| Next changeset 1:2ba834228e9b (2014-06-06) |
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Commit message:
Uploaded |
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added:
bwa_color_wrapper.xml bwa_wrapper.py bwa_wrapper.xml test-data/bwa_wrapper_in1.fastqsanger test-data/bwa_wrapper_in2.fastqsanger test-data/bwa_wrapper_in3.fastqsanger test-data/bwa_wrapper_in4.fastqcssanger test-data/bwa_wrapper_in5.fastqcssanger test-data/bwa_wrapper_in6.fastqcssanger test-data/bwa_wrapper_out1.sam test-data/bwa_wrapper_out2.sam test-data/bwa_wrapper_out3.sam test-data/bwa_wrapper_out4.sam test-data/bwa_wrapper_out5.sam test-data/bwa_wrapper_out6.sam test-data/bwa_wrapper_out7.sam test-data/bwa_wrapper_out8.sam test-data/chr_m.fasta test-data/hg19chrX_midpart.fasta test-data/phiX.fasta tool-data/bwa_index.loc.sample tool-data/bwa_index_color.loc.sample tool_data_table_conf.xml.sample tool_dependencies.xml |
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| diff -r 000000000000 -r 8d92246f41bb bwa_color_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bwa_color_wrapper.xml Thu Jun 05 15:15:34 2014 -0400 |
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| b'@@ -0,0 +1,485 @@\n+<tool id="bwa_color_wrapper" name="Map with BWA for SOLiD" version="1.0.2">\n+ <requirements>\n+ <requirement type="package" version="0.5.9">bwa</requirement>\n+ </requirements>\n+ <description></description>\n+ <parallelism method="basic"></parallelism>\n+ <command interpreter="python">\n+ bwa_wrapper.py \n+ --threads="\\${GALAXY_SLOTS:-4}"\n+ --color-space\n+\n+ ## reference source\n+ --fileSource="${genomeSource.refGenomeSource}"\n+ #if $genomeSource.refGenomeSource == "history":\n+ ##build index on the fly\n+ --ref="${genomeSource.ownFile}"\n+ --dbkey="${dbkey}"\n+ #else:\n+ ##use precomputed indexes\n+ --ref="${genomeSource.indices.fields.path}"\n+ --do_not_build_index\n+ #end if\n+\n+ ## input file(s)\n+ --input1="${paired.input1}"\n+ #if $paired.sPaired == "paired":\n+ --input2="${paired.input2}"\n+ #end if\n+\n+ ## output file\n+ --output="${output}"\n+\n+ ## run parameters\n+ --genAlignType="${paired.sPaired}"\n+ --params="${params.source_select}"\n+ #if $params.source_select != "pre_set":\n+ --maxEditDist="${params.maxEditDist}"\n+ --fracMissingAligns="${params.fracMissingAligns}"\n+ --maxGapOpens="${params.maxGapOpens}"\n+ --maxGapExtens="${params.maxGapExtens}"\n+ --disallowLongDel="${params.disallowLongDel}"\n+ --disallowIndel="${params.disallowIndel}"\n+ --seed="${params.seed}"\n+ --maxEditDistSeed="${params.maxEditDistSeed}"\n+ --mismatchPenalty="${params.mismatchPenalty}"\n+ --gapOpenPenalty="${params.gapOpenPenalty}"\n+ --gapExtensPenalty="${params.gapExtensPenalty}"\n+ --suboptAlign="${params.suboptAlign}"\n+ --noIterSearch="${params.noIterSearch}"\n+ --outputTopN="${params.outputTopN}"\n+ --outputTopNDisc="${params.outputTopNDisc}"\n+ --maxInsertSize="${params.maxInsertSize}"\n+ --maxOccurPairing="${params.maxOccurPairing}"\n+ #if $params.readGroup.specReadGroup == "yes"\n+ --rgid="${params.readGroup.rgid}"\n+ --rgcn="${params.readGroup.rgcn}"\n+ --rgds="${params.readGroup.rgds}"\n+ --rgdt="${params.readGroup.rgdt}"\n+ --rgfo="${params.readGroup.rgfo}"\n+ --rgks="${params.readGroup.rgks}"\n+ --rglb="${params.readGroup.rglb}"\n+ --rgpg="${params.readGroup.rgpg}"\n+ --rgpi="${params.readGroup.rgpi}"\n+ --rgpl="${params.readGroup.rgpl}"\n+ --rgpu="${params.readGroup.rgpu}"\n+ --rgsm="${params.readGroup.rgsm}"\n+ #end if\n+ #end if\n+\n+ ## suppress output SAM header\n+ --suppressHeader="${suppressHeader}"\n+ </command>\n+ <requirements>\n+ <requirement type="package">bwa</requirement>\n+ </requirements>\n+ <inputs>\n+ <conditional name="genomeSource">\n+ <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">\n+ <option value="indexed">Use a built-in index</option>\n+ <option value="history">Use one from the history</option>\n+ </param>\n+ <when value="indexed">\n+ <param name="indices" type="select" label="Select a reference genome">\n+ <options from_data_table="bwa_indexes_color">\n+ <filter type="sort_by" column="2" />\n+ <validator type="no_options" message="No indexes are available for the selected input dataset" />\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 from history" />\n+ </when>\n+ </conditional>\n+ <conditional name="paired">\n+ <param name="sPaired" type="select" label="Is this library mate-paired?">\n+ <option value="single">Single-end</option>\n+ <option value="paired">Paired-end</option>\n+ </param>\n+ <when value="single">\n+ <param '..b"p towards the 3'-end [16]\n+ -i INT Disallow an indel within INT bp towards the ends [5]\n+ -l INT Take the first INT subsequence as seed. If INT is larger than the\n+ query sequence, seeding will be disabled. For long reads, this option \n+ is typically ranged from 25 to 35 for '-k 2'. [inf]\n+ -k INT Maximum edit distance in the seed [2]\n+ -t INT Number of threads (multi-threading mode) [1]\n+ -M INT Mismatch penalty. BWA will not search for suboptimal hits with a score\n+ lower than (bestScore-misMsc). [3]\n+ -O INT Gap open penalty [11]\n+ -E INT Gap extension penalty [4]\n+ -c Reverse query but not complement it, which is required for alignment\n+ in the color space.\n+ -R Proceed with suboptimal alignments even if the top hit is a repeat. By\n+ default, BWA only searches for suboptimal alignments if the top hit is\n+ unique. Using this option has no effect on accuracy for single-end\n+ reads. It is mainly designed for improving the alignment accuracy of\n+ paired-end reads. However, the pairing procedure will be slowed down,\n+ especially for very short reads (~32bp).\n+ -N Disable iterative search. All hits with no more than maxDiff\n+ differences will be found. This mode is much slower than the default.\n+\n+For **samse**::\n+\n+ -n INT Maximum number of alignments to output in the XA tag for reads paired\n+ properly. If a read has more than INT hits, the XA tag will not be\n+ written. [3]\n+ -r STR Specify the read group in a format like '@RG\\tID:foo\\tSM:bar' [null]\n+\n+For **sampe**::\n+\n+ -a INT Maximum insert size for a read pair to be considered as being mapped\n+ properly. Since version 0.4.5, this option is only used when there\n+ are not enough good alignment to infer the distribution of insert\n+ sizes. [500]\n+ -n INT Maximum number of alignments to output in the XA tag for reads paired\n+ properly. If a read has more than INT hits, the XA tag will not be\n+ written. [3]\n+ -N INT Maximum number of alignments to output in the XA tag for disconcordant\n+ read pairs (excluding singletons). If a read has more than INT hits,\n+ the XA tag will not be written. [10]\n+ -o INT Maximum occurrences of a read for pairing. A read with more\n+ occurrences will be treated as a single-end read. Reducing this\n+ parameter helps faster pairing. [100000]\n+ -r STR Specify the read group in a format like '@RG\\tID:foo\\tSM:bar' [null]\n+\n+For specifying the read group in **samse** or **sampe**, use the following::\n+\n+ @RG Read group. Unordered multiple @RG lines are allowed. \n+ ID Read group identi\xef\xac\x81er. Each @RG line must have a unique ID. The value of\n+ ID is used in the RG tags of alignment records. Must be unique among all\n+ read groups in header section. Read group IDs may be modi\xef\xac\x81ed when\n+ merging SAM \xef\xac\x81les in order to handle collisions. \n+ CN Name of sequencing center producing the read. \n+ DS Description. \n+ DT Date the run was produced (ISO8601 date or date/time). \n+ FO Flow order. The array of nucleotide bases that correspond to the\n+ nucleotides used for each flow of each read. Multi-base flows are encoded\n+ in IUPAC format, and non-nucleotide flows by various other characters.\n+ Format : /\\*|[ACMGRSVTWYHKDBN]+/ \n+ KS The array of nucleotide bases that correspond to the key sequence of each read. \n+ LB Library. \n+ PG Programs used for processing the read group. \n+ PI Predicted median insert size. \n+ PL Platform/technology used to produce the reads. Valid values : CAPILLARY,\n+ LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT and PACBIO. \n+ PU Platform unit (e.g. flowcell-barcode.lane for Illumina or slide for\n+ SOLiD). Unique identi\xef\xac\x81er. \n+ SM Sample. Use pool name where a pool is being sequenced. \n+\n+ </help>\n+</tool>\n+\n+\n" |
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| diff -r 000000000000 -r 8d92246f41bb bwa_wrapper.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bwa_wrapper.py Thu Jun 05 15:15:34 2014 -0400 |
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| b'@@ -0,0 +1,348 @@\n+#!/usr/bin/env python\n+\n+"""\n+Runs BWA on single-end or paired-end data.\n+Produces a SAM file containing the mappings.\n+Works with BWA version 0.5.9.\n+\n+usage: bwa_wrapper.py [options]\n+\n+See below for options\n+"""\n+\n+import optparse, os, shutil, subprocess, sys, tempfile\n+\n+def stop_err( msg ):\n+ sys.stderr.write( \'%s\\n\' % msg )\n+ sys.exit()\n+\n+def check_is_double_encoded( fastq ):\n+ # check that first read is bases, not one base followed by numbers\n+ bases = [ \'A\', \'C\', \'G\', \'T\', \'a\', \'c\', \'g\', \'t\', \'N\' ]\n+ nums = [ \'0\', \'1\', \'2\', \'3\' ]\n+ for line in file( fastq, \'rb\'):\n+ if not line.strip() or line.startswith( \'@\' ):\n+ continue\n+ if len( [ b for b in line.strip() if b in nums ] ) > 0:\n+ return False\n+ elif line.strip()[0] in bases and len( [ b for b in line.strip() if b in bases ] ) == len( line.strip() ):\n+ return True\n+ else:\n+ raise Exception, \'First line in first read does not appear to be a valid FASTQ read in either base-space or color-space\'\n+ raise Exception, \'There is no non-comment and non-blank line in your FASTQ file\'\n+\n+def __main__():\n+ #Parse Command Line\n+ parser = optparse.OptionParser()\n+ parser.add_option( \'-t\', \'--threads\', dest=\'threads\', help=\'The number of threads to use\' )\n+ parser.add_option( \'-c\', \'--color-space\', dest=\'color_space\', action=\'store_true\', help=\'If the input files are SOLiD format\' )\n+ parser.add_option( \'-r\', \'--ref\', dest=\'ref\', help=\'The reference genome to use or index\' )\n+ parser.add_option( \'-f\', \'--input1\', dest=\'fastq\', help=\'The (forward) fastq file to use for the mapping\' )\n+ parser.add_option( \'-F\', \'--input2\', dest=\'rfastq\', help=\'The reverse fastq file to use for mapping if paired-end data\' )\n+ parser.add_option( \'-u\', \'--output\', dest=\'output\', help=\'The file to save the output (SAM format)\' )\n+ parser.add_option( \'-g\', \'--genAlignType\', dest=\'genAlignType\', help=\'The type of pairing (single or paired)\' )\n+ parser.add_option( \'-p\', \'--params\', dest=\'params\', help=\'Parameter setting to use (pre_set or full)\' )\n+ parser.add_option( \'-s\', \'--fileSource\', dest=\'fileSource\', help=\'Whether to use a previously indexed reference sequence or one form history (indexed or history)\' )\n+ parser.add_option( \'-n\', \'--maxEditDist\', dest=\'maxEditDist\', help=\'Maximum edit distance if integer\' )\n+ parser.add_option( \'-m\', \'--fracMissingAligns\', dest=\'fracMissingAligns\', help=\'Fraction of missing alignments given 2% uniform base error rate if fraction\' )\n+ parser.add_option( \'-o\', \'--maxGapOpens\', dest=\'maxGapOpens\', help=\'Maximum number of gap opens\' )\n+ parser.add_option( \'-e\', \'--maxGapExtens\', dest=\'maxGapExtens\', help=\'Maximum number of gap extensions\' )\n+ parser.add_option( \'-d\', \'--disallowLongDel\', dest=\'disallowLongDel\', help=\'Disallow a long deletion within specified bps\' )\n+ parser.add_option( \'-i\', \'--disallowIndel\', dest=\'disallowIndel\', help=\'Disallow indel within specified bps\' )\n+ parser.add_option( \'-l\', \'--seed\', dest=\'seed\', help=\'Take the first specified subsequences\' )\n+ parser.add_option( \'-k\', \'--maxEditDistSeed\', dest=\'maxEditDistSeed\', help=\'Maximum edit distance to the seed\' )\n+ parser.add_option( \'-M\', \'--mismatchPenalty\', dest=\'mismatchPenalty\', help=\'Mismatch penalty\' )\n+ parser.add_option( \'-O\', \'--gapOpenPenalty\', dest=\'gapOpenPenalty\', help=\'Gap open penalty\' )\n+ parser.add_option( \'-E\', \'--gapExtensPenalty\', dest=\'gapExtensPenalty\', help=\'Gap extension penalty\' )\n+ parser.add_option( \'-R\', \'--suboptAlign\', dest=\'suboptAlign\', default=None, help=\'Proceed with suboptimal alignments even if the top hit is a repeat\' )\n+ parser.add_option( \'-N\', \'--noIterSearch\', dest=\'noIterSearch\', help=\'Disable iterative search\' )\n+ parser.add_option( \'-T\', \'--outputTopN\', dest=\'outputTopN\', help=\'Maximum number of alignments to output in the XA tag for reads paired properly\' )\n+ parser.a'..b' break\n+ except OverflowError:\n+ pass\n+ tmp_stderr.close()\n+ if returncode != 0:\n+ raise Exception, stderr\n+ except Exception, e:\n+ raise Exception, \'Error aligning sequence. \' + str( e )\n+ # and again if paired data\n+ try:\n+ if cmd2b:\n+ tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name\n+ tmp_stderr = open( tmp, \'wb\' )\n+ proc = subprocess.Popen( args=cmd2b, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )\n+ returncode = proc.wait()\n+ tmp_stderr.close()\n+ # get stderr, allowing for case where it\'s very large\n+ tmp_stderr = open( tmp, \'rb\' )\n+ stderr = \'\'\n+ try:\n+ while True:\n+ stderr += tmp_stderr.read( buffsize )\n+ if not stderr or len( stderr ) % buffsize != 0:\n+ break\n+ except OverflowError:\n+ pass\n+ tmp_stderr.close()\n+ if returncode != 0:\n+ raise Exception, stderr\n+ except Exception, e:\n+ raise Exception, \'Error aligning second sequence. \' + str( e )\n+ # generate align\n+ try:\n+ tmp = tempfile.NamedTemporaryFile( dir=tmp_dir ).name\n+ tmp_stderr = open( tmp, \'wb\' )\n+ proc = subprocess.Popen( args=cmd3, shell=True, cwd=tmp_dir, stderr=tmp_stderr.fileno() )\n+ returncode = proc.wait()\n+ tmp_stderr.close()\n+ # get stderr, allowing for case where it\'s very large\n+ tmp_stderr = open( tmp, \'rb\' )\n+ stderr = \'\'\n+ try:\n+ while True:\n+ stderr += tmp_stderr.read( buffsize )\n+ if not stderr or len( stderr ) % buffsize != 0:\n+ break\n+ except OverflowError:\n+ pass\n+ tmp_stderr.close()\n+ if returncode != 0:\n+ raise Exception, stderr\n+ except Exception, e:\n+ raise Exception, \'Error generating alignments. \' + str( e ) \n+ # remove header if necessary\n+ if options.suppressHeader == \'true\':\n+ tmp_out = tempfile.NamedTemporaryFile( dir=tmp_dir)\n+ tmp_out_name = tmp_out.name\n+ tmp_out.close()\n+ try:\n+ shutil.move( options.output, tmp_out_name )\n+ except Exception, e:\n+ raise Exception, \'Error moving output file before removing headers. \' + str( e )\n+ fout = file( options.output, \'w\' )\n+ for line in file( tmp_out.name, \'r\' ):\n+ if not ( line.startswith( \'@HD\' ) or line.startswith( \'@SQ\' ) or line.startswith( \'@RG\' ) or line.startswith( \'@PG\' ) or line.startswith( \'@CO\' ) ):\n+ fout.write( line )\n+ fout.close()\n+ # check that there are results in the output file\n+ if os.path.getsize( options.output ) > 0:\n+ sys.stdout.write( \'BWA run on %s-end data\' % options.genAlignType )\n+ else:\n+ raise Exception, \'The output file is empty. You may simply have no matches, or there may be an error with your input file or settings.\'\n+ except Exception, e:\n+ stop_err( \'The alignment failed.\\n\' + str( e ) )\n+ finally:\n+ # clean up temp dir\n+ if os.path.exists( tmp_index_dir ):\n+ shutil.rmtree( tmp_index_dir )\n+ if os.path.exists( tmp_dir ):\n+ shutil.rmtree( tmp_dir )\n+\n+if __name__=="__main__": __main__()\n' |
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| diff -r 000000000000 -r 8d92246f41bb bwa_wrapper.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bwa_wrapper.xml Thu Jun 05 15:15:34 2014 -0400 |
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| b'@@ -0,0 +1,480 @@\n+<tool id="bwa_wrapper" name="Map with BWA for Illumina" version="1.2.3">\n+ <requirements>\n+ <requirement type="package" version="0.5.9">bwa</requirement>\n+ </requirements>\n+ <description></description>\n+ <parallelism method="basic"></parallelism>\n+ <command interpreter="python">\n+ bwa_wrapper.py \n+ --threads="\\${GALAXY_SLOTS:-4}"\n+\n+ #if $input1.ext == "fastqillumina":\n+ --illumina1.3\n+ #end if\n+\n+ ## reference source\n+ --fileSource="${genomeSource.refGenomeSource}"\n+ #if $genomeSource.refGenomeSource == "history":\n+ ##build index on the fly\n+ --ref="${genomeSource.ownFile}"\n+ --dbkey="${dbkey}"\n+ #else:\n+ ##use precomputed indexes\n+ --ref="${genomeSource.indices.fields.path}"\n+ --do_not_build_index\n+ #end if\n+\n+ ## input file(s)\n+ --input1="${paired.input1}"\n+ #if $paired.sPaired == "paired":\n+ --input2="${paired.input2}"\n+ #end if\n+\n+ ## output file\n+ --output="${output}"\n+\n+ ## run parameters\n+ --genAlignType="${paired.sPaired}"\n+ --params="${params.source_select}"\n+ #if $params.source_select != "pre_set":\n+ --maxEditDist="${params.maxEditDist}"\n+ --fracMissingAligns="${params.fracMissingAligns}"\n+ --maxGapOpens="${params.maxGapOpens}"\n+ --maxGapExtens="${params.maxGapExtens}"\n+ --disallowLongDel="${params.disallowLongDel}"\n+ --disallowIndel="${params.disallowIndel}"\n+ --seed="${params.seed}"\n+ --maxEditDistSeed="${params.maxEditDistSeed}"\n+ --mismatchPenalty="${params.mismatchPenalty}"\n+ --gapOpenPenalty="${params.gapOpenPenalty}"\n+ --gapExtensPenalty="${params.gapExtensPenalty}"\n+ --suboptAlign="${params.suboptAlign}"\n+ --noIterSearch="${params.noIterSearch}"\n+ --outputTopN="${params.outputTopN}"\n+ --outputTopNDisc="${params.outputTopNDisc}"\n+ --maxInsertSize="${params.maxInsertSize}"\n+ --maxOccurPairing="${params.maxOccurPairing}"\n+ #if $params.readGroup.specReadGroup == "yes"\n+ --rgid="${params.readGroup.rgid}"\n+ --rgcn="${params.readGroup.rgcn}"\n+ --rgds="${params.readGroup.rgds}"\n+ --rgdt="${params.readGroup.rgdt}"\n+ --rgfo="${params.readGroup.rgfo}"\n+ --rgks="${params.readGroup.rgks}"\n+ --rglb="${params.readGroup.rglb}"\n+ --rgpg="${params.readGroup.rgpg}"\n+ --rgpi="${params.readGroup.rgpi}"\n+ --rgpl="${params.readGroup.rgpl}"\n+ --rgpu="${params.readGroup.rgpu}"\n+ --rgsm="${params.readGroup.rgsm}"\n+ #end if\n+\t#if $params.readGroup.specReadGroup == "from_file"\n+ --meta_tsv="$params.readGroup.metadata_tsv"\n+ #end if\n+ #end if\n+\n+ ## suppress output SAM header\n+ --suppressHeader="${suppressHeader}"\n+ </command>\n+ <inputs>\n+ <conditional name="genomeSource">\n+ <param name="refGenomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?">\n+ <option value="indexed">Use a built-in index</option>\n+ <option value="history">Use one from the history</option>\n+ </param>\n+ <when value="indexed">\n+ <param name="indices" type="select" label="Select a reference genome">\n+ <options from_data_table="bwa_indexes">\n+ <filter type="sort_by" column="2" />\n+ <validator type="no_options" message="No indexes are available" />\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 from history" />\n+ </when>\n+ </conditional>\n+ <conditional name="paired">\n+ <param name="sPaired" type="select" label="Is this library mate-paired?">\n+ <option value="single">Single-end</option>\n+ <option value="paired">Paired-end</option'..b"wards the 3'-end [16]\n+ -i INT Disallow an indel within INT bp towards the ends [5]\n+ -l INT Take the first INT subsequence as seed. If INT is larger than the\n+ query sequence, seeding will be disabled. For long reads, this option \n+ is typically ranged from 25 to 35 for '-k 2'. [inf]\n+ -k INT Maximum edit distance in the seed [2]\n+ -t INT Number of threads (multi-threading mode) [1]\n+ -M INT Mismatch penalty. BWA will not search for suboptimal hits with a score\n+ lower than (bestScore-misMsc). [3]\n+ -O INT Gap open penalty [11]\n+ -E INT Gap extension penalty [4]\n+ -c Reverse query but not complement it, which is required for alignment\n+ in the color space.\n+ -R Proceed with suboptimal alignments even if the top hit is a repeat. By\n+ default, BWA only searches for suboptimal alignments if the top hit is\n+ unique. Using this option has no effect on accuracy for single-end\n+ reads. It is mainly designed for improving the alignment accuracy of\n+ paired-end reads. However, the pairing procedure will be slowed down,\n+ especially for very short reads (~32bp).\n+ -N Disable iterative search. All hits with no more than maxDiff\n+ differences will be found. This mode is much slower than the default.\n+\n+For **samse**::\n+\n+ -n INT Maximum number of alignments to output in the XA tag for reads paired\n+ properly. If a read has more than INT hits, the XA tag will not be\n+ written. [3]\n+ -r STR Specify the read group in a format like '@RG\\tID:foo\\tSM:bar' [null]\n+\n+For **sampe**::\n+\n+ -a INT Maximum insert size for a read pair to be considered as being mapped\n+ properly. Since version 0.4.5, this option is only used when there\n+ are not enough good alignment to infer the distribution of insert\n+ sizes. [500]\n+ -n INT Maximum number of alignments to output in the XA tag for reads paired\n+ properly. If a read has more than INT hits, the XA tag will not be\n+ written. [3]\n+ -N INT Maximum number of alignments to output in the XA tag for disconcordant\n+ read pairs (excluding singletons). If a read has more than INT hits,\n+ the XA tag will not be written. [10]\n+ -o INT Maximum occurrences of a read for pairing. A read with more\n+ occurrences will be treated as a single-end read. Reducing this\n+ parameter helps faster pairing. [100000]\n+ -r STR Specify the read group in a format like '@RG\\tID:foo\\tSM:bar' [null]\n+\n+For specifying the read group in **samse** or **sampe**, use the following::\n+\n+ @RG Read group. Unordered multiple @RG lines are allowed. \n+ ID Read group identi\xef\xac\x81er. Each @RG line must have a unique ID. The value of\n+ ID is used in the RG tags of alignment records. Must be unique among all\n+ read groups in header section. Read group IDs may be modi\xef\xac\x81ed when\n+ merging SAM \xef\xac\x81les in order to handle collisions. \n+ CN Name of sequencing center producing the read. \n+ DS Description. \n+ DT Date the run was produced (ISO8601 date or date/time). \n+ FO Flow order. The array of nucleotide bases that correspond to the\n+ nucleotides used for each \xef\xac\x82ow of each read. Multi-base \xef\xac\x82ows are encoded\n+ in IUPAC format, and non-nucleotide \xef\xac\x82ows by various other characters.\n+ Format : /\\*|[ACMGRSVTWYHKDBN]+/ \n+ KS The array of nucleotide bases that correspond to the key sequence of each read. \n+ LB Library. \n+ PG Programs used for processing the read group. \n+ PI Predicted median insert size. \n+ PL Platform/technology used to produce the reads. Valid values : CAPILLARY,\n+ LS454, ILLUMINA, SOLID, HELICOS, IONTORRENT and PACBIO. \n+ PU Platform unit (e.g. \xef\xac\x82owcell-barcode.lane for Illumina or slide for\n+ SOLiD). Unique identi\xef\xac\x81er. \n+ SM Sample. Use pool name where a pool is being sequenced. \n+\n+ </help>\n+</tool>\n+\n+\n" |
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| diff -r 000000000000 -r 8d92246f41bb test-data/bwa_wrapper_in1.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_in1.fastqsanger Thu Jun 05 15:15:34 2014 -0400 |
| b |
| @@ -0,0 +1,120 @@ +@seq1 +GGACTCAGATAGTAATCCACGCTCCTTTAAAATATC ++ +II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B +@seq2 +ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq3 +GTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq4 +AGCCGCTCGTCTTTTATGTAGGTGGTCAACCATTTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq5 +CAGTTATATGGCTTTTGGTTTCTATGTGGCTTAATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq6 +AGGCGCTCGTCTTGGTATGTAGGTGGTCAACAATTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq7 +TGTAGGTGGTCAACCAATTTTAATTGCAGGGGCTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq8 +ACACCCGTCCTTTACGTCATGCGCTCTATTCTCTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq9 +GCCGCTATTCAGGTTGTTTTCTGTTGGTGCTGATAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq10 +ATTCTTTCTTTTCGTATCAGGGCGTTGAGTTCGATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq11 +GCATTTCTACTCCTTCTCATCCCCAATGCTTGGCTT ++ +II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B +@seq12 +CGCGCTTCGATAAAAATGGGATTGGCGTTTCCAACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq13 +ATTTCTACTCTTTCTCATCCCCAATCCTTGCCTTCC ++ +IIIIIIIIIIIIIIIIIIIIIAAIIIIIIIIIIIII +@seq14 +CCCTTTTGAATGTCACGCTGATATTTTGACTTTGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq15 +CCAACTTACCAAGGTGGGTTACGAAACGCGACGCCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq16 +TCAGGGTATTAAAAGAGATTATTTTTCTCCAGCCAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq17 +GTGATGTGCTTGCTACCGAAACAATACTTTAGGCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq18 +TCAATCCCCCATGCTTGGCCGTTCCATAAGCAGATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq19 +TTCCTGCGCTTAATGCTTGAGCGTCCTGGTGCTGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq20 +CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq21 +CTGATACCAATAAAACCCTAAGCATTTGGTTCAGGG ++ +II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B +@seq22 +AATCAAACTTACCAAGGGGTTACGACGCGACGCCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq23 +TGTGCTTCCCCAACTTGATTTAATAACCCTATAGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq24 +TTTCTCAATCCCCAATGCCTTGGCTTCCCTAAGCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq25 +TTGCTACTGACCGCTCTTCGTGCTCGTTGCTGCGTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq26 +CCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq27 +CGCTAATCAAGTTGTTTCTGTTTGGTGCTGATATTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq28 +AAAGAGATTATTTGTCGGTCCAGCCACTAAAGTGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq29 +CAAATTAATGCGCGCTTCGATAATGATTGGGGTATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@seq30 +ATCCCCTATGCTTGGCTTACCATAAGCAGATGGATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII |
| b |
| diff -r 000000000000 -r 8d92246f41bb test-data/bwa_wrapper_in2.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_in2.fastqsanger Thu Jun 05 15:15:34 2014 -0400 |
| b |
| @@ -0,0 +1,120 @@ +@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$5+.(9II +@seq22/1 +AATCAAACTTACCAAGGG ++ +IIIIIIIIIIIIIIIIII +@seq23/1 +TGTGCTTCCCCAACTTGA ++ +IIIIIIIIIIIIIIIIII +@seq24/1 +TTTCTCAATCCCCAATGC ++ +IIIIIIIIIIIIIIIIII +@seq25/1 +TTGCTACTGACCGCTCTT ++ +IIIIIIIIIIIIIIIIII +@seq26/1 +CCGCGTGAAATTTCTATG ++ +IIIIIIIIIIIIIIIIII +@seq27/1 +CGCTAATCAAGTTGTTTC ++ +IIIIIIIIIIIIIIIIII +@seq28/1 +AAAGAGATTATTTGTCGG ++ +IIIIIIIIIIIIIIIIII +@seq29/1 +CAAATTAATGCGCGCTTC ++ +IIIIIIIIIIIIIIIIII +@seq30/1 +ATCCCCTATGCTTGGCTT ++ +IIIIIIIIIIIIIIIIII |
| b |
| diff -r 000000000000 -r 8d92246f41bb test-data/bwa_wrapper_in3.fastqsanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_in3.fastqsanger Thu Jun 05 15:15:34 2014 -0400 |
| b |
| @@ -0,0 +1,120 @@ +@seq1/2 +ACGCTCCTTTAAAATATC ++ +IIIII$%*$G$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 000000000000 -r 8d92246f41bb test-data/bwa_wrapper_in4.fastqcssanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_in4.fastqcssanger Thu Jun 05 15:15:34 2014 -0400 |
| b |
| b'@@ -0,0 +1,800 @@\n+@427_12_390_F3\n+AAGGGAGTGGTGCTGGTGGGAGGCAATTTGTCGGACCTGGGAAGCGAGTC\n++\n+BBB>=;@@A6<A;=>=A?>??@A58@B>9>>@?70?@<=>>@A9/5?=25\n+@427_12_550_F3\n+CGATCTCTGCAACTTCGTGCGCAGGCGATGGGGGGGAAAATGAACGGATA\n++\n+8A=?<BA@=;?A;?><B?;:5@.<:7?9;6<A62<@;8<==@3:>;=339\n+@427_12_941_F3\n+GGGCCAAAGTAAACGCTAATCGAGGAGGACAAAGTAAGGAAGGCGCCTGT\n++\n+B@72=>?A:;<:?>?94B??;3A<?1@<3=<A?8>A6?>=>7A/>=07<@\n+@427_12_1018_F3\n+CTCTTCTCCTCCGGACTAGAGGCCCGGGCAATCAAGGCTGCGTAGACGTA\n++\n+>?<;5@:>>5>7:?<7@><=:>?92<?5>=;@@>?2<?>:?<9<4>56?@\n+@427_13_422_F3\n+AATAACGAAGCGTGTGTGTTAGCGGGAGAGCCGGGCCCCTTCCCGTACGT\n++\n+9>A2,9@9<8<=;;7=7:>@1<:?37<1>1690>7=<:=A/>53.::<=/\n+@427_13_494_F3\n+CGACTACCCCTACCGGTCACCGCTACGGTGAGGCTAAGCTCTTCCAGACG\n++\n+.>>?@;A@?7?@<>39?>=7:==76;=;=65@:::9?8?3=@8=::@2<.\n+@427_13_606_F3\n+TTTAACGCGATAATCCTTCGAAGGAAAAGAAGTGACTTTCCGTACATACC\n++\n+BB?A?@A??>B@A@<=@A==A>>>>AA@7<?:B=9<@A@A@2@>8><;<=\n+@427_13_861_F3\n+CGAGGTGCAGGCCTGCTCTGGGGACCCACTGTGACCAGGCGGCCTGCCAC\n++\n+=>>@<@>BB>>58A=@A<BABA:=>@B:==?A9<AA@7::@;??:A?;2>\n+@427_13_961_F3\n+GACGGGAGACGCTGCGATCGCACCTTAATGGGGGACCGGATGCACAAAAG\n++\n+@BBBBB@BB@B>BBAB@B@AB@ABAABBA?B?B@>@@BA=A?A:<>BBB3\n+@427_14_270_F3\n+GCAGATGCGTGGAGCAACGGTGGTCTGTAGATCGTCAGGATCTGAAACCA\n++\n+A=A@?BB>@9@BAA89>A@:A@@>2@A;383B><;:;>=1=8B:<>=?8=\n+@427_14_376_F3\n+TCACACGCAGGGCCCCGTACGGAGAATACTGCTCAATGAAAATGGAGGGG\n++\n+B9??@BA@;?BB@@>AA?:?>A><=<A:4=5<?;=<?;?:95=61;<:<2\n+@427_14_602_F3\n+GGCCGGTTGGTCGACTAGGCAGGCCGACAATGCCTGAACATACTAGGGCC\n++\n+,B=7==A:9;AA45,=:9/.2<;58>9806:=>:<8=877?=9198>:2:\n+@427_14_665_F3\n+CATACGAGGGAGTCTCTAGCATAAAGCTGGGTCCCCTGACATTGACCTGA\n++\n+<A@@>B7<A5@>@>>>;<@68,9@;<-<<:>9?@?>6.A65=;=8569;5\n+@427_14_1010_F3\n+GCTGCTGTGGCCGGGCGCACCCAGACAGGTAGAAAGCCGACTCACCACGT\n++\n+@??A><@=ABA@?A?A@A??AB@AA@=<?B;<@?A<94?A=5;:@@2?@9\n+@427_15_423_F3\n+GCTGGAGGAGAAAGGGGGGACCCGCAATCGAGCGTCCGATAATGAAATGG\n++\n+>/B@=<A=??@B>A>B@@>9?@=A6@B@9?5@6A7A@>@A?=?A/@@A?=\n+@427_15_646_F3\n+CAGTTCGCTTGGTCAATCAATATAGAGAACCTGGGGAGTAGTGTCCGGAG\n++\n+?@=?>=A?@??B876:@65.B<914;;<06=?914:67997;5<:/7771\n+@427_15_872_F3\n+CGGGTAGACTTTAGTACCTAGACGAAGGGAGTGACATGACGTCGCGTACA\n++\n+<:??A@B@B==>@>A:6=?;5<::30<==63@;;1?=;A5,=7<,4;6@0\n+@427_15_1039_F3\n+AGAGTCAACTGAAGCTTCCGAGTCGTGAACGGGGGGAGGAGAGGGAAGGC\n++\n+BBB@@@B?A?ABB><A>?9=:=<:@:?>51:AA>?87>?979<>><>>=<\n+@427_15_1070_F3\n+CTACTCCCTGCATTAGATACTGGAGCTCGGCTAGAGGGATGGCGTTAAAG\n++\n+=>A<@><?BAA?A?>?4??=;>?@>??=:@<6?98==><<:;<8A:7=@5\n+@427_15_1081_F3\n+GCTCCTCCACGATTAATCGTTGGGGTGCAATGAGAAAACAGCCAATGGCC\n++\n+@=AAAB@?@>?B@?=BB@?@B=@>;B@3:?BA39?>@7==<<<A?A<1A?\n+@427_16_264_F3\n+CCCGATCCTAGGCAGAATCGAGAGAGACCACAACCCGCGAAAACCATTGC\n++\n+@<>?@@?AA?@??@>>?;:A>>A=?>=?>?:A>@@@:A8@@@:>/@>A4=\n+@427_16_565_F3\n+AGCTATGGAATACCAAGACATCCAAGGAACTACTGCCGAAGGTTCCGGAG\n++\n+BB1AABB9@@B>3>=@@,?AB<8A>@@9<=BA8<<>>4A??@:??<?6@<\n+@427_16_1107_F3\n+TGTGTAAGTGAGACACGAGAAGCAAGAACTGATGCCCTGCAGGGTTTAGG\n++\n+<+>B><:;A@B?:>>:A7B5;B@?B>8;:>8=B:B@=;@25A9A=>@1A:\n+@427_17_46_F3\n+CCAATGAATGAAACAGGGTACCCGCGAGCGCCTGCTGAGCTGACAGTCTC\n++\n+:.>A:@>@?7A@<=2?;6?;>;99=<:8;95>0:><14;@4:><:,;:8?\n+@427_17_342_F3\n+AGCTGGAGCTGCTGCCACGGACAAGGTCGGAGCTGAGGCTGGCTGGACTA\n++\n+BA?A?BB>>ABB@;;AA@@>AA>=ABB1??:B6>?>B72>@B49>?@3<<\n+@427_17_446_F3\n+TATGCCGTGAGACGGGGGGAAACAGACCCTACCCCGATGTATAAGGCCGG\n++\n+=B?>8>BA?=>B;?;>A;:<=?937;?=2;6:==;9=@3?9;51;9:149\n+@427_17_917_F3\n+AAGACTACGCGTTAGGCCAAGAGAAAGACTCAAGAGACGACCTCTAAGAT\n++\n+@@=???A6=-;A:3<@?866@94:20<11@3;19:=:/:9<<45B@:48B\n+@427_17_1027_F3\n+CAGTGCAATGGGAGTAAAGCAAATTCGGCAGCCCGTGGCCGAACCGCTTG\n++\n+A@@BAB=>B>BAA?5>=AA8:@B@;=@?@9:>BB::?@A54=B?<0<B@:\n+@427_18_267_F3\n+CTGGCACCGAACGGAGGAAGAAATTGCGTAGATTACAGTAATCAGAAGAC\n++\n+AB@A;>@A@>AAAB:8B<>>@B@A=@?=@;=A<A3>?;@@?<:>+A?;A.\n+@427_18_481_F3\n+GGCTCGCCCCAGTATCGACGTCGTATGAGAGATGACGAGGCCCGGGCGAG\n++\n+AB>?;B@A>=AAA@@@A?=6B=><=B=<8>=7A2=<==5;@5>7<=3=>;\n+@427_18_706_F3\n+CTCTATATGGAAGGTTACTACTCAGTAACCTTAGGGACCAAGAACCGGTT\n++\n+>AAA@B?BAABAAAAA@@@A?B?>=B?@>>B@6??@><@@?:?A;<?=??\n+@427_18_834_F3\n+GGGACCCGACCTAGGACGGACAAAGACAGGGACGACAGATATACGATTCA\n++\n+@@@@><?A><@A?@7@A@@6=><?;<;;7@>=?=:<:<;>=6=/:A?B?4\n+@427_18_846_F3\n+GGACGCGTCACCAGAAAAACTA'..b'?@=<=1=\n+@430_691_1191_F3\n+CTGCAACGCAATCACTTAAGGTGCAGGTGGTGAAGCGGAGATGTTACCCC\n++\n+?ABB@BBB@@BA??@A>@;A==?7A?@@:>@=?8@;@;<9?A>9=@<>?9\n+@430_693_248_F3\n+GACCACACCGCCCTAAAGCCCAGAGTTAAGGGACCCTGAGGGGACGTCCA\n++\n+2>BAA??A@A@B>AA<98@>=B<@@2B?=@>@<A?:A??>@?@B?>A>9:\n+@430_821_1672_F3\n+ATCGGCTGGCGCCAAGAATGTATTTGACGGATGGTCCATCGACGGCAACC\n++\n+A@?AAAAAA@=?:BA>B@>ABA?@A?B>:=@?<<:@>B=74@B;=><@65\n+@430_874_1668_F3\n+GAGAATTAAGGAAGGGAGCTAGCGTACTAAGCATACGGACGAGACACCCG\n++\n+A@AA>A@AB=@BAA@A@>@?B@=@?B@:A@?>:>A>=69@=@8A@@:/9?\n+@430_900_444_F3\n+CCCGTCCAGAAAGAGAGCCCCGACTCCCCAGGGCTACCAGCATAGAACCA\n++\n+=9??BBB@ABABA>A@A=@AA@<<A>A;=@AA?;A>@@:?A<B>@@A?9>\n+@430_1055_244_F3\n+CGATGTTACCCCGCGCGAGACCCATCACACGACGTGCAATCCGCGAACCA\n++\n+?BBBBBBBBBBBBBABB@BB@=<AB<>>B>9?<AB;:>BB@@<B?>3A@@\n+@430_1080_625_F3\n+AGAACTAGGCCTGACACTAGCCAGCCGGGCGTCACTGCAAGGAAACTGCC\n++\n+B=BBBBBBBB>BBBB@?BA@B?@AB>A@AA>A7A@B?+@7A>A?<B-=>@\n+@430_1105_227_F3\n+GAGTAGTACAAAGGACCAAGTGCAGGATCTGCCTTGTCAGCGCGAGCAAC\n++\n+BBBBB=BBABBBAAB??AB@=BA@A;>A;B>A??B5ABBA2@A:@??AB@\n+@430_1195_1598_F3\n+CCTTTTTCAACAAGAGTATTTAATGCTCTGCTGTTTAAGGCCCCTCTCCC\n++\n+@B@BBBBBBABBB@BBBBBBB@AA><6.=>@=5<BA4A5>@8A7B>48:7\n+@430_1270_1392_F3\n+CCTGACACTAGCCAGCCGGGCGTCACTGCAAGGAAACTGCCCTCGGAGTG\n++\n+BBAB:BBABB@BBBBBA>BBB?B-ABB>,@=B?8A>B=;@@B;->;@71A\n+@430_1280_786_F3\n+TGGTTTTCCATGCTCCGCTGGCTCAACCGAAGCCATAACGCGAGCTGGAA\n++\n+A>@BBBAA@BABAAA??@A@A?=82=A<;:@A=<6?@:90>A@:0A?>;<\n+@430_1307_10_F3\n+GCATCACACGACGTGCAATCCGCGAACCACACCGCCCTAAAGCCCAGAGT\n++\n+?ABB@BBBA@>ABB@8>ABA;@?B?7B<A09B?A>?A:B87;BB?<?AA9\n+@430_1403_722_F3\n+AATCCGCGAACCACACCGCCCTAAAGCCCAGAGTTAAGGGACCCTGAGGG\n++\n+BAABBB@@BABA?A?@=>@@ABAAA?A>>ABB<@@BB??A@>@?BA@@=?\n+@430_1406_34_F3\n+GAGCCCCGACCTCCCAGGGCTACCAGCATAGAACCAGTTCGGCCGGGACC\n++\n+BAABBBAB?>A??@><<A@:B@@?<>A4B:AA>A8@>A@=A9??5@@;>7\n+@430_1531_1322_F3\n+GCATTAACCTTCTCCCCTCTCCCCGGAATTTGTCGTCTCGTAATTTATGA\n++\n+=A-:=>B:<@?<>=AA:@:@@@=>@?><@BA@A;>@<>>??=<BB=;=6=\n+@430_1586_641_F3\n+TCCATAACGCGAGAGGGAAAGAGTATACGATCTAAGAATTAAGAGAGGGA\n++\n+@9A?BBABABBBBABA@AAABBA>BBA?;AB@@@B@B;??>B=<><:B2>\n+@430_1684_261_F3\n+CTCAAAGGAACGTCACTGCGGGCCGACCGATCACAGTCCGGATCAAGGGA\n++\n+5@?>?:@>?@4?><@6=?::9@8>91?99;9@:53.A;496:?8=/<=-;\n+@430_1726_1548_F3\n+TTTTCGACGACGAAGCTGCAAAAAGACATAGGCCCGAGGAAGCGCTACAC\n++\n+;BBB=9@BAA3AA@>4=A>?<A@@=8<?;@8@@>>2=>8A69>5>4<==<\n+@430_1779_172_F3\n+GGCAGAACACTGCTAGGGCGTCAACGTTGTTCAGAGCCAAAAACACAACC\n++\n+ABBBBBBBB@BBA@@ABA?@B>A??9BA=BBB@<@?B@AB@@@2@:B@9B\n+@430_1871_988_F3\n+TAGATGCTCTTGCTTAGACTCACCCTTTTCCCTACCCTAAAGGATATGAC\n++\n+A>A@ABAA<@?B?@B=A@<A?B=@+;A=>9:@A>47>??::>:=>;7>>6\n+@430_1994_1381_F3\n+GACTCGGTCTCAGATCCAGGAGACTAACCAACCTTGAGGGAAATTAAGAG\n++\n+@BBBABBAB==ABB@>A@A?A@B?A>B@=?@AAAA=AA@8;ABBBAA?@8\n+@431_44_655_F3\n+GCTATTAGCCCATTGTCAAGGCGACAGACACACAACAATCCGACACCATC\n++\n+>-<=>@@4:=>@?A:>=9=::::=:5<:<66=7865<9;<59=13:+<;;\n+@431_50_371_F3\n+CGGCCCCGTCCAGAAAGAGAGCCCCGACTCCCCAGGGCTACCAGCATAGA\n++\n+=AA@@AAAABBBAB@=@9@A@A@A?>B<??AA>@;?@?@>B?6=B7@8A@\n+@431_274_859_F3\n+AGCCCATTGTCAAGGCGACAGACACACAACAATCCGACACCATCGTTGGC\n++\n+=AAB>BB@@??BB@<?;?@<BAA=<<A?=;BA@BB=A29@<A;>-B@8=9\n+@431_362_522_F3\n+CAGCCATAACGCGAGAAAGAAAGAGTATACGATTCAAGAATTAAGAGAGG\n++\n+?B@?>ABBAA>B?A?@A@A@BA=A<8@>A?2@A@>AA?A?@<@A::779>\n+@431_427_471_F3\n+GAGAGCCCTGAAGACCTAGCACAGTAGAGTGACTTAAATTAGGGGAACGA\n++\n+BB@BABBAB@BB@B@>BA@@=AA?A>BA<B?A?A@.=7?@+>=::0<;:>\n+@431_436_304_F3\n+TTCGGCCGGGATTTCTTACCCAACACAAAAACCAGGACTTGTTGCAATCG\n++\n+9@@AA?A@A?8BBB;<B>>84B?><1A>A=7@6><3?>A65A:;:@<6>5\n+@431_510_914_F3\n+AAAGAGGGCAGATCGGGAATTTCACGCCCAACGTGGCGGGTTTGGAGAGA\n++\n+AB@A@AB@>A@?BA??=>AAAB=??=?=9>;@:>?1=<@:=@4=58<5@<\n+@431_524_1355_F3\n+GAAACTACCGGGCGTAACAAATGGGAGATAGTGCGTTAGTCACGAGCGTC\n++\n+BBBBBBBBBBBBAABBB@BB@ABBA@;BA?>?AB@A@BAB?@?A@@:><?\n+@431_753_1184_F3\n+CGGGAGCCCGGCCAGCTCCGAGAGTTAACCGAAAACGTCAAACACCAACC\n++\n+4=BBB@ABAB>BB@B@BB?BABA@B>BA?A>>?>B>7A>B@?=@<8?;?@\n+@431_933_606_F3\n+GCTTGATCTCAATCAGAGCGAGCTCCGGTAAACCCACAAAGTCATCATCA\n++\n+<<BBB@A?B@ABA@B;AB@A<>>AA8@=A@?AB@@==??A=@<8@=9>9@\n+@431_1029_654_F3\n+CGTAGGAGAGTCAACTCGGTCTCAGATCCAGGAGACTAACCAACCTTGAG\n++\n+@AABBBBBABBB@B@A@B?CB+7BB@@@A<BA=?@ABBB@A??=A=B<=?\n' |
| b |
| diff -r 000000000000 -r 8d92246f41bb test-data/bwa_wrapper_in5.fastqcssanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_in5.fastqcssanger Thu Jun 05 15:15:34 2014 -0400 |
| b |
| b"@@ -0,0 +1,840 @@\n+@853_7_53\n+NNAGNCCGANNGGNGNNGTANGGNTNNATTGCGNCNCNNNNGGGCNNNCG\n++\n+!!14!3.15!!47!4!!8+1!$9!(!!,..1)&!3!(!!!!1/9&!!!,3\n+@853_7_78\n+NNCTNGGGGNNGGNGNNGGGNGGNGNNGGGGCGNGNGNNNNGGGGNNNGG\n++\n+!!##!###$!!##!&!!#$&!$&!&!!%&)'#'!$!#!!!!&)*(!!!&*\n+@853_7_88\n+NNGTNGGGCNNCTNGNNATTNTANCNNACAGGANCNGNNNNGGGGNNNGG\n++\n+!!61!5551!!13!4!!.,)!/,!3!!.)/17+!&!5!!!!-'0.!!!,5\n+@853_7_132\n+NNGGNGATGNNTGNGNNGGGNGGNGNNGGGGGGNGNGNNNNGGGGNNNGG\n++\n+!!$(!,#&#!!&#!#!!#($!%$!#!!#&%#$(!#!#!!!!)(*+!!!,2\n+@853_7_141\n+NNGGNGCCGNNCANGNNGGCNAGNCNNGGACCGNANGNNNNAGGGNNNGG\n++\n+!!54!9518!!1&!5!!/31!)0!6!!)533/:!5!6!!!!)/<:!!!,7\n+@853_7_146\n+NNCGNCACCNNGCNGNNGCTNGGNGNNGGGGGGNGNGNNNNGGGGNNNGG\n++\n+!!10!/240!!0)!2!!#&'!'5!(!!(.-*$3!*!4!!!!+#(.!!!.(\n+@853_7_269\n+NNCGNGGGGNNGGNGNNGGGNGGNGNNGGGGGGNGNGNNNNGGGGNNNGG\n++\n+!!%&!('#%!!#*!#!!/##!&)!$!!'$',%,!%!2!!!!3,,*!!!,2\n+@853_7_321\n+NNGANGTGGNNGCNTNNGGGNCGNCNNCGAACGNTNANNNNGAAANNNGG\n++\n+!!+$!+21(!!*-!.!!)#1!8/!9!!6,3+%6!'!,!!!!2&6,!!!&2\n+@853_7_386\n+NNCGNGTAGNNGANGNNGTCNCGNANNGAAGTGNTNGNNNNAAAGNNNGG\n++\n+!!31!:7-%!!:,!-!!21,!77!)!!227:9:!2!;!!!!)',%!!!86\n+@853_7_405\n+NNGCNAGGCNNTCNGNNAAANGTNGNNAGAAGGNANGNNNNATCTNNNCG\n++\n+!!<8!8;==!!;>!:!!7:7!7;!8!!7:>48=!2!=!!!!536*!!!;:\n+@853_7_411\n+NNCANGAAANNTTNGNNAGGNAGNANNGAAGGGNGNANNNNAAAANNNAA\n++\n+!!,/!13;,!!&,!+!!2/%!*1!$!!%*)+#,!,!&!!!!'-'&!!!++\n+@853_7_445\n+NNTANTGCANNACNCNNCGANCCNTNNTACGGGNCNGNNNNTGGGNNNGG\n++\n+!!&'!*+'#!!'%!&!!,%#!)%!(!!'##$&'!#!$!!!!$$#,!!!#$\n+@853_7_469\n+NNGGNACAGNNGANTNNGAANGCNANNAAGGAGNGNGNNNNAGATNNNAG\n++\n+!!##!*($&!!##!#!!%))!#1!%!!(,##$.!#!(!!!!##'#!!!&$\n+@853_33_1583\n+TATGTATTTCGGTACCGCACAGANCACTCCAACCCGATAGCGTCAAGTCC\n++\n+/&2%,)+,+:&#:;,5*)8/%19!,%*1/%;#<952%:27#%%&4.,#-1\n+@853_33_1649\n+GCTTCGTTCTAACTCCTACATGANGACAGAGCTGCATGCAGATTAGGTGA\n++\n+<9:<9<<=8866<888;87:<8:!24:8691=;)&$)#)$%%1$$#).1%\n+@853_34_1182\n+GTTAAGGGTGTTAGGGAACCCTANAAAGCCCGGGTTTCGTGGGGGCGGGC\n++\n+;7;5*982;:/;,46::69<4<(!4295.6144&::<4*.-+%$#.#,(#\n+@853_34_1358\n+GGCCTGGCCCGAGGGTCAACAGTNTTGATCTGAGGGCAATATTCGAGGCG\n++\n+<<??;=<?>>=<>>=<?>:=@;9!:><>:9<<=;<<=>,=8<:6;9<8/9\n+@853_35_596\n+GTGTTGTGTAGGCAACAACGCAANTATGGTTCAAACCGTTCTGATGTAAA\n++\n+:555079793528;282707:89!*;4;85:):<966.4;547203:978\n+@853_35_669\n+TTGTGCTGTCACGGCAAGGCGGGNGAGTTGGTGCGGCTACTCTCATCTGG\n++\n+#4(,,&5,'-2(&5'10&)&-&3!,)+.*9&););:,8)7&3<&,/1:)&\n+@853_47_795\n+GAAATGTTAACAAACCACTGAAGACTTTATAGCGTATTTTTTCATTACTG\n++\n+?<8;>>=>78<:6:<<&=>><)=;78)?9>/189A0/>>>A36,=<&7<1\n+@853_47_831\n+TGGATACACGTAACAGAGGACCGGGCAGACTACTCGGGGGCCGTCGGTGG\n++\n+.)/'0(,&#*#'#)#(#(#*(#'%%1.3#$-2%$&/#$(#'%'%(##%+,\n+@853_56_1228\n+GCTCAATGCAAACAATCGTTCCCACTGATTCCAACAACACCAACGCTATG\n++\n+=::<:?=?:>@=<><>=>87=<><)>97>=<=3=7=</9;==:67+9<6:\n+@853_56_1324\n+GGGCTTTAACGCGTCGGCACGAGGTAAGTGGAGTGGCGATGGCACGATTC\n++\n+5,(,)5+)57+94*,*3-#*4,2&2$2'(,2)-)22/)$23/1*)24'%$\n+@853_82_2023\n+GTCAGAAGATCTACTCGAAGGGGTTTGTTTACAGCATAAATAAGGTTGGG\n++\n+=7><8<=8<><;9<>=<77>>:>><=;>:?97<:3;;=</64:53:<969\n+@853_83_197\n+GGCAGATGATATGGACTGAGTGGGGGGGGAGGGGGGGGGGGGGGGGGGGG\n++\n+8;95;6:96698;6;89:3=%(-*$&(+$&#%.''+(.-%-/5.*.*4/5\n+@853_112_119\n+CCTAGGATAATACGCGGACAGGGGAGCTCCGGGGGGAGGGGACGGGGCGG\n++\n+7)&8327,(41&&),%1/)%+242(1,)')&15,)&05#$50,$$87&.$\n+@853_112_253\n+GAACGCTTATGGGGTCCGCTAGCTAACGCCGCCTGGCCAATAACTATAGT\n++\n+;9;97857&:;6;&983;4=83/,::2=,8;7(&<;/8+275(/9-1&(;\n+@853_148_1347\n+CTGGCAAATTAACCCCATTTTTCCGCTGCTATTAGAACCTCCAGATGGTA\n++\n+@>A<==;;<<?;A<?:7;=>;;76=6<84?3>6,<=3359>71;595</9\n+@853_148_1509\n+GCTGGGTGAAAAGGCCCCGGCTTCACAGAATGTAATTTCTAATAGTCTTT\n++\n+-'-:+&1.,)&&=(=)?7=<=4&,>:(;,&<))))8)+(,'&(4&,(,3)\n+@853_157_314\n+CTCGCCTGGAATTTAGCCATGGCTATGTTCTAGGTGCTTTGTTAGTTGCG\n++\n+79();(1<))&2(5+&8&+.9-'198,',))&&7&:*,4)(6&2&/:&77\n+@853_157_582\n+CAACAACATCAGGTACCCCATAATCCTCCTGGCTTAGGCAATATCAAAAT\n++\n+=:??::<>;;>:;;A;<;;>=?=<<<:>6==:?:<@<64:<89339==&2\n+@853_158_402\n+GGTTGTTAAACCGTCCCGGGCGTTATCCACGTGTGATACCCGCGCATGTG\n++\n+711&$(-)##.,&((&(4('83><-:94,'.;2&*:<0%&7,3#+02#(#\n+@853_158_569\n+TTCGTAATTATATTTGTCGGGCATTATGAGTACGGAGGTTATTATATAGG\n++\n+8>34:8.56,9/7<=-80.562,994:)3,<#%85(,#7&%,'#3#,#%&\n+@853_216_501\n+CCCTG"..b"GTGCTCCTGAGGCGAGCTGCG\n++\n+?=<<A@=A=>>.?<?;71?A>=<><?2<8>=:749898&=<57&;:49&,\n+@853_1360_1130\n+TGCTTAGACTTTATTGCAGTCATAAATACCTATAATCCTTTGTGGTGACA\n++\n+>A@@<9?A:?>>?8@68?=>>9>/9<<44193577>;:;8?#,5.##4,)\n+@853_1361_389\n+ACAGCTGTATCACGAATGCCCGTCGTTAAGAACTGGATTAAGCCAAAGAT\n++\n+7=9=?>8?4>@7;:==A<?A=<A87=A<<>89789)>6:9)=647):49<\n+@853_1366_1495\n+AACCATAAGGCGCTAACCACAATCGGTGACACCGGCTCCAAGCTTAGCCA\n++\n+?;<9)6)&'&;+22'80:-%:&/3.<&)0(;):69;#)67;(8+&<-'%8\n+@853_1367_802\n+GTTGTTATAGAACAGTCAACCAGCACTGTCTAAGTGGATTTCCGTGGCGG\n++\n+=<?;$%&<<&(5>='(3><+648A+*:<@#46><#70<>#*.<3237=;%\n+@853_1382_1227\n+CTAGTTTTTCATTACTGGAGCGTCAACAAGTAACCAGACTCACAAGCTAG\n++\n+;::::899::898<:96:<99979<;99=93:/999:19667):611.<:\n+@853_1383_1269\n+GGGTGCTGCTGTCTCAACGGGCTGAGGGATAGCTGGTGGGAGCCCTTACC\n++\n+,@)':/)>6:(*'*9&';-(:),4((/,#31;7&/532*8,5:5*75,+1\n+@853_1395_1324\n+ACTTTCGCGGCCAAGGCCTCCTCCCTAGGGCCTTCCCGACCCGCTGCGGG\n++\n+)9-',&9*3)9',(1%6%7/4681)11&+:-1/4205()&3',,+$0#%%\n+@853_1396_1014\n+GGTCCCCTAGAGTGGGGCCTCGAACCTACAGATATTGAGTCGGGAGCCCG\n++\n+@<@:===?<;==98<:9>9:=:;@;:;=68::<:::;>:::><<863>9;\n+@853_1412_1664\n+TGGCGAATATGTCACGACCAACTGACAAGTTATTGTTACACTCCACTATG\n++\n+73A/A(<5,5585/@@4=,)383A,3,/6(3,5?98318,9@1/,9:11=\n+@853_1413_877\n+GACGGTCGTCCCTATTGTATTCGTCTCTCCGTGTCGTGACGTTGCCCGGT\n++\n+&)#*648#,9(.#3&&(#9.2,#/%3)#&555#).%3#19-4#4'3,#2+\n+@853_1437_116\n+AGCTGCGGCAGCCGAACACGGCACAAGGTTGGATAATCACCGGAAGTGGA\n++\n+$;,)42'#2(#&,,#%#2,2%,',42#$))#*428#%$2.%$%4%*#)%&\n+@853_1437_1533\n+CAGTATGGAGGTCCGATGCCGCTATTTATGTCGCATTAAGTTTAATTGCG\n++\n+>@<?:>>8=<:=>?=;>?=5<>:98<A9;6852*+4&$#$%4(#-4(*%#\n+@853_1486_1272\n+TCATGAGTGCGTACGTACAGAGCGCATACCTCGCACGCATTCGTAAAGGA\n++\n+93396@554737/373:5;5,:<=/;:1<1;5/<(/718:<7.<=,<1.7\n+@853_1487_496\n+TTTATTACGGGCGACGAAACGAATGGTATTTCCCTTGCGTTTTTCGCTTG\n++\n+<,'+856638:)0*.,+&.;7&1+;5-&1779<0:+3)/&+;1&,7()((\n+@853_1488_605\n+CCCGTAAGGAACGGGGATTAGAAGGATGGCAGGGGAGTGGAAACGAAGGG\n++\n+(%/)'(32+'))1*6776&2%)8&,7)71'2&$5+%))724&0)$('&('\n+@853_1489_374\n+CTCTTCAAACTGACAGCGCAATGGATGAGGCCACAAAAAGAAACTTTAAA\n++\n+>8786=:8:3:2;;;6(=99.3=5*/,%'(+#7121074(25$0,+%,27\n+@853_1493_452\n+CGCTCTCCCGATTCAGCAAAACAAACAAGGCTCCACCGTCCCGGGGCCGA\n++\n+'$),&/'53(%$((6'*'(&+%694&(2.1'&1(3&2'9/%)(&)()'(/\n+@853_1493_1908\n+CATGATTACGTTGACAACTTGGCCACCAAGGCGTGTCCTTTATACCACAA\n++\n+;@<;?>:::===;<>=;;==<?;==>?88<=<<9;<=?<9;;<7=:9<<;\n+@853_1498_1797\n+CCTCAGCGCCACCCAGCTTGGAAAACTAAACAAACAAATAAACTTTCACT\n++\n+&&&&&#&#######&$##&########$&$###&$$$###$$#$#$####\n+@853_1499_1261\n+ACTGTGCTGCTCGGGCATTGATTGTGAACCATTCCCGGTGTTAAATGAAA\n++\n+:;:=<=;<<5?>><>A9>;98<9<:<7;&7:9<:9<65/)<?&6)=7&2/\n+@853_1509_820\n+GCAACCTGACCGTTTACACAACGTGTGGAAAAGAGGTGGGAGAGGGTTGG\n++\n+18;:.49;5+6/<=879672373=.:;;47$'%06262%562%':5$5&:\n+@853_1510_448\n+ACAAACAACATCAGGTACCCCATAATCCTCCTGGCTGCTGCCCGGTGCGG\n++\n+6280647712'4:*,/72/(,2'28)43%0%)4'+$%''########$##\n+@853_1511_561\n+TTAGAACGCTTATGGGATCCGCTAGCTAACGCCGCCTGGCCAATAACTAT\n++\n+<?;8>>=<9:<599<<,<@;<5@=/<6>?;<;;<@85=<A>,,879296,\n+@853_1511_1886\n+GGATAGTAGGAACGAGATGCGGGGAACCCGTTTGGTGCTCGGCGGGTGTG\n++\n+:A(>/2;&>='7&>::(1678>>:1&(<::11,.<8,(),8>%8</):(<\n+@853_1530_202\n+GGTTCATGGCGGGACATGAGGTGCCATACCGCAACCCTCTAGGCTGATCG\n++\n+/9::8:7;58;0<%;;9=(3;8<1;73;16;1=57686/585:30;/<61\n+@853_1530_1652\n+TTTGCCGAATATATACGGCTGGGCAGGCACTAGCTGAAATGCCGGAATCT\n++\n+85;6%-0<#)75;)165:2597<'0;:;%(;3:#5;*;/2894$&5/5$+\n+@853_1569_1617\n+AAGCGAATACTGAACCAACACAGGTTAACTAGGAAGAAAGATAATTAGGC\n++\n+=A===>>;<><>A@@;AA9>8A>?=1>@9<7:8@@(>>@33573;)<&&:\n+@853_1570_1472\n+CACCGGGACTAAATTAGCTTCTCGTTCCAGGCGCATCGGACTCACGTTAT\n++\n+@A=?<A?@?A=9=AA=@=;>?>?<@=><=:<@9=,A?;<<7<=61;>9/?\n+@853_1585_323\n+GGTCACCCTTGCTAACAAACGTAACTCGCACCGATCCGAAATAAGTTGCG\n++\n+=;<<78<9;<:<:9<88::=<,:;;8/889<79:4;12:;,/88582.:9\n+@853_1585_2023\n+AATAAATATTACCATTTAAGAAGGAATACGAAAAGACGCCGGCGTCCACT\n++\n+:A=>5#:==<+=<==)=?<=&<=<>%<<?;)<=<=#>9<:$<;;:&?3<5\n+@853_1603_500\n+CAAGGAGATCCACACACCAAAACACATTTCCACTATGTTTGTGTCGCGGC\n++\n+=><:=4:;498<9<:9;8:=;>==7;;56;6>;75:9975574624<:1&\n+@853_1603_1995\n+CCAGGGAGATCCTAACGTGGAGCCGCGAATACTCCCAACCACCTATACAG\n++\n+:;;;>=<9A==;9:=;6::?:9@<@:8<<;:6><@<<9;@595:684279\n" |
| b |
| diff -r 000000000000 -r 8d92246f41bb test-data/bwa_wrapper_in6.fastqcssanger --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_in6.fastqcssanger Thu Jun 05 15:15:34 2014 -0400 |
| b |
| b"@@ -0,0 +1,840 @@\n+@853_7_53\n+NNCNNNCGNTNAGTNGGNGGNGNGNNGGNNGNNNGGGGNGGGNGNGNGGN\n++\n+!!0!!!10!)!)0)!,-!##!%!%!!##!!'!!!%+&)!%$/!)!$!/(!\n+@853_7_78\n+NNGNNNAGNGNGTGNGGNCCNGNGNNCGNNCNNNGGGGNGGGNGNTNGGN\n++\n+!!#!!!5,!$!5&+!#8!)#!5!%!!3%!!'!!!$$8+!&)%!)!(!*#!\n+@853_7_88\n+NNTNNNGGNGNATGNCTNGGNGNCNNGTNNANNNGCTANCTGNCNGNTAN\n++\n+!!1!!!42!5!,25!24!77!4!3!!81!!,!!!5147!)/6!,!,!1&!\n+@853_7_132\n+NNGNNNGCNGNGAANGCNTANCNCNNTANNANNNGCCGNGAGNGNANGGN\n++\n+!!&!!!5#!)!)&+!2&!',!&!'!!1)!!1!!!4()$!/&,!'!'!0$!\n+@853_7_141\n+NNGNNNCTNCNCCGNGGNAANANANNAGNNGNNNGGGGNGAANGNGNGGN\n++\n+!!,!!!),!5!3)+!//!),!3!9!!&/!!+!!!**#)!.)(!(!(!43!\n+@853_7_146\n+NNCNNNCGNGNGCGNGANCCNGNCNNCGNNGNNNCTCCNGGTNCNTNGCN\n++\n+!!1!!!33!4!#15!7(!51!1!3!!.5!!5!!!/)/,!&-/!,!.!4,!\n+@853_7_269\n+NNCNNNGCNGNGCGNAGNACNGNCNNGCNNTNNNGGCANCCTNGNTNTGN\n++\n+!!3!!!/.!+!*4,!42!)8!2!3!!62!!0!!!84;)!)7.!5!/!&%!\n+@853_7_321\n+NNCNNNACNGNGAGNCANCCNANGNNGGNNGNNNATTGNCCCNGNANGGN\n++\n+!!$!!!&'!.!*##!6$!#1!+!#!!.+!!)!!!36(#!*5'!#!4!+(!\n+@853_7_386\n+NNGNNNTCNGNGCCNCCNTCNGNANNTCNNANNNGATANTCGNCNANGGN\n++\n+!!;!!!86!=!;9=!%5!58!<!2!!62!!&!!!&3:&!//8!*!7!5*!\n+@853_7_405\n+NNGNNNAANANAAGNTCNGTNANGNNTGNNTNNNCATGNCGANGNCNGGN\n++\n+!!=!!!;:!>!<8=!9<!:<!=!>!!;8!!;!!!;//1!&(&!/!'!*-!\n+@853_7_411\n+NNCNNNAANCNAAGNAGNCGNCNGNNGGNNGNNNCAGANTCGNGNANGCN\n++\n+!!$!!!-#!#!*#+!,&!2*!#!#!!%'!!)!!!'$)$!/-#!#!'!,+!\n+@853_7_445\n+NNGNNNTTNANGTTNATNTCNANCNNCTNNGNNNAAGANGGGNGNGNGGN\n++\n+!!&!!!0%!#!,&'!,'!$$!&!,!!&)!!'!!!..*&!#,7!1!.!10!\n+@853_7_469\n+NNCNNNCANTNTCTNTTNTTNANTNNAGNNCNNNGTTTNGTANGNTNTGN\n++\n+!!#!!!%%!$!))+!$,!*%!.!(!!.#!!#!!!#&##!##&!#!#!##!\n+@853_33_1583\n+CCCGCGCTCCCGATAATATAATCACCGAAACACGAAGACCAACAGGCCCA\n++\n+),+&#,)',$##2$),%2'+#$)2),#$(+#+##&*%(-%1%#(##$$2,\n+@853_33_1649\n+ACTTTCGGTCTACGAGCGCTTGCTACACCATAGTTACCAAACGCGCCCGG\n++\n+:286623:<88:;98367:997<87>/;:7/5<<69&<1;447999923<\n+@853_34_1182\n+GGGAACATTATACGGCTTTCGCCCCCTAGACCGCACTGTGTTGGGCCGTT\n++\n+>>>:9<<>><;58987;::9718859:2;75'3%(720&14%6(,51-&&\n+@853_34_1358\n+CTTATATTAATGCTCCACGTCCTTGACACGCCCATCTTTGCCGTGAAGGA\n++\n+A:8:<<<:<<5==2<6A;:8:>;9;;;==:8=?;:97:;65:5;:2><13\n+@853_35_596\n+GGCTCCTATTTTATTACGTGTCCTTCTCAAACTGACAGCGCAATGCTAAG\n++\n+>978>8=9;>;:2>;;85=3;::=;::7:8:68)<5;859>?<>:<6<58\n+@853_35_669\n+TTCTTATAAAACCGCTTACCCCCTAGGTCCGAACATCTTGCAGGGTCTTG\n++\n+,)&#<&38':&)-2/*4-'*+,5:0(3(+.+&,)9,&%1%*'(+.+-&&'\n+@853_47_795\n+CGGAAGGAGCGAATACTGAACCAACACAGGTTAACTAGGAAGAAAGTGGA\n++\n+>?@;;?>=A@A9:>;:>=<;=>::88<;=8=<:95>08=5.(364,)1,)\n+@853_47_831\n+TAAAATCTCGGATGGTTGCCTTGAACAAAAAGACAGCCCCGTCAAGGGAA\n++\n+5A,&5,))%(()&,13(.9<2++8,>99*(%184,=/&5+)6/)0.&)64\n+@853_56_1228\n+CTGCGAGTATCTGCTGAGTTCAGTCGGGGGGGGGACGGCTCGGCGCAGGG\n++\n+@;>?=?:<==:<??;>>?<<?:=:6621.-&%9&4&%:-&/(5)2(&5-(\n+@853_56_1324\n+ACCATGTATGGAAAAAAAGAGTAGAGGAGGGAAACAATGAAAAACGGACC\n++\n+/6+58//.61366638/)&988).5::15578427=88&0:>;59:(6;<\n+@853_82_2023\n+GTATTAGAATTAGGGAGCCTAAGAGACGCATAAGCCGCGTACAGAGCTAG\n++\n+9;97><<75?<26754=8=<:8?:;;>9;69;8589?17=4566595:57\n+@853_83_197\n+CCGTCTCCCGCGCCGCAGAGACACTACTTCCTCGCCGCGGTGCGCCGGGC\n++\n+/9;58179583997;5591<26;797=55:995$)&$'#-$(&&'(*(%&\n+@853_112_119\n+TCCCGGGACAACGGAATTAACAACCCCCGGGTGGAATCGGGTGGGAGGCG\n++\n+))&)994&,/1(+-+.-('(02)145,.&42,#&).,&(-0.%,',%:(0\n+@853_112_253\n+GTTACACAAGCCCTGTGATAACCAAGTCTGACGTGATCCCAGTGGAGGTA\n++\n+:47675926:45/<9974:+56:;64:;<81;89:<<;56855687<5/&\n+@853_148_1347\n+TAAGGCCCGTGCCGGTCCGTCCAATGATATTGGAGGAGTTCCGGAGCAAG\n++\n+A=;@>>?=@@A@?A@>@A@=9?9<A@;9>>>>>7;=8<=;8;?;18?62=\n+@853_148_1509\n+TGAATGTAAATTAAACGGGAGGAAAAATCTCCCCACAATTGAGGCCTTCC\n++\n+./<&1=35>,/3(6,,1<3*)7,53)69<&(A<8+(;91).8&+7(:&<7\n+@853_157_314\n+GATAGCAAAAAAAGGGGCCGAGCGCAAAAGCCGACCTGAGCACAGACGAA\n++\n+9;:5461242#)#*1####('$$$##'#%#'$$%###/$%($#'#$$#+#\n+@853_157_582\n+AGGAACCGCTAATTACCCCCCTTTTTGAGCTCATAGCGTAGCTTATATTG\n++\n+:9:=>=<:>7>@<:8><><;><:;=;:67<5;4;?4<0<.9=,<6:>,:,\n+@853_158_402\n+TCACAGACCCGAGGAAGCTTCGTATATTTGCCACTAAGGGCGTCGGGGGA\n++\n+5;&35,<55<8<6;<3646:618477::95<92=752071+2339-.#11\n+@853_158_569\n+GTGACTACATGAAGGTGATGAGCTGTCTTCGGTGGCCACCCTCCAATCCG\n++\n+69<7979/5>9:4;9:9+::880:8;37<49<:3:<='6:9=2558<.03\n+@853_216_501\n+CTTTT"..b"AAACAATCGTTCCCACTGGTT\n++\n+<=<<=<<>A?><<=<;=?;;>=?>>9==@<>;>;<7<;>8;<83495&<5\n+@853_1360_1130\n+CAGCTCCATAGCCAATCTATTGCTCACGCAGGTCCGCGCCTACGACGTAT\n++\n+A@AA><:@8>@=AA@>8@A<?<@?@;=<A;A9=?A;<?>:>1>68<6?<;\n+@853_1361_389\n+GTTCACAATCTCTCGAACACCCGCATTCCCCCGGTCTCAATGCGTATGCG\n++\n+=AA>:<8=@@>;>9?=<<487?:=>>A=<?;>;5<8>8/::8;/A/>949\n+@853_1366_1495\n+CTTGAAACGGTACCAAAACCAAAGCGCAACCCTGTCCCGTAAATTTATAT\n++\n+AA;>9>>:<<::?8;>7:>597<>/@6=:8>9=A/:;>:;/9==92/819\n+@853_1367_802\n+GTAGCTTGACTGGGACCGAAAGTAACACTGGTAGCACCGTTGTGCACACC\n++\n+;:?>=>>=?>><;=9?@@=;>?6<<?@7=<?;;:>?99;<?(4<=;:;/<\n+@853_1382_1227\n+CTTGTCCTCTATCATACCAATCTAACTCGACCTTTAGTCTCCTCTCCTCT\n++\n+<;:99:98::8:#5:;:(7:6<#8<6:%0<89,5944,8:9:4/020*),\n+@853_1383_1269\n+CTATTGACCAACACAGTTCAAGCCAATTGAAATTAGACTCCCCAGGCGTT\n++\n+/))3(<(152,3),<8:2)37;.6/&7$)1/,$0'%4$3&74).0&0%13\n+@853_1395_1324\n+TAAGGAACCGCTCAACACTTATGGACTCGATCGGCCGCCGTGGTTGAGCC\n++\n+4*,19./*)96*83;4,/1,)'27)2082,,'*6(&)&*%(*3422-+1+\n+@853_1396_1014\n+TACAAAATGCGTCTGCCGAGGTCGTGGCGGCATGGCGCGTGGGGACCTGA\n++\n+;A5:;:>5;AA>6:><8:<A=<6>:?:9<=<27<<=3<<9=><;><,:<9\n+@853_1412_1664\n+GATCTGGACAGGAATTGAACACAACCCGAGGTCTAATGATTCGTCGTATA\n++\n+545)567,5,/*$$,4/$',+)%*,31#)&-1$.'13$&,1&0).1&&&(\n+@853_1413_877\n+AGGTCAGTTTCCAAGGTGGGGGTTGGCATTACGTACCATTCGATTAGATT\n++\n+?A?<<;A><?;A=<;;>856/>#%###&###%####&&###$$$&#%#$$\n+@853_1437_116\n+CCCAAACCAGGCTCGTCCCCTTTAAGATAGTCTCGCCCCCCCTCAACTTG\n++\n+6>>9;<@7=::=:>=544=54#'8&5-2)#(*)4,&%+#',2-&+&0-*2\n+@853_1437_1533\n+GGCGCATACCTCGCACGCATTCGTAAAGGATTGAGTGAGGCTGCATTGGT\n++\n+@A<:>>>;;<>?=<:>::>A?;=@<;:>>9>?<3:=:8>=39<1<=9?6?\n+@853_1486_1272\n+GCTATGTCCATATCGTGAATGCTTTCTTGCGTCGGGAGGCTTTTCATAGT\n++\n+7(7<<98656955)7:67/98%3(9/#,151#169=861<99%)),-%22\n+@853_1487_496\n+GTCGCACCCCTCCTAAACCCCAGATCAAAAACTGCACCCGCGACCCACTC\n++\n+6969=651<=::86774;7:<9=/69>0366/8,,8=:</6&31(3,/&)\n+@853_1488_605\n+TCGCCGCCAAACGATGCACTAATTTGCTTACCGGCCAGGCACGGATCGAA\n++\n+0)&)&1)/1(6)&(+),1=/*&&(&41,',)&1/(/,9/)1//<)&:15,\n+@853_1489_374\n+TAGTATGAGGACAATGAGTACCGATAGTTAGAGTGTACTTCCCGTCCCCT\n++\n+::;7.;98<;<;:<:<4;35;>95<6==<8/<<=8/==>:5=@/:;<=7<\n+@853_1493_452\n+GAAAGGACCAAACCAGGAGCATCCACCCATGGCCGCTAAACTAGGAGGAG\n++\n+$*)&'#,,,##(*#'%#%##(#))###%$$$##%###$#)###'#%%(%#\n+@853_1493_1908\n+AACATGTGCAAACCCTGCACCGGCAACGGGAGTGAGGACGCGAAAGGGAT\n++\n+@<=<====A@;><>?<==>AA=:?===:99;=:=:<<6:6:;96;<;797\n+@853_1498_1797\n+TGAAGGTCGCATGGCGCGGATTGCACAGCAGATCAACTGTTTCAAAAACA\n++\n+3=#&&04&',.8#*&-:&.*./$'#);%.$21'0&&/&###4$&%%0$#$\n+@853_1499_1261\n+GTGACACCTGTGGACGTCTAACAAGTATACCGTGTTTCAGCGGGCAGGTT\n++\n+>8=36</9587191791<7=<;38@6/51=5<31?9>(:</9:9;5<)7=\n+@853_1509_820\n+ACAAGAGACTACGAGGACACACTCCGGCCCTAAATCGCGAAAAACGGCCC\n++\n+',.1438/1)&1*3.18,72875),/*&://.4&),+/#+3%5*)56((&\n+@853_1510_448\n+TGAGATACTTTCGATCAGACCATCTGCGACCGGGAGAAGCTTTCCAACAA\n++\n+8;<5=6;7547@2;69?5:88>2556:4:88@42:;;72,8:,477<553\n+@853_1511_561\n+GCAAACCGTTCTGATGTAAACAACGTCAATTTGGGCCTTTACAAAGCGTT\n++\n+?A===@A?><A8A>:>9;;=@828;'#+99:#'9;;4#>6-1/89,-&45\n+@853_1511_1886\n+GACGTCGTCGTCGTCGTCGTTAACCCTAAGGTTCGCGGGACCCCTCAACA\n++\n+99;<=:>?<;=8;>=;8=<==9:8::==:9,8?:;)0<6.13;+:*5/:)\n+@853_1530_202\n+GGGGACTGAAGAGCGGCCATTAAGGGAGAATTGAGGAGAAGAGATGAGAA\n++\n+;<;99=:99>6>8:8<?:898A=2<7@88>)6#/+,&)(#,'-%#+-*%(\n+@853_1530_1652\n+GAGCTGGTACGAGTACGCACGTATGAACTTAATGTGCCATACGTAAATAA\n++\n+9:>;:>;<8@>8:;:9=<<;=<::>=>7:;;;;9;<=::85>;966=5/,\n+@853_1569_1617\n+TAATTGTATATAAATGCTGCATGCCGGGAAATTGTGCAGCTACGTGGAAG\n++\n+<A@=>?><<>=@@?=@?;=<=<9A<==;AA>;57:<?<;75>67695@:6\n+@853_1570_1472\n+CGACGCACGTCCGCAGGTACCAGGAACGTCATCCGTAACCGCGGGCACGC\n++\n+<=<>==;=:@>@<@==AA?A@>A?@<@?=A9>@?;>=9?<9>A>><3;=7\n+@853_1585_323\n+CAAGGGACTATAACTGAGGGGTGTGGAGCGGTTGGTTGGCCAGCGCATTA\n++\n+<;:>?<0<;;=;9781&(,95'+$-+2#,#'',1',$,$1/5+#2)6%&(\n+@853_1585_2023\n+AGGGGGATGCAGGCAAGACAAACGGCACGGGCGTGGGGAGAGGTCCCAAG\n++\n+?>@A>=44@@8<5A<7>:=?577<?867=>4588>:;88<59;<=:;)9=\n+@853_1603_500\n+GACCTATTCTGAGTCACCAAACGTTTCCCCTGGACCAAAGTCGGCCTGTT\n++\n+:<:78=:8<8:>2<59<8<<44593:9,&(7:#405:./(66212360/%\n+@853_1603_1995\n+CTGGTACCGGTATGAGCCTAGGATAGAGCGGCAACTCTTATACTGCCGGT\n++\n+9=:8;>>=<==<<>=AA@><A><<=?>?=<<??<<;?;;?<86=<9?=3;\n" |
| b |
| diff -r 000000000000 -r 8d92246f41bb test-data/bwa_wrapper_out1.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out1.sam Thu Jun 05 15:15:34 2014 -0400 |
| b |
| @@ -0,0 +1,30 @@ +seq1 16 phiX174 322 25 36M * 0 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 +seq10 0 phiX174 4149 37 17M1D19M * 0 0 ATTCTTTCTTTTCGTATCAGGGCGTTGAGTTCGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:5G11^G19 +seq11 0 phiX174 4072 37 18M1D18M * 0 0 GCATTTCTACTCCTTCTCATCCCCAATGCTTGGCTT II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:12T5^A18 +seq12 4 * 0 0 * * 0 0 CGCGCTTCGATAAAAATGGGATTGGCGTTTCCAACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq13 4 * 0 0 * * 0 0 ATTTCTACTCTTTCTCATCCCCAATCCTTGCCTTCC IIIIIIIIIIIIIIIIIIIIIAAIIIIIIIIIIIII +seq14 0 phiX174 3998 37 21M1D15M * 0 0 CCCTTTTGAATGTCACGCTGATATTTTGACTTTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:5C15^T15 +seq15 4 * 0 0 * * 0 0 CCAACTTACCAAGGTGGGTTACGAAACGCGACGCCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq16 4 * 0 0 * * 0 0 TCAGGGTATTAAAAGAGATTATTTTTCTCCAGCCAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq17 0 phiX174 3034 37 19M1D17M * 0 0 GTGATGTGCTTGCTACCGAAACAATACTTTAGGCAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:19^T9G7 +seq18 4 * 0 0 * * 0 0 TCAATCCCCCATGCTTGGCCGTTCCATAAGCAGATG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq19 4 * 0 0 * * 0 0 TTCCTGCGCTTAATGCTTGAGCGTCCTGGTGCTGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq2 0 phiX174 141 37 36M * 0 0 ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq20 0 phiX174 1082 37 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq21 0 phiX174 1344 37 15M1D21M * 0 0 CTGATACCAATAAAACCCTAAGCATTTGGTTCAGGG II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:15^T13T7 +seq22 4 * 0 0 * * 0 0 AATCAAACTTACCAAGGGGTTACGACGCGACGCCGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq23 4 * 0 0 * * 0 0 TGTGCTTCCCCAACTTGATTTAATAACCCTATAGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq24 0 phiX174 4084 37 17M1I18M * 0 0 TTTCTCAATCCCCAATGCCTTGGCTTCCCTAAGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:27A7 +seq25 0 phiX174 520 37 16M1I19M * 0 0 TTGCTACTGACCGCTCTTCGTGCTCGTTGCTGCGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:26C8 +seq26 0 phiX174 1976 37 36M * 0 0 CCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq27 0 phiX174 2598 37 20M1I15M * 0 0 CGCTAATCAAGTTGTTTCTGTTTGGTGCTGATATTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:9G25 +seq28 4 * 0 0 * * 0 0 AAAGAGATTATTTGTCGGTCCAGCCACTAAAGTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq29 4 * 0 0 * * 0 0 CAAATTAATGCGCGCTTCGATAATGATTGGGGTATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq3 0 phiX174 505 37 36M * 0 0 GTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq30 0 phiX174 4091 37 18M1I17M * 0 0 ATCCCCTATGCTTGGCTTACCATAAGCAGATGGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:6A28 +seq4 4 * 0 0 * * 0 0 AGCCGCTCGTCTTTTATGTAGGTGGTCAACCATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq5 0 phiX174 4985 25 36M * 0 0 CAGTTATATGGCTTTTGGTTTCTATGTGGCTTAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:13G17A4 +seq6 0 phiX174 925 37 11M1D25M * 0 0 AGGCGCTCGTCTTGGTATGTAGGTGGTCAACAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:11^T25 +seq7 0 phiX174 943 37 13M1I22M * 0 0 TGTAGGTGGTCAACCAATTTTAATTGCAGGGGCTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:35 +seq8 4 * 0 0 * * 0 0 ACACCCGTCCTTTACGTCATGCGCTCTATTCTCTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq9 0 phiX174 2596 37 16M1I19M * 0 0 GCCGCTATTCAGGTTGTTTTCTGTTGGTGCTGATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:7A27 |
| b |
| diff -r 000000000000 -r 8d92246f41bb test-data/bwa_wrapper_out2.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out2.sam Thu Jun 05 15:15:34 2014 -0400 |
| b |
| @@ -0,0 +1,30 @@ +seq1 16 phiX174 322 25 36M * 0 0 GATATTTTAAAGGAGCGTGGATTACTATCTGAGTCC B&&I13A$G$*%$IIIIIII9(.+5$IIIIIII#II XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:2C8A24 +seq2 0 phiX174 141 37 36M * 0 0 ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq3 0 phiX174 505 37 36M * 0 0 GTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq4 4 * 0 0 * * 0 0 AGCCGCTCGTCTTTTATGTAGGTGGTCAACCATTTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq5 0 phiX174 4985 25 36M * 0 0 CAGTTATATGGCTTTTGGTTTCTATGTGGCTTAATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:13G17A4 +seq6 0 phiX174 925 37 11M1D25M * 0 0 AGGCGCTCGTCTTGGTATGTAGGTGGTCAACAATTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:11^T25 +seq7 0 phiX174 943 37 13M1I22M * 0 0 TGTAGGTGGTCAACCAATTTTAATTGCAGGGGCTTC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:0 XO:i:1 XG:i:1 MD:Z:35 +seq8 4 * 0 0 * * 0 0 ACACCCGTCCTTTACGTCATGCGCTCTATTCTCTGG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq9 0 phiX174 2596 37 16M1I19M * 0 0 GCCGCTATTCAGGTTGTTTTCTGTTGGTGCTGATAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:7A27 +seq10 0 phiX174 4149 37 17M1D19M * 0 0 ATTCTTTCTTTTCGTATCAGGGCGTTGAGTTCGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:5G11^G19 +seq11 0 phiX174 4072 37 18M1D18M * 0 0 GCATTTCTACTCCTTCTCATCCCCAATGCTTGGCTT II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:12T5^A18 +seq12 4 * 0 0 * * 0 0 CGCGCTTCGATAAAAATGGGATTGGCGTTTCCAACC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq13 4 * 0 0 * * 0 0 ATTTCTACTCTTTCTCATCCCCAATCCTTGCCTTCC IIIIIIIIIIIIIIIIIIIIIAAIIIIIIIIIIIII +seq14 0 phiX174 3998 37 21M1D15M * 0 0 CCCTTTTGAATGTCACGCTGATATTTTGACTTTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:5C15^T15 +seq15 4 * 0 0 * * 0 0 CCAACTTACCAAGGTGGGTTACGAAACGCGACGCCG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq16 4 * 0 0 * * 0 0 TCAGGGTATTAAAAGAGATTATTTTTCTCCAGCCAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq17 0 phiX174 3034 37 19M1D17M * 0 0 GTGATGTGCTTGCTACCGAAACAATACTTTAGGCAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:19^T9G7 +seq18 4 * 0 0 * * 0 0 TCAATCCCCCATGCTTGGCCGTTCCATAAGCAGATG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq19 4 * 0 0 * * 0 0 TTCCTGCGCTTAATGCTTGAGCGTCCTGGTGCTGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq20 0 phiX174 1082 37 36M * 0 0 CTTATTACCATTTCAACTACTCCGGTTATCGCTGGC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq21 0 phiX174 1344 37 15M1D21M * 0 0 CTGATACCAATAAAACCCTAAGCATTTGGTTCAGGG II#IIIIIII$5+.(9IIIIIII$%*$G$A31I&&B XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:15^T13T7 +seq22 4 * 0 0 * * 0 0 AATCAAACTTACCAAGGGGTTACGACGCGACGCCGT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq23 4 * 0 0 * * 0 0 TGTGCTTCCCCAACTTGATTTAATAACCCTATAGAC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq24 0 phiX174 4084 37 17M1I18M * 0 0 TTTCTCAATCCCCAATGCCTTGGCTTCCCTAAGCAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:27A7 +seq25 0 phiX174 520 37 16M1I19M * 0 0 TTGCTACTGACCGCTCTTCGTGCTCGTTGCTGCGTT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:26C8 +seq26 0 phiX174 1976 37 36M * 0 0 CCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:36 +seq27 0 phiX174 2598 37 20M1I15M * 0 0 CGCTAATCAAGTTGTTTCTGTTTGGTGCTGATATTG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:9G25 +seq28 4 * 0 0 * * 0 0 AAAGAGATTATTTGTCGGTCCAGCCACTAAAGTGAG IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq29 4 * 0 0 * * 0 0 CAAATTAATGCGCGCTTCGATAATGATTGGGGTATC IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +seq30 0 phiX174 4091 37 18M1I17M * 0 0 ATCCCCTATGCTTGGCTTACCATAAGCAGATGGATA IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:1 XO:i:1 XG:i:1 MD:Z:6A28 |
| b |
| diff -r 000000000000 -r 8d92246f41bb test-data/bwa_wrapper_out3.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out3.sam Thu Jun 05 15:15:34 2014 -0400 |
| b |
| b'@@ -0,0 +1,63 @@\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 000000000000 -r 8d92246f41bb test-data/bwa_wrapper_out4.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out4.sam Thu Jun 05 15:15:34 2014 -0400 |
| [ |
| b'@@ -0,0 +1,202 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tXO:i:1\tXG:i:1\tMD:Z:45^A4\n+430_691_1191_F3\t0\tchrX_part\t26852\t0\t49M\t*\t0\t0\tGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCGCCACA\t]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\tXT:A:R\tCM:i:0\tX0:i:2\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:49\tXA:Z:chrX_part,+14746,49M,1;\n+430_693_248_F3\t0\tchrX_part\t14829\t37\t49M\t*\t0\t0\tCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCAC\t-]]]]]]]]]]]]]]]Z]]]]]]][]]]]]]]]]]]]]]]]]]]]]]]\\\tXT:A:U\tCM:i:0\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:49\n+430_78_1025_F3\t0\tchrX_part\t14935\t37\t49M\t*\t0\t0\tTTGTGGTTTTGATTTGCATTTCTCTGATGGCCAGTGATGATGAGCATTT\t]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\\]]]]]]]]]]Z]]]]\tXT:A:U\tCM:i:0\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:49\n+430_821_1672_F3\t4\t*\t0\t0\t*\t*\t0\t0\tATCGGCTGGCGCCAAGAATGTATTTGACGGATGGTCCATCGACGGCAACC\tA@?AAAAAA@=?:BA>B@>ABA?@A?B>:=@?<<:@>B=74@B;=><@65\n+430_874_1668_F3\t4\t*\t0\t0\t*\t*\t0\t0\tGAGAATTAAGGAAGGGAGCTAGCGTACTAAGCATACGGACGAGACACCCG\tA@AA>A@AB=@BAA@A@>@?B@=@?B@:A@?>:>A>=69@=@8A@@:/9?\n+430_89_1672_F3\t4\t*\t0\t0\t*\t*\t0\t0\tGGCGGAGATGTTACCCCGCGCGAGACCCATCACACGACGTGCAATCCGCG\tB?B?9@B@>=A@B=>A>?A@B<@==?=?@;>7A?>53A;>32@BAB>6?;\n+430_900_444_F3\t0\tchrX_part\t26504\t37\t49M\t*\t0\t0\tGTGATGTTCCCCTTCCTGTGTCCATGTGTTCTCATTGTTCAATTCCCAC\t]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\tXT:A:U\tCM:i:1\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:11T37\n+431_1029_654_F3\t0\tchrX_part\t27939\t37\t49M\t*\t0\t0\tGATTCTTCCTACCCATGAGCATGGAATGTTCTTCCATTTGTTTGTATCC\t]]]]]]]]]]]]]]]]]]]]VK]]]]]]]]]]]]]]]]]]]]]]]]]]]\tXT:A:U\tCM:i:1\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:17G31\n+431_274_859_F3\t16\tchrX_part\t14611\t37\t49M\t*\t0\t0\tTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGA\t]]]]XT]]]]]T\\]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\tXT:A:U\tCM:i:0\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:49\n+431_362_522_F3\t4\t*\t0\t0\t*\t*\t0\t0\tCAGCCATAACGCGAGAAAGAAAGAGTATACGATTCAAGAATTAAGAGAGG\t?B@?>ABBAA>B?A?@A@A@BA=A<8@>A?2@A@>AA?A?@<@A::779>\n+431_427_471_F3\t0\tchrX_part\t28034\t37\t49M\t*\t0\t0\tCCTTCACATCCCTTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGA\t]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]WT]]]TR]]]SU]]]\tXT:A:U\tCM:i:1\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:14A34\n+431_436_304_F3\t0\tchrX_part\t26555\t37\t49M\t*\t0\t0\tATGAGTGAGAATATGCGGTGTTTGGTTTTTTGTTCTTGCGATAGTTTAC\t]]]]]]]]]]]]]]]]]]]U]]]]V[]]]]]]]]X[]]]T]]]]]][]\\\tXT:A:U\tCM:i:1\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:11C37\n+431_44_655_F3\t4\t*\t0\t0\t*\t*\t0\t0\tGCTATTAGCCCATTGTCAAGGCGACAGACACACAACAATCCGACACCATC\t>-<=>@@4:=>@?A:>=9=::::=:5<:<66=7865<9;<59=13:+<;;\n+431_50_371_F3\t4\t*\t0\t0\t*\t*\t0\t0\tCGGCCCCGTCCAGAAAGAGAGCCCCGACTCCCCAGGGCTACCAGCATAGA\t=AA@@AAAABBBAB@=@9@A@A@A?>B<??AA>@;?@?@>B?6=B7@8A@\n+431_510_914_F3\t16\tchrX_part\t1438\t37\t49M\t*\t0\t0\tTCCTTCTATAGAGTCTAGTTTGTGACCATATTTCTCATTCCAGAGGAAA\t]]Z]V[Z]]]]]]WY]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\tXT:A:U\tCM:i:0\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:49\n+431_524_1355_F3\t16\tchrX_part\t28191\t37\t49M\t*\t0\t0\tGCTGAAGTTGCTTATCAGCTTAAGGAGATTTTGGGCTGAGACAATGGGG\t]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\tXT:A:U\tCM:i:0\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:49\n+431_753_1184_F3\t0\tchrX_part\t27127\t37\t49M\t*\t0\t0\tGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTG\tZ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\tXT:A:U\tCM:i:1\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:23T25\n+431_933_606_F3\t16\tchrX_part\t27360\t37\t49M\t*\t0\t0\tTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCTATG\t]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\tXT:A:U\tCM:i:0\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:49\n+@PG\tID:bwa\tPN:bwa\tVN:0.5.9-r16\n+@SQ\tSN:chrX_part\tLN:37500\n' |
| b |
| diff -r 000000000000 -r 8d92246f41bb test-data/bwa_wrapper_out5.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out5.sam Thu Jun 05 15:15:34 2014 -0400 |
| [ |
| b"@@ -0,0 +1,420 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|
| b |
| diff -r 000000000000 -r 8d92246f41bb test-data/bwa_wrapper_out6.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out6.sam Thu Jun 05 15:15:34 2014 -0400 |
| [ |
| b'@@ -0,0 +1,203 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_1586_641_F3\t0\tchrX_part\t28277\t25\t49M\t*\t0\t0\tACAATTTGACTTCCTCTTTTCCTAATTGAATGCCCTTTATTTCCTTCTC\t]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]Y\tRG:Z:474747\tXT:A:U\tCM:i:1\tX0:i:1\tX1:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tMD:Z:31A17\n+430_1684_261_F3\t16\tchrX_part\t27257\t25\t49M\t*\t0\t0\tTCTCCCATTCTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGC\tQS]TU]]]YXVX]XJQX]]]][]YS]]]]\\]]]\\]]]]\\]]]]]]]]],\tRG:Z:474747\tXT:A:U\tCM:i:1\tX0:i:1\tX1:i:0\tXM:i:3\tXO:i:0\tXG:i:0\tMD:Z:9T39\n+430_1726_1548_F3\t4\t*\t0\t0\t*\t*\t0\t0\tTTTTCGACGACGAAGCTGCAAAAAGACATAGGCCCGAGGAAGCGCTACAC\t;BBB=9@BAA3AA@>4=A>?<A@@=8<?;@8@@>>2=>8A69>5>4<==<\tRG:Z:474747\n+430_1779_172_F3\t0\tchrX_part\t25672\t37\t49M\t*\t0\t0\tCTGGAAACCATCATTCTCAGCAAACTATCGCAAGGACAAAAAACCAAAC\t]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]][[]]]]]\tRG:Z:474747\tXT:A:U\tCM:i:0\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:49\n+430_1871_988_F3\t0\tchrX_part\t14560\t37\t49M\t*\t0\t0\tAAGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCC\t]]]]]]]]]]]]]]]]]]]]]]]TO]]]]\\]]][T]]]]]]]]]][]]]\tRG:Z:474747\tXT:A:U\tCM:i:1\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:1T47\n+430_1994_1381_F3\t4\t*\t0\t0\t*\t*\t0\t0\tGACTCGGTCTCAGATCCAGGAGACTAACCAACCTTGAGGGAAATTAAGAG\t@BBBABBAB==ABB@>A@A?A@B?A>B@=?@AAAA=AA@8;ABBBAA?@8\tRG:Z:474747\n+431_44_655_F3\t4\t*\t0\t0\t*\t*\t0\t0\tGCTATTAGCCCATTGTCAAGGCGACAGACACACAACAATCCGACACCATC\t>-<=>@@4:=>@?A:>=9=::::=:5<:<66=7865<9;<59=13:+<;;\tRG:Z:474747\n+431_50_371_F3\t4\t*\t0\t0\t*\t*\t0\t0\tCGGCCCCGTCCAGAAAGAGAGCCCCGACTCCCCAGGGCTACCAGCATAGA\t=AA@@AAAABBBAB@=@9@A@A@A?>B<??AA>@;?@?@>B?6=B7@8A@\tRG:Z:474747\n+431_274_859_F3\t16\tchrX_part\t14611\t23\t49M\t*\t0\t0\tTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGA\t]]]]XT]]]]]T\\]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\tRG:Z:474747\tXT:A:U\tCM:i:0\tX0:i:1\tX1:i:1\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:49\tXA:Z:chrX_part,-26717,49M,2;\n+431_362_522_F3\t4\t*\t0\t0\t*\t*\t0\t0\tCAGCCATAACGCGAGAAAGAAAGAGTATACGATTCAAGAATTAAGAGAGG\t?B@?>ABBAA>B?A?@A@A@BA=A<8@>A?2@A@>AA?A?@<@A::779>\tRG:Z:474747\n+431_427_471_F3\t0\tchrX_part\t28034\t37\t49M\t*\t0\t0\tCCTTCACATCCCTTGTAAGTTGGATTCCTAGGTATTTTATTCTCTTTGA\t]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]WT]]]TR]]]SU]]]\tRG:Z:474747\tXT:A:U\tCM:i:1\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:14A34\n+431_436_304_F3\t0\tchrX_part\t26555\t37\t49M\t*\t0\t0\tATGAGTGAGAATATGCGGTGTTTGGTTTTTTGTTCTTGCGATAGTTTAC\t]]]]]]]]]]]]]]]]]]]U]]]]V[]]]]]]]]X[]]]T]]]]]][]\\\tRG:Z:474747\tXT:A:U\tCM:i:1\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:11C37\n+431_510_914_F3\t16\tchrX_part\t1438\t37\t49M\t*\t0\t0\tTCCTTCTATAGAGTCTAGTTTGTGACCATATTTCTCATTCCAGAGGAAA\t]]Z]V[Z]]]]]]WY]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\tRG:Z:474747\tXT:A:U\tCM:i:0\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:49\n+431_524_1355_F3\t16\tchrX_part\t28191\t37\t49M\t*\t0\t0\tGCTGAAGTTGCTTATCAGCTTAAGGAGATTTTGGGCTGAGACAATGGGG\t]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\tRG:Z:474747\tXT:A:U\tCM:i:0\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:49\n+431_753_1184_F3\t0\tchrX_part\t27127\t37\t49M\t*\t0\t0\tGAGAAGTGTCTGTTCATGTCCTTCGCCCACTTTTTGATGGGGTTGTTTG\tZ]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\tRG:Z:474747\tXT:A:U\tCM:i:1\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:23T25\n+431_933_606_F3\t16\tchrX_part\t27360\t37\t49M\t*\t0\t0\tTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCTATG\t]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]\tRG:Z:474747\tXT:A:U\tCM:i:0\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:0\tXG:i:0\tMD:Z:49\n+431_1029_654_F3\t0\tchrX_part\t27939\t37\t49M\t*\t0\t0\tGATTCTTCCTACCCATGAGCATGGAATGTTCTTCCATTTGTTTGTATCC\t]]]]]]]]]]]]]]]]]]]]VK]]]]]]]]]]]]]]]]]]]]]]]]]]]\tRG:Z:474747\tXT:A:U\tCM:i:1\tX0:i:1\tX1:i:0\tXM:i:2\tXO:i:0\tXG:i:0\tMD:Z:17G31\n' |
| b |
| diff -r 000000000000 -r 8d92246f41bb test-data/bwa_wrapper_out7.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out7.sam Thu Jun 05 15:15:34 2014 -0400 |
| [ |
| b"@@ -0,0 +1,422 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|
| b |
| diff -r 000000000000 -r 8d92246f41bb test-data/bwa_wrapper_out8.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/bwa_wrapper_out8.sam Thu Jun 05 15:15:34 2014 -0400 |
| b |
| b'@@ -0,0 +1,60 @@\n+seq1\t113\tphiX174\t340\t37\t18M\t=\t322\t-18\tGGATTACTATCTGAGTCC\tII9(.+5$IIIIIII#II\tXT:A:U\tNM:i:0\tSM:i:37\tAM:i:25\tX0:i:1\tX1:i:0\tXM:i:0\tXO:i:0\tXG:i:0\tMD:Z:18\n+seq1\t177\tphiX174\t322\t25\t18M\t=\t340\t18\tGATATTTTAAAGGAGCGT\tB&&I13A$G$*%$IIIII\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+seq10\t129\tphiX174\t4168\t37\t18M\t=\t4149\t-19\tAGGGCGTTGAGTTCGATA\tIIIIIIIIIIIIIIIIII\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+seq10\t65\tphiX174\t4149\t25\t18M\t=\t4168\t19\tATTCTTTCTTTTCGTATC\tIIIIIIIIIIIIIIIIII\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+seq11\t129\tphiX174\t4091\t37\t18M\t=\t4072\t-19\tATCCCCAATGCTTGGCTT\tIIIII$%*$G$A31I&&B\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+seq11\t65\tphiX174\t4072\t37\t18M\t=\t4091\t19\tGCATTTCTACTCCTTCTC\tII#IIIIIII$5+.(9II\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+seq12\t129\tphiX174\t5365\t25\t18M\t=\t5349\t-16\tGGATTGGCGTTTCCAACC\tIIIIIIIIIIIIIIIIII\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:0T9A7\n+seq12\t65\tphiX174\t5349\t37\t18M\t=\t5365\t16\tCGCGCTTCGATAAAAATG\tIIIIIIIIIIIIIIIIII\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+seq13\t129\tphiX174\t4093\t25\t18M\t=\t4074\t-19\tCCCCAATCCTTGCCTTCC\tIIIAAIIIIIIIIIIIII\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:7G4G5\n+seq13\t65\tphiX174\t4074\t37\t18M\t=\t4093\t19\tATTTCTACTCTTTCTCAT\tIIIIIIIIIIIIIIIIII\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:17A0\n+seq14\t129\tphiX174\t4016\t37\t3M1D15M\t=\t3998\t-18\tTGATATTTTGACTTTGAG\tIIIIIIIIIIIIIIIIII\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:3^T15\n+seq14\t65\tphiX174\t3998\t37\t18M\t=\t4016\t18\tCCCTTTTGAATGTCACGC\tIIIIIIIIIIIIIIIIII\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:5C12\n+seq15\t129\tphiX174\t5216\t37\t5M2I11M\t=\t5198\t-18\tTTACGAAACGCGACGCCG\tIIIIIIIIIIIIIIIIII\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:2\tMD:Z:16\n+seq15\t65\tphiX174\t5198\t37\t18M\t=\t5216\t18\tCCAACTTACCAAGGTGGG\tIIIIIIIIIIIIIIIIII\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:13C4\n+seq16\t129\tphiX174\t2897\t37\t18M\t=\t2880\t-17\tTTATTTTTCTCCAGCCAC\tIIIIIIIIIIIIIIIIII\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+seq16\t65\tphiX174\t2880\t37\t10M1I7M\t=\t2897\t17\tTCAGGGTATTAAAAGAGA\tIIIIIIIIIIIIIIIIII\tXT:A:U\tNM:i:2\tSM:i:37\tAM:i:37\tX0:i:1\tX1:i:0\tXM:i:1\tXO:i:1\tXG:i:1\tMD:Z:5T11\n+seq17\t129\tphiX174\t3053\t25\t18M\t=\t3034\t-19\tAAACAATACTTTAGGCAT\tIIIIIIIIIIIIIIIIII\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:0T9G7\n+seq17\t65\tphiX174\t3034\t37\t18M\t=\t3053\t19\tGTGATGTGCTTGCTACCG\tIIIIIIIIIIIIIIIIII\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+seq18\t133\tphiX174\t4088\t0\t*\t=\t4088\t0\tCCGTTCCATAAGCAGATG\tIIIIIIIIIIIIIIIIII\n+seq18\t73\tphiX174\t4088\t37\t18M\t=\t4088\t0\tTCAATCCCCCATGCTTGG\tIIIIIIIIIIIIIIIIII\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:9A8\n+seq19\t129\tphiX174\t3324\t37\t18M\t=\t3304\t-20\tGAGCGTCCTGGTGCTGAT\tIIIIIIIIIIIIIIIIII\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+seq19\t65\tphiX174\t3304\t37\t18M\t=\t3324\t20\tTTCCTGCGCTTAATGCTT\tIIIIIIIIIIIIIIIIII\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+seq2\t129\tphiX174\t159\t37\t18M\t=\t141\t-18\tCAGCTCGAGAAGCTCTTA\tIIIIIIIIIIIIIIIIII\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\t65\tphiX174\t141\t37\t18M\t=\t159\t18\tATTCGACCTATCCTTGCG\tIIIIIIIIIIIIIIIIII\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\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\t65\tphiX174\t1082\t37\t18M\t=\t1100\t18\tCTTATTACCATTTCAACT\tIIIIIIIIIIIIIIIIII\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\t129\tphiX174\t1363\t37\t18M\t=\t1344\t-19\tTAAGCATTTGGTTCAGGG\tIIIII$%*$G$A'..b'=\t4084\t-17\tCTTGGCTTCCCTAAGCAG\tIIIIIIIIIIIIIIIIII\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+seq24\t65\tphiX174\t4084\t37\t18M\t=\t4101\t17\tTTTCTCAATCCCCAATGC\tIIIIIIIIIIIIIIIIII\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+seq25\t129\tphiX174\t537\t37\t18M\t=\t520\t-17\tCGTGCTCGTTGCTGCGTT\tIIIIIIIIIIIIIIIIII\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+seq25\t65\tphiX174\t520\t37\t18M\t=\t537\t17\tTTGCTACTGACCGCTCTT\tIIIIIIIIIIIIIIIIII\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+seq26\t129\tphiX174\t1994\t37\t18M\t=\t1976\t-18\tAAGGATGTTTTCCGTTCT\tIIIIIIIIIIIIIIIIII\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\t65\tphiX174\t1976\t37\t18M\t=\t1994\t18\tCCGCGTGAAATTTCTATG\tIIIIIIIIIIIIIIIIII\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\t129\tphiX174\t2614\t37\t3M1D15M\t=\t2598\t-16\tTGTTTGGTGCTGATATTG\tIIIIIIIIIIIIIIIIII\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+seq27\t65\tphiX174\t2598\t37\t18M\t=\t2614\t16\tCGCTAATCAAGTTGTTTC\tIIIIIIIIIIIIIIIIII\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+seq28\t129\tphiX174\t2906\t37\t18M\t=\t2890\t-16\tTCCAGCCACTAAAGTGAG\tIIIIIIIIIIIIIIIIII\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+seq28\t65\tphiX174\t2890\t25\t18M\t=\t2906\t16\tAAAGAGATTATTTGTCGG\tIIIIIIIIIIIIIIIIII\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+seq29\t133\tphiX174\t5339\t0\t*\t=\t5339\t0\tGATAATGATTGGGGTATC\tIIIIIIIIIIIIIIIIII\n+seq29\t73\tphiX174\t5339\t37\t18M\t=\t5339\t0\tCAAATTAATGCGCGCTTC\tIIIIIIIIIIIIIIIIII\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+seq3\t129\tphiX174\t523\t37\t18M\t=\t505\t-18\tCTACTGACCGCTCTCGTG\tIIIIIIIIIIIIIIIIII\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\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+seq30\t129\tphiX174\t4108\t37\t18M\t=\t4091\t-17\tACCATAAGCAGATGGATA\tIIIIIIIIIIIIIIIIII\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+seq30\t65\tphiX174\t4091\t37\t18M\t=\t4108\t17\tATCCCCTATGCTTGGCTT\tIIIIIIIIIIIIIIIIII\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+seq4\t137\tphiX174\t945\t37\t18M\t=\t945\t0\tTAGGTGGTCAACCATTTT\tIIIIIIIIIIIIIIIIII\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:12A5\n+seq4\t69\tphiX174\t945\t0\t*\t=\t945\t0\tAGCCGCTCGTCTTTTATG\tIIIIIIIIIIIIIIIIII\n+seq5\t129\tphiX174\t5003\t37\t18M\t=\t4985\t-18\tTTTCTATGTGGCTTAATA\tIIIIIIIIIIIIIIIIII\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+seq5\t65\tphiX174\t4985\t37\t18M\t=\t5003\t18\tCAGTTATATGGCTTTTGG\tIIIIIIIIIIIIIIIIII\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+seq6\t129\tphiX174\t944\t37\t18M\t=\t925\t-19\tGTAGGTGGTCAACAATTT\tIIIIIIIIIIIIIIIIII\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+seq6\t65\tphiX174\t925\t37\t11M1D7M\t=\t944\t19\tAGGCGCTCGTCTTGGTAT\tIIIIIIIIIIIIIIIIII\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+seq7\t129\tphiX174\t960\t37\t18M\t=\t943\t-17\tTTTAATTGCAGGGGCTTC\tIIIIIIIIIIIIIIIIII\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+seq7\t65\tphiX174\t943\t25\t18M\t=\t960\t17\tTGTAGGTGGTCAACCAAT\tIIIIIIIIIIIIIIIIII\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:14A1T1\n+seq8\t137\tphiX174\t1715\t37\t18M\t=\t1715\t0\tATGCGCTCTATTCTCTGG\tIIIIIIIIIIIIIIIIII\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+seq8\t69\tphiX174\t1715\t0\t*\t=\t1715\t0\tACACCCGTCCTTTACGTC\tIIIIIIIIIIIIIIIIII\n+seq9\t129\tphiX174\t2613\t37\t18M\t=\t2596\t-17\tTTCTGTTGGTGCTGATAT\tIIIIIIIIIIIIIIIIII\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+seq9\t65\tphiX174\t2596\t37\t18M\t=\t2613\t17\tGCCGCTATTCAGGTTGTT\tIIIIIIIIIIIIIIIIII\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' |
| b |
| diff -r 000000000000 -r 8d92246f41bb test-data/chr_m.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/chr_m.fasta Thu Jun 05 15:15:34 2014 -0400 |
| b |
| b'@@ -0,0 +1,335 @@\n+>chrM\n+GTTAATGTAGCTTAATAATATAAAGCAAGGCACTGAAAATGCCTAGATGA\n+GTATTCTTACTCCATAAACACATAGGCTTGGTCCTAGCCTTTTTATTAGT\n+TATTAATAGAATTACACATGCAAGTATCCGCACCCCAGTGAGAATGCCCT\n+CTAAATCACGTCTCTACGATTAAAAGGAGCAGGTATCAAGCACACTAGAA\n+AGTAGCTCATAACACCTTGCTCAGCCACACCCCCACGGGACACAGCAGTG\n+ATAAAAATTAAGCTATGAACGAAAGTTCGACTAAGTCATATTAAATAAGG\n+GTTGGTAAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCAAATTA\n+ATAAATCTCCGGCGTAAAGCGTGTCAAAGACTAATACCAAAATAAAGTTA\n+AAACCCAGTTAAGCCGTAAAAAGCTACAACCAAAGTAAAATAGACTACGA\n+AAGTGACTTTAATACCTCTGACTACACGATAGCTAAGACCCAAACTGGGA\n+TTAGATACCCCACTATGCTTAGCCCTAAACTAAAATAGCTTACCACAACA\n+AAGCTATTCGCCAGAGTACTACTAGCAACAGCCTAAAACTCAAAGGACTT\n+GGCGGTGCTTTACATCCCTCTAGAGGAGCCTGTTCCATAATCGATAAACC\n+CCGATAAACCCCACCATCCCTTGCTAATTCAGCCTATATACCGCCATCTT\n+CAGCAAACCCTAAACAAGGTACCGAAGTAAGCACAAATATCCAACATAAA\n+AACGTTAGGTCAAGGTGTAGCCCATGGGATGGAGAGAAATGGGCTACATT\n+TTCTACCCTAAGAACAAGAACTTTAACCCGGACGAAAGTCTCCATGAAAC\n+TGGAGACTAAAGGAGGATTTAGCAGTAAATTAAGAATAGAGAGCTTAATT\n+GAATCAGGCCATGAAGCGCGCACACACCGCCCGTCACCCTCCTTAAATAT\n+CACAAATCATAACATAACATAAAACCGTGACCCAAACATATGAAAGGAGA\n+CAAGTCGTAACAAGGTAAGTATACCGGAAGGTGTACTTGGATAACCAAAG\n+TGTAGCTTAAACAAAGCATCCAGCTTACACCTAGAAGATTTCACTCAAAA\n+TGAACACTTTGAACTAAAGCTAGCCCAAACAATACCTAATTCAATTACCC\n+TTAGTCACTTAACTAAAACATTCACCAAACCATTAAAGTATAGGAGATAG\n+AAATTTTAACTTGGCGCTATAGAGAAAGTACCGTAAGGGAACGATGAAAG\n+ATGCATTAAAAGTACTAAACAGCAAAGCTTACCCCTTTTACCTTTTGCAT\n+AATGATTTAACTAGAATAAACTTAGCAAAGAGAACTTAAGCTAAGCACCC\n+CGAAACCAGACGAGCTACCTATGAACAGTTACAAATGAACCAACTCATCT\n+ATGTCGCAAAATAGTGAGAAGATTCGTAGGTAGAGGTGAAAAGCCCAACG\n+AGCCTGGTGATAGCTGGTTGTCCAGAAACAGAATTTCAGTTCAAATTTAA\n+ATTTACCTAAAAACTACTCAATTCTAATGTAAATTTAAATTATAGTCTAA\n+AAAGGTACAGCTTTTTAGATACAGGTTACAACCTTCATTAGAGAGTAAGA\n+ACAAGATAAACCCATAGTTGGCTTAAAAGCAGCCATCAATTAAGAAAGCG\n+TTCAAGCTCAACGACACATCTATCTTAATCCCAACAATCAACCCAAACTA\n+ACTCCTAATCTCATACTGGACTATTCTATCAACACATAGAAGCAATAATG\n+TTAATATGAGTAACAAGAATTATTTCTCCTTGCATAAGCTTATATCAGAA\n+CGAATACTCACTGATAGTTAACAACAAGATAGGGATAATCCAAAAACTAA\n+TCATCTATTTAAACCATTGTTAACCCAACACAGGCATGCATCTATAAGGA\n+AAGATTAAAAGAAGTAAAAGGAACTCGGCAAACACAAACCCCGCCTGTTT\n+ACCAAAAACATCACCTCTAGCATTTCCAGTATTAGAGGCACTGCCTGCCC\n+AGTGACATCTGTTtaaacggccgcggtatcctaaccgtgcaaaggtagca\n+taatcacttgttccctaaatagggacttgtatgaatggccacacgagggt\n+tttactgtctcttacttccaatcagtgaaattgaccttcccgtgaagagg\n+cgggaatgactaaataagacgagaagaccctatggagcttTAATTAACTG\n+ATTCACAAAAAACAACACACAAACCTTAACCTTCAGGGACAACAAAACTT\n+TTGATTGAATCAGCAATTTCGGTTGGGGTGACCTCGGAGAACAAAACAAC\n+CTCCGAGTGATTTAAATCCAGACTAACCAGTCAAAATATATAATCACTTA\n+TTGATCCAAACCATTGATCAACGGAACAAGTTACCCTAGGGATAACAGCG\n+CAATCCTATTCCAGAGTCCATATCGACAATTAGGGTTTACGACCTCGATG\n+TTGGATCAAGACATCCTAATGGTGCAACCGCTATTAAGGGTTCGTTTGTT\n+CAACGATTAAAGTCTTACGTGATCTGAGTTCAGACCGGAGTAATCCAGGT\n+CGGTTTCTATCTATTCTATACTTTTCCCAGTACGAAAGGACAAGAAAAGT\n+AGGGCCCACTTTACAAGAAGCGCCCTCAAACTAATAGATGACATAATCTA\n+AATCTAACTAATTTATAACTTCTACCGCCCTAGAACAGGGCTCgttaggg\n+tggcagagcccggaaattgcataaaacttaaacctttacactcagaggtt\n+caactcctctccctaacaacaTGTTCATAATTAACGTCCTCCTCCTAATT\n+GTCCCAATCTTGCTCGCCGTAGCATTCCTCACACTAGTTGAACGAAAAGT\n+CTTAGGCTATATGCAACTTCGCAAAGGACCCAACATCGTAGGCCCCTATG\n+GCCTACTACAACCTATTGCCGATGCCCTCAAACTATTTATCAAAGAGCCA\n+CTACAACCACTAACATCATCGACATCCATATTCATCATCGCACCAATCCT\n+AGCCCTAACCCTGGCCTTAACCATATGAATCCCTCTGCCCATACCATACC\n+CACTAATCAACATAAACCTAGGAATTCTATTCATACTAGCCATGTCCAGC\n+CTAGCTGTCTACTCAATCCTTTGATCAGGATGGGCCTCAAACTCAAAATA\n+CGCCCTAATTGGAGCTCTACGAGCAGTAGCACAAACCATCTCATACGAAG\n+TAACTCTAGCAATCATCCTACTCTCAGTCCTCCTAATAAGCGGATCATTC\n+ACATTATCAACACTTATTATTACCCAAGAATACCTCTGATTAATCTTCCC\n+ATCATGACCCTTAGCCATAATGTGATTCATCTCAACATTAGCCGAAACCA\n+ACCGAGCTCCATTTGACCTAACAGAAGGAGAATCAGAACTCGTCTCTGGA\n+TTCAACGTTGAATACGCAGCCGGCCCATTTGCTCTATTCTTCCTAGCAGA\n+ATACGCAAACATCATCATGATAAACATCTTCACAACAACCCTATTTCTAG\n+GAGCATTTCACAACCCCTACCTGCCAGAACTCTACTCAATTAATTTCACC\n+ATTAAAGCTCTCCTTCTAACATGTTCCTTCCTATGAATCCGAGCATCCTA\n+CCCACGATTCCGATATGACCAACTTATACACCTCCTATGAAAGAACTTCC\n+TACCACTCACACTAGCCCTCTGCATATGACACGTCTCACTTCCAATCATA\n+CTATCCAGCATCCCACCACAAACATAGGAAATATGTCTGACAAAAGAGTT\n+ACTTTGATAGAGTAAAACATAGAGGCTCAAACCCTCTTATTTctagaact\n+acaggaattgaacctgctcct'..b'CATTATCCACAGCCTAAATGACGAGCAAGATATC\n+CGAAAAATAGGCGGACTATTTAATGCAATACCCTTCACCACCACATCTCT\n+AATTATTGGCAGCCTTGCACTCACCGGAATTCCTTTCCTCACAGGCTTCT\n+ACTCCAAAGACCTCATCATCGAAACCGCCAACACATCGTACACCAACGCC\n+TGAGCCCTACTAATAACTCTCATTGCCACATCCCTCACAGCTGTCTACAG\n+TACCCGAATCATCTTCTTTGCACTCCTAGGGCAACCCCGCTTCCTCCCTC\n+TGACCTCAATCAACGAAAATAACCCCTTTCTAATTAACTCCATCAAACGC\n+CTCTTAATTGGCAGCATTTTTGCCGGATTCTTCATCTCCAACAATATCTA\n+CCCCACAACCGTCCCAGAAATAACCATACCTACTTACATAAAACTCACCG\n+CCCTCGCAGTAACCATCCTAGGATTTACACTAGCCCTAGAACTAAGCTTG\n+ATAACCCATAACTTAAAACTAGAACACTCCACCAACGTATTCAAATTCTC\n+CAACCTCCTAGGATACTACCCAACAATTATACACCGACTCCCACCGCTCG\n+CTAACCTATCAATAAGCCAAAAATCAGCATCACTTCTACTAGACTCAATC\n+TGACTAGAAAACATCCTGCCAAAATCTATCTCCCAGTTCCAAATAAAAAC\n+CTCGATCCTAATTTCCACCCAAAAAGGACAAATCAAATTATATTTCCTCT\n+CATTCCTCATCACCCTTACCCTAAGCATACTACTTTTTAATCTCCACGAG\n+TAACCTCTAAAATTACCAAGACCCCAACAAGCAACGATCAACCAGTCACA\n+ATCACAACCCAAGCCCCATAACTATACAATGCAGCAGCCCCTATAATTTC\n+CTCACTAAACGCCCCAGAATCTCCAGTATCATAAATAGCTCAAGCCCCCA\n+CACCACTAAACTTAAACACTACCCCCACTTCCTCACTCTTCAGAACATAT\n+AAAACCAACATAACCTCCATCAACAACCCTAAAAGAAATACCCCCATAAC\n+AGTCGTATTAGACACCCATACCTCAGGATACTGCTCAGTAGCCATAGCCG\n+TTGTATAACCAAAAACAACCAACATTCCTCCCAAATAAATCAAAAACACC\n+ATCAACCCCAAAAAGGACCCTCCAAAATTCATAATAATACCACAACCTAC\n+CCCTCCACTTACAATCAGCACTAAACCCCCATAAATAGGTGAAGGTTTTG\n+AAGAAAACCCCACAAAACTAACAACAAAAATAACACTCAAAATAAACACA\n+ATATATGTCATCATTATTCCCACGTGGAATCTAACCACGACCAATGACAT\n+GAAAAATCATCGTTGTATTTCAACTATAAGAACACCAATGACAAACATCC\n+GGAAATCTCACCCACTAATTAAAATCATCAATCACTCTTTTATTGACCTA\n+CCAGCCCCCTCAAACATTTCATCATGATGAAACTTCGGCTCCCTCCTAGG\n+AATCTGCCTAATCCTCCAAATCTTAACAGGCCTATTCCTAGCCATACACT\n+ACACATCAGACACGACAACTGCCTTCTCATCCGTCACTCACATCTGCCGA\n+GACGTTAACTACGGATGAATTATTCGCTACCTCCATGCCAACGGAGCATC\n+AATATTTTTTATCTGCCTCTTCATTCACGTAGGACGCGGCCTCTACTACG\n+GCTCTTACACATTCCTAGAGACATGAAACATTGGAATCATCCTACTTTTC\n+ACAGTTATAGCTACAGCATTCATGGGCTATGTCCTACCATGAGGCCAAAT\n+ATCCTTTTGAGGAGCAACAGTCATCACGAACCTCCTATCAGCAATTCCCT\n+ACATCGGTACTACCCTCGTCGAGTGAATCTGAGGTGGATTCTCAGTAGAC\n+AAAGCCACCCTTACCCGATTTTTTGCTTTCCACTTCATCCTACCCTTCAT\n+CATCACAGCCCTGGTAGTCGTACATTTACTATTTCTTCACGAAACAGGAT\n+CTAATAACCCCTCAGGAATCCCATCCGATATGGACAAAATCCCATTCCAC\n+CCATATTATACAATTAAAGACATCCTAGGACTCCTCCTCCTGATCTTGCT\n+CCTACTAACTCTAGTATTATTCTCCCCCGACCTCCTAGGAGACCCAGACA\n+ACTACACCCCAGCTAACCCTCTCAGCACTCCCCCTCATATTAAACCAGAA\n+TGGTACTTCCTGTTTGCCTACGCCATCCTACGCTCCATTCCCAACAAACT\n+AGGCGGCGTATTAGCCCTAATCCTCTCCATCCTGATCCTAGCACTCATCC\n+CCACCCTCCACATATCAAAACAACGAAGCATAATATTCCGGCCTCTCAGC\n+CAATGCGTATTCTGACTCTTAGTGGCAGACTTACTGACACTAACATGAAT\n+CGGCGGACAGCCAGTGGAACACCCATACGTAATTATCGGCCAACTGGCCT\n+CAATCCTCTACTTCTCCCTAATTCTCATTTTTATACCACTCGCAAGCACC\n+ATCGAAAACAATCTTCTAAAATGAAGAGTCCCTGTAGTATATCGCACATT\n+ACCCTGGTCTTGTAAACCAGAAAAGGGGGAAAACGTTTCCTCCCAAGGAC\n+TATCAAGGAAGAAGCTCTAGCTCCACCATCAACACCCAAAGCTGAAATTC\n+TACTTAAACTATTCCTTGATTTCTTCCCCTAAACGACAACAATTTACCCT\n+CATGTGCTATGTCAGTATCAGATTATACCCCCACATAACACCATACCCAC\n+CTGACATGCAATATCTTATGAATGGCCTATGTACGTCGTGCATTAAATTG\n+TCTGCCCCATGAATAATAAGCATGTACATAATATCATTTATCTTACATAA\n+GTACATTATATTATTGATCGTGCATACCCCATCCAAGTCAAATCATTTCC\n+AGTCAACACGCATATCACAGCCCATGTTCCACGAGCTTAATCACCAAGCC\n+GCGGGAAATCAGCAACCCTCCCAACTACGTGTCCCAATCCTCGCTCCGGG\n+CCCATCCAAACGTGGGGGTTTCTACAATGAAACTATACCTGGCATCTGGT\n+TCTTTCTTCAGGGCCATTCCCACCCAACCTCGCCCATTCTTTCCCCTTAA\n+ATAAGACATCTCGATGGACTAATGACTAATCAGCCCATGCTCACACATAA\n+CTGTGATTTCATGCATTTGGTATCTTTTTATATTTGGGGATGCTATGACT\n+CAGCTATGGCCGTCAAAGGCCTCGACGCAGTCAATTAAATTGAAGCTGGA\n+CTTAAATTGAACGTTATTCCTCCGCATCAGCAACCATAAGGTGTTATTCA\n+GTCCATGGTAGCGGGACATAGGAAACAAgtgcacctgtgcacctgtgcac\n+ctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacct\n+gtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgt\n+gcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgc\n+acctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcac\n+ctgtgcacctACCCGCGCAGTAAGCAAGTAATATAGCTTTCTTAATCAAA\n+CCCCCCCTACCCCCCATTAAACTCCACATATGTACATTCAACACAATCTT\n+GCCAAACCCCAAAAACAAGACTAAACAATGCACAATACTTCATGAAGCTT\n+AACCCTCGCATGCCAACCATAATAACTCAACACACCTAACAATCTTAACA\n+GAACTTTCCCCCCGCCATTAATACCAACATGCTACTTTAATCAATAAAAT\n+TTCCATAGACAGGCATCCCCCTAGATCTAATTTTCTAAATCTGTCAACCC\n+TTCTTCCCCC\n' |
| b |
| diff -r 000000000000 -r 8d92246f41bb test-data/hg19chrX_midpart.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hg19chrX_midpart.fasta Thu Jun 05 15:15:34 2014 -0400 |
| b |
| b'@@ -0,0 +1,751 @@\n+>chrX_part\n+TCTGTTAGACTCACTCAGGACTGTATGAGCATCACCTGTGCTGCACTGTG\n+ACTTTACAGATATTAACGAAGAATCCTCAAGGATCTGTGTTTCGGAGGCA\n+ATCTGGTGACCAGCAGCATTCTCAGCATTCAAATGATGACCCTCAAAATA\n+GGCAGTAGCATTTTTATCTGCTCTGTCATTGGCTACAAAAGACGGCACCA\n+CTGGTACTGATCTTGGTAGCTGATATTCAGGAGAAAGGCTGACCAAGGGT\n+GTATATATGCTGGTGTACTGGGGCAAACCTGGTAACACATTTATGTATGC\n+TGGCGATGTCCGGGTGTTATCAAATCTCTGGAAAGGAAGATACGTACAGT\n+ATCCTGTGACCAAATGGGATTGAGCCCAATAAGTTGGTTTCACATCCTCA\n+AGAACCGGTTTGGGAGAATTAGAGGAGACTCGCTTGTAATTTGCATCCTC\n+AGAGCCTGGTTTGGGAGAATTAGAAGAGAACCCTTTGGGTTTCCCATCCT\n+CAGAAACTTGTCTAGAAGAATTATCGGATACTGGTTTGGCCTTCACATCT\n+TCACAAGCTGGCTTGGGAGAATTTGCAGACAAAGGTTTGGGTTTCACATC\n+TTCAGAAGCTGGTGCTGAAGATGAACCTGATACTGGTTTAGACTTTACAT\n+CTGGTTTAAATTCCCTAGCAGCTGAATTAAGTGGTAGTTTAACTTGTAAA\n+TACTCTCCTGCTTTTGAAATGTCTTCTACTTTTGTTTTAATGTTTTTCTT\n+CTTTCTTTTTTTCTTGAGCCGTGATGCAACTTTCTTCAATGCAATACAGT\n+TGTCAATCACAACAAAACGGGGACATCCCAAGAGAAAAGATTTTAAACCT\n+CCTGCTTTTTCTAGTATTGGTCGAGTTTCTTCTGGGAAAAACTCATATTC\n+TTCAGAGAACATCTTGTGACTCATGTCCAAGGGACCATGTTCCTCCAACA\n+ACTGAGAGAAGTAATCATATAGAGTTGAACATTTTTGTTTTGGGTTCATG\n+TCCCATAGCTTCTTATTGCGGACAACATATTCATTACTGTGTTGGTCATA\n+GAGAGCTTCAAATTCTTCTACGTCTTGCCGAAGATGGTCAGGCACTGCAA\n+ATGGGCCTGCAGTATCTGAATTTTGATTGCTATGGTCTTCACTTGAAGTG\n+ATGATCTCATTATTTGGAGTTACTGAAGTTGTTCCAGACCCAACTAACAT\n+AGGCTTTGAATCCTTTGGTTTCTTTTTCTTGCCTTTGTTTTTCACCTTGG\n+TAGAACTAAACGGTGCTTCGCCACTGTCTTGTTTCCTTAACACAGTACAG\n+CGGCTGTCCATTATATCAAAGAATTCATCTAAAGCACTATGTAATGCTGG\n+GAACTTGTCTCTGTGTTCTTCTAGCAGCCATATTAAACAGCGGGCTTCCT\n+TCGATGATGTTGGCTCAAAGAAATAATCAAGTTGCTTTCCTTCTATAGAG\n+TCTAGTTTGTGACCATATTTCTCATTCCAGAGGAAAGTCATGATGCTAAA\n+ATCAAGCTGTTTAAGAGATGCTTCATACCGAGAAAAGAAAGGTCCTGTGG\n+CATCTAAGCCAAAGCTATTAAGTTTTCGGATCCAGGCGGCTAATTTGGGC\n+TCCACTTCTTTAAGCTCACTCAAAACATGCAGAAATATTCTTGTCTTTAC\n+TCTGTTCTTTTCTTGAATCAAGTGACGAATAACATAGTCCACTGCTTCAT\n+TTAGAAAATTTCTGCTTGAAAAACAGGTTGTATAGTCCTCTGTGCTCAAA\n+ACTTTCCAAGAAAGTAATTCTTTGAGAAGCGTGGCTGTATTCCATATGCC\n+GGATTTAATCTTGTCAGCATACTGCTTTATACACTGTAGAATTCTGTCAT\n+CAAGGAACTGACAATGCTGAACATTGTCTACAGTTTCTTTCTGCTCTTCG\n+TTTTTGGGTGGATTACTTTCTCTTAAGTCCTCCTCCATTCTTTCTTGTGC\n+TAATTTTTTTGCTTCTTTTTTTTGGATCTTTCTCTTCAATTTTTTGTCTT\n+CTTTCAGTCTTAGTTTCTCTAGGCTAGAACATTTCTGTTTCAGAATAGGT\n+CTTGGAGGAACCTTTTCTTTTATGACCTTGTGTTCAAATTCACATTTAAC\n+TTGACCACCACTGCTGAAGATGATAATCTTAGAAATGACACCTTCACAGT\n+CAGGGGTAAGACATATTCCTTGTAGAAAATCCTTGTCAATTTTATCATTA\n+AAGGTTGTGGTTTTTAACTTCTTCCAGCAATTCATGTGAAATTCTATTTT\n+ACAGTACTGGCAACAGCTGATGCGTATAAAACCCTTAAAGTCTGGATCAG\n+TTATGTATATCTGGATCTTAGAATATCCACAGCACTTCTGATAGCAACAA\n+ATGGCATCTGGCACTGGAGGGAACTTGCATTCTTCAACAAATTTCTCTAA\n+CAGCATCTTTATTTTTTCTGGCTGAGACTCTTCAATAATCACATTACTTG\n+TGGGCCAAGTTAACACTCCAGGAAGACGATAAATCAAGGTTCTTGCTTTC\n+TCAAAGTGATTGAGAGCTTCTAGAAATCTGTTTTTTTTCAAATATACTTT\n+TCCAATTCCACAGTAGGCCAAGCAATCAAGTCCCTCATTGTGGTAGTGTT\n+CAATAATCCTCTTAAACTGGTTTTCAGCTTCAGATAGTTCTTCAGGCTGT\n+CCTATTCCAAGGAGTGAAATGGCAAGTCCATAGACAACCAAGACATAGTT\n+AATCATGGCCAGATTCAATTGCTTTATTTTTTGAGGATCTAAACCATTCA\n+GCAACTCTGTAAAGGCATGTGCGGCACTGCGGCAACGCTGCTCCAATAAG\n+GCTGTATAGCCATCTTGAATTAAGCTTCTCAGCATTGTCATTATATTAGC\n+AAAATCCTGGTGTGCACCTCTGGAAGATTTAGAAAACTGTTTCTCCAAGA\n+TGTTCTTCAAATCTGCTGGTAAAGTCAATTGTGAACTAGAACTGAACTTT\n+TCTGATTCATTGTTTCGAGATTTTTGTTTTCCTTTATGTTTCGGAGGCTG\n+ACTTGATGGTGGTGAAAATTCAGGATGACAGTCACAATCATCTACCATCA\n+ATGCCTCATCCATCACCTTTAGATTCTGATTACCACCGTTAGCCATTTCG\n+TGATTAATTTTTCTGAAATCTCTTTCCTTCTCCACAAAGTTAAGTGAAGT\n+ACTAAATACAGGTGCTGATAAACTCCTAGGTGTGTAGGCCCTGTTTTCAT\n+AAAAGGCTTTAATTGGATTCTTATTTGCTGTTCGACCTTGTAGGTCTTCT\n+ATTTGTTTTTGTAACTTTACATGCTGCTGAATTAGATCCTTGATTCCCTC\n+AGGGTCATTTTTACAGAGTTTTTGAGCTGTTATGTTTGCTTGCAGGGCCC\n+AGTTATATTCCCCCAGCATAGAAAGAGCATCACAATAACGATAATGACCC\n+TTTGGCCAAGTGTTCTTCAGAATAGTGGCTCTCTTTCCATCACCAAGTGC\n+ATTTCTAAACTGTCCAGTACGAAGAAAACAAAGAGCTCGGTTACCATAAA\n+GAAGGTGGTTTTCAGGTCTATATTCAATGGCTCTGGTGTAATAGATAATA\n+GCTATATCAAATCTTTCTTTGGAAAACTCTTCATTTCCTTTCATTTTCAT\n+TAGTTCTCCTTGCTCTATACAATCCATACAACTTTGGGTTTTAAGTTCTT\n+CAAGCAAATTGCAGTCTTCCATTACAATTTTAGTTATGTGGTACTTGTAT\n+TCAGTAAAGAAAATACTTAACATAGGCCAACAATTGTCAATTGATCCTAA\n+TTTAGTTAGAATTGTTACATCGCCTGCATATTTTATCCAATTCAGAGCTT\n+CTTCCATTGCCAAGAT'..b'gtgtggaagcatgacaccggcagatatgaaactagtgccctccatg\n+catgcattcacacaagcagcagtggcaacacagggtggaggccagggctt\n+ctggtctctatgcacacatgcaagcaatggtggtgcagcaggagtgggca\n+gggtgtgctcacatacagagtagtggcatagtggggtgcatacataaatg\n+catgctggcagggaagggagttgaggtcaaccagcatgcacatgcactga\n+caaagcaatgtcaggggtagctgtgggcaaatttgtgctgccaaaggggc\n+acagaggaggctgtagttgggggagtgtgtgggtgggcttgtgtgcacca\n+gtagaagctgctctgctggagctctgcaaatgtgaggcatggtctgtcag\n+tgcaggaactgtgatgtgtgtctccaggaggcattccagctgggcaccca\n+aggctgcactgcaagcatgtgcactaggggagtaaaggtgagccttgggg\n+gatggacatccctggctgtactccactgacgacactcacacaccaaatcc\n+cttgggttccacactggctggtcttctgcctctaccacttctctaagcag\n+ctctgcctgccactacaagtgtccatgcaggttagggggtctcctgctgc\n+cagaattccagagatccatggtgtgggcaggttgctcctcacctgctcaa\n+cttaccttttccctgggagtggctggtggccaggaacaagtcccagtgca\n+tggaagtcccttgcagggttcccaccttcctttctctatagcccagcatc\n+tgagtcttccctccatcaattctcattgtctttcctccaaatatatgctt\n+ggagtgtgccaggcttcccaatgtcctagtctcttggtggcagatatttc\n+acttggctgcactgagtgagccaccttgccTATAATTTTTagaaggcttt\n+taactagatattatctcatttatccatttttgctttggttgtctgtgctt\n+gtgaggtactactcgaatctttgcctagtccagtgtcttggagaatttct\n+gtgatattttcttgtagtagttttatagtttgaagtgttagatAATAATC\n+AGACTCAACAAATGGCAGAATTCACAATTAATGAAACACACAATAGTAGA\n+TCAATGTAAAAATAACTTTAAAGATAAATCTGGTTTAAATATTGAAAGAG\n+ACGAAAAAGGGACTGTAATTTGTAAGACAAGAACAGGAATCTTCTTTAAC\n+AATAAGGTATATTTTAAAAAAGAAACAACTGGAAATTTTATAAATGAAAC\n+AGGTATGCACTGAAATAAAACCATTAATAGATTGCTCATATATTTCGACA\n+GAGTCAAGGCTGAGTATTGAGTTAGAACACAGATTAgacaggggtcacat\n+ctaattcatccctgtaccccagtgtctaatacaATAAGGCCAACATATAA\n+CAAGTGTTTCAAAATTGCTTATTAAATTGAACTGGGTAAGTGGTCTTCAG\n+ATAGGCCAGACATCTCTGGGCTTCTCCAGTGTATAGGGGTTTCAGGGGGG\n+CAGGACAGCCTCAAGTGGAACTACCTGAGGGCTGGGCAGAGCTGGGTGTG\n+GTTCCTCGTGGGTGGAGTAGGCAATAAAGGCTATCTAGAAAAGAGGTACT\n+GGCTTTACCATTCACCTCAGGGACTAACTAGTTTGTTCCCTCTCAGAGCT\n+GGAGAGTGAATTATCTTCATTCAGCACATGTCTGGCTACTATTCATCCTC\n+CCCGTGTCAAAGAtacttaaagtagtgaaaacagatcttattcagtaact\n+actaacaatgctgaaaaaagctgagctccattccaatttgtgcaaaggtg\n+gtttgggcattttaaagggagaatgatgttgggggctgagtagagtcaga\n+gaagtgaaaactacaaaatattggtcagtgtaaatgcactgtgtttaggc\n+catctgtgtttgttagccggcagttatcaaagttaggatttgtccttcca\n+cagagactggaagacagggttcctatctttcttgattacatttcaaagaa\n+atggctctcaggtccttgggagagacatttctaaattgtaagagatacat\n+attcactgtaataagcccttttaaataagtgctctaaaaaagggaggtca\n+gggtcttatcatcagattttggcaagaacaaacagtatattttcctggca\n+gcattgaactttctcaggcagtcattttagtggggtttggggtcaattat\n+agggacccagccttaggctgtgagaaaccatgctagagtttagttagttc\n+ccttactactacaggggtttggacagaagtgttagttccaggagttctgc\n+agttctcCCCTGTTAGAAACTCTAAGGATGTCCATGGCTATATTTATGTG\n+ACAAAACATTATATAAATGGTTGATGTTAACAACCTGCCAAAGATTATTT\n+TTCTTACTCCCTCCCTCCTAGGCCTTTTGCAACCCCCACCCCCATTACAG\n+AGAAAGGGGAACAATCCTGTGTGCAACCAGCTCTCCATACCTGGCCCCCA\n+CAGCTGGATCTCAGGGTGATCTCCTTTACCACCTGGAATGATAAATACCT\n+TCTTCCAGGACAGCAGCCCTCTTTATCTTGCAGAAGGAGGCAATCCAGGC\n+TGGGTCCTTCGCCAGGGTACCATTTTCCTGCAGCCTCTACAGGAAAATAA\n+GCTCGTCTGAGCTGTGGCCTGAGCAGGTCAAGTCTTCAGTAGAGAGGTCA\n+ACTTTAGAAACAATGGCTATTCTTGTGTCTTCCCTTTCTCTATCCTCCTT\n+CCCTTCTATATTACCAAAGAAGTGAACACTTAGAGGACAGAAACTTTATC\n+CTGTCTAGCCCATGCCAAAGAAGATGTTCTCAAGAGAAGAACAGTTTGAA\n+AGAGGCTGCTTGGACCTTAGGCCTCAGCTCCCAACTCCCTCCCTAACTCT\n+TTCCCCTTAGAAAGGAAATCATCCTCACTGACTGAAGCCCTGAGTGGCAA\n+GTCAGCAGGTGGTTTCCTGTAGGACACTGAGGTCTGCTTAAATAGACCAC\n+CCATATGCTTCCATAAAAATATCTTGTGTATTGGAGTCTACAAATAATAT\n+ATTCTTGATGCACCTAAACCTCACTAATTCATAACCACCTGGGGTTAACA\n+TTTGCCTGAAGTATTTTCTAAAGAAAACAAAGACTAGTGATTCTAACAAC\n+CCAGATGTTGTTTGACTTCAGCTACCCAGGTGTTGACAAGTAGTAGTTTT\n+AAAAGCAGTTGTATGGCATGGAAATATCACTAGACTAAGATACAACTGGT\n+TTGGGTCACAGTTCTGAAATCATCAAATGGTAGATATGTGACTGGGATTT\n+TCTATCAATTTATTGAAAACAGCATTAAGTggcctagaaagatgtgagta\n+actttcccaagttcacacagctagtaagtgacagaaaaagtaccgtccag\n+atctagagttcttaaccattccaaatatattgccccatccTTATCAGGTG\n+CTTGTTTATTCCTATGGTTTCTAGAGAGCAAAAGTATTAATATTTCAGGG\n+TACACTTTTTTGCAACTTTTTTTGGCAACTATCTTCAAATCCTGCCTGCA\n+GAGAATTCCTAAAGATATTGTTGAGCACTCATTGAGATGGAAGACAAACC\n+CTGTTCAACGAGAAATCTTACTGTCTGGAGATCCCCTCTAAGAAAGAAGA\n+AGGAGACTGCAGGGGTCTTGTCTGAACATGAAAGACACTTATGAGTTGGt\n+ctagattgtcagtattggaggatttaggggcagcaatccttggggcaggg\n+ggaatttccttgaaatccacatatgccagtctagctcagcttttgcttgg\n' |
| b |
| diff -r 000000000000 -r 8d92246f41bb test-data/phiX.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phiX.fasta Thu Jun 05 15:15:34 2014 -0400 |
| b |
| @@ -0,0 +1,79 @@ +>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 000000000000 -r 8d92246f41bb tool-data/bwa_index.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/bwa_index.loc.sample Thu Jun 05 15:15:34 2014 -0400 |
| b |
| @@ -0,0 +1,38 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of BWA indexed sequences data files. You will need +#to create these data files and then create a bwa_index.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bwa_index.loc +#file has this format (longer white space characters are TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, for example, if you had phiX indexed stored in +#/depot/data2/galaxy/phiX/base/, +#then the bwa_index.loc entry would look like this: +# +#phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa +# +#and your /depot/data2/galaxy/phiX/base/ directory +#would contain phiX.fa.* files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt +#...etc... +# +#Your bwa_index.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: +# +#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa +#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa +#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa +#...etc... +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +# |
| b |
| diff -r 000000000000 -r 8d92246f41bb tool-data/bwa_index_color.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/bwa_index_color.loc.sample Thu Jun 05 15:15:34 2014 -0400 |
| b |
| @@ -0,0 +1,38 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of BWA indexed sequences data files. You will need +#to create these data files and then create a bwa_index_color.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bwa_index_color.loc +#file has this format (longer white space characters are TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, for example, if you had phiX indexed stored in +#/depot/data2/galaxy/phiX/color/, +#then the bwa_index.loc entry would look like this: +# +#phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/color/phiX.fa +# +#and your /depot/data2/galaxy/phiX/color/ directory +#would contain phiX.fa.* files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann +#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt +#...etc... +# +#Your bwa_index_color.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: +# +#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/color/phiX.fa +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/color/hg18canon.fa +#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/color/hg18full.fa +#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/color/hg19.fa +#...etc... +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +# |
| b |
| diff -r 000000000000 -r 8d92246f41bb tool_data_table_conf.xml.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_data_table_conf.xml.sample Thu Jun 05 15:15:34 2014 -0400 |
| b |
| @@ -0,0 +1,13 @@ +<!-- Use the file tool_data_table_conf.xml.oldlocstyle if you don't want to update your loc files as changed in revision 4550:535d276c92bc--> +<tables> + <!-- Locations of indexes in the BWA mapper format --> + <table name="bwa_indexes" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bwa_index.loc" /> + </table> + <!-- Locations of indexes in the BWA color-space mapper format --> + <table name="bwa_indexes_color" comment_char="#"> + <columns>value, dbkey, name, path</columns> + <file path="tool-data/bwa_index_color.loc" /> + </table> +</tables> \ No newline at end of file |
| b |
| diff -r 000000000000 -r 8d92246f41bb tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Jun 05 15:15:34 2014 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="bwa" version="0.5.9"> + <repository changeset_revision="0eb3d3c40344" name="package_bwa_0_5_9" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |