFCHGGED.;0CEF.F99B0CFFEEFGGG0FBFBBF0F/FFBDE?/9//9B.FFBFFFFFFBF..A..;@B--\n+@M01368:8:000000000-A3GHV:1:1101:5446:12248/1\n+AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTAT\n++\n+CCCCDFFFFCCFGGGGGGGGFGHHHHHGGGGHHHHHHHHHHHHHHHHGBGHGGHGGHHHHHHHHHHGHGHGGGGGHHHHHHHHGHHHHHHHHHGGGGGHHHHFFGHHHGGGGGGHHHGFGGHHGGGGHHHHHHGGGGGGHGHHGGGGGGGHGGGGGGHHHHHHHHHHHHHFHGGGHHHHGGGGGG:FE;EGEGGGGG/;?FGGGGGGGFFFFGGFFFFFFFFFBFFFFFFFFFFBFFFFFFEFFFFFEFFF\n+@M01368:8:000000000-A3GHV:1:1101:5861:6452/1\n+ATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTT\n++\n+ABCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHGHHHHGHHHHHHHHHHHGGGGHHHHHHHHFHHHHHHGGHGHGGHGGHHHHHHHGGHFHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHHEGGHHGGGGGGHHHGGGGHGGGGGHHHHHHGGGDCGHHHHGGGGGGGHEFGGGGHGHHHGHGGGFGGGGGGGEGGGGGGG?E0CEFGGGGGFEE9EEFFFFFBFFFFFFFBFFBD.AFFFFFFF0\n+@M01368:8:000000000-A3GHV:1:1102:10403:6021/1\n+CGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTG\n++\n+>A@AAAAD2ADDFFGGGGGFGGHA?EAEFBEAGHFABFGG5FDF5DB1EEGAFDFB53FF5FH@G5FFEHGHEFHFFHBE333GF43GCGGGGE@0?BFGGB0B?FHGFDGGHHHBFFDEGGHGFFFDFE@<1>@FFFGHHHHFHEFGDABFFGG/@DCE<CG1<GF0/DD000=<DHGBDFDCECE/:AC?-;-;9B/ABBB-AD9BFB99AB?BDFBAD-.9..@;=;;..9..9/9;BEF;A:9/BFF\n+@M01368:8:000000000-A3GHV:1:1102:10677:23253/1\n+CCTTAAATAAGACATCACGATGGATCACAGGTCTATCAC'..b'HHHHHHHHHFGHHGHDCA@DGA@DFDGGGGGGFEFFFFFFFFFFFFFFFEFFFBBFFFFDADFEFFFFFF/BABFFEFFFF?FFFBFF?EFFFFFBBBFF?EEB\n+@M01368:8:000000000-A3GHV:1:2105:20721:7004/1\n+AAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGGACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTT\n++\n+CCDCCFFFFFFFGGGGGGGGGGHHHHGGGGGHHHHHHHHHHGGHHHGGHHHHHHHGHHGGHHHHHHHHHHHHHHHHHHHGHHHGGHHHHHHHGHHHHHHHHHHHHHHHHGGGHHHHHHHGHHHHHHHHHHHHHHHGHHHHHGGGHGHHFHGGHGGHGHHHHGFHHHHCGGGGHEHFHHHHHHHHHHHC?EED0GFGFFHFHHHGDGFCCGGF?GG?:BFFFGCBFFGF0:FFGFF00:B0FF0FAD.:A:B\n+@M01368:8:000000000-A3GHV:1:2107:4010:17094/1\n+TTATTGGGGAGGGGGTGATCTAAAACACTCTTTACGCCGGCTTCTATTGACTTGGGTTAATCGTGTGACCGCGGTGGCTGGCACGAAATTGACCAACCCTGGGGTTAGTATAGCTTAGTTAAACTTTCGTTTATTGCTAAAGGTTAATCACTGCTGTTTCCCGTGGGGGTGTGGCTAGGCTAAGCGTTTTGAGCTGCATTGCTGCGTGCTTGATGCTTGTCCCTTTTGATCGTGGTGATTTAGAGGGTGAA\n++\n+BBAAAFFBBCC@GGGEEEFGGGHHHHGHHHHHHHGGGGGGGGGHHFHHHGHGGHFG1FHFHHGHH?GHHHGGGGEGGHGGGGHHGGGGHHHHHHHGFGGHFHGGCCGHGBHHHHHHHHHDHHHHHHHHGFGGHHHHHHHGFHHDGHGHHHHHHHHFHHHGFHGHGGFGGDGBFGGGFGFFFFBFFCADAFFFFFFFFFFFFFFFFFADDFFFFFFFFFFFF/BFFFFFFFFFFFFEEFFFFFBBFFFDFE/\n+@M01368:8:000000000-A3GHV:1:1112:20478:8885/1\n+GCTTTATTGGGGAGGGGGTGATCTAAAACACTCTTTACGCCGGCTTCTATTGACTTGGGTTAATCGTGTGACCGCGGTGGCTGGCACGAAATTGACCAACCCTGGGGTTAGTATAGCTTAGTTAAACTTTCGTTTATTGCTAAAGGTTAATCACTGCTGTTTCCCGTGGGGGTGTGGCTAGGCTAAGCGTTTTGAGCTGCATTGCTGCGTGCTTGATGCTTGTCCCTTTTGATCGTGGTGATTTAGAGGGG\n++\n+BBCCCFFFFFCCGGGGGGEEGGHHHHGHHGHHHHHHHHGGGGFGGGHHHHHEHHHHHHHEFHHHHGHH1FDGHEGGGEEFHHEGGBFDAC?GGHHGHHHGGGHHHGGGGHHHGHBBGFHFFHHHEFGHHHHGHHGGHHHEHHGHHGDGHDGGGFGFFFHHHHGHHGHGG-CFGGGDF?FFFFEFFBFFFFFFF.9./BBFFFFFFFFFF..;A9B9BBFFFFABFFFFFFF.BB.:ADEFBBFFFF/B/A-\n+@M01368:8:000000000-A3GHV:1:2105:16915:2522/1\n+GTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGGACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACAC\n++\n+BABBCFFFFBFFGGGGGGFGGGHHHHHHHHHHHHHHHHHHGHHHHGHHHHGGGHHGHFHHHHHHGHHHHHHHHHHHGHGHHHGGHHGHHHHCFHFGHHHHHHHHHHHHGGGGGHHHHFHHGHHHFHHHGGGGGGHHFHHHGHHHDDGGGGGCGGGFHHHHGGFGCGHGGFHHHHHFFGHHHHHHHGGE?DGHHFFHEHGBGFHHHHHHHHGGGDFE?;FAFDGGGGBFFBF?EEBFF.AB.:-9-;@A/B/\n+@M01368:8:000000000-A3GHV:1:2110:11901:13185/1\n+AACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGGACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCACACCCC\n++\n+BBCCCCCCFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHGHEFHHHHHGGGGGHHHHHHGHHHGGHHHGHHEHHHHHGHHGGHHHHHHHFHHHGHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHHHGHGGGHHHHGGHHHGHHHHHGHHHHFHFHHHHHHGGFHGGHHHGGEGEHGHGHGHHHHHF;@FAFGGGGEFFFFGFFBFA?DGGFFFFFFFF/;FFFDAB\n+@M01368:8:000000000-A3GHV:1:2101:24037:24448/1\n+TAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGGACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGATTAACCCAAGTCAATAGAAGC\n++\n+ABC3AFFFFFFFGGGGGGGGGGHHHHHGGGHHHHHHHHCHHGHFHHHHHHHHHHHHHHHGGHHGHHHHGGHGGHHGGHHHHGHHHGGGGGHGHGHHHHHHHGHHHGGGGGHHHHHHHHHHHGGGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHFHHGGGGGDGHHHHHHGGHHHHHHHHHFHHGGGGGHHGGGGGGGGGBFFGGGGGGFGBFGGGFDFFFFFFFFFFFBFFFFEFFFFFFFFFFB\n+@M01368:8:000000000-A3GHV:1:2105:25110:7111/1\n+CCCTCTAAATCACCACGATCAAAAGGGACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGAACAA\n++\n+3A?ABFFFFFFFGGGGGGGGGGHGHCGHGGHHGGHGHFCHGHFGGGGHHFHGHFHHHHHHHG?FEGGFEHHHHHHFHHGGGGGGGGGFEGHHHGGGFHHGHHGHHHHHGHFGHHHHHHHGGGCF?FGHFHF2FGFHHHHHHHHHHHGGGGGHHCCDHHHHHHGGGGFGHGGGHHGD-CGADDHFFGGGFG0BBFGGGGGEF??GGBEGGGFFDFBBFEFFFF--./;..;B/BFF9@.99BBBFFB.;/;;\n' |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_FastqToSam_read2.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_FastqToSam_read2.fq Tue Dec 16 19:03:21 2014 -0500 |
| b |
| b'@@ -0,0 +1,4000 @@\n+@M01368:8:000000000-A3GHV:1:1101:6911:8255/2\n+TCGCCTTACCGCTACTCACCCACGGCGGCCATCAGCCGATACTAAGTTTGGGGTATGGTGGGGGGGATAATGAATTAGGTTGTGGGGGAGGGTTTGTGGTTGAGAGAAACACAAAAAACAATCTTATATATGGGTAGTCGTTTTGTATTGGTTTTTTGTTTTGTTTGTGTTTTGAGTGTCGGTTTAGTTCGGTGTACTAGGGGGGGTGGATGGGGTCGGCTGGTGAGGGGGTCTTAGTGTATTGAGTGTGG\n++\n+1>11111@11111A111A100000000////011110//>>/12@1@22B/////1@>21/>>/-----9/;////9////--;-;-;-----;--------9/-/-///9-;-------9//////9/////-//-/9-;-;9--/////99-;--9-:-;----/---/-----////---9-/////--;A-//////---------9/-----;-----/-/-----;--;//////////9;///-\n+@M01368:8:000000000-A3GHV:1:1101:14518:9998/2\n+CATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAA\n++\n+CCCCCFCCCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGFHHHHGGGGGHGFHHHHHHHHHHHHHHHHHHHGHGGEHGGGGCGGGHHGGCGGGGGHHGHHHGGGGGGGG.BFFFGAGADFGAFDGFGGCFFF;DDFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFF09FFFE00;BE@;DABBFFFFFBBFB00;F:9;FFBFFF9BFFFFFFFFFFFFF90/::BFFFBF0\n+@M01368:8:000000000-A3GHV:1:1101:18422:19051/2\n+CTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGG\n++\n+BCCCCFFCFFFFGGGGGGGGGGHHHGHHHHHHHHHHHHHHHHGGGGHHHHHHHHEHHHHHHHGGHHGGHGGHHHHHHHGHGGHHHGGGGGHGHHHHGGGHFHFHHHHHGGGGGHBFFCGDHHHGGGGGGHGGGGGGHHGCGGGFGHHBGGGGGFFFHEGGGGGCDCCE@EFGHHHHFHEGHGFFHHGB;ECBFGGGEFEFFGF0AFGFGFFG.;;DFFFFFFFFFF090BFFFE?FEFBBFBFFFB990BF\n+@M01368:8:000000000-A3GHV:1:1101:25545:21098/2\n+GCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTTCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCAACCTATGTCGCAGTATCTGTCTTTGAT\n++\n+3AAA34BFFFFFGCGGCGGGCGHHHGHHHHCGHFGHFHGFGGCDGGBD5FGFFFHFHGGGHAEBFGHHHEHGGFHBGGFHHHGGGEEFHHHFHFFHDHGHGHHHHFFHHGGFAEGFFFFFBGHHHFFHHHHHHHFHFHHFHGFHGHGA/<@EFHEHH1GGHFFFHG1>=FGHFHGF.GE//-<BB?9.9BFFFB==AA/FFFFFA-@BA.;;D?F9FAB;---./99BFFFBBAE-.9B/BFB9F/9BFBB\n+@M01368:8:000000000-A3GHV:1:1101:5446:12248/2\n+ATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTT\n++\n+CCDDDCCCCFFFGGGGGGGGGGHHHHHGHHHHHHHHGHHHHHHGHHHHGGGGHHHHHHHHHHHHHHHHHHHHHHGGGGGHHHHHHHGFGHHHHHHHHHHHHHHHHHGHHHHHGGGGGHHHHHHHHHHHHHHHGHHHHHHGHGHGHHGGGGGGGGGGGFFFFFFFFFFFFFFAFFFFFFFFFFFFFBFC?.EAFFFFFFFFAFFFFFFFFFFFFFFFEFFFF0FFFFFFF0BFFFFFFFFF?.BDCFFEDA/\n+@M01368:8:000000000-A3GHV:1:1101:5861:6452/2\n+TTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\n++\n+BCCCCFBBCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHHHHGGGGHHHHHHHHGHHHHHHHHHHHHHGGHGGHHHHHHHGHHHHHHHHHHHHHHHHHHHGGHHHHGGGGGGEHGHHHHHHHHHHHGHHHHHHGHGHGHGGGGCGGGGGFFFFFFFFFFFFFFFFFFFFFFFF?FFEAF:DAEF9DEFFFFFFF-A.BFFFFFEFFFFEFFFFFFFF0FFEB0FFFFBFFFFFFADEFCF0/.\n+@M01368:8:000000000-A3GHV:1:1102:10403:6021/2\n+GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGGGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGGGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGAGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACGCTGAAGTAGGAACCAGATGTCGGATACAGTTGACTTTAGGTAACCCA\n++\n+AA?A34BF>AADEBGGGGFFCGGHHA5DFGAE?AAEDFHG2AEE1FBE00A1BGE0?E1FFGEEEGB4F43?EE/>///F??//@BCBAC<<BAGHB?11F/FGFGGBFBGBD.11><.<<<C0<A</<<=0GFHC@-.;FF09BFFGB00B0;FE.C/:CCF0;0C0;BBBFF@.9AF.:9EFF.;.BFF/FF/;/./BFB/..;;ABF/9FF//.;AAF9BBBA;-A.B/9///9/BF////;///:9.\n+@M01368:8:000000000-A3GHV:1:1102:10677:23253/2\n+AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATT'..b'HCCGCCFHHHGGFFHFHHHHHHC-CFFHHHHHFHEHHHGFAC--.::-C-GBBB9/:/.:CFFB0BBCCB0BFFBB0FGA?A.9;BBFFFBFF/;:F/B/9//:\n+@M01368:8:000000000-A3GHV:1:2105:20721:7004/2\n+TTATTGGGGAGGGGGTGATCTAAAACACTCTTTACGCCGGCTTCTATTGACTTGGGTTAATCGTGTGACCGCGGTGGCTGGCACGAAATTGACCAACCCTGGGGTTAGTATAGCTTAGTTAAACTTTCGTTTATTGCTAAAGGTTAATCACTGCTGTTTCCCGTGGGGGTGTGGCTAGGCTAAGCGTTTTGAGCTGCATTGCTGCGGGCTTGATGCTTGTCCCTTTTGATCGTGGGGATTTAGAGGGTGAA\n++\n+BBBBBFFBBBDBGGGEFGGGGGFHHHFHHHHHHHHGGGCGGGGHHFFHF5EGFFHG?FFFHHFHHHAHEHGGGCEFGAFEFDBGFAFGGHEFFGHHGGGHHHGG/@<G1FGHGGGHHFDDF<DDHHHHGHGGEHBDFFHGHHHFFGDGB0GHHEGFHHHGHFDEDCGGG;:BGG?FG?FBFFFFFDDDFA...;/::9FB/////----9.:./::B:B9;9:/BFFF.;/;BFD--..//////;..;./\n+@M01368:8:000000000-A3GHV:1:2107:4010:17094/2\n+TTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGGACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACC\n++\n+BBCBBFBFFFFFGGGGGGGGGGHHHHHHHHGHHHHHHHHHHGGHGHGGFGGHHHHHHHHHHGGHHHHHHHHHHHHHHHGFGHHHHFHHGHHHHGHHHHHGHHHHHHHHHHHHHHHGHHHHHHHHHHGHHGGGHHFHHFHHHHHGHGHHHHHHHHHHHHCGHCFHHGEHGGDFHGGHHGHHHHHHGBFCDGGGFHFEHHGHBGHHHGHCCGGFHFF0CFFFGGGG.;@?CGABBDAFFFFFFFBFFF0BF0:\n+@M01368:8:000000000-A3GHV:1:1112:20478:8885/2\n+GCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGGACAAGCATCAAGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAACCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCA\n++\n+ABBBBFFFFBFFGGGGGGGGGGHHHHHGFHHHHHHGGHHGGGGGHHGHFHFHHHGGHHHHHHHFFFHHHHHGGHHHHGFHHHHHHHGHHHGHHHHFHHHHGHHHGGHHHHHGGHHFHHHHHHGGGHHHHHHHHHHHHGHGHHGHHHHHHHHHHHGGGHGHHFFDFEFGHHHFHHHGHHHHGG-<@AHFGHHBHFHFCGGG--AEDCFHHH/;CGAEFFGG--C:@ADCEGGFEFF//BFFFE/;B9/BBFB\n+@M01368:8:000000000-A3GHV:1:2105:16915:2522/2\n+GCTTTATTGGGGAGGGGGTGATCTAAAACACTCTTTACGCCGGCTTCTATTGACTTGGGTTAATCGTGTGACCGCGGTGGCTGGCACGAAATTGACCAACCCTGGGGTTAGTATAGCTTAGTTAAACTTTCGTTTATTGCTAAAGGTTAATCACTGCTGTTTCCCGTGGGGGTGTGGCTAGGCTAAGCGTTTTGAGCTGCATTGCTGCGTGCTTGATGCTTGTCCCTTTTGATCGTGGTGATTTAGAGGGG\n++\n+ABBBBFFFFFBBGGGGGGEEGGHFGHHHHGHHHHHHHGGGGGGGGGCGGHHHGFHHHHH1FGHHHFAFEHHHHGGGGGGGGH/ED23C?DCGHHHHHGHGGGFHHGG/CCGFHHHFHHHHHHHHFHHGHHBGFHEAHHFBGFGDFH<DHHHHGF0::CGGFFCCGGAEDBCF-A9AD..9A?//BBB/B;.@E9AE/BFFFFE////:;.9.9BBA/FBFFB.9BB/BFFF.BFA..;.9/;BB//;BFB-\n+@M01368:8:000000000-A3GHV:1:2110:11901:13185/2\n+GCTTTATTGGGGAGGGGGTGATCTAAAACACTCTTTACGCCGGCTTCTATTGACTTGGGTTAATCGTGTGACCGCGGTGGCTGGCACGAAATTGACCAACCCTGGGGTTAGTATAGCTTAGTTAAACTTTCGTTTATTGCTAAAGGTTAATCACTGCTGTTTCCCGTGGGGGTGTGGCTAGGCTAAGCGTTTTGAGCTGCATTGCTGCGTGCTTGATGCTTGTCCCTTTTGATCGTGGGGGTTTAGAGGGG\n++\n+BBBBBBFFFFBBGGGGGGGGGGHHHHHGHHHFHGHHHHGGGGGGGGGHFGHHEFFFHHHFGGHGHGHFGHFHHGGGGGGGHHGGFBGGCDDGHGFGFFEGGGGHHGGDGHHHEHFHEFHGHGHHFGHHHHFDHHGGHHHFHHHGHHHG<0==:C0:C0CCFFHHHGHDCCGG;--CE?.;9./BFFFFD.:@E?AABFF//9//9BFBFFF?EFB?FF////.;;9BB//B.9/:.:A---;-.////F?-\n+@M01368:8:000000000-A3GHV:1:2101:24037:24448/2\n+GGGAGGGGGTGATCTAAAACACTCTTTACGCCGGCTTCTATTGACTTGGGTTAATCGTGTGACCGCGGTGGCTGGCACGAAATTGACCAACCCTGGGGTTAGTATAGCTTAGTTAAACTTTCGTTTATTGCTAAAGGTTAATCACTGCTGTTTCCCGTGGGGGTGTGGCTAGGCTAAGCGTTTTGAGCTGCATTGCTGCGTGCTTGATGCTTGTCCCTTTTGATCGTGGTGATTTAGAGGGGGGACTCAGT\n++\n+BBBBBBBBBBBBGGGGGGGGGGHHHGHHHGGGEEGGGHHFHHHGHHHEHHGGHHHHGGFEHHHGGGGG?EEFGEGDEHG/?EGHFHHHHHGGGHEFGCGGHHFGHHHHHFHFHEFH1FHHHHDFHG<GHHHEHHGHFFDHHHHH<GGGGHHHHGEFG.CFFGG-:BDDE.BAFFFFGG/BACBEFFEB;FFFFFFFFFFC.ADFFFFFFF/F/:F/FFFF/F.;9AFFD9EBBB/://;B.-----:9///\n+@M01368:8:000000000-A3GHV:1:2105:25110:7111/2\n+ACCGCGGTGGCTGGCACGAAATTGACCAACCCTGGGGTTAGTATAGCTTAGTTAAACTTTCGTTTATTGCTAAAGGTTAATCACTGCTGTTTCCCGTGGGGGTGTGGCTAGGCTAAGCGTTTTGAGCTGCATTGCTGCGTGCTTGATGCTTGTCCCTTTTGATCGTGGTGATTTAGAGGGCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATTTCGGTTGTCGCCCGGTCCTTT\n++\n+BCCCCCCCCCFFGGGGGGGGGGHHHHHHHGGGHHHGGGGHHHHHHHGHHHHHHHHHHHHHHGHHGHHHGHHHHHGHGGHHHHHHHHHGHHHHHGGGGGGGGGEGGGGHHHGEFHHFHHGGGGGAEAHHHHHHHBHHFHCADDGFHGFHHHHHHHHHEHHHGGHHEHHGHGGFHHFGHGFEFHFC0BBFFFGFGF0B90BBFBFDDDFF??DDCF;A-:..0;B000000900/-..:.0....9----::0\n' 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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_FastqToSam_test1.bam |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_FilterSamReads.bam |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_FilterSamReads_exclude_reads_test2.bam |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_FilterSamReads_include_reads_test1.bam |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_FilterSamReads_read_list_file.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_FilterSamReads_read_list_file.tab Tue Dec 16 19:03:21 2014 -0500 |
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| @@ -0,0 +1,20 @@ +M01368:8:000000000-A3GHV:1:1101:6911:8255 +M01368:8:000000000-A3GHV:1:1101:14518:9998 +M01368:8:000000000-A3GHV:1:1101:18422:19051 +M01368:8:000000000-A3GHV:1:1101:25545:21098 +M01368:8:000000000-A3GHV:1:1101:5446:12248 +M01368:8:000000000-A3GHV:1:1101:5861:6452 +M01368:8:000000000-A3GHV:1:1102:10403:6021 +M01368:8:000000000-A3GHV:1:1102:10677:23253 +M01368:8:000000000-A3GHV:1:1102:13809:1733 +M01368:8:000000000-A3GHV:1:1102:17584:10050 +M01368:8:000000000-A3GHV:1:1102:18842:24844 +M01368:8:000000000-A3GHV:1:1102:21788:11027 +M01368:8:000000000-A3GHV:1:1102:5728:8777 +M01368:8:000000000-A3GHV:1:1102:5983:21093 +M01368:8:000000000-A3GHV:1:1102:7765:18353 +M01368:8:000000000-A3GHV:1:1103:10405:17879 +M01368:8:000000000-A3GHV:1:1103:13493:8205 +M01368:8:000000000-A3GHV:1:1103:14060:21273 +M01368:8:000000000-A3GHV:1:1103:14528:12993 +M01368:8:000000000-A3GHV:1:1103:17657:20856 |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_FixMateInformation.bam |
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| Binary file test-data/picard_FixMateInformation.bam has changed |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_FixMateInformation_test1.bam |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_MD_output1.txt --- a/test-data/picard_MD_output1.txt Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,112 +0,0 @@ -## net.sf.picard.metrics.StringHeader -# net.sf.picard.sam.MarkDuplicates INPUT=picard_input_tiny_coord.bam OUTPUT=picard_MD_output2.bam METRICS_FILE=picard_MD_output1.txt REMOVE_DUPLICATES=false ASSUME_SORTED=true READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 TMP_DIR=/tmp/kpvincent VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -## net.sf.picard.metrics.StringHeader -# Started on: Tue Apr 19 15:28:21 EDT 2011 - -## METRICS CLASS net.sf.picard.sam.DuplicationMetrics -LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE - 1 3 1 1 1 0 0.428571 3 - -## HISTOGRAM java.lang.Double -BIN VALUE -1.0 0.948181 -2.0 1.296997 -3.0 1.425319 -4.0 1.472527 -5.0 1.489893 -6.0 1.496282 -7.0 1.498632 -8.0 1.499497 -9.0 1.499815 -10.0 1.499932 -11.0 1.499975 -12.0 1.499991 -13.0 1.499997 -14.0 1.499999 -15.0 1.5 -16.0 1.5 -17.0 1.5 -18.0 1.5 -19.0 1.5 -20.0 1.5 -21.0 1.5 -22.0 1.5 -23.0 1.5 -24.0 1.5 -25.0 1.5 -26.0 1.5 -27.0 1.5 -28.0 1.5 -29.0 1.5 -30.0 1.5 -31.0 1.5 -32.0 1.5 -33.0 1.5 -34.0 1.5 -35.0 1.5 -36.0 1.5 -37.0 1.5 -38.0 1.5 -39.0 1.5 -40.0 1.5 -41.0 1.5 -42.0 1.5 -43.0 1.5 -44.0 1.5 -45.0 1.5 -46.0 1.5 -47.0 1.5 -48.0 1.5 -49.0 1.5 -50.0 1.5 -51.0 1.5 -52.0 1.5 -53.0 1.5 -54.0 1.5 -55.0 1.5 -56.0 1.5 -57.0 1.5 -58.0 1.5 -59.0 1.5 -60.0 1.5 -61.0 1.5 -62.0 1.5 -63.0 1.5 -64.0 1.5 -65.0 1.5 -66.0 1.5 -67.0 1.5 -68.0 1.5 -69.0 1.5 -70.0 1.5 -71.0 1.5 -72.0 1.5 -73.0 1.5 -74.0 1.5 -75.0 1.5 -76.0 1.5 -77.0 1.5 -78.0 1.5 -79.0 1.5 -80.0 1.5 -81.0 1.5 -82.0 1.5 -83.0 1.5 -84.0 1.5 -85.0 1.5 -86.0 1.5 -87.0 1.5 -88.0 1.5 -89.0 1.5 -90.0 1.5 -91.0 1.5 -92.0 1.5 -93.0 1.5 -94.0 1.5 -95.0 1.5 -96.0 1.5 -97.0 1.5 -98.0 1.5 -99.0 1.5 -100.0 1.5 - |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_MD_output2.bam |
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| Binary file test-data/picard_MD_output2.bam has changed |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_MD_output3.txt --- a/test-data/picard_MD_output3.txt Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,112 +0,0 @@ -## net.sf.picard.metrics.StringHeader -# net.sf.picard.sam.MarkDuplicates INPUT=picard_input_tiny_coord.sam OUTPUT=picard_MD_output4_.sam METRICS_FILE=picard_MD_output3_.txt REMOVE_DUPLICATES=true ASSUME_SORTED=false READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 TMP_DIR=/tmp/kpvincent VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -## net.sf.picard.metrics.StringHeader -# Started on: Tue Apr 19 15:32:38 EDT 2011 - -## METRICS CLASS net.sf.picard.sam.DuplicationMetrics -LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE - 1 3 1 1 1 0 0.428571 3 - -## HISTOGRAM java.lang.Double -BIN VALUE -1.0 0.948181 -2.0 1.296997 -3.0 1.425319 -4.0 1.472527 -5.0 1.489893 -6.0 1.496282 -7.0 1.498632 -8.0 1.499497 -9.0 1.499815 -10.0 1.499932 -11.0 1.499975 -12.0 1.499991 -13.0 1.499997 -14.0 1.499999 -15.0 1.5 -16.0 1.5 -17.0 1.5 -18.0 1.5 -19.0 1.5 -20.0 1.5 -21.0 1.5 -22.0 1.5 -23.0 1.5 -24.0 1.5 -25.0 1.5 -26.0 1.5 -27.0 1.5 -28.0 1.5 -29.0 1.5 -30.0 1.5 -31.0 1.5 -32.0 1.5 -33.0 1.5 -34.0 1.5 -35.0 1.5 -36.0 1.5 -37.0 1.5 -38.0 1.5 -39.0 1.5 -40.0 1.5 -41.0 1.5 -42.0 1.5 -43.0 1.5 -44.0 1.5 -45.0 1.5 -46.0 1.5 -47.0 1.5 -48.0 1.5 -49.0 1.5 -50.0 1.5 -51.0 1.5 -52.0 1.5 -53.0 1.5 -54.0 1.5 -55.0 1.5 -56.0 1.5 -57.0 1.5 -58.0 1.5 -59.0 1.5 -60.0 1.5 -61.0 1.5 -62.0 1.5 -63.0 1.5 -64.0 1.5 -65.0 1.5 -66.0 1.5 -67.0 1.5 -68.0 1.5 -69.0 1.5 -70.0 1.5 -71.0 1.5 -72.0 1.5 -73.0 1.5 -74.0 1.5 -75.0 1.5 -76.0 1.5 -77.0 1.5 -78.0 1.5 -79.0 1.5 -80.0 1.5 -81.0 1.5 -82.0 1.5 -83.0 1.5 -84.0 1.5 -85.0 1.5 -86.0 1.5 -87.0 1.5 -88.0 1.5 -89.0 1.5 -90.0 1.5 -91.0 1.5 -92.0 1.5 -93.0 1.5 -94.0 1.5 -95.0 1.5 -96.0 1.5 -97.0 1.5 -98.0 1.5 -99.0 1.5 -100.0 1.5 - |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_MD_output4.sam --- a/test-data/picard_MD_output4.sam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,11 +0,0 @@ -@HD VN:1.0 SO:coordinate -@SQ SN:chr1 LN:101 -@SQ SN:chr7 LN:404 -@SQ SN:chr8 LN:202 -@RG ID:0 SM:Hi,Mom! -@PG ID:1 PN:Hey! VN:2.0 -both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 -both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_MarkDuplicates.bam |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_MarkDuplicatesWithMateCigar.bam |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_MarkDuplicatesWithMateCigar_test1.bam |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_MarkDuplicates_test1.bam |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_MeanQualityByCycle.bam |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_MeanQualityByCycle_ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_MeanQualityByCycle_ref.fa Tue Dec 16 19:03:21 2014 -0500 |
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| b'@@ -0,0 +1,239 @@\n+>chrM\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG\n+GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC\n+CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA\n+ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC\n+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC\n+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA\n+CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC\n+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC\n+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC\n+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA\n+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA\n+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT\n+CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC\n+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC\n+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA\n+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC\n+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA\n+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA\n+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA\n+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA\n+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA\n+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC\n+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA\n+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT\n+AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG\n+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC\n+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG\n+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC\n+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC\n+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA\n+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT\n+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA\n+TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG\n+TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA\n+GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG\n+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG\n+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA\n+ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT\n+TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA\n+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC\n+CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC\n+CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG\n+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC\n+AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC\n+TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG\n+CCATAATATGATT'..b'GTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA\n+CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA\n+TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT\n+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT\n+CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA\n+TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC\n+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC\n+AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC\n+CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC\n+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA\n+AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC\n+TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC\n+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA\n+CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC\n+AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA\n+TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA\n+ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA\n+TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA\n+CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA\n+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC\n+CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC\n+CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG\n+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC\n+CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC\n+CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA\n+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA\n+CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC\n+ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC\n+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC\n+TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA\n+GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT\n+CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT\n+TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC\n+TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA\n+GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC\n+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC\n+TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC\n+CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA\n+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC\n+ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA\n+ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA\n+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG\n+TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC\n+TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC\n+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n+\n' |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_MeanQualityByCycle_test1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_MeanQualityByCycle_test1.tab Tue Dec 16 19:03:21 2014 -0500 |
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| @@ -0,0 +1,511 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.analysis.MeanQualityByCycle CHART_OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_924.dat ALIGNED_READS_ONLY=false PF_READS_ONLY=false INPUT=/Users/anton/galaxy-central/database/files/000/dataset_882.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_923.dat REFERENCE_SEQUENCE=localref.fa ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +## htsjdk.samtools.metrics.StringHeader +# Started on: Mon Oct 13 16:54:21 EDT 2014 + + +## HISTOGRAM java.lang.Integer +CYCLE MEAN_QUALITY +1 30.92 +2 32.06 +3 31.93 +4 32.2 +5 32.11 +6 35.73 +7 35.77 +8 35.93 +9 34.98 +10 35.63 +11 35.38 +12 36.14 +13 37.72 +14 37.39 +15 37.27 +16 37.29 +17 37.21 +18 37.13 +19 37.28 +20 36.9 +21 37.12 +22 36.77 +23 37.81 +24 37.64 +25 38.32 +26 38.15 +27 37.97 +28 37.8 +29 37.86 +30 37.85 +31 38.21 +32 38.36 +33 38.24 +34 38.2 +35 38.04 +36 37.52 +37 37.68 +38 38.12 +39 37.46 +40 37.66 +41 37.23 +42 37.25 +43 37.28 +44 37.61 +45 37.49 +46 37.67 +47 38.02 +48 37.43 +49 37.91 +50 38.02 +51 38.01 +52 37.97 +53 37.53 +54 37.46 +55 37.83 +56 37.38 +57 37.54 +58 37.39 +59 37.69 +60 37.99 +61 37.65 +62 37.19 +63 38.03 +64 37.54 +65 38.06 +66 37.6 +67 37.17 +68 37.91 +69 37.51 +70 37.97 +71 37.78 +72 37.88 +73 37.54 +74 36.84 +75 37.3 +76 37.89 +77 37.64 +78 37.54 +79 37.73 +80 37.23 +81 36.97 +82 37.45 +83 36.68 +84 36.87 +85 36.82 +86 37.47 +87 37.18 +88 37.42 +89 37.4 +90 36.42 +91 37.12 +92 37.63 +93 37.37 +94 37.38 +95 37.55 +96 37.84 +97 38.14 +98 37.42 +99 38.12 +100 36.51 +101 36.54 +102 37.02 +103 36.53 +104 37.57 +105 37.4 +106 37.28 +107 37.32 +108 37.44 +109 37.4 +110 36.82 +111 37.73 +112 37.42 +113 37.53 +114 36.52 +115 36.44 +116 36.06 +117 37.45 +118 36.9 +119 36.53 +120 37.15 +121 36.28 +122 37.27 +123 37.05 +124 37.34 +125 35.58 +126 36.2 +127 36.72 +128 36.17 +129 36.99 +130 36.39 +131 37.17 +132 36.61 +133 36.34 +134 36.7 +135 36.18 +136 36.07 +137 37.15 +138 36.16 +139 35.52 +140 36.35 +141 36.77 +142 35.8 +143 36.47 +144 36.07 +145 36.32 +146 36.53 +147 36.16 +148 35.99 +149 35.58 +150 35.99 +151 35.37 +152 34.34 +153 34.51 +154 35.34 +155 35.83 +156 36.26 +157 36.28 +158 36.68 +159 36.18 +160 36.44 +161 35.34 +162 34.81 +163 35.58 +164 35.72 +165 35.63 +166 36.01 +167 35.22 +168 35.82 +169 35.29 +170 35 +171 35.46 +172 34.78 +173 34.54 +174 33.67 +175 34.51 +176 34.47 +177 35.38 +178 34.74 +179 35.6 +180 34.5 +181 34.27 +182 34.26 +183 35.11 +184 34.54 +185 33.99 +186 33.22 +187 33.8 +188 33.43 +189 34.4 +190 32.97 +191 33.59 +192 33.29 +193 32.52 +194 34.05 +195 33.54 +196 32.56 +197 33.88 +198 33.03 +199 32.74 +200 31.84 +201 33.09 +202 32.95 +203 32.85 +204 33.79 +205 33.35 +206 33.05 +207 32.71 +208 32.83 +209 32.76 +210 31.26 +211 31.29 +212 32.19 +213 33.79 +214 33.22 +215 32.27 +216 32.03 +217 31.8 +218 32.67 +219 32.57 +220 32.32 +221 31.24 +222 31.27 +223 31.22 +224 31.59 +225 30.77 +226 30.36 +227 30.66 +228 30.16 +229 30.91 +230 32.04 +231 32.24 +232 32.04 +233 30.92 +234 30.78 +235 31.59 +236 31.73 +237 32.32 +238 30.25 +239 29.03 +240 29.61 +241 30.03 +242 29.38 +243 28.82 +244 29.32 +245 28.41 +246 28.49 +247 29.24 +248 29.71 +249 29.51 +250 28.9 +251 20.13 +252 32.02 +253 33.03 +254 33.14 +255 33.32 +256 32.92 +257 35.86 +258 36.02 +259 35.97 +260 35.76 +261 36.03 +262 35.9 +263 36.35 +264 37.5 +265 37.28 +266 37.61 +267 37.7 +268 37.66 +269 37.48 +270 37.68 +271 37.59 +272 37.66 +273 37.73 +274 38.05 +275 38.42 +276 38.12 +277 38.37 +278 38.41 +279 38.32 +280 38.39 +281 38.2 +282 38.26 +283 38.34 +284 38.22 +285 38.37 +286 38.33 +287 38.39 +288 38.17 +289 38.1 +290 38.16 +291 37.86 +292 37.77 +293 38.23 +294 37.79 +295 37.64 +296 38.02 +297 37.77 +298 38.2 +299 38.02 +300 37.83 +301 38.26 +302 38.2 +303 38.04 +304 37.86 +305 38.14 +306 38.25 +307 37.88 +308 38.39 +309 38.3 +310 37.82 +311 37.71 +312 38.23 +313 38.07 +314 38.06 +315 37.71 +316 37.92 +317 37.78 +318 37.89 +319 37.37 +320 37.2 +321 37.59 +322 37.88 +323 37.35 +324 37.8 +325 37.11 +326 37.34 +327 36.97 +328 37.34 +329 37.27 +330 37.6 +331 37.4 +332 37.31 +333 37.57 +334 37.12 +335 37.46 +336 37.45 +337 37.47 +338 37.27 +339 37.62 +340 37.6 +341 37.78 +342 37.51 +343 37.81 +344 37.92 +345 37.86 +346 37.22 +347 37.75 +348 37.5 +349 37.12 +350 37.2 +351 36.71 +352 37.26 +353 37.27 +354 37.96 +355 38 +356 37.49 +357 37.61 +358 36.68 +359 37.02 +360 37.23 +361 36.35 +362 36.78 +363 36.51 +364 36.98 +365 36.74 +366 36.98 +367 36.4 +368 36.89 +369 37.09 +370 36.85 +371 36.94 +372 37.03 +373 37.27 +374 36.99 +375 37.22 +376 36.68 +377 37.01 +378 37.16 +379 36.63 +380 37.02 +381 36.7 +382 37.36 +383 36.97 +384 36.61 +385 36.4 +386 36.31 +387 36.38 +388 36.57 +389 36.17 +390 35.9 +391 36.52 +392 36.31 +393 35.73 +394 35.6 +395 35.14 +396 35.58 +397 34.47 +398 36.4 +399 36.35 +400 35.78 +401 35.94 +402 36.15 +403 35.06 +404 34.94 +405 35.2 +406 35.3 +407 35.66 +408 36.08 +409 35.26 +410 35.19 +411 35.12 +412 34.92 +413 35.04 +414 34.72 +415 35.31 +416 35.41 +417 35.76 +418 34.93 +419 34.61 +420 31.67 +421 33.03 +422 34.43 +423 33.21 +424 34.64 +425 34.09 +426 33.68 +427 33.42 +428 33.14 +429 34.06 +430 33.51 +431 33.3 +432 34.18 +433 34.35 +434 34.16 +435 34.4 +436 33.83 +437 32.62 +438 32.52 +439 32.2 +440 31.23 +441 30.53 +442 31.09 +443 31.4 +444 32.42 +445 32.48 +446 32.09 +447 32.82 +448 32.44 +449 31.59 +450 31.29 +451 31.51 +452 31.44 +453 29.73 +454 30.59 +455 31.49 +456 29.87 +457 30.48 +458 30.45 +459 31.44 +460 29.87 +461 30.61 +462 30.39 +463 30.65 +464 28.86 +465 28.55 +466 28.77 +467 30 +468 30.1 +469 30.27 +470 31.21 +471 30.62 +472 31.14 +473 29.87 +474 28.56 +475 28.48 +476 29.52 +477 28.14 +478 28.27 +479 28.02 +480 28.57 +481 27.39 +482 28.5 +483 28.68 +484 27.18 +485 27.42 +486 27.09 +487 25.93 +488 27.18 +489 26.68 +490 26.65 +491 26.27 +492 25.41 +493 25.3 +494 26.21 +495 26.68 +496 26.32 +497 25.83 +498 24.29 +499 24.26 +500 24.58 +501 24.86 +502 19.15 + |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_MergeBamAlignment_aligned.bam |
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| Binary file test-data/picard_MergeBamAlignment_aligned.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_MergeBamAlignment_ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_MergeBamAlignment_ref.fa Tue Dec 16 19:03:21 2014 -0500 |
| b |
| b'@@ -0,0 +1,239 @@\n+>chrM\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG\n+GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC\n+CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA\n+ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC\n+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC\n+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA\n+CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC\n+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC\n+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC\n+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA\n+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA\n+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT\n+CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC\n+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC\n+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA\n+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC\n+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA\n+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA\n+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA\n+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA\n+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA\n+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC\n+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA\n+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT\n+AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG\n+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC\n+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG\n+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC\n+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC\n+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA\n+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT\n+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA\n+TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG\n+TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA\n+GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG\n+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG\n+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA\n+ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT\n+TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA\n+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC\n+CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC\n+CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG\n+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC\n+AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC\n+TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG\n+CCATAATATGATT'..b'GTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA\n+CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA\n+TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT\n+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT\n+CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA\n+TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC\n+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC\n+AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC\n+CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC\n+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA\n+AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC\n+TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC\n+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA\n+CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC\n+AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA\n+TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA\n+ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA\n+TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA\n+CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA\n+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC\n+CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC\n+CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG\n+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC\n+CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC\n+CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA\n+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA\n+CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC\n+ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC\n+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC\n+TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA\n+GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT\n+CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT\n+TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC\n+TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA\n+GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC\n+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC\n+TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC\n+CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA\n+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC\n+ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA\n+ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA\n+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG\n+TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC\n+TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC\n+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n+\n' |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_MergeBamAlignment_test1.bam |
| b |
| Binary file test-data/picard_MergeBamAlignment_test1.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_MergeBamAlignment_unaligned.bam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_MergeBamAlignment_unaligned.bam Tue Dec 16 19:03:21 2014 -0500 |
| b |
| b'@@ -0,0 +1,202 @@\n+@HD\tVN:1.4\tSO:queryname\n+@RG\tID:A\tSM:sample-a\n+M01368:8:000000000-A3GHV:1:1101:14518:9998\t77\t*\t0\t0\t*\t*\t0\t0\tGTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGAT\tAAAAAFFFFFFFGGGGGGGGGGHGGHHHHGHHHHHHHGCGHHHHHHHHHHHHHHHGGGGGHHHHHHHHHGHHGFHFE5BGEEHFGGGHHHHHHHHFBHHGGGGFHGHHFGHHHHGHHHHHHGEGGGGFHFHGEGHHGGCDGDGHGGGDGGHGGCGGGHGHHH/ACDG?.1FGCDCCGCA.CC@CDCHFHGFFGGGEBFGAB//CEFBFGG.:;D;;A0AFFFFFB..:@ABFF//;BFFFFFBF/9D:A//\tRG:Z:A\n+M01368:8:000000000-A3GHV:1:1101:14518:9998\t141\t*\t0\t0\t*\t*\t0\t0\tCATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAA\tCCCCCFCCCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGFHHHHGGGGGHGFHHHHHHHHHHHHHHHHHHHGHGGEHGGGGCGGGHHGGCGGGGGHHGHHHGGGGGGGG.BFFFGAGADFGAFDGFGGCFFF;DDFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFF09FFFE00;BE@;DABBFFFFFBBFB00;F:9;FFBFFF9BFFFFFFFFFFFFF90/::BFFFBF0\tRG:Z:A\n+M01368:8:000000000-A3GHV:1:1101:18422:19051\t77\t*\t0\t0\t*\t*\t0\t0\tGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG\tCCCCCFDDDDDFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHFHHHHGGGGHHHHHHHHHGHHHHHHHHHHHHGGHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHGCGGGHHHHHHHHHHHHHHHHHHHHHHGFDHGFHCFGGGGFGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;FFFFFFFFFFFFFFFFFFFFFFFFFFFFEFBFFFFFFFFFF:FFF.\tRG:Z:A\n+M01368:8:000000000-A3GHV:1:1101:18422:19051\t141\t*\t0\t0\t*\t*\t0\t0\tCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGG\tBCCCCFFCFFFFGGGGGGGGGGHHHGHHHHHHHHHHHHHHHHGGGGHHHHHHHHEHHHHHHHGGHHGGHGGHHHHHHHGHGGHHHGGGGGHGHHHHGGGHFHFHHHHHGGGGGHBFFCGDHHHGGGGGGHGGGGGGHHGCGGGFGHHBGGGGGFFFHEGGGGGCDCCE@EFGHHHHFHEGHGFFHHGB;ECBFGGGEFEFFGF0AFGFGFFG.;;DFFFFFFFFFF090BFFFE?FEFBBFBFFFB990BF\tRG:Z:A\n+M01368:8:000000000-A3GHV:1:1101:25545:21098\t77\t*\t0\t0\t*\t*\t0\t0\tATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATAAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGGCTTATTTAAGGGGAACGGGTGGGG\t33AA?DFD5BDFGGGFEBDGEGHEGHGEGHCEGGHHCHGHHFFHHGFGAGE53FF2FAFFGDE5FFFE5GFBFGAEE1GHHHGHHHEHE3FGHF@GEGEGGHHGG3FAGFFDE?EEE3GFEGFGFGGCG?GHHHFHGGGC@DHFFHD/A<C@EGFDCGGGHFHHHEGFGHBFHG0:CEHFCHGGED.;0CEF.F99B0CFFEEFGGG0FBFBBF0F/FFBDE?/9//9B.FFBFFFFFFBF..A..;@B--\tRG:Z:A\n+M01368:8:000000000-A3GHV:1:1101:25545:21098\t141\t*\t0\t0\t*\t*\t0\t0\tGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTTCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCAACCTATGTCGCAGTATCTGTCTTTGAT\t3AAA34BFFFFFGCGGCGGGCGHHHGHHHHCGHFGHFHGFGGCDGGBD5FGFFFHFHGGGHAEBFGHHHEHGGFHBGGFHHHGGGEEFHHHFHFFHDHGHGHHHHFFHHGGFAEGFFFFFBGHHHFFHHHHHHHFHFHHFHGFHGHGA/<@EFHEHH1GGHFFFHG1>=FGHFHGF.GE//-<BB?9.9BFFFB==AA/FFFFFA-@BA.;;D?F9FAB;---./99BFFFBBAE-.9B/BFB9F/9BFBB\tRG:Z:A\n+M01368:8:000000000-A3GHV:1:1101:5446:12248\t77\t*\t0\t0\t*\t*\t0\t0\tAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTAT\tCCCCDFFFFCCFGGGGGGGGFGHHHHHGGGGHHHHHHHHHHHHHHHHGBGHGGHGGHHHHHHHHHHGHGHGGGGGHHHHHHHHGHHHHHHHHHGGGGGHHHHFFGHHHGGGGGGHHHGFGGHHGGGGHHHHHHGGGGGGHGHHGGGGGGGHGGGGGGHHHHHHHHHHHHHFHGGGHHHHGGG'..b'000000000-A3GHV:1:1114:15066:16302\t141\t*\t0\t0\t*\t*\t0\t0\tTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGTGG\tCCCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHDGHHHHFHHGHHGHHHHHGGGGEHHHHFHHFF5FHHFEGHHHGDHGGHGHGFGGGEHFGHHGGGGGHGHHHGHHFHHB3FGHHFGGGG?GFFHCCEBGFFECCDFEGFCFGCHHGFDDHHHGHHCFGGGGGFBFDGFG?-:..AFG.-C0C009;:00;00:9/:CEFFF?AE::9;9?0:FEF0;0..--./00::B/090000000;A....\tRG:Z:A\n+M01368:8:000000000-A3GHV:1:1114:16639:15258\t77\t*\t0\t0\t*\t*\t0\t0\tCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGCGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTCCAATATTACAGGCGAACATACTTACTAAATTGTGT\t11>>ABFFFFFFGGCGC1BBF1GHHHBHHHHGFHGH1A100AA/GGEHGFBAA1FFD2FHHHHECG2F1BB/E0FC/A>EE/FGGFGEF1EGBBEHHCGGGHBGEHFHE0B?E--;C?CCGGG@A@GBFBBBB09?@??A-AB--ABE@=-=-9AE9A;FFFFFE=9-//;//;9FF/////;;///9B///;/B////9FFBB;--A@-;/9;9-:-/;;FFFE9BF?@;-9-99/B9F/://///99/;\tRG:Z:A\n+M01368:8:000000000-A3GHV:1:1114:16639:15258\t141\t*\t0\t0\t*\t*\t0\t0\tTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCGCACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATG\tCDCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHGHHHHHHGGGGGHGIHHHIH5DEGHHHF?FGHGGHGGHEGGHFHHGHGEHHGGGGGFFFGHFBG2GHEBGHHGHGGEG/GFGABEDFGHEED?GGHHFFGGGCFEGD/GFHFFGEFGCGG?CC??D-EF@EEEFGCDDBBFGGGEBBFFF09090A.BFGA.9CCA0;EBAB00BBFF.@-./;BB;BFFF0:00099AAFFF0\tRG:Z:A\n+M01368:8:000000000-A3GHV:1:1114:2404:13066\t77\t*\t0\t0\t*\t*\t0\t0\tTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCTGTCTATTATACACATC\tCCCCCFFFFCFFGGGGGGGGGGHHHHHGHHHHHHHHHFFHHHHHGGGGHHHHHHHHFHHHHHHFGGHHGGHGGHHHHHHGHHFHHHHGGGGGGHHHHHHGHHHHHHHHHHGGGGGGGHH?FGHHHGGGGGGHHGGFGGHHGGGGHHHHHFGGGGFGHGHHGGGGGGGHGGGEGGHHGHHHHHHHHHGFBFFDA0FGGGFFGG0:EFGGGGGGGG;AEBF0B0BFFBFFFFFFFFFFFFFFFFFFFFFEFF0\tRG:Z:A\n+M01368:8:000000000-A3GHV:1:1114:2404:13066\t141\t*\t0\t0\t*\t*\t0\t0\tATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGACCATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACTGTCTCTTATACACATT\tCCCCCFFFFFFCGGGGGGGGGGHHHHHHHHHFFHHHHGGGGGHFFFHHFHHHHHHHHHHHHHHHGFEGGGHGEDFCDFHGHFG@@DGGHHHHHHGGGGCGGGGGEHGGCGBB?CF99EGFGGFGG?D9CFFFF/BBFFFFFEF9BFFAFFFFEFFFFFFFFFFFFFFFFFFFFF.FFBBFFFFFFFFFFFF-9;;;BFFFFFB9BFBFBFABFFEFFFFFFFFFF::BFFBFFFF.9//;FFFFF/BFFB/\tRG:Z:A\n+M01368:8:000000000-A3GHV:1:1114:9184:6959\t77\t*\t0\t0\t*\t*\t0\t0\tGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTTCTGTCTCTTA\tAABBBFFFCCCBFGGGGGGGGGHHHHHHHHGGGGGGHHHG3FFHHHFGFGGGHHHGGGEHHGGGGHHHHHHGGGGGGHGHGGGGGGGDEGGGGEGGFHHHHHHHHHHHHGGGFGEHHGGFDGGGDFFGFHHHHGFCFHHHHHEFHFHGGFFGHHGGGHHHHDGHHHFHHHFFFFGFGGG.EFGGGGFGEBFGGGFGFGGGGFFBFGGBBFFFFFB/FEFF?///;A::AABBFFFBFFFFFFFFFBFFFF/\tRG:Z:A\n+M01368:8:000000000-A3GHV:1:1114:9184:6959\t141\t*\t0\t0\t*\t*\t0\t0\tAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCTGTCTCTTA\tCCCCBFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHEHIHHGGGGHHHHHHHHHHHHHGHHHHHHHHGGGGGHHFHHHHHBGHHHHHHHHHHHHHHHHHGHHHHHGGGGGHHHHGHHHHHHHHHHHHHHHHHGHGHGHHGGGGCFFFFFFFFFFFFFFFFFFFFFFFFFF.CFFFFAF=D=EAEFFF0B:0AF-DAFBFFFFFFFFFBFFFFFFFFFFBFFFEFF9B900B0\tRG:Z:A\n' |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_MergeSamFiles_input1.bam |
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| Binary file test-data/picard_MergeSamFiles_input1.bam has changed |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_MergeSamFiles_input2.bam |
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| Binary file test-data/picard_MergeSamFiles_input2.bam has changed |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_MergeSamFiles_input3.bam |
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| Binary file test-data/picard_MergeSamFiles_input3.bam has changed |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_MergeSamFiles_test1.bam |
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| Binary file test-data/picard_MergeSamFiles_test1.bam has changed |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_NormalizeFasta_ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_NormalizeFasta_ref.fa Tue Dec 16 19:03:21 2014 -0500 |
| b |
| b'@@ -0,0 +1,239 @@\n+>chrM\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG\n+GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC\n+CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA\n+ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC\n+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC\n+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA\n+CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC\n+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC\n+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC\n+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA\n+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA\n+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT\n+CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC\n+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC\n+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA\n+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC\n+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA\n+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA\n+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA\n+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA\n+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA\n+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC\n+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA\n+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT\n+AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG\n+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC\n+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG\n+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC\n+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC\n+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA\n+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT\n+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA\n+TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG\n+TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA\n+GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG\n+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG\n+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA\n+ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT\n+TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA\n+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC\n+CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC\n+CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG\n+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC\n+AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC\n+TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG\n+CCATAATATGATT'..b'GTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA\n+CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA\n+TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT\n+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT\n+CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA\n+TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC\n+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC\n+AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC\n+CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC\n+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA\n+AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC\n+TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC\n+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA\n+CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC\n+AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA\n+TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA\n+ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA\n+TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA\n+CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA\n+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC\n+CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC\n+CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG\n+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC\n+CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC\n+CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA\n+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA\n+CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC\n+ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC\n+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC\n+TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA\n+GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT\n+CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT\n+TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC\n+TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA\n+GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC\n+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC\n+TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC\n+CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA\n+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC\n+ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA\n+ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA\n+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG\n+TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC\n+TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC\n+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n+\n' |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_NormalizeFasta_test1.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_NormalizeFasta_test1.fa Tue Dec 16 19:03:21 2014 -0500 |
| b |
| b'@@ -0,0 +1,416 @@\n+>chrM\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCT\n+CTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGC\n+GATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC\n+GCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTA\n+TCGCACCTACGTTCAATATTACAGGCGAACATACTTACTA\n+AAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA\n+ACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC\n+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTC\n+TGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAAAA\n+ACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTT\n+TATCTTTTGGCGGTATGCACTTTTAACAGTCACCCCCCAA\n+CTAACACATTATTTTCCCCTCCCACTCCCATACTACTAAT\n+CTCATCAATACAACCCCCGCCCATCCTACCCAGCACACAC\n+ACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC\n+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAA\n+GCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCC\n+ATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCT\n+TAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGAGT\n+TCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCA\n+AGCACGCAGCAATGCAGCTCAAAACGCTTAGCCTAGCCAC\n+ACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA\n+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTC\n+AATTTCGTGCCAGCCACCGCGGTCACACGATTAACCCAAG\n+TCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCC\n+TCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACT\n+CCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACAT\n+ATCTGAACACACAATAGCTAAGACCCAAACTGGGATTAGA\n+TACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC\n+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAA\n+AACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGAGG\n+AGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCA\n+CCTCTTGCTCAGCCTATATACCGCCATCTTCAGCAAACCC\n+TGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAG\n+ACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATG\n+GGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAG\n+AGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACA\n+CACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACAT\n+TTAACTAAAACCCCTACGCATTTATATAGAGGAGACAAGT\n+CGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAA\n+CCAGAGTGTAGCTTAACACAAAGCACCCAACTTACACTTA\n+GGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA\n+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGC\n+CAAACCATTTACCCAAATAAAGTATAGGCGATAGAAATTG\n+AAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATG\n+AAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCC\n+TATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGC\n+AAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGACGAGCT\n+ACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA\n+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTAC\n+CGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTTAG\n+TTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCT\n+TGTAAATTTAACTGTTAGTCCAAAGAGGAACAGCTCTTTG\n+GACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTA\n+ACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAA\n+GCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC\n+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATC\n+ACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAA\n+ACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACT\n+GAACTGACAATTAACAGCCCAATATCTACAATCAACCAAC\n+AAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATG\n+CTCATAAGGAAAGGTTAAAAAAAGTAAAAGGAACTCGGCA\n+AATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC\n+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATG\n+TTTAACGGCCGCGGTACCCTAACCGTGCAAAGGTAGCATA\n+ATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCC\n+ACGAGGGTTCAGCTGTCTCTTACTTTTAACCAGTGAAATT\n+GACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGA\n+GAAGACCCTATGGAGCTTTAATTTATTAATGCAAACAGTA\n+CCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACC\n+TCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCGAA\n+CTACTATACTCAATTGATCCAATAACTTGACCAACGGAAC\n+AAGTTACCCTAGGGATAACAGCGCAATCCTATTCTAGAGT\n+CCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCA\n+GGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTG\n+TTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG\n+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCC\n+CTGTACGAAAGGACAAGAGAAATAAGGCCTACTTCACAAA\n+GCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATT\n+ATACCCACACCCACCCAAGAACAGGGTTTGTTAAGATGGC\n+AGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCA\n+GAGGTTCAATTCCTCTTCTTAACAACATACCCATGGCCAA\n+CCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA\n+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATAC\n+AACTACGCAAAGGCCCCAACGTTGTAGGCCCCTACGGGCT\n+ACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAA\n+GAGCCCCTAAAACCCGCCACATCTACCATCACCCTCTACA\n+TCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACT\n+ATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCTC\n+AACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG\n+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTC\n+AAACTACGCCCTGATCGGCGCACTGCGAGCAGTAGCCCAA\n+ACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTAT\n+CAACATTACTAATAAGTGGCTCCTT'..b'CGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCAT\n+CAGTTGATGATACGCCCGAGCAGATGCCAACACAGCAGCC\n+ATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT\n+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTC\n+ATGAGACCCACAACAAATAGCCCTTCTAAACGCTAATCCA\n+AGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAG\n+GCAAATCAGCCCAATTAGGTCTCCACCCCTGACTCCCCTC\n+AGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCAC\n+TCAAGCACTATAGTTGTAGCAGGAATCTTCTTACTCATCC\n+GCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC\n+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCA\n+GCAGTCTGCGCCCTTACACAAAATGACATCAAAAAAATCG\n+TAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGT\n+TACAATCGGCATCAACCAACCACACCTAGCATTCCTGCAC\n+ATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGT\n+GCTCCGGGTCCATCATCCACAACCTTAACAATGAACAAGA\n+TATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC\n+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAG\n+GAATACCTTTCCTCACAGGTTTCTACTCCAAAGACCACAT\n+CATCGAAACCGCAAACATATCATACACAAACGCCTGAGCC\n+CTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCT\n+ATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACC\n+TCGCTTCCCCACCCTTACTAACATTAACGAAAATAACCCC\n+ACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC\n+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGC\n+ATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACTC\n+ACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCC\n+TAGACCTCAACTACCTAACCAACAAACTTAAAATAAAATC\n+CCCACTATGCACATTTTATTTCTCCAACATACTCGGATTC\n+TACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCC\n+TTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAG\n+CACCAAATCTCCACCTCCATCATCACCTCAACCCAAAAAG\n+GCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACT\n+CATCCTAACCCTACTCCTAATCACATAACCTATTCCCCCG\n+AGCAATCTCAATTACAATATATACACCAACAAACAATGTT\n+CAACCAGTAACTACTACTAATCAACGCCCATAATCATACA\n+AAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA\n+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTA\n+AAGTTTACCACAACCACCACCCCATCATACTCTTTCACCC\n+ACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAAC\n+ACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGA\n+TACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAA\n+CCATCATTCCCCCTAAATAAATTAAAAAAACTATTAAACC\n+CATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG\n+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAG\n+GAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTAA\n+ACCCACACTCAACAGAAACAAAGCATACATCATTATTCTC\n+GCACGGACTACAACCACGACCAATGATATGAAAAACCATC\n+GTTGTATTTCAACTACAAGAACACCAATGACCCCAATACG\n+CAAAACTAACCCCCTAATAAAATTAATTAACCACTCATTC\n+ATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA\n+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAAT\n+CACCACAGGACTATTCCTAGCCATGCACTACTCACCAGAC\n+GCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAG\n+ACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCAA\n+TGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATC\n+GGGCGAGGCCTATATTACGGATCATTTCTCTACTCAGAAA\n+CCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC\n+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATA\n+TCATTCTGAGGGGCCACAGTAATTACAAACTTACTATCCG\n+CCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTG\n+AGGAGGCTACTCAGTAGACAGTCCCACCCTCACACGATTC\n+TTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCC\n+TAGCAACACTCCACCTCCTATTCTTGCACGAAACGGGATC\n+AAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCT\n+TACTTCTCTTCCTTCTCTCCTTAATGACATTAACACTATT\n+CTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTA\n+GCCAACCCCTTAAACACCCCTCCCCACATCAAGCCCGAAT\n+GATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCC\n+TAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATC\n+CTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC\n+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTA\n+TTGACTCCTAGCCGCAGACCTCCTCATTCTAACCTGAATC\n+GGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGAC\n+AAGTAGCATCCGTACTATACTTCACAACAATCCTAATCCT\n+AATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAA\n+TGGGCCTGTCCTTGTAGTATAAACTAATACACCAGTCTTG\n+TAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA\n+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAG\n+ATTCTAATTTAAACTATTCTCTGTTCTTTCATGGGGAAGC\n+AGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACA\n+ACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAA\n+TATTGTACGGTACCATAAATACTTGACCACCTGTAGTACA\n+TAAAAACCCAATCCACATCAAAACCCCCTCCCCATGCTTA\n+CAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA\n+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCA\n+ACAAACCTACCCACCCTTAACAGTACATAGTACATAAAGC\n+CATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTC\n+GTCCCCATGGATGACCCCCCTCAGATAGGGGTCCCTTGAC\n+CACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCT\n+ACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTA\n+AAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC\n+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGAC\n+ATCACGATG\n' |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_QualityScoreDistribution.bam |
| b |
| Binary file test-data/picard_QualityScoreDistribution.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_QualityScoreDistribution_ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_QualityScoreDistribution_ref.fa Tue Dec 16 19:03:21 2014 -0500 |
| b |
| b'@@ -0,0 +1,239 @@\n+>chrM\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG\n+GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC\n+CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA\n+ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC\n+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC\n+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA\n+CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC\n+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC\n+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC\n+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA\n+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA\n+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT\n+CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC\n+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC\n+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA\n+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC\n+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA\n+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA\n+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA\n+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA\n+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA\n+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC\n+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA\n+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT\n+AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG\n+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC\n+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG\n+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC\n+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC\n+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA\n+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT\n+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA\n+TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG\n+TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA\n+GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG\n+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG\n+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA\n+ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT\n+TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA\n+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC\n+CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC\n+CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG\n+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC\n+AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC\n+TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG\n+CCATAATATGATT'..b'GTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA\n+CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA\n+TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT\n+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT\n+CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA\n+TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC\n+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC\n+AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC\n+CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC\n+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA\n+AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC\n+TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC\n+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA\n+CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC\n+AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA\n+TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA\n+ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA\n+TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA\n+CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA\n+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC\n+CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC\n+CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG\n+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC\n+CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC\n+CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA\n+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA\n+CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC\n+ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC\n+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC\n+TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA\n+GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT\n+CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT\n+TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC\n+TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA\n+GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC\n+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC\n+TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC\n+CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA\n+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC\n+ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA\n+ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA\n+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG\n+TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC\n+TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC\n+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n+\n' |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_QualityScoreDistribution_test1.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_QualityScoreDistribution_test1.tab Tue Dec 16 19:03:21 2014 -0500 |
| b |
| @@ -0,0 +1,44 @@ +## htsjdk.samtools.metrics.StringHeader +# picard.analysis.QualityScoreDistribution CHART_OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_968.dat ALIGNED_READS_ONLY=false PF_READS_ONLY=false INCLUDE_NO_CALLS=false INPUT=/Users/anton/galaxy-central/database/files/000/dataset_966.dat OUTPUT=/Users/anton/galaxy-central/database/files/000/dataset_967.dat REFERENCE_SEQUENCE=localref.fa ASSUME_SORTED=true VERBOSITY=ERROR QUIET=true VALIDATION_STRINGENCY=LENIENT STOP_AFTER=0 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +## htsjdk.samtools.metrics.StringHeader +# Started on: Wed Oct 15 14:31:45 EDT 2014 + + +## HISTOGRAM java.lang.Byte +QUALITY COUNT_OF_Q +6 704 +7 2044 +8 745 +9 2761 +10 1193 +11 723 +12 1766 +13 1467 +14 1400 +15 1463 +16 478 +17 831 +18 330 +19 904 +20 1538 +21 2953 +22 565 +23 4270 +24 1496 +25 5178 +26 3992 +27 3779 +28 3074 +29 2909 +30 19446 +31 3520 +32 13368 +33 9203 +34 22271 +35 24655 +36 64306 +37 38212 +38 95777 +39 67370 +40 36926 + |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_RSH_input1.bam |
| b |
| Binary file test-data/picard_RSH_input1.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_RSH_input1.sam --- a/test-data/picard_RSH_input1.sam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,14 +0,0 @@ -@HD VN:1.0 SO:coordinate -@SQ SN:chr1 LN:101 -@SQ SN:chr7 LN:404 -@SQ SN:chr8 LN:202 -@RG ID:0 SM:What_is_that_sound? -@PG ID:1 PN:Greetings! VN:2.0 -both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 -read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 -both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_RSH_output1.sam --- a/test-data/picard_RSH_output1.sam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,14 +0,0 @@ -@HD VN:1.0 SO:coordinate -@SQ SN:chr1 LN:101 -@SQ SN:chr7 LN:404 -@SQ SN:chr8 LN:202 -@RG ID:0 SM:What_is_that_sound? -@PG ID:1 PN:Greetings! VN:2.0 -both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 -read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 -both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_RSH_output2.bam |
| b |
| Binary file test-data/picard_RSH_output2.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_RSH_output2.sam --- a/test-data/picard_RSH_output2.sam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,14 +0,0 @@ -@HD VN:1.0 SO:coordinate -@SQ SN:chr1 LN:101 -@SQ SN:chr7 LN:404 -@SQ SN:chr8 LN:202 -@RG ID:0 SM:What_is_that_sound? -@PG ID:1 PN:Greetings! VN:2.0 -both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 -read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 -both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_RS_input1.bam |
| b |
| Binary file test-data/picard_RS_input1.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_RS_input2.sam --- a/test-data/picard_RS_input2.sam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,22 +0,0 @@ -@HD VN:1.0 SO:unsorted -@SQ SN:phiX174 LN:5386 -@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 |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_RS_input3.bam |
| b |
| Binary file test-data/picard_RS_input3.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_RS_input3.sam --- a/test-data/picard_RS_input3.sam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,26 +0,0 @@ -@HD VN:1.0 SO:unsorted -@SQ SN:phiX1 LN:1120 -@SQ SN:phiX2 LN:1190 -@SQ SN:phiX3 LN:1330 -@SQ SN:phiX4 LN:910 -@SQ SN:phiX5 LN:828 -@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:1:1:1578:331/1 0 phiX1 209 255 50M * 0 0 TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1761:343/1 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:1:1:1647:512/1 0 phiX1 401 255 50M * 0 0 TACTGAACAATCCGTACGTTTCCAGACCGCTTTGGCCTCTATTAAGCTCA IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1746:351/1 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:1:1:1570:620/1 4 * 0 0 * * 0 0 GAGTAACAAAGTAAAGTTTGGACCGTTTTTGTCTCGTGCTCGTCGCTGCG IIIIIII""IIIIIIIIIIIIIBIIIIIIIIIIII"IIIIIII000IIII XM: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:1:1:1572:324/1 4 * 0 0 * * 0 0 AAGGTGCTTAAATTCGTGGGTCCTGAGCTGGCGACCCTGTTTTGTATGGC IIIIIII""IIIIIIIIIIIIIIIIIIII+7I05I"IIIIIII000IIII XM: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:1:1:1652:270/1 4 * 0 0 * * 0 0 AGCGTAAAGGCGCTCGTCTTTGGTATGTAGGACTTTGCATTGTTTAATTG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII6II"IIIIIII000IIII XM: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:1:1:1629:446/1 4 * 0 0 * * 0 0 AGGTTATAACGCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGT IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"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:1:1:1785:1272/1 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:1:1:1634:330/1 0 phiX4 778 255 50M * 0 0 GGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATG IIIIIII""IIIIIIIIIIIIIIIIIIIIIII8II"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_RS_input4.fasta --- a/test-data/picard_RS_input4.fasta Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,82 +0,0 @@ ->phiX1 length=1120 -GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT -GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA -ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG -TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA -GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC -TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT -TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT -CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT -TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG -TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC -GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA -CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCGGAAGGAG -TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT -AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC -CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA -TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC ->phiX2 length=1190 -TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA -CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA -GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT -GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA -ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC -TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT -TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC -ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCATGATGTTATTTCTTCATTTGGAGGTAAAAC -CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT -GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC -CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC -TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG -TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT -TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA -AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT -TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT -ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC ->phiX3 length=1330 -GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC -TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT -TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA -TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG -TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC -CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG -AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC -CGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT -TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG -CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA -AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT -GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG -GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA -TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT -CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG -TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA -GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC -CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA -TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA ->phiX4 length=910 -AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC -TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT -CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA -TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG -TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT -CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT -TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC -ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG -TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA -ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG -GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC -CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT -GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTGCTATTCAGCGTTTGATGAATGCAATGCGACAG ->phiX5 length=828 -GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT -ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG -CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC -CGTCTTCATTTCCATGCGGTGCACTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC -GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT -CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG -CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA -TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT -TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG -TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC -AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC -TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCC |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_RS_output1.bam |
| b |
| Binary file test-data/picard_RS_output1.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_RS_output2.sam --- a/test-data/picard_RS_output2.sam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -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 |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_RS_output3.sam --- a/test-data/picard_RS_output3.sam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,26 +0,0 @@ -@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 -@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:1:1:1578:331/1 0 phiX1 209 255 50M * 0 0 TGTCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1582:633/1 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:1:1:1616:363/1 0 phiX3 408 255 50M * 0 0 TGTTTATCCTTTGAATGGTCGCCATGATGGTGGTTATTATACCGTCAAGG IIIIIII""IIIIIIIIIIIIIIIIIIIIIIDIII"IIIIIII000IIII XA:i:0 MD:Z:50 NM:i:0 -HWI-EAS91_1_30788AAXX:1:1:1629:446/1 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 |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_ReorderSam.bam |
| b |
| Binary file test-data/picard_ReorderSam.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_ReorderSam_ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_ReorderSam_ref.fa Tue Dec 16 19:03:21 2014 -0500 |
| b |
| b'@@ -0,0 +1,239 @@\n+>chrM\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG\n+GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC\n+CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA\n+ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC\n+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC\n+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA\n+CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC\n+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC\n+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC\n+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA\n+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA\n+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT\n+CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC\n+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC\n+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA\n+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC\n+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA\n+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA\n+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA\n+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA\n+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA\n+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC\n+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA\n+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT\n+AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG\n+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC\n+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG\n+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC\n+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC\n+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA\n+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT\n+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA\n+TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG\n+TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA\n+GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG\n+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG\n+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA\n+ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT\n+TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA\n+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC\n+CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC\n+CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG\n+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC\n+AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC\n+TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG\n+CCATAATATGATT'..b'GTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA\n+CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA\n+TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT\n+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT\n+CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA\n+TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC\n+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC\n+AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC\n+CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC\n+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA\n+AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC\n+TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC\n+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA\n+CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC\n+AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA\n+TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA\n+ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA\n+TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA\n+CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA\n+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC\n+CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC\n+CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG\n+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC\n+CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC\n+CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA\n+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA\n+CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC\n+ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC\n+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC\n+TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA\n+GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT\n+CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT\n+TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC\n+TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA\n+GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC\n+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC\n+TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC\n+CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA\n+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC\n+ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA\n+ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA\n+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG\n+TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC\n+TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC\n+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n+\n' |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_ReorderSam_test1.bam |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_ReplaceSamHeader.bam |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_ReplaceSamHeader_header.bam |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_RevertOriginalBaseQualitiesAndAddMateCigar.bam |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_RevertOriginalBaseQualitiesAndAddMateCigar_test1.bam |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_RevertSam.bam |
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| Binary file test-data/picard_RevertSam.bam has changed |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_RevertSam_test1.bam |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_SamToFastq.bam |
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| Binary file test-data/picard_SamToFastq.bam has changed |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_SamToFastq_test1.fq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_SamToFastq_test1.fq Tue Dec 16 19:03:21 2014 -0500 |
| b |
| b"@@ -0,0 +1,8000 @@\n+@M01368:28:000000000-A5KYY:1:1101:10045:12104/1\n+ATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGCTTTATGG\n++\n+?????B/B-<5BBA<B/+,6>@AEHFF>CFBA>EC=C>>CED?CFCEDA-AC/AE=ACE,CCCDHHHH-5C5EG>><<EHGHCEDE+?7<CCD?D@DF?:DAE=EDEDDDD;@<BBEE@2.?8:::?EEEEEEA::*?A:88//?A20?8A0/8:AEEEEC:A*00?:?E?CE:/:/?::C??AC?**:0:*??CEA?EE?*8?8CE8A*888A*??://?AEEAAACAE\n+@M01368:28:000000000-A5KYY:1:1101:10045:12104/2\n+CCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCATTATTTATCGCACCTACGTTCAATAT\n++\n+?????<<<B<BBBBB<>CFFFFHEHHH?-CEFFB?ECC??EFFDDGDEHFFDD?A?C??;5AEAEGCFFDFBEDC-AFHHFFFHHD*<DDDCGHHHHHFHFFF@@+77D@=DEFHFFBBA=8.?CEECC????8EEEEECC?.8??AA;A?'8??E;;'82AC*8AECCEEEE2AEEE?EE:?AC::AE?AEE::*0:C?A?EC?C*:?E:/?A?848:?CECEEEEECE\n+@M01368:28:000000000-A5KYY:1:1101:10126:23848/1\n+CTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCG\n++\n+??AAABAADDDDDDDEGGGGGGIIIHIHIHHEEHHIIIIIEGHHIIIHGHIIHHHHHIIIIGFHHIIIIIIIHHHHHHHHHHHHHHHHHHHFHHHGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGCEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGGGCGGGG<CGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGGCGG\n+@M01368:28:000000000-A5KYY:1:1101:10126:23848/2\n+GTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGCTTTATGGCCCTGAAGTAGGAACCAG\n++\n+?????BBBDDDEDDDDGCFFDEHHHIIIIIIIIHGHFHHIHHHEHIHHHHHHFHIIIIHIIHHHHEDFHIGBCEHHHHHHHEHHHHHDHHHHGHEEHHHG?DEGG:BGGGGGCCEBEEGEGBD>EGGGGGEGGGGGGGGGGGGGGCG?CD0?CECCEC8CEGGCEE*8?CEECCEEGCGGGGGGEEECGGEEGECCCE:CCGECCA8)?CCE:CEGGCEGGC?CEE?EEGGGGC*8*9C*?EGG?*:9)?8\n+@M01368:28:000000000-A5KYY:1:1101:10229:22034/1\n+CACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAA\n++\n+?????BBBDDDDEDDDGGFGGGHHHHHHIIHFHHFFHIICGGHHIIIIIIIIIHIIHHHFHHHHHHEEDFIIIIIIHIIIGIIIDHHHIIHHIHHHHHHHGDGCEGGGGGGGGGGGGGGGGGGGGGGGCC>EGGGGGGGGGGGGGGEGGGGGGGCGGGGGGGGGGGGGGGEEEEGGEGGGGGGGGGGGGGGGCE?>GGGGGCEEEEGGGGGGEEGGGGGGGEEGGGGGGGGGGEGEEEEEECGGG\n+@M01368:28:000000000-A5KYY:1:1101:10229:22034/2\n+TTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTG\n++\n+?A???BBBDDDDDDDDGFFFFGFFHHHHHHHHHIIIIIHIIGHHIIDDHH9DECEFEHHIIIIIIIFFEGGFDEHHHHHHHHIIHHHHFFGIIHHHDHHHHHHH-DDFFHEEGEGFEDDB=DDECGGEEGGEGEGGGG<<EGGEEEEE>>>EGGGGGG8EC?CGGEGGGEGGGGGGGEEEEGACC?C1:8*0*CCGGGG:??CEGGCEEE:CEGGECCECECC*:::?CC?CG:C:CCAECCEC8\n+@M01368:28:000000000-A5KYY:1:1101:10278:20774/1\n+CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGCTTTA\n++\n+?????BBBDDDDDDDDGGGGGGHFFHHIICGHIFEFFECFFHHHHHHIHIIIHIIIHHIHHHHE@FHIIIGIIIIIFHIHHHHHHHHHFHHHDFHFHGHHHHEHHHHGGGGGGGGGGEEGGGGGGG@EGGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGEEGGGGGGGGGCCEECEE:CEGGGGGGGGEGGGGGGEGGGGGGGGCEEEGEGGEEGGGGGEGEGGEGGGEGC80?EEEGGG?CEGEEGGGE\n+@M01368:28:000000000-A5KYY:1:1101:10278:20774/2\n+CATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGG"..b'TACAGGCGAACATACTTACTAAAGT\n++\n+AAAA????DDDDBDDDGCFGGGIIIIIIIIIIIHIIIIIIIIHHHHHHIIIIFGHHIIIIIICGHHIIFHEHFHIIHHG?EGGGGGGGGGGGGGGGGGGGGGGGGDGGGGGGGGAGGGGGGGGGGGGGGGGGEGGGGGEGGGGGGGG?CEGGGGGGE*:CGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGC\n+@M01368:28:000000000-A5KYY:1:1106:20079:20293/2\n+ACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATAATGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGA\n++\n+????ABBBDDDDDDDDGGGGGGIFBFFBF>ECDGFFHHHCFGHHIHHHHHIIIIIFHHFHIIHHHHIFHHIIIIIHIFHG-AEHHHHHHIIFHFHHFHHHHHEHHHHFDEGDGGGGGGGGGGGGGGGG@CCGGCACGDGGGCEGGGGGEEGGGCCGGEGEGEECECEC:CED*)0?CCECEEEGECGG:CEG?CEEGCCGGEE?:CGCEEGG\n+@M01368:28:000000000-A5KYY:1:1106:20084:8979/1\n+ATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCATTATTTATCGCACCTACGTTCAATATT\n++\n+????5.<?BDDDDDDDF?FFEEHHEHFCHHGF?CFHGFFFHHDHCAEFHHHHHHHCDFGHHFHHFFHHHHHHHFFFHHHFFGHDGBEGHHCEFGHDGHFHHFHHHDHHHHHHHHHFFFFFFFFFBADEFEEFEEEFFCC@6>DEEFFFFF>DDDA.?*ACEFED>>EE8?E8C8AA82;>DEFFEFEEAEFFF>E):AEEFEFFFFFEEEFEFE?EECEFAA?CEEFFFFFEF?AE8DFAC??:CEEFFFF\n+@M01368:28:000000000-A5KYY:1:1106:20084:8979/2\n+GTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGCTTTATGGC\n++\n+?<???BBBDDDDDEDAFF?FFFHFFCF;C,7CCAEG>@CEEHGHCFFHFFHHGFDFEEA:EFFFHHDFFFHHFFFGHF@CA>CFHFF8E+@DCE7CHHFCCFC@EDFFFEE@BD=BDDAEE@EECEE=BEEE>;A.8>;D?>E?EEEE8:?CE?EA::A?E?EEE>8A)?*:?:8*:**0A80).::CEE?AEC:*:AECEEA8AACEEECC:CAACCAE*4.?8A?EEEEEAEEAE?EC**::A**:CC\n+@M01368:28:000000000-A5KYY:1:1106:20271:14486/1\n+GGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCC\n++\n+???????BBDDDD<?DFGGGGGHIIHHHHHIIIIIHHIIIIHIFHHIIHHHIIIIIIIIIIIHFEHHHIIHHDHIIHHHHHIIIIIIIIIHHHIIHHHHHHHHHHHHHCFFHHHHHHHHGGGGGGGGGGGGGGEBGGGGGGGGGGGGGGEGGGECEGEGGGEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG<EGGGGDGGGGGGGGGGGGGGGGGEEECAEEGGGGGGGGGGGGGGGCECEGGGGGGG\n+@M01368:28:000000000-A5KYY:1:1106:20271:14486/2\n+GTAATATTGAACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGCTTTATGGCACTGAAGTAGGAACCAG\n++\n+?????BBBBBBBB?BDEFFFFEHEHAAC>FFHHEHEHGHHHHHHIFFF@FGHHF=FGGGGGFD>EHEGHHIFHEHHIHHBDEFHHHHEHHHHHHHHHFFFFFDEFEEEFFFEEEFEEEEEEEDDEDFFFFECAACEFFEFCEEEAEFFFDFECEEFECEFFFFFEE:AC?CC?*:ACEEFFFFFFFEEE??C?:AEFFACA:ACEDEAEAAAEFEEA?EFCFFEEEEECEECC?*1:?::?EFEA:C?0*?\n+@M01368:28:000000000-A5KYY:1:1106:20363:9345/1\n+TCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCATTATTTATCGCACCTACG\n++\n+?<????BBDBBDDBDBFCFFFFHHHHHHHFFGHDFEHHEHHHHHHHHFHHHHHHHHFHHHHHHHEHFHHHHHHEFGFHHHHHHFFHHF=EHHHHHHHHEDEEHHHHHHFFFFHHHFFFAFFFFFFEFEEDBEE@D4AECEFFED>>DAEEEFCAEE;88AEDEEDFFFE?DDDDEFFEFFFE?AAEDE?AC*A?ECEEEEEFFEEF:EEEFEFFFFFFFAEEEFFFEEEDDFACA\n+@M01368:28:000000000-A5KYY:1:1106:20363:9345/2\n+CGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCATACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGCTTTATGGCCCTGAAGTAGGA\n++\n+AA?AA?BBDBDDDDDDGGFGFFCFH8CAF,7C@7ADEDHGHHHHHHIHFGGEECCHIGIICFDFHDHHH@EFDFFHHHEFFFEHHHHHHHHEHCGGGGGGGEEGGDGEEEGBGGBGGEGGCCEGGGGGEGGGCCEGGGGC?8?C:C:CCCECCEGCEGGCEGGGGGEG*:CC?CEEEGCEGEEEG?EEE:C?EGD8???CC:?CEGCCGEE?CEGGGGCEEEEE*8??EECGGGG\n' |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_SortSam.bam |
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| Binary file test-data/picard_SortSam.bam has changed |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_SortSam_test1.bam |
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| Binary file test-data/picard_SortSam_test1.bam has changed |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_ValidateSamFile.bam |
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| Binary file test-data/picard_ValidateSamFile.bam has changed |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_ValidateSamFile_ref.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_ValidateSamFile_ref.fa Tue Dec 16 19:03:21 2014 -0500 |
| b |
| b'@@ -0,0 +1,239 @@\n+>chrM\n+GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGG\n+GTATGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTC\n+CTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTA\n+ATTAATTAATGCTTGTAGGACATAATAATAACAATTGAATGTCTGCACAGCCACTTTCCACACAGACATC\n+ATAACAAAAAATTTCCACCAAACCCCCCCTCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCA\n+AACCCCAAAAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTTGGCGGTATGCAC\n+TTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTAATCTCATCAATA\n+CAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCATACCCCGAACCAACCAAACCCC\n+AAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCAAAGCAATACACTGAAAATGTTTAGACGGGCTC\n+ACATCACCCCATAAACAAATAGGTTTGGTCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAA\n+GCATCCCCGTTCCAGTGAGTTCACCCTCTAAATCACCACGATCAAAAGGAACAAGCATCAAGCACGCAGC\n+AATGCAGCTCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAATAA\n+ACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCACACGA\n+TTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCCCCTCCCCAATAAAGCTAAAACT\n+CACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAGACTACGAAAGTGGCTTTAACATATCTGAACAC\n+ACAATAGCTAAGACCCAAACTGGGATTAGATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATC\n+AACAAAACTGCTCGCCAGAACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATC\n+CCTCTAGAGGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATATA\n+CCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAAAGACGTTAGGTC\n+AAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCCAGAAAACTACGATAGCCCTTAT\n+GAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTAAGAGTAGAGTGCTTAGTTGAACAGGGCCCTGA\n+AGCGCGTACACACCGCCCGTCACCCTCCTCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCA\n+TTTATATAGAGGAGACAAGTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTA\n+GCTTAACACAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACCTA\n+GCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAATAAAGTATAGGCG\n+ATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGATGAAAAATTATAACCAAGCATA\n+ATATAGCAAGGACTAACCCCTATACCTTCTGCATAATGAATTAACTAGAAATAACTTTGCAAGGAGAGCC\n+AAAGCTAAGACCCCCGAAACCAGACGAGCTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCA\n+AAATAGTGGGAAGATTTATAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGAT\n+AGAATCTTAGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAGTC\n+CAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATTTAACACCCATAG\n+TAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACCCACTACCTAAAAAATCCCAAAC\n+ATATAACTGAACTCCTCACACCCAATTGGACCAATCTATCACCCTATAGAAGAACTAATGTTAGTATAAG\n+TAACATGAAAACATTCTCCTCCGCATAAGCCTGCGTCAGATTAAAACACTGAACTGACAATTAACAGCCC\n+AATATCTACAATCAACCAACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGA\n+AAGGTTAAAAAAAGTAAAAGGAACTCGGCAAATCTTACCCCGCCTGTTTACCAAAAACATCACCTCTAGC\n+ATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACCCTAACCGTGCAA\n+AGGTAGCATAATCACTTGTTCCTTAAATAGGGACCTGTATGAATGGCTCCACGAGGGTTCAGCTGTCTCT\n+TACTTTTAACCAGTGAAATTGACCTGCCCGTGAAGAGGCGGGCATAACACAGCAAGACGAGAAGACCCTA\n+TGGAGCTTTAATTTATTAATGCAAACAGTACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATT\n+AAAAATTTCGGTTGGGGCGACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAG\n+TCAAAGCGAACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAACA\n+GCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGATCAGGACATCCCG\n+ATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCTACGTGATCTGAGTTCAGACCGG\n+AGTAATCCAGGTCGGTTTCTATCTACNTTCAAATTCCTCCCTGTACGAAAGGACAAGAGAAATAAGGCCT\n+ACTTCACAAAGCGCCTTCCCCCGTAAATGATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGA\n+ACAGGGTTTGTTAAGATGGCAGAGCCCGGTAATCGCATAAAACTTAAAACTTTACAGTCAGAGGTTCAAT\n+TCCTCTTCTTAACAACATACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGCA\n+TTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAACGTTGTAGGCC\n+CCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAAAGAGCCCCTAAAACCCGCCAC\n+ATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGCTCTCACCATCGCTCTTCTACTATGAACCCCC\n+CTCCCCATACCCAACCCCCTGGTCAACCTCAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAG\n+CCGTTTACTCAATCCTCTGATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGC\n+AGTAGCCCAAACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGGC\n+TCCTTTAACCTCTCCACCCTTATCACAACACAAGAACACCTCTGATTACTCCTGCCATCATGACCCTTGG\n+CCATAATATGATT'..b'GTTCTTCAAATATCTACTCATCTTCCTAATTACCATACTAATCTTAGTTACCGCTAA\n+CAACCTATTCCAACTGTTCATCGGCTGAGAGGGCGTAGGAATTATATCCTTCTTGCTCATCAGTTGATGA\n+TACGCCCGAGCAGATGCCAACACAGCAGCCATTCAAGCAATCCTATACAACCGTATCGGCGATATCGGTT\n+TCATCCTCGCCTTAGCATGATTTATCCTACACTCCAACTCATGAGACCCACAACAAATAGCCCTTCTAAA\n+CGCTAATCCAAGCCTCACCCCACTACTAGGCCTCCTCCTAGCAGCAGCAGGCAAATCAGCCCAATTAGGT\n+CTCCACCCCTGACTCCCCTCAGCCATAGAAGGCCCCACCCCAGTCTCAGCCCTACTCCACTCAAGCACTA\n+TAGTTGTAGCAGGAATCTTCTTACTCATCCGCTTCCACCCCCTAGCAGAAAATAGCCCACTAATCCAAAC\n+TCTAACACTATGCTTAGGCGCTATCACCACTCTGTTCGCAGCAGTCTGCGCCCTTACACAAAATGACATC\n+AAAAAAATCGTAGCCTTCTCCACTTCAAGTCAACTAGGACTCATAATAGTTACAATCGGCATCAACCAAC\n+CACACCTAGCATTCCTGCACATCTGTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTC\n+CATCATCCACAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCTC\n+ACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGGTTTCTACTCCA\n+AAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGCCCTATCTATTACTCTCATCGC\n+TACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCTTCTCACCCTAACAGGTCAACCTCGCTTCCCC\n+ACCCTTACTAACATTAACGAAAATAACCCCACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCC\n+TATTCGCAGGATTTCTCATTACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTA\n+CCTAAAACTCACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAACC\n+AACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATTCTACCCTAGCA\n+TCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCTGCCCCTACTCCTCCTAGACCT\n+AACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACAGCACCAAATCTCCACCTCCATCATCACCTCA\n+ACCCAAAAAGGCATAATTAAACTTTACTTCCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAA\n+TCACATAACCTATTCCCCCGAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAA\n+CTACTACTAATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTGA\n+CCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCACCCCATCATAC\n+TCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAACACTCACCAAGACCTCAACCC\n+CTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCGCTGTAGTATATCCAAAGACAACCATCATTCC\n+CCCTAAATAAATTAAAAAAACTATTAAACCCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCG\n+ACCACACCGCTAACAATCAATACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACC\n+CCATTACTAAACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGAC\n+CAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATACGCAAAACTAAC\n+CCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCATCCAACATCTCCGCATGATGAA\n+ACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAATCACCACAGGACTATTCCTAGCCATGCACTA\n+CTCACCAGACGCCTCAACCGCCTTTTCATCAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATC\n+ATCCGCTACCTTCACGCCAATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCC\n+TATATTACGGATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAGC\n+AACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAGTAATTACAAAC\n+TTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCTGAGGAGGCTACTCAGTAGACA\n+GTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCTTGCCCTTCATTATTGCAGCCCTAGCAACACT\n+CCACCTCCTATTCTTGCACGAAACGGGATCAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATC\n+ACCTTCCACCCTTACTACACAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACAT\n+TAACACTATTCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCCC\n+TCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCCCTAACAAACTA\n+GGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCCCCATCCTCCATATATCCAAAC\n+AACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTTATTGACTCCTAGCCGCAGACCTCCTCATTCT\n+AACCTGAATCGGAGGACAACCAGTAAGCTACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATAC\n+TTCACAACAATCCTAATCCTAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTC\n+CTTGTAGTATAAACTAATACACCAGTCTTGTAAACCGGAGATGAAAACCTTTTTCCAAGGACAAATCAGA\n+GAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTCTCTGTTCTTTC\n+ATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAACAACCGCTATGTATTTCGTACA\n+TTACTGCCAGCCACCATGAATATTGTACGGTACCATAAATACTTGACCACCTGTAGTACATAAAAACCCA\n+ATCCACATCAAAACCCCCTCCCCATGCTTACAAGCAAGTACAGCAATCAACCCTCAACTATCACACATCA\n+ACTGCAACTCCAAAGCCACCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAG\n+TACATAAAGCCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCCCC\n+TCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTGCTACTCTCCTCG\n+CTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTC\n+ATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATG\n+\n' |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_ValidateSamFile_test1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/picard_ValidateSamFile_test1.txt Tue Dec 16 19:03:21 2014 -0500 |
| [ |
| b'@@ -0,0 +1,101 @@\n+ERROR: Read groups is empty\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:15130:6486, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:19193:4910, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:19687:27581, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:25123:14783, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1102:16897:10864, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1102:18180:25039, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1102:18745:16268, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1102:28904:12081, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1103:13486:23487, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1103:13545:26345, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1103:19673:17954, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1103:3642:12806, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1104:21319:16719, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1104:26456:9833, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1105:14672:12340, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1105:24128:14251, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1105:24520:20516, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1105:7598:17197, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1106:15870:27794, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1106:18833:21202, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:15130:6486, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:19193:4910, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:19687:27581, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:22554:16461, A record is missing a read group\n+ERROR: Record 24, Read name M01368:28:000000000-A5KYY:1:1101:22554:16461, Mate negative strand flag does not match read negative strand flag of mate\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:22554:16461, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:25123:14783, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:7459:20893, A record is missing a read group\n+ERROR: Record 28, Read name M01368:28:000000000-A5KYY:1:1101:7459:20893, Mate negative strand flag does not match read negative strand flag of mate\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:7459:20893, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1102:16897:10864, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1102:18180:25039, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1102:18745:16268, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1102:28904:12081, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1103:13120:19662, A record is missing a read group\n+ERROR: Record 33, Read name M01368:28:000000000-A5KYY:1:1103:13120:19662, Mate negative strand flag does not match read negative strand flag of mate\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1103:13120:19662, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1103:13486:23487, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1'..b'mate\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1104:9455:13351, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1105:14672:12340, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1105:21471:18067, A record is missing a read group\n+ERROR: Record 54, Read name M01368:28:000000000-A5KYY:1:1105:21471:18067, Mate negative strand flag does not match read negative strand flag of mate\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1105:21471:18067, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1105:24128:14251, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1105:24520:20516, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1105:7598:17197, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1106:15870:27794, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1106:18833:21202, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1106:19331:13430, A record is missing a read group\n+ERROR: Record 61, Read name M01368:28:000000000-A5KYY:1:1106:19331:13430, Mate negative strand flag does not match read negative strand flag of mate\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1106:19331:13430, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:10045:12104, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:10045:12104, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:10126:23848, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:10126:23848, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:10229:22034, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:10229:22034, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:10278:20774, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:10278:20774, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:10291:14859, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:10291:14859, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:10479:22035, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:10479:22035, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:10581:22138, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:10581:22138, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:10696:7547, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:10696:7547, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:10891:2447, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:10891:2447, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:11083:9831, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:11083:9831, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:11136:11974, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:11136:11974, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:11197:4908, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:11197:4908, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:11224:22137, A record is missing a read group\n+WARNING: Read name M01368:28:000000000-A5KYY:1:1101:11224:22137, A record is missing a read group\n+Maximum output of [100] errors reached.\n' |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_fastq_to_sam_out1.bam |
| b |
| Binary file test-data/picard_fastq_to_sam_out1.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_fastq_to_sam_out1.bam.bai |
| b |
| Binary file test-data/picard_fastq_to_sam_out1.bam.bai has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_fastq_to_sam_out2.bam |
| b |
| Binary file test-data/picard_fastq_to_sam_out2.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_fastq_to_sam_out2.bam.bai |
| b |
| Binary file test-data/picard_fastq_to_sam_out2.bam.bai has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_input_bait.bed --- a/test-data/picard_input_bait.bed Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,8 +0,0 @@ -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 |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_input_coordinate_sorted.bam |
| b |
| Binary file test-data/picard_input_coordinate_sorted.bam has changed |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_input_hg18.trimmed.fasta --- a/test-data/picard_input_hg18.trimmed.fasta Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,302 +0,0 @@\n->chrM\n-GATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTT\n-CGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTC\n-GCAGTATCTGTCTTTGATTCCTGCCTCATTCTATTATTTATCGCACCTACGTTCAATATT\n-ACAGGCGAACATACCTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATA\n-ACAATTGAATGTCTGCACAGCCGCTTTCCACACAGACATCATAACAAAAAATTTCCACCA\n-AACCCCCCCCTCCCCCCGCTTCTGGCCACAGCACTTAAACACATCTCTGCCAAACCCCAA\n-AAACAAAGAACCCTAACACCAGCCTAACCAGATTTCAAATTTTATCTTTAGGCGGTATGC\n-ACTTTTAACAGTCACCCCCCAACTAACACATTATTTTCCCCTCCCACTCCCATACTACTA\n-ATCTCATCAATACAACCCCCGCCCATCCTACCCAGCACACACACACCGCTGCTAACCCCA\n-TACCCCGAACCAACCAAACCCCAAAGACACCCCCCACAGTTTATGTAGCTTACCTCCTCA\n-AAGCAATACACTGAAAATGTTTAGACGGGCTCACATCACCCCATAAACAAATAGGTTTGG\n-TCCTAGCCTTTCTATTAGCTCTTAGTAAGATTACACATGCAAGCATCCCCGTTCCAGTGA\n-GTTCACCCTCTAAATCACCACGATCAAAAGGGACAAGCATCAAGCACGCAGCAATGCAGC\n-TCAAAACGCTTAGCCTAGCCACACCCCCACGGGAAACAGCAGTGATTAACCTTTAGCAAT\n->chr1\n-AAACGAAAGTTTAACTAAGCTATACTAACCCCAGGGTTGGTCAATTTCGTGCCAGCCACC\n-GCGGTCACACGATTAACCCAAGTCAATAGAAGCCGGCGTAAAGAGTGTTTTAGATCACCC\n-CCTCCCCAATAAAGCTAAAACTCACCTGAGTTGTAAAAAACTCCAGTTGACACAAAATAG\n-ACTACGAAAGTGGCTTTAACATATCTGAACACACAATAGCTAAGACCCAAACTGGGATTA\n-GATACCCCACTATGCTTAGCCCTAAACCTCAACAGTTAAATCAACAAAACTGCTCGCCAG\n-AACACTACGAGCCACAGCTTAAAACTCAAAGGACCTGGCGGTGCTTCATATCCCTCTAGA\n-GGAGCCTGTTCTGTAATCGATAAACCCCGATCAACCTCACCACCTCTTGCTCAGCCTATA\n-TACCGCCATCTTCAGCAAACCCTGATGAAGGCTACAAAGTAAGCGCAAGTACCCACGTAA\n-AGACGTTAGGTCAAGGTGTAGCCCATGAGGTGGCAAGAAATGGGCTACATTTTCTACCCC\n-AGAAAACTACGATAGCCCTTATGAAACTTAAGGGTCGAAGGTGGATTTAGCAGTAAACTG\n-AGAGTAGAGTGCTTAGTTGAACAGGGCCCTGAAGCGCGTACACACCGCCCGTCACCCTCC\n->chr2\n-TCAAGTATACTTCAAAGGACATTTAACTAAAACCCCTACGCATTTATATAGAGGAGACAA\n-GTCGTAACATGGTAAGTGTACTGGAAAGTGCACTTGGACGAACCAGAGTGTAGCTTAACA\n-CAAAGCACCCAACTTACACTTAGGAGATTTCAACTTAACTTGACCGCTCTGAGCTAAACC\n-TAGCCCCAAACCCACTCCACCTTACTACCAGACAACCTTAGCCAAACCATTTACCCAAAT\n-AAAGTATAGGCGATAGAAATTGAAACCTGGCGCAATAGATATAGTACCGCAAGGGAAAGA\n-TGAAAAATTATAACCAAGCATAATATAGCAAGGACTAACCCCTATACCTTCTGCATAATG\n-AATTAACTAGAAATAACTTTGCAAGGAGAGCCAAAGCTAAGACCCCCGAAACCAGACGAG\n-CTACCTAAGAACAGCTAAAAGAGCACACCCGTCTATGTAGCAAAATAGTGGGAAGATTTA\n-TAGGTAGAGGCGACAAACCTACCGAGCCTGGTGATAGCTGGTTGTCCAAGATAGAATCTT\n->chr3\n-AGTTCAACTTTAAATTTGCCCACAGAACCCTCTAAATCCCCTTGTAAATTTAACTGTTAG\n-TCCAAAGAGGAACAGCTCTTTGGACACTAGGAAAAAACCTTGTAGAGAGAGTAAAAAATT\n-TAACACCCATAGTAGGCCTAAAAGCAGCCACCAATTAAGAAAGCGTTCAAGCTCAACACC\n-CACTACCTAAAAAATCCCAAACATATAACTGAACTCCTCACACCCAATTGGACCAATCTA\n-TCACCCTATAGAAGAACTAATGTTAGTATAAGTAACATGAAAACATTCTCCTCCGCATAA\n-GCCTGCGTCAGATCAAAACACTGAACTGACAATTAACAGCCCAATATCTACAATCAACCA\n-ACAAGTCATTATTACCCTCACTGTCAACCCAACACAGGCATGCTCATAAGGAAAGGTTAA\n-AAAAAGTAAAAGGAACTCGGCAAACCTTACCCCGCCTGTTTACCAAAAACATCACCTCTA\n-GCATCACCAGTATTAGAGGCACCGCCTGCCCAGTGACACATGTTTAACGGCCGCGGTACC\n-CTAACCGTGCAaaggtagcataatcacttgttccttaaatagggacctgtatgaatggct\n-ccacgagggttcagctgtctcttacttttaaccagtgaaattgacctgcccgtgaagagg\n-cgggcatgacacagcaagacgagaagaccctatggagctttaatttaTTAATGCAAACAG\n-TACCTAACAAACCCACAGGTCCTAAACTACCAAACCTGCATTAAAAATTTCGGTTGGGGC\n-GACCTCGGAGCAGAACCCAACCTCCGAGCAGTACATGCTAAGACTTCACCAGTCAAAGCG\n-AACTACTATACTCAATTGATCCAATAACTTGACCAACGGAACAAGTTACCCTAGGGATAA\n-CAGCGCAATCCTATTCTAGAGTCCATATCAACAATAGGGTTTACGACCTCGATGTTGGAT\n-CAGGACATCCCGATGGTGCAGCCGCTATTAAAGGTTCGTTTGTTCAACGATTAAAGTCCT\n-ACGTGATCTGAGTTCAGACCGGAGTAATCCAGGTCGGTTTCTATCTACTTCAAATTCCTC\n-CCTGTACGAAAGGACAAGAGAAATAAGGCCTACTTCACAAAGCGCCTTCCCCCGTAAATG\n-ATATCATCTCAACTTAGTATTATACCCACACCCACCCAAGAACAGGGTTTgttaagatgg\n-cagagcccggtaatcgcataaaacttaaaactttacagtcagaggttcaattcctcttct\n-taacaacaTACCCATGGCCAACCTCCTACTCCTCATTGTACCCATTCTAATCGCAATGGC\n-ATTCCTAATGCTTACCGAACGAAAAATTCTAGGCTATATACAACTACGCAAAGGCCCCAA\n-CGTTGTAGGCCCCTACGGGCTACTACAACCCTTCGCTGACGCCATAAAACTCTTCACCAA\n-AGAGCCCCTAAAACCCGCCACATCTACCATCACCCTCTACATCACCGCCCCGACCTTAGC\n-TCTCACCATCGCTCTTCTACTATGAACCCCCCTCCCCATACCCAACCCCCTGGTCAACCT\n-CAACCTAGGCCTCCTATTTATTCTAGCCACCTCTAGCCTAGCCGTTTACTCAATCCTCTG\n->chr4\n-ATCAGGGTGAGCATCAAACTCAAACTACGCCCTGATCGGCGCACTGCGAGCAGTAGCCCA\n-AACAATCTCATATGAAGTCACCCTAGCCATCATTCTACTATCAACATTACTAATAAGTGG\n-CTCCTTTAACCTCTCCACCCTTATCACAACACAAGAACA'..b'GTACCCACGCCTTCTTCAAAGCCATACTATTTATGTGCTCCGGGTCCATCATCCA\n-CAACCTTAACAATGAACAAGATATTCGAAAAATAGGAGGACTACTCAAAACCATACCTCT\n-CACTTCAACCTCCCTCACCATTGGCAGCCTAGCATTAGCAGGAATACCTTTCCTCACAGG\n-TTTCTACTCCAAAGACCACATCATCGAAACCGCAAACATATCATACACAAACGCCTGAGC\n-CCTATCTATTACTCTCATCGCTACCTCCCTGACAAGCGCCTATAGCACTCGAATAATTCT\n-TCTCACCCTAACAGGTCAACCTCGCTTCCCCACCCTTACTAACATTAACGAAAATAACCC\n-CACCCTACTAAACCCCATTAAACGCCTGGCAGCCGGAAGCCTATTCGCAGGATTTCTCAT\n-TACTAACAACATTTCCCCCGCATCCCCCTTCCAAACAACAATCCCCCTCTACCTAAAACT\n->chr12\n-CACAGCCCTCGCTGTCACTTTCCTAGGACTTCTAACAGCCCTAGACCTCAACTACCTAAC\n-CAACAAACTTAAAATAAAATCCCCACTATGCACATTTTATTTCTCCAACATACTCGGATT\n-CTACCCTAGCATCACACACCGCACAATCCCCTATCTAGGCCTTCTTACGAGCCAAAACCT\n-GCCCCTACTCCTCCTAGACCTAACCTGACTAGAAAAGCTATTACCTAAAACAATTTCACA\n-GCACCAAATCTCCACCTCCATCATCACCTCAACCCAAAAAGGCATAATTAAACTTTACTT\n-CCTCTCTTTCTTCTTCCCACTCATCCTAACCCTACTCCTAATCACATAACCTATTCCCCC\n-GAGCAATCTCAATTACAATATATACACCAACAAACAATGTTCAACCAGTAACCACTACTA\n-ATCAACGCCCATAATCATACAAAGCCCCCGCACCAATAGGATCCTCCCGAATCAACCCTG\n-ACCCCTCTCCTTCATAAATTATTCAGCTTCCTACACTATTAAAGTTTACCACAACCACCA\n-CCCCATCATACTCTTTCACCCACAGCACCAATCCTACCTCCATCGCTAACCCCACTAAAA\n-CACTCACCAAGACCTCAACCCCTGACCCCCATGCCTCAGGATACTCCTCAATAGCCATCG\n-CTGTAGTATATCCAAAGACAACCATCATTCCCCCTAAATAAATTAAAAAAACTATTAAAC\n-CCATATAACCTCCCCCAAAATTCAGAATAATAACACACCCGACCACACCGCTAACAATCA\n-GTACTAAACCCCCATAAATAGGAGAAGGCTTAGAAGAAAACCCCACAAACCCCATTACTA\n-AACCCACACTCAACAGAAACAAAGCATACATCATTATTCTCGCACGGACTACAACCACGA\n-CCAATGATATGAAAAACCATCGTTGTATTTCAACTACAAGAACACCAATGACCCCAATAC\n-GCAAAATTAACCCCCTAATAAAATTAATTAACCACTCATTCATCGACCTCCCCACCCCAT\n-CCAACATCTCCGCATGATGAAACTTCGGCTCACTCCTTGGCGCCTGCCTGATCCTCCAAA\n-TCACCACAGGACTATTCCTAGCCATACACTACTCACCAGACGCCTCAACCGCCTTTTCAT\n-CAATCGCCCACATCACTCGAGACGTAAATTATGGCTGAATCATCCGCTACCTTCACGCCA\n-ATGGCGCCTCAATATTCTTTATCTGCCTCTTCCTACACATCGGGCGAGGCCTATATTACG\n-GATCATTTCTCTACTCAGAAACCTGAAACATCGGCATTATCCTCCTGCTTGCAACTATAG\n-CAACAGCCTTCATAGGCTATGTCCTCCCGTGAGGCCAAATATCATTCTGAGGGGCCACAG\n-TAATTACAAACTTACTATCCGCCATCCCATACATTGGGACAGACCTAGTTCAATGAATCT\n-GAGGAGGCTACTCAGTAGACAGTCCCACCCTCACACGATTCTTTACCTTTCACTTCATCT\n-TACCCTTCATTATTGCAGCCCTAGCAGCACTCCACCTCCTATTCTTGCACGAAACGGGAT\n-CAAACAACCCCCTAGGAATCACCTCCCATTCCGATAAAATCACCTTCCACCCTTACTACA\n-CAATCAAAGACGCCCTCGGCTTACTTCTCTTCCTTCTCTCCTTAATGACATTAACACTAT\n-TCTCACCAGACCTCCTAGGCGACCCAGACAATTATACCCTAGCCAACCCCTTAAACACCC\n-CTCCCCACATCAAGCCCGAATGATATTTCCTATTCGCCTACACAATTCTCCGATCCGTCC\n-CTAACAAACTAGGAGGCGTCCTTGCCCTATTACTATCCATCCTCATCCTAGCAATAATCC\n-CCATCCTCCATATATCCAAACAACAAAGCATAATATTTCGCCCACTAAGCCAATCACTTT\n-ATTGACTCCTAGCCGCAGACCTCCTCATTCTAACCTGAATCGGAGGACAACCAGTAAGCT\n->chr13\n-ACCCTTTTACCATCATTGGACAAGTAGCATCCGTACTATACTTCACAACAATCCTAATCC\n-TAATACCAACTATCTCCCTAATTGAAAACAAAATACTCAAATGGGCCTGTCCTTGTAGTA\n-TAAACTAATACACCAGTCTTGTAAACCGGAGACGAAAACCTTTTTCCAAGGACAAATCAG\n-AGAAAAAGTCTTTAACTCCACCATTAGCACCCAAAGCTAAGATTCTAATTTAAACTATTC\n-TCTGTTCTTTCATGGGGAAGCAGATTTGGGTACCACCCAAGTATTGACTCACCCATCAAC\n-AACCGCTATGTATTTCGTACATTACTGCCAGCCACCATGAATATTGTACGGTACCATAAA\n-TACTTGACCACCTGTAGTACATAAAAACCCAACCCACATCAAACCCCCCCCCCCCATGCT\n-TACAAGCAAGTACAGCAATCAACCTTCAACTATCACACATCAACTGCAACTCCAAAGCCA\n-CCCCTCACCCACTAGGATACCAACAAACCTACCCACCCTTAACAGTACATAGTACATAAA\n-GTCATTTACCGTACATAGCACATTACAGTCAAATCCCTTCTCGTCCCCATGGATGACCCC\n-CCTCAGATAGGGGTCCCTTGACCACCATCCTCCGTGAAATCAATATCCCGCACAAGAGTG\n-CTACTCTCCTCGCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGAC\n-ATCTGGTTCCTACTTCAGGGCCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAG\n-ACATCACGATG\n->chr20\n-NNNNNNNNNNNNNNNNNNNNGATCCAgaggtggaagaggaaggaagcttggaaccctata\n-gagttgctgagtgccaggaccagatcctggccctaaacaggtggtaaggaaggagagagt\n-gaaggaactgccaggtgacacactcccaccatggacctctgggatcctagctttaagaga\n-tcccatcacccacatgaacgtttgaattgacagggggagctgcctggagagtaggcagat\n-gcagagctcaagcctgtgcagagcccaggttttgtgagtgggacagttgcagcaaaacac\n-aaccataggtgcccatccaccaaggcaggctctccatcttgctcagagtggctctagccc\n-ttgctgactgctgggcagggagagagcagagctaacttcctcatgggacctgggtgtgtc\n-tgatctgtgcacaccactatccaaccgatcccgaggctccaccctggccactcttgtgtg\n-cacacagcacagcctctactgctacacctgagtactttgccagtggcctggaagcacttt\n-gtcccccctggcacaaatggtgctggaccacgaggggccagagaacaaagccttgggcgt\n' |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_input_sorted_pair.bam --- a/test-data/picard_input_sorted_pair.bam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,10 +0,0 @@ -bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:2 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:2 141 chr2 30 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:3 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:3 141 chr3 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:4 77 chr1 1 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:4 141 chr1 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:5 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:5 141 chr3 40 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_input_sorted_pair.sam --- a/test-data/picard_input_sorted_pair.sam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,15 +0,0 @@ -@HD VN:1.0 SO:coordinate -@SQ SN:chr1 LN:10001 -@SQ SN:chr2 LN:10001 -@SQ SN:chr3 LN:10001 -@RG ID:rg1 SM:Z -bar:record:1 77 chr1 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:1 141 chr1 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:2 77 chr1 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:2 141 chr1 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:3 77 chr2 10 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:3 141 chr2 20 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:4 77 chr2 50 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:4 141 chr2 60 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:5 77 chr3 40 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:5 141 chr3 50 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_input_summary_alignment_stats.sam --- a/test-data/picard_input_summary_alignment_stats.sam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,28 +0,0 @@ -@HD VN:1.0 SO:coordinate -@SQ SN:chr1 LN:255 -@SQ SN:chr2 LN:255 -@SQ SN:chr3 LN:255 -@SQ SN:chr4 LN:255 -@SQ SN:chr5 LN:255 -@SQ SN:chr6 LN:255 -@SQ SN:chr7 LN:255 -@SQ SN:chr8 LN:255 -@RG ID:0 SM:Hi,Mom! -SL-XAV:1:1:0:764#0/1 89 chr1 1 255 101M * 0 0 TTCATGCTGANGCNCTCTTACGATCGTACAGATGCAAATATTAACANNCNTTNAAGNNCANNNNNNNNNCAATACAATANTAGAGTACGTNAACACTCCAN &/,&-.1/6/&&)&).)/,&0768)&/.,/874,&.4137572)&/&&,&1-&.0/&&*,&&&&&&&&&&18775799,&16:8775-56256/69::;0& RG:Z:0 XN:i:1 -SL-XAV:1:1:0:1668#0/2 153 chr2 1 255 101M * 0 0 CATCTCTACANGCGCGTCCTACCAGACGCGCTTCCGATCTGAGAGCATACTTTTCATTGGATTCCAGCACAACTCCATTTTTGATCCACTNGACACCTTTN (/,'-/'0////(1'&&1&&&&'2''-6/,/3-33653.6:1'.86/-++32.-4864653/5/583/346423203+28888644446688456/4880& RG:Z:0 XN:i:1 -SL-XAV:1:1:0:1914#0/2 153 chr3 1 255 101M * 0 0 CGTATGCGCTNTTTATGTCGCCCACAGTGCCTAGTATAGCCCCTGCTAATAAAAAGAGATGAATACGTTTACTTAAAAAACTGAAACTAGNAATGTGCAAN (0,7&&*/*0*,)10/).-*&.&*/6669.&-337599;3,&,6/.,5::999987893+387020775777547999::668997448:::9;999::0& RG:Z:0 -SL-XAV:1:1:0:1639#0/2 153 chr4 1 255 101M * 0 0 CGTGATACCANCTCATGTTCACAGCCAAAGCCTGAAGCTGTCTATTATATTTCTCAACCATAAACTTTTGCCTCAGGCATCCGCAGAATGNTTTGCAGCCN '.&.&&'.0+01'2(1'(''-)','+0041/.+032;:867115/5267-.0/)-5.&-26200224,,0+0/0275/5605688::646875568882*& RG:Z:0 -SL-XAV:1:1:0:68#0/2 137 chr5 1 255 101M * 0 0 NTCTCATTTANAAATGGTTATAAAAACATTTATGCTGAAAAGGTGAAGTTCATTAATGAACAGGCTGACTGTCTCACTATCGCGTTCGCANGACGTTATCT &1<<999;;;;<<<87579:556972789977444.'.023.&,7621/54.49.)/53055-22--''+(.'-))6-168/(3&&0(<).))*&&&&&'0 RG:Z:0 -SL-XAV:1:1:0:700#0/2 137 chr6 1 255 101M * 0 0 NAATTGTTCTNAGTTTCTCGGTTTATGTGCTCTTCCAGGTGGGTAACACAATAATGGCCTTCCAGATCGTAAGAGCGACGTGTGTTGCACNAGTGTCGATC &0::887::::6/646::838388811/679:87640&./2+/-4/28:3,536/4''&&.78/(/554/./02*)*',-(57()&.6(6:(0601'/(,* RG:Z:0 -SL-XAV:1:1:0:1721#0/1 83 chr7 1 255 101M = 102 40 CAACAGAAGGNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCGAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -SL-XAV:1:1:0:1721#0/2 163 chr7 102 255 101M = 1 -40 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTCACTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 -SL-XAV:1:1:0:105#0/2 147 chr8 1 255 101M = 102 79 CACATCGTGANTCTTACAATCTGCGGTTTCAGATGTGGAGCGATGTGTGAGAGATTGAGCAACTGATCTGAAAAGCAGACACAGCTATTCNTAAGATGACN /))3--/&*()&)&&+'++.'-&,(.))'4,)&'&&,')8,&&*'.&*0'225/&)3-8//)*,5-*).7851453583.3568526:863688:::85.& RG:Z:0 -SL-XAV:1:1:0:105#0/1 99 chr8 102 255 101M = 1 -79 NCAGGTTCAANTGTGCAGCCCNTTTTGAGAGATNNNNNNNNTGNNCTGNAANANNGACACAGCTATTCCTAAGATGACAAGATCAGANAANAAGTCAAGCA &06665578::41.*/7577/&/77403-324.&&&&&&&&/.&&..&&.0&&&&',:9:/-/(55002020+3'12+2/&.2-&//&),&*&&&&&&&51 RG:Z:0 -SL-XAV:1:1:0:1300#0/1 77 * 0 0 * * 0 0 NAAACACAAGNNANAGTCTTANCNGCTATTCCNNNNNNNNNCTNNNCTNAGNANNACATACAACAGTATCCACACAAGTGTACTCGTNCANACATGTGAAC &*5535)*-,,&.&.*-1)*,&'&)&1&&.,)&&&&&&&&&)0&&&0'&&&&.&&*2'/4''0/**&)&,'-&*,&,&&&.0.&)&&&**&,.&&&')&&) RG:Z:0 -SL-XAV:1:1:0:1300#0/2 141 * 0 0 * * 0 0 NGATCATGGANGACTCTCCCCATCCCCCGCTCCAGCGCTCAGTTATATGCCTAGCCTCGGACACGTCACCAACATCTCACGCACTCTGCANAGTCTCTCAC &&'+''3*&-/)/1'26/*-2-/542-*&-&/'/*/&-'&)-')&.'-/&&2+122*'&+,(/-&)((,/-,,.'2(2'+)/&/&-66-&&/16&)&*&'3 RG:Z:0 -SL-XAV:1:1:0:1639#0/1 101 * 0 0 * chr1 1 0 NCCCTCTCAGNNTNTCTGCCANANCCTTAAGCNNNNNNNNNTANNNCTNAANCNNAAACTTTTGCCTCAGGCATCCGCAGAATGTTTNTCNGCCTATATCG &1::::::64/&/&0:3.280&/&087881,/&&&&&&&&&..&&&..&,,&-&&,265341-)/5680&-.5552-25/322/42/&)&&).421&-&-/ RG:Z:0 -SL-XAV:1:1:0:1668#0/1 101 * 0 0 * chr2 1 0 NATAGCATACNNTNCATTGGANTNCAGCACAANNNNNNNNNTGNNNCANTNNANNCCTTTGAGATCGGAAGAGCGGTTCAGCAGGAANNCNCAGACCGATC &1988998890&0&.8863//&.&.0-2875.&&&&&&&&&.)&&&..&.&&.&&.5782-2+262)&-0-0510*.332-2.-,0*&&*&'.&-2-)0., RG:Z:0 -SL-XAV:1:1:0:1914#0/1 101 * 0 0 * chr3 1 0 NTTTTTCTCCNNCNGTGCCTANTNTAGCCCCTNNNNNNNNNAANNNATNANNANNTTTACTTAAAAAACTGAAACTAGTAATGTGCANNANATCGNAAGAG &0::::<<;90&/&.244760&,&.414798/&&&&&&&&&00&&&0.&/&&-&&.4475687363504.&.557/.*)65.&/*./&&.&.+*)&..).& RG:Z:0 -SL-XAV:1:1:0:68#0/1 581 * 0 0 * chr4 1 0 NAATATTCATNNGNTCAGCCTNTNCATTAATTNNNNNNNNNTTNNNATNATNANNTTTTTTATAACCATTTATAAATGAGAGAGATCNTANCACAATATCA &0<<:::::</&&&.73'290&.&0;:::90&&&&&&&&&&..&&&0)&0-&0&&&.743799995253348597921.,.'050.*&.0&)*)&&&&*). RG:Z:0 -SL-XAV:1:1:0:700#0/1 581 * 0 0 * chr5 1 0 NGAAGCCCATNNTNGTGTTACNCNCCTGGAAGNNNNNNNNNACNNNGANACNTNNAACAATTCAGATCGGAAGAGCGGTTCAGCAGANNTNCCGAGACCGA &.88888:88/&0&,03189.&/&.8/))12/&&&&&&&&&./&&&&.&1.&)&&/35962/6432-3&),0&/2+0,),61&-6,&&&'&/,.0&...)0 RG:Z:0 -SL-XAV:1:1:0:764#0/2 165 * 0 0 * chr6 1 0 NACAGATGCANATATTAACAGGCTTTAAAGGACAGATGGACTGCAATACAATAATAGAGTACGTCAACACTCCACAGATCGCTAGAGCATNACATCGGTGT &/:5358::9999::99998255::7275,,/5567-'+387537857:54-4.51'31059547320;73/720+22.4(6.;((.;(;8()(''&&2&& RG:Z:0 |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_input_tiny.sam --- a/test-data/picard_input_tiny.sam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,14 +0,0 @@ -@HD VN:1.0 SO:queryname -@SQ SN:chr1 LN:101 -@SQ SN:chr7 LN:404 -@SQ SN:chr8 LN:202 -@RG ID:0 SM:Hi,Mom! -@PG ID:1 PN:Hey! VN:2.0 -both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 -both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 -read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_input_tiny_coord.bam |
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| Binary file test-data/picard_input_tiny_coord.bam has changed |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_input_tiny_coord.sam --- a/test-data/picard_input_tiny_coord.sam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,14 +0,0 @@ -@HD VN:1.0 SO:coordinate -@SQ SN:chr1 LN:101 -@SQ SN:chr7 LN:404 -@SQ SN:chr8 LN:202 -@RG ID:0 SM:Hi,Mom! -@PG ID:1 PN:Hey! VN:2.0 -both_reads_align_clip_marked 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_present_only_first_aligns 89 chr7 1 255 101M * 0 0 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -read_2_too_many_gaps 83 chr7 1 255 101M = 302 201 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_align_clip_adapter 147 chr7 16 255 101M = 21 -96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_align_clip_adapter 99 chr7 21 255 101M = 16 96 CAACAGAAGCNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCAAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -both_reads_align_clip_marked 163 chr7 302 255 101M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 -read_2_too_many_gaps 163 chr7 302 255 10M1D10M5I76M = 1 -201 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 -both_reads_present_only_first_aligns 165 * 0 0 * chr7 1 0 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTTATTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_output_AsMetrics_indexed_hg18_sorted_pair.html --- a/test-data/picard_output_AsMetrics_indexed_hg18_sorted_pair.html Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,57 +0,0 @@ -<style type="text/css"> - tr.d0 td {background-color: oldlace; color: black;} - tr.d1 td {background-color: aliceblue; color: black;} - </style><?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"> -<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 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"> -Galaxy tool CollectAlignmentSummaryMetrics run at 11/11/2011 08:07:27</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.log">CollectAlignmentSummaryMetrics.log</a></td></tr> -<tr><td><a href="CollectAlignmentSummaryMetrics.metrics.txt">CollectAlignmentSummaryMetrics.metrics.txt</a></td></tr> -</table><p/> -<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 colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_4.dat OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/hg19.fa_fake.fasta ASSUME_SORTED=true TMP_DIR=[/tmp] VALIDATION_STRINGENCY=LENIENT METRIC_ACCUMULATION_LEVEL=[ALL_READS] 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 colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Fri Nov 11 08:07:22 EST 2011</td></tr><tr class="d0"><td colspan="2">## 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>5 </td></tr> -<tr class="d0"><td>PF_READS</td><td>5 </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_ALIGNED_BASES</td><td>0 </td></tr> -<tr class="d0"><td>PF_HQ_ALIGNED_READS</td><td>0 </td></tr> -<tr class="d1"><td>PF_HQ_ALIGNED_BASES</td><td>0 </td></tr> -<tr class="d0"><td>PF_HQ_ALIGNED_Q20_BASES</td><td>0 </td></tr> -<tr class="d1"><td>PF_HQ_MEDIAN_MISMATCHES</td><td>0 </td></tr> -<tr class="d0"><td>PF_MISMATCH_RATE</td><td>0 </td></tr> -<tr class="d1"><td>PF_HQ_ERROR_RATE</td><td>0 </td></tr> -<tr class="d0"><td>PF_INDEL_RATE</td><td>0 </td></tr> -<tr class="d1"><td>MEAN_READ_LENGTH</td><td>13 </td></tr> -<tr class="d0"><td>READS_ALIGNED_IN_PAIRS</td><td>0 </td></tr> -<tr class="d1"><td>PCT_READS_ALIGNED_IN_PAIRS</td><td>0 </td></tr> -<tr class="d0"><td>BAD_CYCLES</td><td>0 </td></tr> -<tr class="d1"><td>STRAND_BALANCE</td><td>0 </td></tr> -<tr class="d0"><td>PCT_CHIMERAS</td><td>0 </td></tr> -<tr class="d1"><td>PCT_ADAPTER</td><td>0 </td></tr> -<tr class="d0"><td>SAMPLE</td><td> </td></tr> -<tr class="d1"><td>LIBRARY</td><td> </td></tr> -<tr class="d0"><td>READ_GROUP -</td><td> - </td></tr> -</table> -<b>Picard Tool Run Log</b><hr/> -<pre>INFO:root:## executing java -Xmx4g -jar /data/home/rlazarus/galaxy/tool-data/shared/jars/picard/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/CollectAlignmentSummaryMetrics.metrics.txt R=/data/home/rlazarus/galaxy/database/job_working_directory/5/dataset_5_files/hg19.fa_fake.fasta TMP_DIR=/tmp INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_4.dat 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> - |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_output_GcBias_uploaded_hg18_summary_alignment_stats.html --- a/test-data/picard_output_GcBias_uploaded_hg18_summary_alignment_stats.html Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,28 +0,0 @@ -@HD VN:1.0 SO:coordinate -@SQ SN:chr1 LN:255 -@SQ SN:chr2 LN:255 -@SQ SN:chr3 LN:255 -@SQ SN:chr4 LN:255 -@SQ SN:chr5 LN:255 -@SQ SN:chr6 LN:255 -@SQ SN:chr7 LN:255 -@SQ SN:chr8 LN:255 -@RG ID:0 SM:Hi,Mom! -SL-XAV:1:1:0:764#0/1 89 chr1 1 255 101M * 0 0 TTCATGCTGANGCNCTCTTACGATCGTACAGATGCAAATATTAACANNCNTTNAAGNNCANNNNNNNNNCAATACAATANTAGAGTACGTNAACACTCCAN &/,&-.1/6/&&)&).)/,&0768)&/.,/874,&.4137572)&/&&,&1-&.0/&&*,&&&&&&&&&&18775799,&16:8775-56256/69::;0& RG:Z:0 XN:i:1 -SL-XAV:1:1:0:1668#0/2 153 chr2 1 255 101M * 0 0 CATCTCTACANGCGCGTCCTACCAGACGCGCTTCCGATCTGAGAGCATACTTTTCATTGGATTCCAGCACAACTCCATTTTTGATCCACTNGACACCTTTN (/,'-/'0////(1'&&1&&&&'2''-6/,/3-33653.6:1'.86/-++32.-4864653/5/583/346423203+28888644446688456/4880& RG:Z:0 XN:i:1 -SL-XAV:1:1:0:1914#0/2 153 chr3 1 255 101M * 0 0 CGTATGCGCTNTTTATGTCGCCCACAGTGCCTAGTATAGCCCCTGCTAATAAAAAGAGATGAATACGTTTACTTAAAAAACTGAAACTAGNAATGTGCAAN (0,7&&*/*0*,)10/).-*&.&*/6669.&-337599;3,&,6/.,5::999987893+387020775777547999::668997448:::9;999::0& RG:Z:0 -SL-XAV:1:1:0:1639#0/2 153 chr4 1 255 101M * 0 0 CGTGATACCANCTCATGTTCACAGCCAAAGCCTGAAGCTGTCTATTATATTTCTCAACCATAAACTTTTGCCTCAGGCATCCGCAGAATGNTTTGCAGCCN '.&.&&'.0+01'2(1'(''-)','+0041/.+032;:867115/5267-.0/)-5.&-26200224,,0+0/0275/5605688::646875568882*& RG:Z:0 -SL-XAV:1:1:0:68#0/2 137 chr5 1 255 101M * 0 0 NTCTCATTTANAAATGGTTATAAAAACATTTATGCTGAAAAGGTGAAGTTCATTAATGAACAGGCTGACTGTCTCACTATCGCGTTCGCANGACGTTATCT &1<<999;;;;<<<87579:556972789977444.'.023.&,7621/54.49.)/53055-22--''+(.'-))6-168/(3&&0(<).))*&&&&&'0 RG:Z:0 -SL-XAV:1:1:0:700#0/2 137 chr6 1 255 101M * 0 0 NAATTGTTCTNAGTTTCTCGGTTTATGTGCTCTTCCAGGTGGGTAACACAATAATGGCCTTCCAGATCGTAAGAGCGACGTGTGTTGCACNAGTGTCGATC &0::887::::6/646::838388811/679:87640&./2+/-4/28:3,536/4''&&.78/(/554/./02*)*',-(57()&.6(6:(0601'/(,* RG:Z:0 -SL-XAV:1:1:0:1721#0/1 83 chr7 1 255 101M = 102 40 CAACAGAAGGNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCGAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -SL-XAV:1:1:0:1721#0/2 163 chr7 102 255 101M = 1 -40 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTCACTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 -SL-XAV:1:1:0:105#0/2 147 chr8 1 255 101M = 102 79 CACATCGTGANTCTTACAATCTGCGGTTTCAGATGTGGAGCGATGTGTGAGAGATTGAGCAACTGATCTGAAAAGCAGACACAGCTATTCNTAAGATGACN /))3--/&*()&)&&+'++.'-&,(.))'4,)&'&&,')8,&&*'.&*0'225/&)3-8//)*,5-*).7851453583.3568526:863688:::85.& RG:Z:0 -SL-XAV:1:1:0:105#0/1 99 chr8 102 255 101M = 1 -79 NCAGGTTCAANTGTGCAGCCCNTTTTGAGAGATNNNNNNNNTGNNCTGNAANANNGACACAGCTATTCCTAAGATGACAAGATCAGANAANAAGTCAAGCA &06665578::41.*/7577/&/77403-324.&&&&&&&&/.&&..&&.0&&&&',:9:/-/(55002020+3'12+2/&.2-&//&),&*&&&&&&&51 RG:Z:0 -SL-XAV:1:1:0:1300#0/1 77 * 0 0 * * 0 0 NAAACACAAGNNANAGTCTTANCNGCTATTCCNNNNNNNNNCTNNNCTNAGNANNACATACAACAGTATCCACACAAGTGTACTCGTNCANACATGTGAAC &*5535)*-,,&.&.*-1)*,&'&)&1&&.,)&&&&&&&&&)0&&&0'&&&&.&&*2'/4''0/**&)&,'-&*,&,&&&.0.&)&&&**&,.&&&')&&) RG:Z:0 -SL-XAV:1:1:0:1300#0/2 141 * 0 0 * * 0 0 NGATCATGGANGACTCTCCCCATCCCCCGCTCCAGCGCTCAGTTATATGCCTAGCCTCGGACACGTCACCAACATCTCACGCACTCTGCANAGTCTCTCAC &&'+''3*&-/)/1'26/*-2-/542-*&-&/'/*/&-'&)-')&.'-/&&2+122*'&+,(/-&)((,/-,,.'2(2'+)/&/&-66-&&/16&)&*&'3 RG:Z:0 -SL-XAV:1:1:0:1639#0/1 101 * 0 0 * chr1 1 0 NCCCTCTCAGNNTNTCTGCCANANCCTTAAGCNNNNNNNNNTANNNCTNAANCNNAAACTTTTGCCTCAGGCATCCGCAGAATGTTTNTCNGCCTATATCG &1::::::64/&/&0:3.280&/&087881,/&&&&&&&&&..&&&..&,,&-&&,265341-)/5680&-.5552-25/322/42/&)&&).421&-&-/ RG:Z:0 -SL-XAV:1:1:0:1668#0/1 101 * 0 0 * chr2 1 0 NATAGCATACNNTNCATTGGANTNCAGCACAANNNNNNNNNTGNNNCANTNNANNCCTTTGAGATCGGAAGAGCGGTTCAGCAGGAANNCNCAGACCGATC &1988998890&0&.8863//&.&.0-2875.&&&&&&&&&.)&&&..&.&&.&&.5782-2+262)&-0-0510*.332-2.-,0*&&*&'.&-2-)0., RG:Z:0 -SL-XAV:1:1:0:1914#0/1 101 * 0 0 * chr3 1 0 NTTTTTCTCCNNCNGTGCCTANTNTAGCCCCTNNNNNNNNNAANNNATNANNANNTTTACTTAAAAAACTGAAACTAGTAATGTGCANNANATCGNAAGAG &0::::<<;90&/&.244760&,&.414798/&&&&&&&&&00&&&0.&/&&-&&.4475687363504.&.557/.*)65.&/*./&&.&.+*)&..).& RG:Z:0 -SL-XAV:1:1:0:68#0/1 581 * 0 0 * chr4 1 0 NAATATTCATNNGNTCAGCCTNTNCATTAATTNNNNNNNNNTTNNNATNATNANNTTTTTTATAACCATTTATAAATGAGAGAGATCNTANCACAATATCA &0<<:::::</&&&.73'290&.&0;:::90&&&&&&&&&&..&&&0)&0-&0&&&.743799995253348597921.,.'050.*&.0&)*)&&&&*). RG:Z:0 -SL-XAV:1:1:0:700#0/1 581 * 0 0 * chr5 1 0 NGAAGCCCATNNTNGTGTTACNCNCCTGGAAGNNNNNNNNNACNNNGANACNTNNAACAATTCAGATCGGAAGAGCGGTTCAGCAGANNTNCCGAGACCGA &.88888:88/&0&,03189.&/&.8/))12/&&&&&&&&&./&&&&.&1.&)&&/35962/6432-3&),0&/2+0,),61&-6,&&&'&/,.0&...)0 RG:Z:0 -SL-XAV:1:1:0:764#0/2 165 * 0 0 * chr6 1 0 NACAGATGCANATATTAACAGGCTTTAAAGGACAGATGGACTGCAATACAATAATAGAGTACGTCAACACTCCACAGATCGCTAGAGCATNACATCGGTGT &/:5358::9999::99998255::7275,,/5567-'+387537857:54-4.51'31059547320;73/720+22.4(6.;((.;(;8()(''&&2&& RG:Z:0 |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_output_alignment_summary_metrics.html --- a/test-data/picard_output_alignment_summary_metrics.html Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,59 +0,0 @@ -<style type="text/css"> - tr.d0 td {background-color: oldlace; color: black;} - tr.d1 td {background-color: aliceblue; color: black;} - </style><?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"> -<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 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"> -Galaxy tool CollectAlignmentSummaryMetrics run at 11/11/2011 08:07:10</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.log">CollectAlignmentSummaryMetrics.log</a></td></tr> -<tr><td><a href="CollectAlignmentSummaryMetrics.metrics.txt">CollectAlignmentSummaryMetrics.metrics.txt</a></td></tr> -</table><p/> -<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 colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG, IS_BISULFITE_SEQUENCED=false] INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_2.dat OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt REFERENCE_SEQUENCE=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsfq2hit.fasta_fake.fasta ASSUME_SORTED=true TMP_DIR=[/tmp] VALIDATION_STRINGENCY=LENIENT METRIC_ACCUMULATION_LEVEL=[ALL_READS] 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 colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># Started on: Fri Nov 11 08:07:10 EST 2011</td></tr><tr class="d0"><td colspan="2">## 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>4 </td></tr> -<tr class="d0"><td>PCT_PF_READS_ALIGNED</td><td>1 </td></tr> -<tr class="d1"><td>PF_ALIGNED_BASES</td><td>404 </td></tr> -<tr class="d0"><td>PF_HQ_ALIGNED_READS</td><td>4 </td></tr> -<tr class="d1"><td>PF_HQ_ALIGNED_BASES</td><td>404 </td></tr> -<tr class="d0"><td>PF_HQ_ALIGNED_Q20_BASES</td><td>28 </td></tr> -<tr class="d1"><td>PF_HQ_MEDIAN_MISMATCHES</td><td>78 </td></tr> -<tr class="d0"><td>PF_MISMATCH_RATE</td><td>0.777228 </td></tr> -<tr class="d1"><td>PF_HQ_ERROR_RATE</td><td>0.777228 </td></tr> -<tr class="d0"><td>PF_INDEL_RATE</td><td>0 </td></tr> -<tr class="d1"><td>MEAN_READ_LENGTH</td><td>101 </td></tr> -<tr class="d0"><td>READS_ALIGNED_IN_PAIRS</td><td>3 </td></tr> -<tr class="d1"><td>PCT_READS_ALIGNED_IN_PAIRS</td><td>0.75 </td></tr> -<tr class="d0"><td>BAD_CYCLES</td><td>63 </td></tr> -<tr class="d1"><td>STRAND_BALANCE</td><td>0.25 </td></tr> -<tr class="d0"><td>PCT_CHIMERAS</td><td>0 </td></tr> -<tr class="d1"><td>PCT_ADAPTER</td><td>0 </td></tr> -<tr class="d0"><td>SAMPLE</td><td> </td></tr> -<tr class="d1"><td>LIBRARY</td><td> </td></tr> -<tr class="d0"><td>READ_GROUP -</td><td> - </td></tr> -</table> -<b>Picard Tool Run Log</b><hr/> -<pre>INFO:root:## executing java -Xmx4g -jar /data/home/rlazarus/galaxy/tool-data/shared/jars/picard/CreateSequenceDictionary.jar REFERENCE=/tmp/CollectAlignmentSummaryMetricsfq2hit.fasta OUTPUT=/tmp/CollectAlignmentSummaryMetricsfq2hit.dict URI=dataset_1.dat TRUNCATE_NAMES_AT_WHITESPACE=None returned status 0 and nothing on stderr - -INFO:root:## executing java -Xmx4g -jar /data/home/rlazarus/galaxy/tool-data/shared/jars/picard/CollectAlignmentSummaryMetrics.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true ADAPTER_SEQUENCE= IS_BISULFITE_SEQUENCED=false MAX_INSERT_SIZE=100000 OUTPUT=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetrics.metrics.txt R=/data/home/rlazarus/galaxy/database/job_working_directory/3/dataset_3_files/CollectAlignmentSummaryMetricsfq2hit.fasta_fake.fasta TMP_DIR=/tmp INPUT=/data/tmp/tmpLLcl1w/database/files/000/dataset_2.dat 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> - |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_output_collect_AS_sorted_pair.txt --- a/test-data/picard_output_collect_AS_sorted_pair.txt Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,12 +0,0 @@ -## net.sf.picard.metrics.StringHeader -# net.sf.picard.analysis.CollectAlignmentSummaryMetrics INPUT=testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam OUTPUT=output_test_as/test_as_sorted-pair.txt REFERENCE_SEQUENCE=testdata/picard/reference/Homo_sapiens_assembly18.trimmed.fasta ASSUME_SORTED=true MAX_INSERT_SIZE=100000 ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] IS_BISULFITE_SEQUENCED=false TMP_DIR=/tmp/raphael VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -## net.sf.picard.metrics.StringHeader -# Started on: Tue Oct 26 14:06:32 EDT 2010 - -## METRICS CLASS net.sf.picard.analysis.AlignmentSummaryMetrics -CATEGORY TOTAL_READS PF_READS PCT_PF_READS PF_NOISE_READS PF_READS_ALIGNED PCT_PF_READS_ALIGNED PF_HQ_ALIGNED_READS PF_HQ_ALIGNED_BASES PF_HQ_ALIGNED_Q20_BASES PF_HQ_MEDIAN_MISMATCHES PF_HQ_ERROR_RATE MEAN_READ_LENGTH READS_ALIGNED_IN_PAIRS PCT_READS_ALIGNED_IN_PAIRS BAD_CYCLES STRAND_BALANCE PCT_CHIMERAS PCT_ADAPTER -FIRST_OF_PAIR 5 5 1 0 0 0 0 0 0 0 ? 13 0 ? 0 ? ? 0 -SECOND_OF_PAIR 5 5 1 0 0 0 0 0 0 0 ? 13 0 ? 0 ? ? 0 -PAIR 10 10 1 0 0 0 0 0 0 0 ? 13 0 ? 0 ? ? 0 - - |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_output_estlibcomplexity_tinysam.html --- a/test-data/picard_output_estlibcomplexity_tinysam.html Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,38 +0,0 @@ -<style type="text/css"> - tr.d0 td {background-color: oldlace; color: black;} - tr.d1 td {background-color: aliceblue; color: black;} - </style><?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"> -<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 rgEstLibComplexity.py tool output - see http://g2.trac.bx.psu.edu/" /> -<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 rgEstLibComplexity.py run at 10/04/2011 14:52:24</b><b>Your job produced the following output files.</b><hr/> -<table> -<tr><td><a href="estlibcompout.txt">estlibcompout.txt</a></td></tr> -</table><p/> -<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.sam.EstimateLibraryComplexity INPUT=[/export/tmp/tmpBfU1Um/database/files/000/dataset_111.dat] OUTPUT=estlibcompout.txt MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT 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>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># Started on: Sun Apr 10 14:52:24 EDT 2011</td></tr></table> -<b>Picard log</b><hr/> -<pre>## executing java -Xmx2g -jar /udd/rerla/rgalaxy/tool-data/shared/jars/EstimateLibraryComplexity.jar MIN_IDENTICAL_BASES=5 O=estlibcompout.txt VALIDATION_STRINGENCY=LENIENT MIN_MEAN_QUALITY=20 READ_NAME_REGEX="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 I=/export/tmp/tmpBfU1Um/database/files/000/dataset_111.dat MAX_DIFF_RATE=0.03 returned status 0 and log (stdout/stderr) records: -[Sun Apr 10 14:52:24 EDT 2011] net.sf.picard.sam.EstimateLibraryComplexity INPUT=[/export/tmp/tmpBfU1Um/database/files/000/dataset_111.dat] OUTPUT=estlibcompout.txt MIN_IDENTICAL_BASES=5 MAX_DIFF_RATE=0.03 MIN_MEAN_QUALITY=20 READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -INFO 2011-04-10 14:52:24 EstimateLibraryComplexity Will store 3098916 read pairs in memory before sorting. -INFO 2011-04-10 14:52:24 EstimateLibraryComplexity Finished reading - moving on to scanning for duplicates. -[Sun Apr 10 14:52:24 EDT 2011] net.sf.picard.sam.EstimateLibraryComplexity done. -Runtime.totalMemory()=33947648 - - -</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/EstimateLibraryComplexity.jar MIN_IDENTICAL_BASES=5 O=estlibcompout.txt VALIDATION_STRINGENCY=LENIENT MIN_MEAN_QUALITY=20 READ_NAME_REGEX="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 I=/export/tmp/tmpBfU1Um/database/files/000/dataset_111.dat MAX_DIFF_RATE=0.03</pre> -</div></body></html> - |
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| @@ -1,15 +0,0 @@ -@HD VN:1.0 SO:coordinate -@SQ SN:chr1 LN:10001 -@SQ SN:chr2 LN:10001 -@SQ SN:chr3 LN:10001 -@RG ID:rg1 SM:Z -bar:record:1 77 * 0 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:1 141 * 0 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:2 77 * 0 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:2 141 * 0 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:3 77 * 0 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:3 141 * 0 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:4 77 * 0 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:4 141 * 0 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 -bar:record:5 77 * 0 0 * * 0 0 AAAAAAAAAAAAA 1111111111111 RG:Z:rg1 -bar:record:5 141 * 0 0 * * 0 0 CCCCCCCCCCCCC 2222222222222 RG:Z:rg1 |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_output_gc_summary_alignment_stats.txt --- a/test-data/picard_output_gc_summary_alignment_stats.txt Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,102 +0,0 @@ -## net.sf.picard.metrics.StringHeader -# net.sf.picard.analysis.CollectGcBiasMetrics REFERENCE_SEQUENCE=testdata/picard/reference/Homo_sapiens_assembly18.trimmed.nodict.fasta INPUT=testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=output_test_gc_nodict/test_nodic_ref_gc_summary_alignment_stats_test.txt CHART_OUTPUT=output_test_gc_nodict/test_nodic_ref_gc_summary_alignment_stats_test.pdf WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 TMP_DIR=/tmp/raphael VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -## net.sf.picard.metrics.StringHeader -# Started on: Tue Oct 26 13:54:53 EDT 2010 - -## METRICS CLASS net.sf.picard.analysis.GcBiasDetailMetrics -GC WINDOWS READ_STARTS MEAN_BASE_QUALITY NORMALIZED_COVERAGE ERROR_BAR_WIDTH -6 3 0 0 0 0 -7 7 0 0 0 0 -8 6 0 0 0 0 -9 45 0 0 0 0 -10 54 0 0 0 0 -11 83 0 0 0 0 -12 110 0 0 0 0 -13 83 0 0 0 0 -14 130 0 0 0 0 -15 178 0 0 0 0 -16 276 0 0 0 0 -17 352 0 0 0 0 -18 519 0 0 0 0 -19 658 0 0 0 0 -20 1073 0 0 0 0 -21 1543 0 0 0 0 -22 2024 0 0 0 0 -23 2631 0 0 0 0 -24 3758 0 0 0 0 -25 5087 0 0 0 0 -26 6543 0 0 0 0 -27 8020 0 0 0 0 -28 10251 0 0 0 0 -29 12241 0 0 0 0 -30 14189 0 0 0 0 -31 16295 0 0 0 0 -32 17995 0 0 0 0 -33 20131 0 0 0 0 -34 22194 0 0 0 0 -35 23848 0 0 0 0 -36 25355 0 0 0 0 -37 27310 0 0 0 0 -38 28274 0 0 0 0 -39 28818 0 0 0 0 -40 28806 0 0 0 0 -41 29651 0 0 0 0 -42 30773 0 0 0 0 -43 31217 0 0 0 0 -44 31743 0 0 0 0 -45 32727 0 0 0 0 -46 34084 0 0 0 0 -47 35307 0 0 0 0 -48 36752 0 0 0 0 -49 36917 0 0 0 0 -50 36561 0 0 0 0 -51 36399 0 0 0 0 -52 35677 0 0 0 0 -53 34354 1 1 29.352448 29.352448 -54 32401 0 0 0 0 -55 30417 0 0 0 0 -56 28588 0 0 0 0 -57 27083 0 0 0 0 -58 24090 0 0 0 0 -59 20995 0 0 0 0 -60 17702 0 0 0 0 -61 14252 0 0 0 0 -62 11595 0 0 0 0 -63 9077 0 0 0 0 -64 6863 0 0 0 0 -65 5394 0 0 0 0 -66 4304 0 0 0 0 -67 3551 0 0 0 0 -68 2776 0 0 0 0 -69 2321 0 0 0 0 -70 1999 0 0 0 0 -71 1777 0 0 0 0 -72 1444 0 0 0 0 -73 1367 0 0 0 0 -74 1182 0 0 0 0 -75 975 0 0 0 0 -76 807 0 0 0 0 -77 852 0 0 0 0 -78 867 0 0 0 0 -79 925 0 0 0 0 -80 786 0 0 0 0 -81 762 0 0 0 0 -82 578 0 0 0 0 -83 475 0 0 0 0 -84 391 0 0 0 0 -85 219 0 0 0 0 -86 184 0 0 0 0 -87 75 0 0 0 0 -88 36 0 0 0 0 -89 37 0 0 0 0 -90 24 0 0 0 0 -91 40 0 0 0 0 -92 33 0 0 0 0 -93 11 0 0 0 0 -94 24 0 0 0 0 -95 12 0 0 0 0 -96 11 0 0 0 0 -97 11 0 0 0 0 -98 9 0 0 0 0 - - |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_output_hs_transposed_summary_alignment_stats.html --- a/test-data/picard_output_hs_transposed_summary_alignment_stats.html Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,167 +0,0 @@\n-<style type="text/css">\n- tr.d0 td {background-color: oldlace; color: black;}\n- tr.d1 td {background-color: aliceblue; color: black;}\n- </style><?xml version="1.0" encoding="utf-8" ?>\n-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">\n-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">\n-<head>\n-<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />\n-<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" />\n-<title></title>\n-<link rel="stylesheet" href="/static/style/base.css" type="text/css" />\n-</head>\n-<body>\n-<div class="document">\n-Galaxy tool wrapper run picard_wrapper at 07/05/2011 00:15:30</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table>\n-<tr><td><a href="tempSamHead.txt">tempSamHead.txt</a></td></tr>\n-<tr><td><a href="rgPicardHsMetrics.bait">rgPicardHsMetrics.bait</a></td></tr>\n-<tr><td><a href="CalculateHsMetrics.metrics.txt">CalculateHsMetrics.metrics.txt</a></td></tr>\n-</table><p/>\n-<b>Picard on line resources - maxrows=100</b><ul>\n-<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>\n-<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>\n-<b>Picard output (transposed to make it easier to see)</b><hr/>\n-<table cellpadding="3" >\n-<tr class="d0"><td>## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td># net.sf.picard.analysis.directed.CalculateHsMetrics BAIT_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait TARGET_INTERVALS=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/rgPicardHsMetrics.bait INPUT=/tmp/6728811.1.all.q/tmpCsP1vm/database/files/000/dataset_95.dat OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/95/dataset_97_files/CalculateHsMetrics.metrics.txt TMP_DIR=/tmp/6728811.1.all.q/tmpCsP1vm/database/tmp VALIDATION_STRINGENCY=LENIENT 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: Sat May 07 00:15:15 EDT 2011</td></tr><tr class="d0"><td>## METRICS CLASS\tnet.sf.picard.analysis.directed.HsMetrics</td></tr><tr class="d0"><td>BAIT_SET</td><td>rgPicardHsMetrics</td></tr>\n-<tr class="d1"><td>GENOME_SIZE</td><td>2040</td></tr>\n-<tr class="d0"><td>BAIT_TERRITORY</td><td>14601938</td></tr>\n-<tr class="d1"><td>TARGET_TERRITORY</td><td>14601938</td></tr>\n-<tr class="d0"><td>BAIT_DESIGN_EFFICIENCY</td><td>1</td></tr>\n-<tr class="d1"><td>TOTAL_READS</td><td>18</td></tr>\n-<tr class="d0"><td>PF_READS</td><td>16</td></tr>\n-<tr class="d1"><td>PF_UNIQUE_READS</td><td>16</td></tr>\n-<tr class="d0"><td>PCT_PF_READS</td><td>0.888889</td></tr>\n-<tr class="d1"><td>PCT_PF_UQ_READS</td><td>0.888889</td></tr>\n-<tr class="d0"><td>PF_UQ_READS_ALIGNED</td><td>10</td></tr>\n-<tr class="d1"><td>PCT_PF_UQ_READS_ALIGNED</td><td>0.625</td></tr>\n-<tr class="d0"><td>PF_UQ_BASES_ALIGNED</td><td>1010</td></tr>\n-<tr class="d1"><td>ON_BAIT_BASES</td><td>0</td></tr>\n-<tr class="d0"><td>NEAR_BAIT_BASES</td><td>0</td></tr>\n-<tr class="d1"><td>OFF_BAIT_BASES</td><td>1010</td></tr>\n-<tr class="d0"><td>ON_TARGET_BASES</td><td>0</td></tr>\n-<tr class="d1"><td>PCT_SELECTED_BASES</td><td>0</td></tr>\n-<tr class="d0"><td>PCT_OFF_BAIT</td><td>1</td></tr>\n-<tr class="d1"><td>ON_BAIT_VS_SELECTED</td><td>?</td></tr>\n-<tr class="d0"><td>MEAN_BAIT_COVERAGE</td><td>0</td></tr>\n-<tr class="d1"><td>MEAN_TARGET_COVERAGE</td><td>?</td></tr>\n-<tr class="d0"><td>PCT_USABLE_BASES_ON_BAIT</td><td>0</td></tr>\n-<tr class="d1"><td>PCT_USABLE_BASES_ON_TARGET</td><td>0</td></tr>\n-<tr class="d0"><td>FOLD_ENRICHMENT</td><td>0</td></tr>\n-<tr cla'..b'\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:8514924-8515035\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:8518590-8518779\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:8623316-8623458\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:8626698-8626844\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:8723779-8723843\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:16408986-16409647\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:16425552-16427522\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:16542527-16542763\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:16572980-16573083\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:16717794-16717995\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:16728357-16728483\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:16860643-16860646\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:125814448-125814568\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:125816060-125816263\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:125817221-125817625\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:125823198-125823404\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:125834519-125834807\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:2019022-2019247\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:2022951-2023081\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:2029465-2029900\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:2037228-2037484\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:2044596-2044723\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:2046671-2046845\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:2048290-2048464\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:2050815-2050986\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:2060417-2060471\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:2063211-2063342\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:2063565-2063623\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:2066228-2066329\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:2067628-2067776\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:2071831-2071995\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:2073346-2073413\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:2074085-2074196\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:2076828-2077071\n-WARNING\t2011-05-07 00:15:16\tIntervalList\tIgnoring interval for unknown reference: chr9:2078499-2078613\n-\n-<b>## WARNING - 434559 log lines truncated - CalculateHsMetrics.log contains entire output</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> \n-generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>\n-\n' |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_output_insertsize_tinysam.html --- a/test-data/picard_output_insertsize_tinysam.html Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,53 +0,0 @@ -<style type="text/css"> - tr.d0 td {background-color: oldlace; color: black;} - tr.d1 td {background-color: aliceblue; color: black;} - </style><?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"> -<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 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"> -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> -<tr><td><a href="CollectInsertSizeMetrics.metrics.txt">CollectInsertSizeMetrics.metrics.txt</a></td></tr> -<tr><td><a href="CollectInsertSizeMetrics.log">CollectInsertSizeMetrics.log</a></td></tr> -<tr><td><a href="InsertSizeHist.pdf">InsertSizeHist.pdf</a></td></tr> -<tr><td><a href="InsertSizeHist.jpg">InsertSizeHist.jpg</a></td></tr> -</table><p/> -<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 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>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 - - -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 - -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> - |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_output_markdups_remdupes.bam |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_output_markdups_sortedpairsam.bam |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_output_markdups_sortedpairsam.html --- a/test-data/picard_output_markdups_sortedpairsam.html Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,160 +0,0 @@\n-<style type="text/css">\n- tr.d0 td {background-color: oldlace; color: black;}\n- tr.d1 td {background-color: aliceblue; color: black;}\n- </style><?xml version="1.0" encoding="utf-8" ?>\n-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">\n-<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">\n-<head>\n-<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />\n-<meta name="generator" content="Galaxy picard_wrapper tool output - see http://getgalaxy.org/" />\n-<title></title>\n-<link rel="stylesheet" href="/static/style/base.css" type="text/css" />\n-</head>\n-<body>\n-<div class="document">\n-Galaxy tool MarkDuplicates run at 12/05/2011 14:34:29</b><br/><b>The following output files were created (click the filename to view/download a copy):</b><hr/><table>\n-<tr><td><a href="MarkDuplicates.log">MarkDuplicates.log</a></td></tr>\n-<tr><td><a href="MarkDuplicates.metrics.txt">MarkDuplicates.metrics.txt</a></td></tr>\n-</table><p/>\n-<b>Picard on line resources</b><ul>\n-<li><a href="http://picard.sourceforge.net/index.shtml">Click here for Picard Documentation</a></li>\n-<li><a href="http://picard.sourceforge.net/picard-metric-definitions.shtml">Click here for Picard Metrics definitions</a></li></ul><hr/>\n-<b>Picard output (transposed to make it easier to see)</b><hr/>\n-<table cellpadding="3" >\n-<tr class="d0"><td colspan="2">## net.sf.picard.metrics.StringHeader</td></tr><tr class="d1"><td colspan="2"># net.sf.picard.sam.MarkDuplicates INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1097.dat OUTPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1098.dat METRICS_FILE=/udd/rerla/galaxy-central/database/job_working_directory/1032/dataset_1099_files/MarkDuplicates.metrics.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 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 14:34:28 EDT 2011</td></tr><tr class="d0"><td colspan="2">## METRICS CLASS\tnet.sf.picard.sam.DuplicationMetrics</td></tr><tr class="d0"><td>LIBRARY</td><td> </td></tr>\n-<tr class="d1"><td>UNPAIRED_READS_EXAMINED</td><td>1 </td></tr>\n-<tr class="d0"><td>READ_PAIRS_EXAMINED</td><td>3 </td></tr>\n-<tr class="d1"><td>UNMAPPED_READS</td><td>1 </td></tr>\n-<tr class="d0"><td>UNPAIRED_READ_DUPLICATES</td><td>1 </td></tr>\n-<tr class="d1"><td>READ_PAIR_DUPLICATES</td><td>1 </td></tr>\n-<tr class="d0"><td>READ_PAIR_OPTICAL_DUPLICATES</td><td>0 </td></tr>\n-<tr class="d1"><td>PERCENT_DUPLICATION</td><td>0.428571 </td></tr>\n-<tr class="d0"><td>ESTIMATED_LIBRARY_SIZE\n-</td><td>3\n- </td></tr>\n-<tr class="d0"><td colspan="2">## HISTOGRAM\tjava.lang.Double</td></tr><tr class="d0"><td colspan="2">BIN\tVALUE</td></tr>\n-<tr class="d1"><td colspan="2">1.0\t0.948181</td></tr>\n-<tr class="d0"><td colspan="2">2.0\t1.296997</td></tr>\n-<tr class="d1"><td colspan="2">3.0\t1.425319</td></tr>\n-<tr class="d0"><td colspan="2">4.0\t1.472527</td></tr>\n-<tr class="d1"><td colspan="2">5.0\t1.489893</td></tr>\n-<tr class="d0"><td colspan="2">6.0\t1.496282</td></tr>\n-<tr class="d1"><td colspan="2">7.0\t1.498632</td></tr>\n-<tr class="d0"><td colspan="2">8.0\t1.499497</td></tr>\n-<tr class="d1"><td colspan="2">9.0\t1.499815</td></tr>\n-<tr class="d0"><td colspan="2">10.0\t1.499932</td></tr>\n-<tr class="d1"><td colspan="2">11.0\t1.499975</td></tr>\n-<tr class="d0"><td colspan="2">12.0\t1.499991</td></tr>\n-<tr class="d1"><td colspan="2">13.0\t1.499997</td></tr>\n-<tr class="d0"><td colspan="2">14.0\t1.499999</t'..b'pan="2">84.0\t1.5</td></tr>\n-<tr class="d1"><td colspan="2">85.0\t1.5</td></tr>\n-<tr class="d0"><td colspan="2">86.0\t1.5</td></tr>\n-<tr class="d1"><td colspan="2">87.0\t1.5</td></tr>\n-<tr class="d0"><td colspan="2">88.0\t1.5</td></tr>\n-<tr class="d1"><td colspan="2">89.0\t1.5</td></tr>\n-<tr class="d0"><td colspan="2">90.0\t1.5</td></tr>\n-<tr class="d1"><td colspan="2">91.0\t1.5</td></tr>\n-<tr class="d0"><td colspan="2">92.0\t1.5</td></tr>\n-<tr class="d1"><td colspan="2">93.0\t1.5</td></tr>\n-<tr class="d0"><td colspan="2">94.0\t1.5</td></tr>\n-<tr class="d1"><td colspan="2">95.0\t1.5</td></tr>\n-<tr class="d0"><td colspan="2">96.0\t1.5</td></tr>\n-<tr class="d1"><td colspan="2">97.0\t1.5</td></tr>\n-<tr class="d0"><td colspan="2">98.0\t1.5</td></tr>\n-<tr class="d1"><td colspan="2">99.0\t1.5</td></tr>\n-</table>\n-<b>Picard Tool Run Log</b><hr/>\n-<pre>Thu, 12 May 2011 14:34:29 INFO\n- ## executing java -Xmx2g -jar /udd/rerla/galaxy-central/tool-data/shared/jars/MarkDuplicates.jar VALIDATION_STRINGENCY=LENIENT ASSUME_SORTED=true INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1097.dat OUTPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1098.dat METRICS_FILE=/udd/rerla/galaxy-central/database/job_working_directory/1032/dataset_1099_files/MarkDuplicates.metrics.txt REMOVE_DUPLICATES=true READ_NAME_REGEX="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 returned status 0 and stderr: \n-[Thu May 12 14:34:28 EDT 2011] net.sf.picard.sam.MarkDuplicates INPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1097.dat OUTPUT=/tmp/6729253.1.all.q/tmpM5wI_h/database/files/001/dataset_1098.dat METRICS_FILE=/udd/rerla/galaxy-central/database/job_working_directory/1032/dataset_1099_files/MarkDuplicates.metrics.txt REMOVE_DUPLICATES=true ASSUME_SORTED=true READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 VALIDATION_STRINGENCY=LENIENT MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 TMP_DIR=/tmp/rerla VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false\n-INFO\t2011-05-12 14:34:28\tMarkDuplicates\tStart of doWork freeMemory: 8644632; totalMemory: 9109504; maxMemory: 1908932608\n-INFO\t2011-05-12 14:34:28\tMarkDuplicates\tReading input file and constructing read end information.\n-INFO\t2011-05-12 14:34:28\tMarkDuplicates\tWill retain up to 7575129 data points before spilling to disk.\n-INFO\t2011-05-12 14:34:28\tMarkDuplicates\tRead 7 records. 0 pairs never matched.\n-INFO\t2011-05-12 14:34:29\tMarkDuplicates\tAfter buildSortedReadEndLists freeMemory: 8316168; totalMemory: 130351104; maxMemory: 1908932608\n-INFO\t2011-05-12 14:34:29\tMarkDuplicates\tWill retain up to 59654144 duplicate indices before spilling to disk.\n-INFO\t2011-05-12 14:34:29\tMarkDuplicates\tTraversing read pair information and detecting duplicates.\n-INFO\t2011-05-12 14:34:29\tMarkDuplicates\tTraversing fragment information and detecting duplicates.\n-INFO\t2011-05-12 14:34:29\tMarkDuplicates\tSorting list of duplicate records.\n-INFO\t2011-05-12 14:34:29\tMarkDuplicates\tAfter generateDuplicateIndexes freeMemory: 129615120; totalMemory: 607649792; maxMemory: 1908932608\n-INFO\t2011-05-12 14:34:29\tMarkDuplicates\tMarking 3 records as duplicates.\n-INFO\t2011-05-12 14:34:29\tMarkDuplicates\tFound 0 optical duplicate clusters.\n-INFO\t2011-05-12 14:34:29\tMarkDuplicates\tBefore output close freeMemory: 128997520; totalMemory: 607649792; maxMemory: 1908932608\n-INFO\t2011-05-12 14:34:29\tMarkDuplicates\tAfter output close freeMemory: 128997280; totalMemory: 607649792; maxMemory: 1908932608\n-[Thu May 12 14:34:29 EDT 2011] net.sf.picard.sam.MarkDuplicates done.\n-Runtime.totalMemory()=607649792\n-\n-\n-</pre><hr/>The freely available <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> \n-generated all outputs reported here running as a <a href="http://getgalaxy.org">Galaxy</a> tool</div></body></html>\n-\n' |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_output_markdups_sortedpairsam.sam --- a/test-data/picard_output_markdups_sortedpairsam.sam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,63 +0,0 @@ -<?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"> -<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 rgPicardMarkDups.py tool output - see http://g2.trac.bx.psu.edu/" /> - <link rel="stylesheet" href="/static/style/base.css" type="text/css" /> - </head> - <body> - <div class="document"> - <h3><a href="http://rgenetics.org">Rgenetics</a> tool rgPicardMarkDups.py run at 19/11/2010 18:25:23</h3> - <b>Your job produced the following outputs - check here for a record of what was done and any unexpected events</b> - <hr /> - <div> - <b>Output files.</b> - <table> - <tr><td><a href="rgPicardMarkDups.txt">rgPicardMarkDups.txt (1.8 KB)</a></td></tr> - </table> - </div> - <hr /> - <div> - <b>Log of activity</b> - <hr/> - ## executing java -Xmx2g -jar /share/shared/relul.galaxy/tool-data/shared/jars/MarkDuplicates.jar I= /share/shared/relul.galaxy/database/files/000/dataset_57.dat O= /share/shared/relul.galaxy/database/files/000/dataset_99.dat M= rgPicardMarkDupsMetrics.txt READ_NAME_REGEX="[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*" OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 returned status 1 and log (stdout/stderr) records: -<BR /> -[Fri Nov 19 18:25:23 EST 2010] net.sf.picard.sam.MarkDuplicates INPUT=/share/shared/relul.galaxy/database/files/000/dataset_57.dat OUTPUT=/share/shared/relul.galaxy/database/files/000/dataset_99.dat METRICS_FILE=rgPicardMarkDupsMetrics.txt READ_NAME_REGEX=[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 REMOVE_DUPLICATES=false ASSUME_SORTED=false MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 TMP_DIR=/tmp/relul VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -<BR /> -INFO 2010-11-19 18:25:23 MarkDuplicates Start of doWork freeMemory: 8645600; totalMemory: 9109504; maxMemory: 1908932608 -<BR /> -INFO 2010-11-19 18:25:23 MarkDuplicates Reading input file and constructing read end information. -<BR /> -INFO 2010-11-19 18:25:23 MarkDuplicates Will retain up to 7575129 data points before spilling to disk. -<BR /> -[Fri Nov 19 18:25:23 EST 2010] net.sf.picard.sam.MarkDuplicates done. -<BR /> -Runtime.totalMemory()=130351104 -<BR /> -Exception in thread "main" net.sf.picard.PicardException: /share/shared/relul.galaxy/database/files/000/dataset_57.dat is not coordinate sorted. -<BR /> - at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:248) -<BR /> - at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:109) -<BR /> - at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:165) -<BR /> - at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:93) -<BR /> - -<BR /> - - </div> - - <div> - <p>Note: The freely available - <a href="http://picard.sourceforge.net/command-line-overview.shtml">Picard software</a> - generated all outputs reported here. These third party tools were orchestrated by the Galaxy - rgPicardMarkDups.py wrapper and this command line from the Galaxy form: - </p> - <hr /> - <div>/share/shared/relul.galaxy/tools/development/rgPicardMarkDups.py -i /share/shared/relul.galaxy/database/files/000/dataset_57.dat -n Dupes Marked --tmp_dir /export/tmp/relul -o /share/shared/relul.galaxy/database/files/000/dataset_99.dat --remdups false --assumesorted true --readregex [a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).* --optdupedist 100 -j /share/shared/relul.galaxy/tool-data/shared/jars/MarkDuplicates.jar -d /share/shared/relul.galaxy/database/job_working_directory/81/dataset_98_files -t /share/shared/relul.galaxy/database/files/000/dataset_98.dat</div> - </div> - </body> -</html> |
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| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_output_validate_tiny_sam.html --- a/test-data/picard_output_validate_tiny_sam.html Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,46 +0,0 @@ -<style type="text/css"> - tr.d0 td {background-color: oldlace; color: black;} - tr.d1 td {background-color: aliceblue; color: black;} - </style><?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"> -<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 rgPicardValidate.py tool output - see http://g2.trac.bx.psu.edu/" /> -<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 rgPicardValidate.py run at 19/04/2011 11:19:17</b><br/><b>Running this Galaxy tool produced the following output files (click the filename to view/download a copy).</b><hr/><table> -<tr><td><a href="rgPicardValidate.out">rgPicardValidate.out</a></td></tr> -</table><p/> -<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</b><hr/> -<table cellpadding="3" > -<tr class="d0"><td>['WARNING: Record 1, Read name both_reads_align_clip_marked, NM tag (nucleotide differences) is missing\n']</td></tr> -<tr class="d1"><td>['WARNING: Record 2, Read name both_reads_present_only_first_aligns, NM tag (nucleotide differences) is missing\n']</td></tr> -<tr class="d0"><td>['WARNING: Record 3, Read name read_2_too_many_gaps, NM tag (nucleotide differences) is missing\n']</td></tr> -<tr class="d1"><td>['ERROR: Record 4, Read name both_reads_align_clip_adapter, The record is out of [queryname] order, prior read name [read_2_too_many_gaps], prior coodinates [1:1]\n']</td></tr> -<tr class="d0"><td>['WARNING: Record 4, Read name both_reads_align_clip_adapter, NM tag (nucleotide differences) is missing\n']</td></tr> -<tr class="d1"><td>['WARNING: Record 5, Read name both_reads_align_clip_adapter, NM tag (nucleotide differences) is missing\n']</td></tr> -<tr class="d0"><td>['WARNING: Record 6, Read name both_reads_align_clip_marked, NM tag (nucleotide differences) is missing\n']</td></tr> -<tr class="d1"><td>['WARNING: Record 7, Read name read_2_too_many_gaps, NM tag (nucleotide differences) is missing\n']</td></tr> -<tr class="d0"><td>['ERROR: Record 8, Read name both_reads_present_only_first_aligns, The record is out of [queryname] order, prior read name [read_2_too_many_gaps], prior coodinates [1:302]\n']</td></tr> -</table> -<b>Picard log</b><hr/> -<pre>## executing samtools sort /udd/rerla/rgalaxy/database/job_working_directory/98/dataset_100_files/tmpELItj4rgSortBamTemp.bam /udd/rerla/rgalaxy/database/job_working_directory/98/dataset_100_files/rgcleansam.sorted returned status 0. Nothing appeared on stderr/stdout - -rectory/98/dataset_100_files/rgPicardValidate.out IGNORE=INVALID_TAG_NM MAX_OUTPUT=100 TMP_DIR=/tmp returned status 1 and log (stdout/stderr) records: -[Tue Apr 19 11:19:17 EDT 2011] net.sf.picard.sam.ValidateSamFile INPUT=/udd/rerla/rgalaxy/database/job_working_directory/98/dataset_100_files/rgcleansam.sorted.bam OUTPUT=/udd/rerla/rgalaxy/database/job_working_directory/98/dataset_100_files/rgPicardValidate.out IGNORE=[INVALID_TAG_NM] MAX_OUTPUT=100 REFERENCE_SEQUENCE=/share/shared/data/hg18/hg18.fasta TMP_DIR=/tmp MODE=VERBOSE IGNORE_WARNINGS=false VALIDATE_INDEX=true IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false -[Tue Apr 19 11:19:17 EDT 2011] net.sf.picard.sam.ValidateSamFile 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 -Xmx8g -jar /udd/rerla/rgalaxy/tool-data/shared/jars/ValidateSamFile.jar I=/udd/rerla/rgalaxy/database/job_working_directory/98/dataset_100_files/rgcleansam.sorted.bam R=/share/shared/data/hg18/hg18.fasta O=/udd/rerla/rgalaxy/database/job_working_directory/98/dataset_100_files/rgPicardValidate.out IGNORE=INVALID_TAG_NM MAX_OUTPUT=100 TMP_DIR=/tmp</pre> -</div></body></html> - |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/picard_summary_alignment_stats.sam --- a/test-data/picard_summary_alignment_stats.sam Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,28 +0,0 @@ -@HD VN:1.0 SO:coordinate -@SQ SN:chr1 LN:101 -@SQ SN:chr2 LN:101 -@SQ SN:chr3 LN:101 -@SQ SN:chr4 LN:101 -@SQ SN:chr5 LN:101 -@SQ SN:chr6 LN:101 -@SQ SN:chr7 LN:202 -@SQ SN:chr8 LN:202 -@RG ID:0 SM:Hi,Mom! -SL-XAV:1:1:0:764#0/1 89 chr1 1 255 101M * 0 0 TTCATGCTGANGCNCTCTTACGATCGTACAGATGCAAATATTAACANNCNTTNAAGNNCANNNNNNNNNCAATACAATANTAGAGTACGTNAACACTCCAN &/,&-.1/6/&&)&).)/,&0768)&/.,/874,&.4137572)&/&&,&1-&.0/&&*,&&&&&&&&&&18775799,&16:8775-56256/69::;0& RG:Z:0 XN:i:1 -SL-XAV:1:1:0:1668#0/2 153 chr2 1 255 101M * 0 0 CATCTCTACANGCGCGTCCTACCAGACGCGCTTCCGATCTGAGAGCATACTTTTCATTGGATTCCAGCACAACTCCATTTTTGATCCACTNGACACCTTTN (/,'-/'0////(1'&&1&&&&'2''-6/,/3-33653.6:1'.86/-++32.-4864653/5/583/346423203+28888644446688456/4880& RG:Z:0 XN:i:1 -SL-XAV:1:1:0:1914#0/2 153 chr3 1 255 101M * 0 0 CGTATGCGCTNTTTATGTCGCCCACAGTGCCTAGTATAGCCCCTGCTAATAAAAAGAGATGAATACGTTTACTTAAAAAACTGAAACTAGNAATGTGCAAN (0,7&&*/*0*,)10/).-*&.&*/6669.&-337599;3,&,6/.,5::999987893+387020775777547999::668997448:::9;999::0& RG:Z:0 -SL-XAV:1:1:0:1639#0/2 153 chr4 1 255 101M * 0 0 CGTGATACCANCTCATGTTCACAGCCAAAGCCTGAAGCTGTCTATTATATTTCTCAACCATAAACTTTTGCCTCAGGCATCCGCAGAATGNTTTGCAGCCN '.&.&&'.0+01'2(1'(''-)','+0041/.+032;:867115/5267-.0/)-5.&-26200224,,0+0/0275/5605688::646875568882*& RG:Z:0 -SL-XAV:1:1:0:68#0/2 137 chr5 1 255 101M * 0 0 NTCTCATTTANAAATGGTTATAAAAACATTTATGCTGAAAAGGTGAAGTTCATTAATGAACAGGCTGACTGTCTCACTATCGCGTTCGCANGACGTTATCT &1<<999;;;;<<<87579:556972789977444.'.023.&,7621/54.49.)/53055-22--''+(.'-))6-168/(3&&0(<).))*&&&&&'0 RG:Z:0 -SL-XAV:1:1:0:700#0/2 137 chr6 1 255 101M * 0 0 NAATTGTTCTNAGTTTCTCGGTTTATGTGCTCTTCCAGGTGGGTAACACAATAATGGCCTTCCAGATCGTAAGAGCGACGTGTGTTGCACNAGTGTCGATC &0::887::::6/646::838388811/679:87640&./2+/-4/28:3,536/4''&&.78/(/554/./02*)*',-(57()&.6(6:(0601'/(,* RG:Z:0 -SL-XAV:1:1:0:1721#0/1 83 chr7 1 255 101M = 102 40 CAACAGAAGGNGGNATCTGTGTTTGTGTTTCGGATTTCCTGCTGAANNGNTTNTCGNNTCNNNNNNNNATCCCGATTTCNTTCCGCAGCTNACCTCCCGAN )'.*.+2,))&&'&*/)-&*-)&.-)&)&),/-&&..)./.,.).*&&,&.&&-)&&&0*&&&&&&&&/32/,01460&&/6/*0*/2/283//36868/& RG:Z:0 -SL-XAV:1:1:0:1721#0/2 163 chr7 102 255 101M = 1 -40 NCGCGGCATCNCGATTTCTTTCCGCAGCTAACCTCCCGACAGATCGGCAGCGCGTCGTGTAGGTCACTATGGTACATCTTGTCGTGCGGCNAGAGCATACA &/15445666651/566666553+2/14/&/555512+3/)-'/-&-'*+))*''13+3)'//++''/'))/3+&*5++)&'2+&+/*&-&&*)&-./1'1 RG:Z:0 -SL-XAV:1:1:0:105#0/2 147 chr8 1 255 101M = 102 79 CACATCGTGANTCTTACAATCTGCGGTTTCAGATGTGGAGCGATGTGTGAGAGATTGAGCAACTGATCTGAAAAGCAGACACAGCTATTCNTAAGATGACN /))3--/&*()&)&&+'++.'-&,(.))'4,)&'&&,')8,&&*'.&*0'225/&)3-8//)*,5-*).7851453583.3568526:863688:::85.& RG:Z:0 -SL-XAV:1:1:0:105#0/1 99 chr8 102 255 101M = 1 -79 NCAGGTTCAANTGTGCAGCCCNTTTTGAGAGATNNNNNNNNTGNNCTGNAANANNGACACAGCTATTCCTAAGATGACAAGATCAGANAANAAGTCAAGCA &06665578::41.*/7577/&/77403-324.&&&&&&&&/.&&..&&.0&&&&',:9:/-/(55002020+3'12+2/&.2-&//&),&*&&&&&&&51 RG:Z:0 -SL-XAV:1:1:0:1300#0/1 77 * 0 0 * * 0 0 NAAACACAAGNNANAGTCTTANCNGCTATTCCNNNNNNNNNCTNNNCTNAGNANNACATACAACAGTATCCACACAAGTGTACTCGTNCANACATGTGAAC &*5535)*-,,&.&.*-1)*,&'&)&1&&.,)&&&&&&&&&)0&&&0'&&&&.&&*2'/4''0/**&)&,'-&*,&,&&&.0.&)&&&**&,.&&&')&&) RG:Z:0 -SL-XAV:1:1:0:1300#0/2 141 * 0 0 * * 0 0 NGATCATGGANGACTCTCCCCATCCCCCGCTCCAGCGCTCAGTTATATGCCTAGCCTCGGACACGTCACCAACATCTCACGCACTCTGCANAGTCTCTCAC &&'+''3*&-/)/1'26/*-2-/542-*&-&/'/*/&-'&)-')&.'-/&&2+122*'&+,(/-&)((,/-,,.'2(2'+)/&/&-66-&&/16&)&*&'3 RG:Z:0 -SL-XAV:1:1:0:1639#0/1 101 * 0 0 * chr1 1 0 NCCCTCTCAGNNTNTCTGCCANANCCTTAAGCNNNNNNNNNTANNNCTNAANCNNAAACTTTTGCCTCAGGCATCCGCAGAATGTTTNTCNGCCTATATCG &1::::::64/&/&0:3.280&/&087881,/&&&&&&&&&..&&&..&,,&-&&,265341-)/5680&-.5552-25/322/42/&)&&).421&-&-/ RG:Z:0 -SL-XAV:1:1:0:1668#0/1 101 * 0 0 * chr2 1 0 NATAGCATACNNTNCATTGGANTNCAGCACAANNNNNNNNNTGNNNCANTNNANNCCTTTGAGATCGGAAGAGCGGTTCAGCAGGAANNCNCAGACCGATC &1988998890&0&.8863//&.&.0-2875.&&&&&&&&&.)&&&..&.&&.&&.5782-2+262)&-0-0510*.332-2.-,0*&&*&'.&-2-)0., RG:Z:0 -SL-XAV:1:1:0:1914#0/1 101 * 0 0 * chr3 1 0 NTTTTTCTCCNNCNGTGCCTANTNTAGCCCCTNNNNNNNNNAANNNATNANNANNTTTACTTAAAAAACTGAAACTAGTAATGTGCANNANATCGNAAGAG &0::::<<;90&/&.244760&,&.414798/&&&&&&&&&00&&&0.&/&&-&&.4475687363504.&.557/.*)65.&/*./&&.&.+*)&..).& RG:Z:0 -SL-XAV:1:1:0:68#0/1 581 * 0 0 * chr4 1 0 NAATATTCATNNGNTCAGCCTNTNCATTAATTNNNNNNNNNTTNNNATNATNANNTTTTTTATAACCATTTATAAATGAGAGAGATCNTANCACAATATCA &0<<:::::</&&&.73'290&.&0;:::90&&&&&&&&&&..&&&0)&0-&0&&&.743799995253348597921.,.'050.*&.0&)*)&&&&*). RG:Z:0 -SL-XAV:1:1:0:700#0/1 581 * 0 0 * chr5 1 0 NGAAGCCCATNNTNGTGTTACNCNCCTGGAAGNNNNNNNNNACNNNGANACNTNNAACAATTCAGATCGGAAGAGCGGTTCAGCAGANNTNCCGAGACCGA &.88888:88/&0&,03189.&/&.8/))12/&&&&&&&&&./&&&&.&1.&)&&/35962/6432-3&),0&/2+0,),61&-6,&&&'&/,.0&...)0 RG:Z:0 -SL-XAV:1:1:0:764#0/2 165 * 0 0 * chr6 1 0 NACAGATGCANATATTAACAGGCTTTAAAGGACAGATGGACTGCAATACAATAATAGAGTACGTCAACACTCCACAGATCGCTAGAGCATNACATCGGTGT &/:5358::9999::99998255::7275,,/5567-'+387537857:54-4.51'31059547320;73/720+22.4(6.;((.;(;8()(''&&2&& RG:Z:0 |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e test-data/random_phiX_1.fastqsanger --- a/test-data/random_phiX_1.fastqsanger Fri Feb 21 12:07:49 2014 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,80 +0,0 @@ -@random_phiX_region_0 -TTGAGGCTTGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTT -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@random_phiX_region_1 -GTTAGTGCTGAGGTTGACTTAGTTCATCAGCAAACGCAGAATCAGCGGTA -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@random_phiX_region_2 -AATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTTTCCA -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@random_phiX_region_3 -GGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTC -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@random_phiX_region_4 -ACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGAC -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@random_phiX_region_5 -AGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACTTCCCA -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@random_phiX_region_6 -CACGTTTATGGTGAACAGTGGATTAAGTTCATGAAGGATGGTGTTAATGC -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@random_phiX_region_7 -AACTACTCCGGTTATCGCTGGCGACTCCTTCGAGATGGACGCCGTTGGCG -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@random_phiX_region_8 -CTCGTGCTCGTCGCTGCGTTGAGGCTTGCGTTTATGGTACGCTGGACTTT -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@random_phiX_region_9 -CAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGACTTAGTTCA -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@random_phiX_region_10 -TACAGTATGCCCATCGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTC -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@random_phiX_region_11 -TATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGA -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@random_phiX_region_12 -AGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATA -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@random_phiX_region_13 -TTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGACTAAAGAGATTCA -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@random_phiX_region_14 -CCGGGCAATAACGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGC -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@random_phiX_region_15 -AACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTT -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@random_phiX_region_16 -GCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCA -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@random_phiX_region_17 -CATGATTATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAG -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@random_phiX_region_18 -TGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -@random_phiX_region_19 -GCTGTCGCTACTTCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACT -+ -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
| b |
| diff -r ab1f60c26526 -r 3d4f1fa26f0e tool_dependencies.xml --- a/tool_dependencies.xml Fri Feb 21 12:07:49 2014 -0500 +++ b/tool_dependencies.xml Tue Dec 16 19:03:21 2014 -0500 |
| b |
| @@ -1,6 +1,6 @@ <?xml version="1.0"?> <tool_dependency> - <package name="picard" version="1.56.0"> - <repository changeset_revision="61e41d21cb6f" name="package_picard_1_56_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <package name="picard" version="1.126.0"> + <repository changeset_revision="b455d70e90b8" name="package_picard_1_126_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> </tool_dependency> |