| Next changeset 1:047a20d4258f (2021-04-02) |
|
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 29e40a76f1e249c3ed73f9129ad711beba34eb07" |
|
added:
clip_overlap.xml macros.xml test-data/input.bam test-data/input.sam test-data/input_qname_sorted.bam test-data/output.sam test-data/output_qname_sorted.bam test-data/output_stats.txt |
| b |
| diff -r 000000000000 -r 79725ecf10a3 clip_overlap.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clip_overlap.xml Mon Mar 29 14:15:42 2021 +0000 |
| [ |
| b'@@ -0,0 +1,157 @@\n+<tool id="bamutil_clip_overlap" name="BamUtil clipOverlap" version="@WRAPPER_VERSION@" profile="@PROFILE@">\n+ <description></description>\n+ <macros>\n+ <import>macros.xml</import>\n+ </macros>\n+ <expand macro="requirements"/>\n+ <expand macro="edam"/>\n+ <command detect_errors="exit_code"><![CDATA[\n+## clipOverlap uses the output file\n+## extension to determine the output format.\n+#if $input.ext.endswith(\'bam\'):\n+ #set tmp_out = \'output.bam\'\n+#else:\n+ #set tmp_out = \'output.sam\'\n+#end if\n+trap \'>&2 cat output.log\' EXIT;\n+touch \'output.log\' &&\n+bam clipOverlap\n+--in \'$input\'\n+#if str($storeOrig):\n+ --storeOrig \'$storeOrig\'\n+#end if\n+$stats\n+#if str($input.ext) == \'qname_sorted.bam\':\n+ --readName\n+#end if\n+$overlapsOnly\n+#if str($excludeFlags):\n+ --excludeFlags $excludeFlags\n+#end if\n+$unmapped\n+--noPhoneHome\n+--out \'$tmp_out\'\n+2> \'output.log\'\n+&& mv \'$tmp_out\' \'$output\'\n+#if str($stats):\n+ && cp \'output.log\' \'$output_stats\'\n+#end if\n+ ]]></command>\n+ <inputs>\n+ <param name="input" type="data" format="sam,bam,qname_sorted.bam" label="Select SAM or BAM file on which to clip overlapping read pairs"/>\n+ <param argument="--storeOrig" type="text" value="" label="Enter a tag in which to store the original CIGAR" help="Leave blank to skip">\n+ <sanitizer invalid_char="">\n+ <valid initial="string.letters,string.digits"/>\n+ </sanitizer>\n+ </param>\n+ <param argument="--stats" type="boolean" truevalue="--stats" falsevalue="" checked="false" label="Output statistics on the overlaps?"/>\n+ <param argument="--overlapsOnly" type="boolean" truevalue="--overlapsOnly" falsevalue="" checked="false" label="Only output overlapping read pairs?"/>\n+ <param argument="--excludeFlags" type="integer" optional="true" value="" label="Enter an integer representation of a flag to skip records with any of the specified flags set" help="See the help section below for information about this option"/>\n+ <param argument="--unmapped" type="boolean" truevalue="--unmapped" falsevalue="" checked="false" label="Mark records that would be completely clipped as unmapped?"/>\n+ </inputs>\n+ <outputs>\n+ <data name="output" format_source="input" metadata_source="input"/>\n+ <data name="output_stats" format="txt" label="${tool.name} on ${on_string}: Statistics">\n+ <filter>stats</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test expect_num_outputs="1">\n+ <param name="input" value="input.sam" ftype="sam"/>\n+ <output name="output" file="output.sam" ftype="sam"/>\n+ </test>\n+ <test expect_num_outputs="2">\n+ <param name="input" value="input.bam" ftype="bam"/>\n+ <param name="storeOrig" value="6M"/>\n+ <param name="stats" value="--stats"/>\n+ <output name="output" file="input.bam" ftype="bam"/>\n+ <output name="output_stats" file="output_stats.txt" ftype="txt"/>\n+ </test>\n+ <test expect_num_outputs="1">\n+ <param name="input" value="input_qname_sorted.bam" ftype="qname_sorted.bam"/>\n+ <output name="output" file="output_qname_sorted.bam" ftype="qname_sorted.bam"/>\n+ </test>\n+ </tests>\n+ <help>\n+**What it does**\n+\n+Clips overlapping read pairs in a SAM or BAM file based on criteria.\n+\n+The input file and resulting output file are sorted by coordinate (or readName if specified in the options).\n+\n+When a read is clipped from the front:\n+\n+ * the read start position is updated to reflect the clipping\n+ * the mate\'s mate start position is updated to reflect the record\'s new position\n+ * the record is placed in the output file in the correct location based on the updated position\n+\n+To handle coordinate-sorted files, SAM/BAM records are buffered up until it is known that all following records will have a later start position. To prevent the program from running aw'..b'ped, 0-based position is left as the original (not modified) |\n++------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------+\n+| Clip occurs after the read ends | Entire read is soft clipped, 0-based position is left as the original (not modified) |\n++------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------+\n+| Clip occurs before the read starts | Nothing is clipped. The read is not changed. |\n++------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------+\n+\n+**Clipping from the back**\n+\n++----------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------+\n+| Clip location | How it is handled |\n++==================+=========================================================+===================================================================================================================+\n+| If the clip position falls in a skip/deletion | Removes the entire skip/deletion |\n++----------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------+\n+| If the position immediately before the clip is a deletion/skip/pad | Remove the deletion/skip/pad |\n++----------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------+\n+| If the position immediately before the clip is an insertion | Leave the insertion, even if it results in a 70M3I27S |\n++----------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------+\n+| Clip occurs at the first position of the read (the entire read is clipped) | Entire read is soft clipped, preceding insertions remain, 0-based position is left as the original (not modified) |\n++----------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------+\n+| Clip occurs before the read starts | Entire read is soft clipped, 0-based position is left as the original (not modified) |\n++----------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------+\n+| Clip occurs after the read ends | Nothing is clipped. The read is not changed. |\n++----------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------+\n+\n+ </help>\n+ <expand macro="citations"/>\n+</tool>\n+\n' |
| b |
| diff -r 000000000000 -r 79725ecf10a3 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Mar 29 14:15:42 2021 +0000 |
| b |
| @@ -0,0 +1,24 @@ +<macros> + <token name="@WRAPPER_VERSION@">1.0.15</token> + <token name="@PROFILE@">20.09</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@WRAPPER_VERSION@">bamutil</requirement> + </requirements> + </xml> + <xml name="edam"> + <edam_topics> + <edam_topic>topic_0091</edam_topic> + <edam_topic>topic_0080</edam_topic> + </edam_topics> + <edam_operations> + <edam_operation>operation_0369</edam_operation> + </edam_operations> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1101/gr.176552.114</citation> + </citations> + </xml> +</macros> + |
| b |
| diff -r 000000000000 -r 79725ecf10a3 test-data/input.bam |
| b |
| Binary file test-data/input.bam has changed |
| b |
| diff -r 000000000000 -r 79725ecf10a3 test-data/input.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.sam Mon Mar 29 14:15:42 2021 +0000 |
| b |
| b'@@ -0,0 +1,178 @@\n+@SQ\tSN:>chrM\tLN:0\n+@SQ\tSN:GTATTCTTACTCCATAAACACATAGGCTTGGTCCTAGCCTTTTTATTAGT\tLN:0\n+@SQ\tSN:CTAAATCACGTCTCTACGATTAAAAGGAGCAGGTATCAAGCACACTAGAA\tLN:0\n+@SQ\tSN:ATAAAAATTAAGCTATGAACGAAAGTTCGACTAAGTCATATTAAATAAGG\tLN:0\n+@SQ\tSN:ATAAATCTCCGGCGTAAAGCGTGTCAAAGACTAATACCAAAATAAAGTTA\tLN:0\n+@SQ\tSN:AAGTGACTTTAATACCTCTGACTACACGATAGCTAAGACCCAAACTGGGA\tLN:0\n+@SQ\tSN:AAGCTATTCGCCAGAGTACTACTAGCAACAGCCTAAAACTCAAAGGACTT\tLN:0\n+@SQ\tSN:CCGATAAACCCCACCATCCCTTGCTAATTCAGCCTATATACCGCCATCTT\tLN:0\n+@SQ\tSN:AACGTTAGGTCAAGGTGTAGCCCATGGGATGGAGAGAAATGGGCTACATT\tLN:0\n+@SQ\tSN:TGGAGACTAAAGGAGGATTTAGCAGTAAATTAAGAATAGAGAGCTTAATT\tLN:0\n+@SQ\tSN:CACAAATCATAACATAACATAAAACCGTGACCCAAACATATGAAAGGAGA\tLN:0\n+@SQ\tSN:TGTAGCTTAAACAAAGCATCCAGCTTACACCTAGAAGATTTCACTCAAAA\tLN:0\n+@SQ\tSN:TTAGTCACTTAACTAAAACATTCACCAAACCATTAAAGTATAGGAGATAG\tLN:0\n+@SQ\tSN:ATGCATTAAAAGTACTAAACAGCAAAGCTTACCCCTTTTACCTTTTGCAT\tLN:0\n+@SQ\tSN:CGAAACCAGACGAGCTACCTATGAACAGTTACAAATGAACCAACTCATCT\tLN:0\n+@SQ\tSN:AGCCTGGTGATAGCTGGTTGTCCAGAAACAGAATTTCAGTTCAAATTTAA\tLN:0\n+@SQ\tSN:AAAGGTACAGCTTTTTAGATACAGGTTACAACCTTCATTAGAGAGTAAGA\tLN:0\n+@SQ\tSN:TTCAAGCTCAACGACACATCTATCTTAATCCCAACAATCAACCCAAACTA\tLN:0\n+@SQ\tSN:TTAATATGAGTAACAAGAATTATTTCTCCTTGCATAAGCTTATATCAGAA\tLN:0\n+@SQ\tSN:TCATCTATTTAAACCATTGTTAACCCAACACAGGCATGCATCTATAAGGA\tLN:0\n+@SQ\tSN:ACCAAAAACATCACCTCTAGCATTTCCAGTATTAGAGGCACTGCCTGCCC\tLN:0\n+@SQ\tSN:taatcacttgttccctaaatagggacttgtatgaatggccacacgagggt\tLN:0\n+@SQ\tSN:cgggaatgactaaataagacgagaagaccctatggagcttTAATTAACTG\tLN:0\n+@SQ\tSN:TTGATTGAATCAGCAATTTCGGTTGGGGTGACCTCGGAGAACAAAACAAC\tLN:0\n+@SQ\tSN:TTGATCCAAACCATTGATCAACGGAACAAGTTACCCTAGGGATAACAGCG\tLN:0\n+@SQ\tSN:TTGGATCAAGACATCCTAATGGTGCAACCGCTATTAAGGGTTCGTTTGTT\tLN:0\n+@SQ\tSN:CGGTTTCTATCTATTCTATACTTTTCCCAGTACGAAAGGACAAGAAAAGT\tLN:0\n+@SQ\tSN:AATCTAACTAATTTATAACTTCTACCGCCCTAGAACAGGGCTCgttaggg\tLN:0\n+@SQ\tSN:caactcctctccctaacaacaTGTTCATAATTAACGTCCTCCTCCTAATT\tLN:0\n+@SQ\tSN:CTTAGGCTATATGCAACTTCGCAAAGGACCCAACATCGTAGGCCCCTATG\tLN:0\n+@SQ\tSN:CTACAACCACTAACATCATCGACATCCATATTCATCATCGCACCAATCCT\tLN:0\n+@SQ\tSN:CACTAATCAACATAAACCTAGGAATTCTATTCATACTAGCCATGTCCAGC\tLN:0\n+@SQ\tSN:CGCCCTAATTGGAGCTCTACGAGCAGTAGCACAAACCATCTCATACGAAG\tLN:0\n+@SQ\tSN:ACATTATCAACACTTATTATTACCCAAGAATACCTCTGATTAATCTTCCC\tLN:0\n+@SQ\tSN:ACCGAGCTCCATTTGACCTAACAGAAGGAGAATCAGAACTCGTCTCTGGA\tLN:0\n+@SQ\tSN:ATACGCAAACATCATCATGATAAACATCTTCACAACAACCCTATTTCTAG\tLN:0\n+@SQ\tSN:ATTAAAGCTCTCCTTCTAACATGTTCCTTCCTATGAATCCGAGCATCCTA\tLN:0\n+@SQ\tSN:TACCACTCACACTAGCCCTCTGCATATGACACGTCTCACTTCCAATCATA\tLN:0\n+@SQ\tSN:ACTTTGATAGAGTAAAACATAGAGGCTCAAACCCTCTTATTTctagaact\tLN:0\n+@SQ\tSN:ttacaccatgtcctaCAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCAT\tLN:0\n+@SQ\tSN:CTTCACAACTATTCTAATAACAGTTCTTCTAGGAACTATAATCGTTATAA\tLN:0\n+@SQ\tSN:GCCATTATCCCTATCCTAATAAAAAAGTACAATCCCCGAACCATAGAAGC\tLN:0\n+@SQ\tSN:TAGCGATCATCATTAACCTCATACACTCAGGCCAATGAACAATCACAAAA\tLN:0\n+@SQ\tSN:ACTTGGACTCACACCATTCCACTTCTGAGTACCCGAAGTCACACAGGGCA\tLN:0\n+@SQ\tSN:ATATCAATCCTATATCAAATCTCACCCTCAATTAACCTAAATATCTTATT\tLN:0\n+@SQ\tSN:AAACCCAACTACGAAAAATCATAGCATACTCGTCAATCGCGCATATAGGA\tLN:0\n+@SQ\tSN:ATTAATTTACATTATAATAACACTCACAATATTCATACTATTTATCCACA\tLN:0\n+@SQ\tSN:CTAACCACTACACTAATCTTAATTACCTTACTATCCATAGGAGGCCTCCC\tLN:0\n+@SQ\tSN:AAAATAGCAGCATCATCCTCCCCACACTAATAGCCATTATAGCACTACTC\tLN:0\n+@SQ\tSN:CCCATCCACAAACAACATAAAAATAAAATGACAATTCGAAACCAAACGAA\tLN:0\n+@SQ\tSN:ACCCCCATACTATCAATTTTGGACTAGGAATTTAGGTTAACATCCCAGAC\tLN:0\n+@SQ\tSN:TAAGGACTGCGAGACTCTATCTCACATCAATTGAACGCAAATCAAACTCT\tLN:0\n+@SQ\tSN:TTTAGTTAACAGCTAAATACCCTAATCAACTGGCTTCAATCTACTTCTCC\tLN:0\n+@SQ\tSN:TCCTTTGAATTTGCAATTCAATGTGAAAATTCACCACGGGACTTGATAAG\tLN:0\n+@SQ\tSN:CCATCTTACCTATGTTCATCAACCGCTGACTATTTTCAACTAACCACAAA\tLN:0\n+@SQ\tSN:AACTGCCCTAAGCCTCCTAATCCGTGCTGAATTAGGCCAACCTGGGACCC\tLN:0\n+@SQ\tSN:GTAATAATTTTCTTTATGGTCATACCCATTATAATCGGAGGATTCGGAAA\tLN:0\n+@SQ\tSN:TAAACAACATAAGCTTCTGATTACTTCCCCCATCATTCCTACTTCTTCTC\tLN:0\n+@SQ\tSN:TCCTCTAGCTGGAAATCTGGCGCATGCAGGAGCCTCTGTTGACTTAACCA\tLN:0\n+@SQ\tSN:TTTATTACCACAATCATTAACATAAAACCACCAGCCCTATCCCAATATCA\tLN:0\n+@SQ\tSN:TAGCCCTCCCGGTCCTAGCAGCAGGCATTACCATGCTTCTCACAGACCGT\tLN:0\n+@SQ\tSN:TTATCAACACCTATTCTGATTCTTCGGACACCCCGAAGTCTATATTCTTA\tLN:0\n+@SQ\tSN:AAAAAGGAACCTTTTGGCTACATGGGTATAGTGTGAGCTATAATATCCAT'..b'CACATCTCT\tLN:0\n+@SQ\tSN:ACTCCAAAGACCTCATCATCGAAACCGCCAACACATCGTACACCAACGCC\tLN:0\n+@SQ\tSN:TACCCGAATCATCTTCTTTGCACTCCTAGGGCAACCCCGCTTCCTCCCTC\tLN:0\n+@SQ\tSN:CTCTTAATTGGCAGCATTTTTGCCGGATTCTTCATCTCCAACAATATCTA\tLN:0\n+@SQ\tSN:CCCTCGCAGTAACCATCCTAGGATTTACACTAGCCCTAGAACTAAGCTTG\tLN:0\n+@SQ\tSN:CAACCTCCTAGGATACTACCCAACAATTATACACCGACTCCCACCGCTCG\tLN:0\n+@SQ\tSN:TGACTAGAAAACATCCTGCCAAAATCTATCTCCCAGTTCCAAATAAAAAC\tLN:0\n+@SQ\tSN:CATTCCTCATCACCCTTACCCTAAGCATACTACTTTTTAATCTCCACGAG\tLN:0\n+@SQ\tSN:ATCACAACCCAAGCCCCATAACTATACAATGCAGCAGCCCCTATAATTTC\tLN:0\n+@SQ\tSN:CACCACTAAACTTAAACACTACCCCCACTTCCTCACTCTTCAGAACATAT\tLN:0\n+@SQ\tSN:AGTCGTATTAGACACCCATACCTCAGGATACTGCTCAGTAGCCATAGCCG\tLN:0\n+@SQ\tSN:ATCAACCCCAAAAAGGACCCTCCAAAATTCATAATAATACCACAACCTAC\tLN:0\n+@SQ\tSN:AAGAAAACCCCACAAAACTAACAACAAAAATAACACTCAAAATAAACACA\tLN:0\n+@SQ\tSN:GAAAAATCATCGTTGTATTTCAACTATAAGAACACCAATGACAAACATCC\tLN:0\n+@SQ\tSN:CCAGCCCCCTCAAACATTTCATCATGATGAAACTTCGGCTCCCTCCTAGG\tLN:0\n+@SQ\tSN:ACACATCAGACACGACAACTGCCTTCTCATCCGTCACTCACATCTGCCGA\tLN:0\n+@SQ\tSN:AATATTTTTTATCTGCCTCTTCATTCACGTAGGACGCGGCCTCTACTACG\tLN:0\n+@SQ\tSN:ACAGTTATAGCTACAGCATTCATGGGCTATGTCCTACCATGAGGCCAAAT\tLN:0\n+@SQ\tSN:ACATCGGTACTACCCTCGTCGAGTGAATCTGAGGTGGATTCTCAGTAGAC\tLN:0\n+@SQ\tSN:CATCACAGCCCTGGTAGTCGTACATTTACTATTTCTTCACGAAACAGGAT\tLN:0\n+@SQ\tSN:CCATATTATACAATTAAAGACATCCTAGGACTCCTCCTCCTGATCTTGCT\tLN:0\n+@SQ\tSN:ACTACACCCCAGCTAACCCTCTCAGCACTCCCCCTCATATTAAACCAGAA\tLN:0\n+@SQ\tSN:AGGCGGCGTATTAGCCCTAATCCTCTCCATCCTGATCCTAGCACTCATCC\tLN:0\n+@SQ\tSN:CAATGCGTATTCTGACTCTTAGTGGCAGACTTACTGACACTAACATGAAT\tLN:0\n+@SQ\tSN:CAATCCTCTACTTCTCCCTAATTCTCATTTTTATACCACTCGCAAGCACC\tLN:0\n+@SQ\tSN:ACCCTGGTCTTGTAAACCAGAAAAGGGGGAAAACGTTTCCTCCCAAGGAC\tLN:0\n+@SQ\tSN:TACTTAAACTATTCCTTGATTTCTTCCCCTAAACGACAACAATTTACCCT\tLN:0\n+@SQ\tSN:CTGACATGCAATATCTTATGAATGGCCTATGTACGTCGTGCATTAAATTG\tLN:0\n+@SQ\tSN:GTACATTATATTATTGATCGTGCATACCCCATCCAAGTCAAATCATTTCC\tLN:0\n+@SQ\tSN:GCGGGAAATCAGCAACCCTCCCAACTACGTGTCCCAATCCTCGCTCCGGG\tLN:0\n+@SQ\tSN:TCTTTCTTCAGGGCCATTCCCACCCAACCTCGCCCATTCTTTCCCCTTAA\tLN:0\n+@SQ\tSN:CTGTGATTTCATGCATTTGGTATCTTTTTATATTTGGGGATGCTATGACT\tLN:0\n+@SQ\tSN:CTTAAATTGAACGTTATTCCTCCGCATCAGCAACCATAAGGTGTTATTCA\tLN:0\n+@SQ\tSN:ctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacct\tLN:0\n+@SQ\tSN:gcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgc\tLN:0\n+@SQ\tSN:ctgtgcacctACCCGCGCAGTAAGCAAGTAATATAGCTTTCTTAATCAAA\tLN:0\n+@SQ\tSN:GCCAAACCCCAAAAACAAGACTAAACAATGCACAATACTTCATGAAGCTT\tLN:0\n+@SQ\tSN:GAACTTTCCCCCCGCCATTAATACCAACATGCTACTTTAATCAATAAAAT\tLN:0\n+@SQ\tSN:TTCTTCCCCC\tLN:0\n+HWI-EAS91_1_30788AAXX:1:1:1698:516\t16\t*\t2735\t25\t36M\t*\t0\t0\tTTTACACTCAGAGGTTCAACTCCTCTCNNTAACAAC\tI9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\n+HWI-EAS91_1_30788AAXX:1:1:1398:854\t16\t*\t3921\t25\t36M\t*\t0\t0\tCACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC\tIIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\n+HWI-EAS91_1_30788AAXX:1:1:1716:413\t0\t*\t6040\t25\t36M\t*\t0\t0\tGATCCAANNCTTTATCAACACCTATTCTGATTCTTC\tIIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\n+HWI-EAS91_1_30788AAXX:1:1:1634:211\t0\t*\t9350\t25\t36M\t*\t0\t0\tGAAGCAGNNGCTTGATACTGACACTTCGTCGACGTA\tIIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\n+HWI-EAS91_1_30788AAXX:1:1:1513:715\t16\t*\t9563\t25\t36M\t*\t0\t0\tCTGACTACCACAACTAAACATCTATGCNNAAAAAAC\tI+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\n+HWI-EAS91_1_30788AAXX:1:1:1310:991\t16\t*\t10002\t25\t36M\t*\t0\t0\tCTCCTATGCCTAGAAGGAATAATACTANNACTATTC\tI:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\n+HWI-EAS91_1_30788AAXX:1:1:1711:249\t16\t*\t10617\t25\t36M\t*\t0\t0\tACCAAACAGAACGCCTGAACGCAGGCCNNTACTTCC\tIIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\n+HWI-EAS91_1_30788AAXX:1:1:1491:637\t16\t*\t10864\t25\t36M\t*\t0\t0\tTGTAGAAGCCCCAATTGCCGGATCCATNNTGCTAGC\tDBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\n+HWI-EAS91_1_30788AAXX:1:1:1630:59\t16\t*\t12387\t25\t36M\t*\t0\t0\tTCATACTCGACCCCAACCTTACCAACCNNCCGCTCC\tFIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\n+HWI-EAS91_1_30788AAXX:1:1:1218:141\t16\t*\t14062\t25\t36M\t*\t0\t0\tACAAAACTAACAACAAAAATAACACTCNNAATAAAC\tI+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII\tNM:i:1\tX1:i:1\tMD:Z:7N0N27\n' |
| b |
| diff -r 000000000000 -r 79725ecf10a3 test-data/input_qname_sorted.bam |
| b |
| Binary file test-data/input_qname_sorted.bam has changed |
| b |
| diff -r 000000000000 -r 79725ecf10a3 test-data/output.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.sam Mon Mar 29 14:15:42 2021 +0000 |
| b |
| b'@@ -0,0 +1,178 @@\n+@SQ\tSN:>chrM\tLN:0\n+@SQ\tSN:GTATTCTTACTCCATAAACACATAGGCTTGGTCCTAGCCTTTTTATTAGT\tLN:0\n+@SQ\tSN:CTAAATCACGTCTCTACGATTAAAAGGAGCAGGTATCAAGCACACTAGAA\tLN:0\n+@SQ\tSN:ATAAAAATTAAGCTATGAACGAAAGTTCGACTAAGTCATATTAAATAAGG\tLN:0\n+@SQ\tSN:ATAAATCTCCGGCGTAAAGCGTGTCAAAGACTAATACCAAAATAAAGTTA\tLN:0\n+@SQ\tSN:AAGTGACTTTAATACCTCTGACTACACGATAGCTAAGACCCAAACTGGGA\tLN:0\n+@SQ\tSN:AAGCTATTCGCCAGAGTACTACTAGCAACAGCCTAAAACTCAAAGGACTT\tLN:0\n+@SQ\tSN:CCGATAAACCCCACCATCCCTTGCTAATTCAGCCTATATACCGCCATCTT\tLN:0\n+@SQ\tSN:AACGTTAGGTCAAGGTGTAGCCCATGGGATGGAGAGAAATGGGCTACATT\tLN:0\n+@SQ\tSN:TGGAGACTAAAGGAGGATTTAGCAGTAAATTAAGAATAGAGAGCTTAATT\tLN:0\n+@SQ\tSN:CACAAATCATAACATAACATAAAACCGTGACCCAAACATATGAAAGGAGA\tLN:0\n+@SQ\tSN:TGTAGCTTAAACAAAGCATCCAGCTTACACCTAGAAGATTTCACTCAAAA\tLN:0\n+@SQ\tSN:TTAGTCACTTAACTAAAACATTCACCAAACCATTAAAGTATAGGAGATAG\tLN:0\n+@SQ\tSN:ATGCATTAAAAGTACTAAACAGCAAAGCTTACCCCTTTTACCTTTTGCAT\tLN:0\n+@SQ\tSN:CGAAACCAGACGAGCTACCTATGAACAGTTACAAATGAACCAACTCATCT\tLN:0\n+@SQ\tSN:AGCCTGGTGATAGCTGGTTGTCCAGAAACAGAATTTCAGTTCAAATTTAA\tLN:0\n+@SQ\tSN:AAAGGTACAGCTTTTTAGATACAGGTTACAACCTTCATTAGAGAGTAAGA\tLN:0\n+@SQ\tSN:TTCAAGCTCAACGACACATCTATCTTAATCCCAACAATCAACCCAAACTA\tLN:0\n+@SQ\tSN:TTAATATGAGTAACAAGAATTATTTCTCCTTGCATAAGCTTATATCAGAA\tLN:0\n+@SQ\tSN:TCATCTATTTAAACCATTGTTAACCCAACACAGGCATGCATCTATAAGGA\tLN:0\n+@SQ\tSN:ACCAAAAACATCACCTCTAGCATTTCCAGTATTAGAGGCACTGCCTGCCC\tLN:0\n+@SQ\tSN:taatcacttgttccctaaatagggacttgtatgaatggccacacgagggt\tLN:0\n+@SQ\tSN:cgggaatgactaaataagacgagaagaccctatggagcttTAATTAACTG\tLN:0\n+@SQ\tSN:TTGATTGAATCAGCAATTTCGGTTGGGGTGACCTCGGAGAACAAAACAAC\tLN:0\n+@SQ\tSN:TTGATCCAAACCATTGATCAACGGAACAAGTTACCCTAGGGATAACAGCG\tLN:0\n+@SQ\tSN:TTGGATCAAGACATCCTAATGGTGCAACCGCTATTAAGGGTTCGTTTGTT\tLN:0\n+@SQ\tSN:CGGTTTCTATCTATTCTATACTTTTCCCAGTACGAAAGGACAAGAAAAGT\tLN:0\n+@SQ\tSN:AATCTAACTAATTTATAACTTCTACCGCCCTAGAACAGGGCTCgttaggg\tLN:0\n+@SQ\tSN:caactcctctccctaacaacaTGTTCATAATTAACGTCCTCCTCCTAATT\tLN:0\n+@SQ\tSN:CTTAGGCTATATGCAACTTCGCAAAGGACCCAACATCGTAGGCCCCTATG\tLN:0\n+@SQ\tSN:CTACAACCACTAACATCATCGACATCCATATTCATCATCGCACCAATCCT\tLN:0\n+@SQ\tSN:CACTAATCAACATAAACCTAGGAATTCTATTCATACTAGCCATGTCCAGC\tLN:0\n+@SQ\tSN:CGCCCTAATTGGAGCTCTACGAGCAGTAGCACAAACCATCTCATACGAAG\tLN:0\n+@SQ\tSN:ACATTATCAACACTTATTATTACCCAAGAATACCTCTGATTAATCTTCCC\tLN:0\n+@SQ\tSN:ACCGAGCTCCATTTGACCTAACAGAAGGAGAATCAGAACTCGTCTCTGGA\tLN:0\n+@SQ\tSN:ATACGCAAACATCATCATGATAAACATCTTCACAACAACCCTATTTCTAG\tLN:0\n+@SQ\tSN:ATTAAAGCTCTCCTTCTAACATGTTCCTTCCTATGAATCCGAGCATCCTA\tLN:0\n+@SQ\tSN:TACCACTCACACTAGCCCTCTGCATATGACACGTCTCACTTCCAATCATA\tLN:0\n+@SQ\tSN:ACTTTGATAGAGTAAAACATAGAGGCTCAAACCCTCTTATTTctagaact\tLN:0\n+@SQ\tSN:ttacaccatgtcctaCAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCAT\tLN:0\n+@SQ\tSN:CTTCACAACTATTCTAATAACAGTTCTTCTAGGAACTATAATCGTTATAA\tLN:0\n+@SQ\tSN:GCCATTATCCCTATCCTAATAAAAAAGTACAATCCCCGAACCATAGAAGC\tLN:0\n+@SQ\tSN:TAGCGATCATCATTAACCTCATACACTCAGGCCAATGAACAATCACAAAA\tLN:0\n+@SQ\tSN:ACTTGGACTCACACCATTCCACTTCTGAGTACCCGAAGTCACACAGGGCA\tLN:0\n+@SQ\tSN:ATATCAATCCTATATCAAATCTCACCCTCAATTAACCTAAATATCTTATT\tLN:0\n+@SQ\tSN:AAACCCAACTACGAAAAATCATAGCATACTCGTCAATCGCGCATATAGGA\tLN:0\n+@SQ\tSN:ATTAATTTACATTATAATAACACTCACAATATTCATACTATTTATCCACA\tLN:0\n+@SQ\tSN:CTAACCACTACACTAATCTTAATTACCTTACTATCCATAGGAGGCCTCCC\tLN:0\n+@SQ\tSN:AAAATAGCAGCATCATCCTCCCCACACTAATAGCCATTATAGCACTACTC\tLN:0\n+@SQ\tSN:CCCATCCACAAACAACATAAAAATAAAATGACAATTCGAAACCAAACGAA\tLN:0\n+@SQ\tSN:ACCCCCATACTATCAATTTTGGACTAGGAATTTAGGTTAACATCCCAGAC\tLN:0\n+@SQ\tSN:TAAGGACTGCGAGACTCTATCTCACATCAATTGAACGCAAATCAAACTCT\tLN:0\n+@SQ\tSN:TTTAGTTAACAGCTAAATACCCTAATCAACTGGCTTCAATCTACTTCTCC\tLN:0\n+@SQ\tSN:TCCTTTGAATTTGCAATTCAATGTGAAAATTCACCACGGGACTTGATAAG\tLN:0\n+@SQ\tSN:CCATCTTACCTATGTTCATCAACCGCTGACTATTTTCAACTAACCACAAA\tLN:0\n+@SQ\tSN:AACTGCCCTAAGCCTCCTAATCCGTGCTGAATTAGGCCAACCTGGGACCC\tLN:0\n+@SQ\tSN:GTAATAATTTTCTTTATGGTCATACCCATTATAATCGGAGGATTCGGAAA\tLN:0\n+@SQ\tSN:TAAACAACATAAGCTTCTGATTACTTCCCCCATCATTCCTACTTCTTCTC\tLN:0\n+@SQ\tSN:TCCTCTAGCTGGAAATCTGGCGCATGCAGGAGCCTCTGTTGACTTAACCA\tLN:0\n+@SQ\tSN:TTTATTACCACAATCATTAACATAAAACCACCAGCCCTATCCCAATATCA\tLN:0\n+@SQ\tSN:TAGCCCTCCCGGTCCTAGCAGCAGGCATTACCATGCTTCTCACAGACCGT\tLN:0\n+@SQ\tSN:TTATCAACACCTATTCTGATTCTTCGGACACCCCGAAGTCTATATTCTTA\tLN:0\n+@SQ\tSN:AAAAAGGAACCTTTTGGCTACATGGGTATAGTGTGAGCTATAATATCCAT'..b'CACATCTCT\tLN:0\n+@SQ\tSN:ACTCCAAAGACCTCATCATCGAAACCGCCAACACATCGTACACCAACGCC\tLN:0\n+@SQ\tSN:TACCCGAATCATCTTCTTTGCACTCCTAGGGCAACCCCGCTTCCTCCCTC\tLN:0\n+@SQ\tSN:CTCTTAATTGGCAGCATTTTTGCCGGATTCTTCATCTCCAACAATATCTA\tLN:0\n+@SQ\tSN:CCCTCGCAGTAACCATCCTAGGATTTACACTAGCCCTAGAACTAAGCTTG\tLN:0\n+@SQ\tSN:CAACCTCCTAGGATACTACCCAACAATTATACACCGACTCCCACCGCTCG\tLN:0\n+@SQ\tSN:TGACTAGAAAACATCCTGCCAAAATCTATCTCCCAGTTCCAAATAAAAAC\tLN:0\n+@SQ\tSN:CATTCCTCATCACCCTTACCCTAAGCATACTACTTTTTAATCTCCACGAG\tLN:0\n+@SQ\tSN:ATCACAACCCAAGCCCCATAACTATACAATGCAGCAGCCCCTATAATTTC\tLN:0\n+@SQ\tSN:CACCACTAAACTTAAACACTACCCCCACTTCCTCACTCTTCAGAACATAT\tLN:0\n+@SQ\tSN:AGTCGTATTAGACACCCATACCTCAGGATACTGCTCAGTAGCCATAGCCG\tLN:0\n+@SQ\tSN:ATCAACCCCAAAAAGGACCCTCCAAAATTCATAATAATACCACAACCTAC\tLN:0\n+@SQ\tSN:AAGAAAACCCCACAAAACTAACAACAAAAATAACACTCAAAATAAACACA\tLN:0\n+@SQ\tSN:GAAAAATCATCGTTGTATTTCAACTATAAGAACACCAATGACAAACATCC\tLN:0\n+@SQ\tSN:CCAGCCCCCTCAAACATTTCATCATGATGAAACTTCGGCTCCCTCCTAGG\tLN:0\n+@SQ\tSN:ACACATCAGACACGACAACTGCCTTCTCATCCGTCACTCACATCTGCCGA\tLN:0\n+@SQ\tSN:AATATTTTTTATCTGCCTCTTCATTCACGTAGGACGCGGCCTCTACTACG\tLN:0\n+@SQ\tSN:ACAGTTATAGCTACAGCATTCATGGGCTATGTCCTACCATGAGGCCAAAT\tLN:0\n+@SQ\tSN:ACATCGGTACTACCCTCGTCGAGTGAATCTGAGGTGGATTCTCAGTAGAC\tLN:0\n+@SQ\tSN:CATCACAGCCCTGGTAGTCGTACATTTACTATTTCTTCACGAAACAGGAT\tLN:0\n+@SQ\tSN:CCATATTATACAATTAAAGACATCCTAGGACTCCTCCTCCTGATCTTGCT\tLN:0\n+@SQ\tSN:ACTACACCCCAGCTAACCCTCTCAGCACTCCCCCTCATATTAAACCAGAA\tLN:0\n+@SQ\tSN:AGGCGGCGTATTAGCCCTAATCCTCTCCATCCTGATCCTAGCACTCATCC\tLN:0\n+@SQ\tSN:CAATGCGTATTCTGACTCTTAGTGGCAGACTTACTGACACTAACATGAAT\tLN:0\n+@SQ\tSN:CAATCCTCTACTTCTCCCTAATTCTCATTTTTATACCACTCGCAAGCACC\tLN:0\n+@SQ\tSN:ACCCTGGTCTTGTAAACCAGAAAAGGGGGAAAACGTTTCCTCCCAAGGAC\tLN:0\n+@SQ\tSN:TACTTAAACTATTCCTTGATTTCTTCCCCTAAACGACAACAATTTACCCT\tLN:0\n+@SQ\tSN:CTGACATGCAATATCTTATGAATGGCCTATGTACGTCGTGCATTAAATTG\tLN:0\n+@SQ\tSN:GTACATTATATTATTGATCGTGCATACCCCATCCAAGTCAAATCATTTCC\tLN:0\n+@SQ\tSN:GCGGGAAATCAGCAACCCTCCCAACTACGTGTCCCAATCCTCGCTCCGGG\tLN:0\n+@SQ\tSN:TCTTTCTTCAGGGCCATTCCCACCCAACCTCGCCCATTCTTTCCCCTTAA\tLN:0\n+@SQ\tSN:CTGTGATTTCATGCATTTGGTATCTTTTTATATTTGGGGATGCTATGACT\tLN:0\n+@SQ\tSN:CTTAAATTGAACGTTATTCCTCCGCATCAGCAACCATAAGGTGTTATTCA\tLN:0\n+@SQ\tSN:ctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacct\tLN:0\n+@SQ\tSN:gcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgc\tLN:0\n+@SQ\tSN:ctgtgcacctACCCGCGCAGTAAGCAAGTAATATAGCTTTCTTAATCAAA\tLN:0\n+@SQ\tSN:GCCAAACCCCAAAAACAAGACTAAACAATGCACAATACTTCATGAAGCTT\tLN:0\n+@SQ\tSN:GAACTTTCCCCCCGCCATTAATACCAACATGCTACTTTAATCAATAAAAT\tLN:0\n+@SQ\tSN:TTCTTCCCCC\tLN:0\n+HWI-EAS91_1_30788AAXX:1:1:1698:516\t16\t*\t2735\t25\t36M\t*\t0\t0\tTTTACACTCAGAGGTTCAACTCCTCTCNNTAACAAC\tI9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII\tMD:Z:7N0N27\tNM:i:1\tX1:i:1\n+HWI-EAS91_1_30788AAXX:1:1:1398:854\t16\t*\t3921\t25\t36M\t*\t0\t0\tCACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC\tIIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII\tMD:Z:7N0N27\tNM:i:1\tX1:i:1\n+HWI-EAS91_1_30788AAXX:1:1:1716:413\t0\t*\t6040\t25\t36M\t*\t0\t0\tGATCCAANNCTTTATCAACACCTATTCTGATTCTTC\tIIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII\tMD:Z:7N0N27\tNM:i:1\tX1:i:1\n+HWI-EAS91_1_30788AAXX:1:1:1634:211\t0\t*\t9350\t25\t36M\t*\t0\t0\tGAAGCAGNNGCTTGATACTGACACTTCGTCGACGTA\tIIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF\tMD:Z:7N0N27\tNM:i:1\tX1:i:1\n+HWI-EAS91_1_30788AAXX:1:1:1513:715\t16\t*\t9563\t25\t36M\t*\t0\t0\tCTGACTACCACAACTAAACATCTATGCNNAAAAAAC\tI+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII\tMD:Z:7N0N27\tNM:i:1\tX1:i:1\n+HWI-EAS91_1_30788AAXX:1:1:1310:991\t16\t*\t10002\t25\t36M\t*\t0\t0\tCTCCTATGCCTAGAAGGAATAATACTANNACTATTC\tI:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII\tMD:Z:7N0N27\tNM:i:1\tX1:i:1\n+HWI-EAS91_1_30788AAXX:1:1:1711:249\t16\t*\t10617\t25\t36M\t*\t0\t0\tACCAAACAGAACGCCTGAACGCAGGCCNNTACTTCC\tIIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII\tMD:Z:7N0N27\tNM:i:1\tX1:i:1\n+HWI-EAS91_1_30788AAXX:1:1:1491:637\t16\t*\t10864\t25\t36M\t*\t0\t0\tTGTAGAAGCCCCAATTGCCGGATCCATNNTGCTAGC\tDBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII\tMD:Z:7N0N27\tNM:i:1\tX1:i:1\n+HWI-EAS91_1_30788AAXX:1:1:1630:59\t16\t*\t12387\t25\t36M\t*\t0\t0\tTCATACTCGACCCCAACCTTACCAACCNNCCGCTCC\tFIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII\tMD:Z:7N0N27\tNM:i:1\tX1:i:1\n+HWI-EAS91_1_30788AAXX:1:1:1218:141\t16\t*\t14062\t25\t36M\t*\t0\t0\tACAAAACTAACAACAAAAATAACACTCNNAATAAAC\tI+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII\tMD:Z:7N0N27\tNM:i:1\tX1:i:1\n' |
| b |
| diff -r 000000000000 -r 79725ecf10a3 test-data/output_qname_sorted.bam |
| b |
| Binary file test-data/output_qname_sorted.bam has changed |
| b |
| diff -r 000000000000 -r 79725ecf10a3 test-data/output_stats.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_stats.txt Mon Mar 29 14:15:42 2021 +0000 |
| b |
| @@ -0,0 +1,8 @@ +Overlap Statistics: +Number of overlapping pairs: 0 +Average # Reference Bases Overlapped: 0 +Variance of Reference Bases overlapped: 0 +Number of times orientation causes additional clipping: 0 +Number of times the forward strand was clipped: 0 +Number of times the reverse strand was clipped: 0 +Completed ClipOverlap Successfully. |