Mercurial > repos > iuc > bamutil_clip_overlap
changeset 0:79725ecf10a3 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bamutil commit 29e40a76f1e249c3ed73f9129ad711beba34eb07"
| author | iuc |
|---|---|
| date | Mon, 29 Mar 2021 14:15:42 +0000 |
| parents | |
| children | 047a20d4258f |
| files | 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 |
| diffstat | 8 files changed, 545 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/clip_overlap.xml Mon Mar 29 14:15:42 2021 +0000 @@ -0,0 +1,157 @@ +<tool id="bamutil_clip_overlap" name="BamUtil clipOverlap" version="@WRAPPER_VERSION@" profile="@PROFILE@"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements"/> + <expand macro="edam"/> + <command detect_errors="exit_code"><![CDATA[ +## clipOverlap uses the output file +## extension to determine the output format. +#if $input.ext.endswith('bam'): + #set tmp_out = 'output.bam' +#else: + #set tmp_out = 'output.sam' +#end if +trap '>&2 cat output.log' EXIT; +touch 'output.log' && +bam clipOverlap +--in '$input' +#if str($storeOrig): + --storeOrig '$storeOrig' +#end if +$stats +#if str($input.ext) == 'qname_sorted.bam': + --readName +#end if +$overlapsOnly +#if str($excludeFlags): + --excludeFlags $excludeFlags +#end if +$unmapped +--noPhoneHome +--out '$tmp_out' +2> 'output.log' +&& mv '$tmp_out' '$output' +#if str($stats): + && cp 'output.log' '$output_stats' +#end if + ]]></command> + <inputs> + <param name="input" type="data" format="sam,bam,qname_sorted.bam" label="Select SAM or BAM file on which to clip overlapping read pairs"/> + <param argument="--storeOrig" type="text" value="" label="Enter a tag in which to store the original CIGAR" help="Leave blank to skip"> + <sanitizer invalid_char=""> + <valid initial="string.letters,string.digits"/> + </sanitizer> + </param> + <param argument="--stats" type="boolean" truevalue="--stats" falsevalue="" checked="false" label="Output statistics on the overlaps?"/> + <param argument="--overlapsOnly" type="boolean" truevalue="--overlapsOnly" falsevalue="" checked="false" label="Only output overlapping read pairs?"/> + <param argument="--excludeFlags" type="integer" optional="true" value="" label="Enter an integer representation of a flag to skip records with any of the specified flags set" help="See the help section below for information about this option"/> + <param argument="--unmapped" type="boolean" truevalue="--unmapped" falsevalue="" checked="false" label="Mark records that would be completely clipped as unmapped?"/> + </inputs> + <outputs> + <data name="output" format_source="input" metadata_source="input"/> + <data name="output_stats" format="txt" label="${tool.name} on ${on_string}: Statistics"> + <filter>stats</filter> + </data> + </outputs> + <tests> + <test expect_num_outputs="1"> + <param name="input" value="input.sam" ftype="sam"/> + <output name="output" file="output.sam" ftype="sam"/> + </test> + <test expect_num_outputs="2"> + <param name="input" value="input.bam" ftype="bam"/> + <param name="storeOrig" value="6M"/> + <param name="stats" value="--stats"/> + <output name="output" file="input.bam" ftype="bam"/> + <output name="output_stats" file="output_stats.txt" ftype="txt"/> + </test> + <test expect_num_outputs="1"> + <param name="input" value="input_qname_sorted.bam" ftype="qname_sorted.bam"/> + <output name="output" file="output_qname_sorted.bam" ftype="qname_sorted.bam"/> + </test> + </tests> + <help> +**What it does** + +Clips overlapping read pairs in a SAM or BAM file based on criteria. + +The input file and resulting output file are sorted by coordinate (or readName if specified in the options). + +When a read is clipped from the front: + + * the read start position is updated to reflect the clipping + * the mate's mate start position is updated to reflect the record's new position + * the record is placed in the output file in the correct location based on the updated position + +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 away with memory, a limit is set to the number of records that can be buffered, see --poolSize for more information. + +When two mates overlap, this tool will clip the record's whose clipped region would have the lowest average quality. + +It also checks strand. If a forward strand extends past the end of a reverse strand, that will be clipped. Similarly, if a reverse strand starts before the forward strand, the region prior to the forward strand will be clipped. If the reverse strand occurs entirely before the forward strand, both strands will be entirely clipped. If the --unmapped option is specified, then rather than clipping an entire read, it will be marked as unmapped. +The qualities on the two strands remain unchanged even with clipping. + +The excludeFlags option accepts a decimal value and skips the records with the specified flags set. The default is 3852 (0xF0C hex), so records with any of the following flags set will be skipped: + + * unmapped + * mate unmapped + * secondary alignment + * fails QC checks + * duplicate + * supplementary + +**Assumptions/ Restrictions** + + * Assumes the file is sorted by Coordinate (or ReadName if using --readName option) + * Assumes only 2 reads have matching ReadNames (Supplementary and Secondary reads are ignored/skipped by default so will not cause a problem) + + * It matches in pairs, so if there are 3, the first 2 will be matched and compared, but the 3rd won't. If there are 4, the first 2 will be matched and the last 2 will be matched and compared. + + * Only mapped reads will be clipped + * Assumes that mate information in records are accurate + +**Clipping from the front** + +The first operation after the softclip will be a Match/Mismatch, meaning that any trailing pads, deletions, insertions, or skips will also be soft clipped. + ++------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------+ +| Clip location | How it is handled | ++================================+=========================================================+======================================================================================+ +| If the clip position falls in a skip/deletion | Removes the entire skip/deletion | ++------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------+ +| If the position immediately after the clip is a skip/deletion | Also removes the skip/deletion | ++------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------+ +| If the position immediately after the clip is an Insert | Softclips the insert | ++------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------+ +| If the position immediately after the clip is a Pad | Removes the pad | ++------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------+ +| Clip occurs at the last match/mismatch position of the read (the entire read is clipped) | Entire read is soft clipped, 0-based position is left as the original (not modified) | ++------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------+ +| Clip occurs after the read ends | Entire read is soft clipped, 0-based position is left as the original (not modified) | ++------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------+ +| Clip occurs before the read starts | Nothing is clipped. The read is not changed. | ++------------------------------------------------------------------------------------------+--------------------------------------------------------------------------------------+ + +**Clipping from the back** + ++----------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------+ +| Clip location | How it is handled | ++==================+=========================================================+===================================================================================================================+ +| If the clip position falls in a skip/deletion | Removes the entire skip/deletion | ++----------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------+ +| If the position immediately before the clip is a deletion/skip/pad | Remove the deletion/skip/pad | ++----------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------+ +| If the position immediately before the clip is an insertion | Leave the insertion, even if it results in a 70M3I27S | ++----------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------+ +| 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) | ++----------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------+ +| Clip occurs before the read starts | Entire read is soft clipped, 0-based position is left as the original (not modified) | ++----------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------+ +| Clip occurs after the read ends | Nothing is clipped. The read is not changed. | ++----------------------------------------------------------------------------+-------------------------------------------------------------------------------------------------------------------+ + + </help> + <expand macro="citations"/> +</tool> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Mar 29 14:15:42 2021 +0000 @@ -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> +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/input.sam Mon Mar 29 14:15:42 2021 +0000 @@ -0,0 +1,178 @@ +@SQ SN:>chrM LN:0 +@SQ SN:GTATTCTTACTCCATAAACACATAGGCTTGGTCCTAGCCTTTTTATTAGT LN:0 +@SQ SN:CTAAATCACGTCTCTACGATTAAAAGGAGCAGGTATCAAGCACACTAGAA LN:0 +@SQ SN:ATAAAAATTAAGCTATGAACGAAAGTTCGACTAAGTCATATTAAATAAGG LN:0 +@SQ SN:ATAAATCTCCGGCGTAAAGCGTGTCAAAGACTAATACCAAAATAAAGTTA LN:0 +@SQ SN:AAGTGACTTTAATACCTCTGACTACACGATAGCTAAGACCCAAACTGGGA LN:0 +@SQ SN:AAGCTATTCGCCAGAGTACTACTAGCAACAGCCTAAAACTCAAAGGACTT LN:0 +@SQ SN:CCGATAAACCCCACCATCCCTTGCTAATTCAGCCTATATACCGCCATCTT LN:0 +@SQ SN:AACGTTAGGTCAAGGTGTAGCCCATGGGATGGAGAGAAATGGGCTACATT LN:0 +@SQ SN:TGGAGACTAAAGGAGGATTTAGCAGTAAATTAAGAATAGAGAGCTTAATT LN:0 +@SQ SN:CACAAATCATAACATAACATAAAACCGTGACCCAAACATATGAAAGGAGA LN:0 +@SQ SN:TGTAGCTTAAACAAAGCATCCAGCTTACACCTAGAAGATTTCACTCAAAA LN:0 +@SQ SN:TTAGTCACTTAACTAAAACATTCACCAAACCATTAAAGTATAGGAGATAG LN:0 +@SQ SN:ATGCATTAAAAGTACTAAACAGCAAAGCTTACCCCTTTTACCTTTTGCAT LN:0 +@SQ SN:CGAAACCAGACGAGCTACCTATGAACAGTTACAAATGAACCAACTCATCT LN:0 +@SQ SN:AGCCTGGTGATAGCTGGTTGTCCAGAAACAGAATTTCAGTTCAAATTTAA LN:0 +@SQ SN:AAAGGTACAGCTTTTTAGATACAGGTTACAACCTTCATTAGAGAGTAAGA LN:0 +@SQ SN:TTCAAGCTCAACGACACATCTATCTTAATCCCAACAATCAACCCAAACTA LN:0 +@SQ SN:TTAATATGAGTAACAAGAATTATTTCTCCTTGCATAAGCTTATATCAGAA LN:0 +@SQ SN:TCATCTATTTAAACCATTGTTAACCCAACACAGGCATGCATCTATAAGGA LN:0 +@SQ SN:ACCAAAAACATCACCTCTAGCATTTCCAGTATTAGAGGCACTGCCTGCCC LN:0 +@SQ SN:taatcacttgttccctaaatagggacttgtatgaatggccacacgagggt LN:0 +@SQ SN:cgggaatgactaaataagacgagaagaccctatggagcttTAATTAACTG LN:0 +@SQ SN:TTGATTGAATCAGCAATTTCGGTTGGGGTGACCTCGGAGAACAAAACAAC LN:0 +@SQ SN:TTGATCCAAACCATTGATCAACGGAACAAGTTACCCTAGGGATAACAGCG LN:0 +@SQ SN:TTGGATCAAGACATCCTAATGGTGCAACCGCTATTAAGGGTTCGTTTGTT LN:0 +@SQ SN:CGGTTTCTATCTATTCTATACTTTTCCCAGTACGAAAGGACAAGAAAAGT LN:0 +@SQ SN:AATCTAACTAATTTATAACTTCTACCGCCCTAGAACAGGGCTCgttaggg LN:0 +@SQ SN:caactcctctccctaacaacaTGTTCATAATTAACGTCCTCCTCCTAATT LN:0 +@SQ SN:CTTAGGCTATATGCAACTTCGCAAAGGACCCAACATCGTAGGCCCCTATG LN:0 +@SQ SN:CTACAACCACTAACATCATCGACATCCATATTCATCATCGCACCAATCCT LN:0 +@SQ SN:CACTAATCAACATAAACCTAGGAATTCTATTCATACTAGCCATGTCCAGC LN:0 +@SQ SN:CGCCCTAATTGGAGCTCTACGAGCAGTAGCACAAACCATCTCATACGAAG LN:0 +@SQ SN:ACATTATCAACACTTATTATTACCCAAGAATACCTCTGATTAATCTTCCC LN:0 +@SQ SN:ACCGAGCTCCATTTGACCTAACAGAAGGAGAATCAGAACTCGTCTCTGGA LN:0 +@SQ SN:ATACGCAAACATCATCATGATAAACATCTTCACAACAACCCTATTTCTAG LN:0 +@SQ SN:ATTAAAGCTCTCCTTCTAACATGTTCCTTCCTATGAATCCGAGCATCCTA LN:0 +@SQ SN:TACCACTCACACTAGCCCTCTGCATATGACACGTCTCACTTCCAATCATA LN:0 +@SQ SN:ACTTTGATAGAGTAAAACATAGAGGCTCAAACCCTCTTATTTctagaact LN:0 +@SQ SN:ttacaccatgtcctaCAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCAT LN:0 +@SQ SN:CTTCACAACTATTCTAATAACAGTTCTTCTAGGAACTATAATCGTTATAA LN:0 +@SQ SN:GCCATTATCCCTATCCTAATAAAAAAGTACAATCCCCGAACCATAGAAGC LN:0 +@SQ SN:TAGCGATCATCATTAACCTCATACACTCAGGCCAATGAACAATCACAAAA LN:0 +@SQ SN:ACTTGGACTCACACCATTCCACTTCTGAGTACCCGAAGTCACACAGGGCA LN:0 +@SQ SN:ATATCAATCCTATATCAAATCTCACCCTCAATTAACCTAAATATCTTATT LN:0 +@SQ SN:AAACCCAACTACGAAAAATCATAGCATACTCGTCAATCGCGCATATAGGA LN:0 +@SQ SN:ATTAATTTACATTATAATAACACTCACAATATTCATACTATTTATCCACA LN:0 +@SQ SN:CTAACCACTACACTAATCTTAATTACCTTACTATCCATAGGAGGCCTCCC LN:0 +@SQ SN:AAAATAGCAGCATCATCCTCCCCACACTAATAGCCATTATAGCACTACTC LN:0 +@SQ SN:CCCATCCACAAACAACATAAAAATAAAATGACAATTCGAAACCAAACGAA LN:0 +@SQ SN:ACCCCCATACTATCAATTTTGGACTAGGAATTTAGGTTAACATCCCAGAC LN:0 +@SQ SN:TAAGGACTGCGAGACTCTATCTCACATCAATTGAACGCAAATCAAACTCT LN:0 +@SQ SN:TTTAGTTAACAGCTAAATACCCTAATCAACTGGCTTCAATCTACTTCTCC LN:0 +@SQ SN:TCCTTTGAATTTGCAATTCAATGTGAAAATTCACCACGGGACTTGATAAG LN:0 +@SQ SN:CCATCTTACCTATGTTCATCAACCGCTGACTATTTTCAACTAACCACAAA LN:0 +@SQ SN:AACTGCCCTAAGCCTCCTAATCCGTGCTGAATTAGGCCAACCTGGGACCC LN:0 +@SQ SN:GTAATAATTTTCTTTATGGTCATACCCATTATAATCGGAGGATTCGGAAA LN:0 +@SQ SN:TAAACAACATAAGCTTCTGATTACTTCCCCCATCATTCCTACTTCTTCTC LN:0 +@SQ SN:TCCTCTAGCTGGAAATCTGGCGCATGCAGGAGCCTCTGTTGACTTAACCA LN:0 +@SQ SN:TTTATTACCACAATCATTAACATAAAACCACCAGCCCTATCCCAATATCA LN:0 +@SQ SN:TAGCCCTCCCGGTCCTAGCAGCAGGCATTACCATGCTTCTCACAGACCGT LN:0 +@SQ SN:TTATCAACACCTATTCTGATTCTTCGGACACCCCGAAGTCTATATTCTTA LN:0 +@SQ SN:AAAAAGGAACCTTTTGGCTACATGGGTATAGTGTGAGCTATAATATCCAT LN:0 +@SQ SN:TAGACGTTGACACACGAGCATACTTCACATCAGCTACCATAATCATCGCT LN:0 +@SQ SN:AAATATCAAATGATCTCCAGCTATACTCTGAGCTCTAGGCTTCATCTTCT LN:0 +@SQ SN:GATATTGTTCTCCACGATACTTATTATGTAGTAGCACATTTCCATTATGT LN:0 +@SQ SN:TCCCTCTATTCTCAGGATACACACTCAACCAAACCTGAGCAAAAATCCAC LN:0 +@SQ SN:CCTTGGCCTCTCAGGAATGCCACGACGCTATTCTGATTATCCAGACGCAT LN:0 +@SQ SN:GCAGTGATACTAATAATTTTCATAATTTGAGAAGCGTTCGCATCCAAACG LN:0 +@SQ SN:GATGCCCCCCACCATACCACACATTTGAAGAACCCACCTACGTAAACCTA LN:0 +@SQ SN:tcataaccactatgtctttctcCATCAATTGAGGTATTAGTAAAAATTAC LN:0 +@SQ SN:GCCTACCCCTTCCAACTAGGATTCCAAGACGCAACATCCCCTATTATAGA LN:0 +@SQ SN:GCTCTCTAGTATTATATATTATCTCATCAATACTAACAACTAAATTAACC LN:0 +@SQ SN:ACCAGCCATCATCCTTATTCTAATCGCCCTCCCATCCCTACGAATTCTAT LN:0 +@SQ SN:CACCAATGATACTGAAGCTACGAGTATACCGATTACGAAGACTTGACCTT LN:0 +@SQ SN:TTCTAGAAGTCGACAATCGAGTGGTTCTCCCCATAGAAATAACCATCCGA LN:0 +@SQ SN:AGGCCTAAAAACAGACGCTATCCCTGGGCGCCTAAATCAGACAACTCTCG LN:0 +@SQ SN:TCAAACCACAGCTTTATACCAATTGTCCTTGAACTAGTTCCACTGAAACA LN:0 +@SQ SN:TAGCATTAACCTTTTAAGTTAAAGATTGAGGGTTCAACCCCCTCCCTAGT LN:0 +@SQ SN:AATCCTAACTCTATTTATTGTATTTCAACTAAAAATCTCAAAGCACTCCT LN:0 +@SQ SN:CCTTGAGAATCAAAATGAACGAAAATCTATTCGCCTCTTTCGCTACCCCA LN:0 +@SQ SN:CCTATTCCCCTCACCCAACCGACTAATCAACAATCGCCTAATCTCAATTC LN:0 +@SQ SN:AGCAAAGGACAAACCTGAACTCTTATACTCATATCACTGATCCTATTCAT LN:0 +@SQ SN:CACAACTATCAATAAACCTAGGCATAGCTATTCCCCTATGGGCAGGGACA LN:0 +@SQ SN:ACCTCAAGGGACGCCCATTTTCCTCATCCCCATACTAGTAATTATCGAGA LN:0 +@SQ SN:AACATTACCGCCGGACACCTCCTAATACACCTCATCGGAGGGGCAACACT LN:0 +@SQ SN:TAATTCTACTAACTATCCTCGAATTCGCAGTAGCTATAATCCAAGCCTAC LN:0 +@SQ SN:CACCAAACCCACGCTTACCACATAGTAAACCCCAGCCCATGACCACTTAC LN:0 +@SQ SN:ACTTTAACTCAACCTTACTTCTAGCTATAGGGCTATTAACTAACATCCTT LN:0 +@SQ SN:CCATCACACATCAATCGTTCAAAAGGGACTCCGATATGGCATAATCCTTT LN:0 +@SQ SN:CACTCAAGCCTAGCCCCCACACCCGAACTAGGCGGCTGCTGACCACCCAC LN:0 +@SQ SN:TGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCACCATAGCCTAATA LN:0 +@SQ SN:AGGCGTATACTTCACCCTTCTCCAAGCCTCAGAATACTATGAAGCCTCAT LN:0 +@SQ SN:TTCCACGGACTACACGTAATTATCGGATCTACCTTCCTCATTGTATGTTT LN:0 +@SQ SN:AAGCAGCCGCTTGATACTGACACTTCGTCGACGTAGTCTGACTATTCTTG LN:0 +@SQ SN:CAATTGACTTCCAATCAATCAGCTTCGGTATAACCCGAAAAAGAATAATA LN:0 +@SQ SN:ACTCATCGCATTCTGACTACCACAACTAAACATCTATGCAGAAAAAACCA LN:0 +@SQ SN:TCAATAAAATTTTTCTTAGTGGCCATTACATTTCTGCTATTCGACTTAGA LN:0 +@SQ SN:ACACTATACTTATCATAGCACTAGTCCTAATCTCTCTTCTAGCCATCAGC LN:0 +@SQ SN:TTAGTTTAAACCAAAACAAATGATTTCGACTCATTAAACTATGATTAACT LN:0 +@SQ SN:ACAGTATCCCTCGTAGGCCTACTAATGTACCGATCCCACCTAATATCCTC LN:0 +@SQ SN:TAATAGTCCTAAACACCCACTTCACACTAGCTAGTATAATACCTATCATC LN:0 +@SQ SN:CATAGTCTCCAATACTTATGGAGTAGACCACGTACAAAACCTTAACCTCC LN:0 +@SQ SN:GACTATCAAAAAAGAATATAATCTGAATCAACACTACAACCTATAGTCTA LN:0 +@SQ SN:CCTAAACTTCTCACTAATATTCTTCTCCGATCCCCTATCAGCCCCACTTC LN:0 +@SQ SN:CATCTATCTAAGGAACCACTAATCCGAAAAAAACTCTACATCACCATGCT LN:0 +@SQ SN:TCTCCTTCTACATCCTATTTGAAGCCACATTAGTTCCAACACTAATTATC LN:0 +@SQ SN:CCTATTCTACACACTAATAGGTTCCCTCCCACTCTTAGTTGCACTAATCT LN:0 +@SQ SN:AACCAAGCACTACCCGACTCTTGATCCAATATTTTCCTATGACTAGCATG LN:0 +@SQ SN:TCCCAAAAGCCCATGTAGAAGCCCCAATTGCCGGATCCATAGTGCTAGCA LN:0 +@SQ SN:ACTAAACCCCCAAACTAGCTTTATAGCCTACCCCTTCCTCATACTATCCC LN:0 +@SQ SN:AAATCACTTATTGCATACTCCTCTGTCAGCCACATAGCCCTAGTAATCGT LN:0 +@SQ SN:TAATCGCTCACGGCCTTACATCATCAATACTATTCTGCCTGGCAAACTCA LN:0 +@SQ SN:AACACTTCTTCCCCTTATAGCAGCCTGATGACTATTAGCCAGCCTAACCA LN:0 +@SQ SN:ATATCATCATTCTCATGATCAAATATTACCATTATCCTAATAGGAGCCAA LN:0 +@SQ SN:GAGGGAAATACACACACCATATCAACAGCATTAAACCTTCATTTACACGA LN:0 +@SQ SN:TAACCCTAAAATTATCCTAGGCTTTACGTACTGTAAATATAGTTTAACAA LN:0 +@SQ SN:CGAGAAAGTATGCAAGAACTGCTAATTCATGCCCCCATGTCCAACAAACA LN:0 +@SQ SN:CCAAAAAATTGGTGCAACTCCAAATAAAAGTAATCAACATGTTCTCCTCC LN:0 +@SQ SN:CTTCAATACCTACAAAAACAGCACGTTCCCGCATCATGTAAAAAACACTA LN:0 +@SQ SN:TCTGGACAAGAAACAATTATCTCAAACTGACACTGAATAACCATACAAAC LN:0 +@SQ SN:TACCAGTAGCCCTATTCGTAACATGATCTATTATGGAATTCTCCCTATGA LN:0 +@SQ SN:ATTCCTCATCACTATAATAATTCTAGTCACAGCTAACAACCTTTTCCAAC LN:0 +@SQ SN:TGATGATACGGCCGAACAGATGCCAACACCGCGGCCCTTCAAGCAATCCT LN:0 +@SQ SN:TATTCAACACCAACACATGAGACCTCCAACAAATCTTCATACTCGACCCC LN:0 +@SQ SN:ATCCGCTCAATTTGGACTCCACCCATGACTTCCTTCAGCCATAGAGGGCC LN:0 +@SQ SN:GTCTTCCTGCTAATCCGCTTCCATCCACTAATAGAAAACAACAAAACAAT LN:0 +@SQ SN:TCTGCGCACTCACTCAAAACGATATCAAAAAAATCATTGCTTTCTCCACC LN:0 +@SQ SN:CCTAGCATTCCTCCACATTTGCACTCACGCATTCTTCAAAGCTATACTAT LN:0 +@SQ SN:CGAAAAATAGGCGGACTATTTAATGCAATACCCTTCACCACCACATCTCT LN:0 +@SQ SN:ACTCCAAAGACCTCATCATCGAAACCGCCAACACATCGTACACCAACGCC LN:0 +@SQ SN:TACCCGAATCATCTTCTTTGCACTCCTAGGGCAACCCCGCTTCCTCCCTC LN:0 +@SQ SN:CTCTTAATTGGCAGCATTTTTGCCGGATTCTTCATCTCCAACAATATCTA LN:0 +@SQ SN:CCCTCGCAGTAACCATCCTAGGATTTACACTAGCCCTAGAACTAAGCTTG LN:0 +@SQ SN:CAACCTCCTAGGATACTACCCAACAATTATACACCGACTCCCACCGCTCG LN:0 +@SQ SN:TGACTAGAAAACATCCTGCCAAAATCTATCTCCCAGTTCCAAATAAAAAC LN:0 +@SQ SN:CATTCCTCATCACCCTTACCCTAAGCATACTACTTTTTAATCTCCACGAG LN:0 +@SQ SN:ATCACAACCCAAGCCCCATAACTATACAATGCAGCAGCCCCTATAATTTC LN:0 +@SQ SN:CACCACTAAACTTAAACACTACCCCCACTTCCTCACTCTTCAGAACATAT LN:0 +@SQ SN:AGTCGTATTAGACACCCATACCTCAGGATACTGCTCAGTAGCCATAGCCG LN:0 +@SQ SN:ATCAACCCCAAAAAGGACCCTCCAAAATTCATAATAATACCACAACCTAC LN:0 +@SQ SN:AAGAAAACCCCACAAAACTAACAACAAAAATAACACTCAAAATAAACACA LN:0 +@SQ SN:GAAAAATCATCGTTGTATTTCAACTATAAGAACACCAATGACAAACATCC LN:0 +@SQ SN:CCAGCCCCCTCAAACATTTCATCATGATGAAACTTCGGCTCCCTCCTAGG LN:0 +@SQ SN:ACACATCAGACACGACAACTGCCTTCTCATCCGTCACTCACATCTGCCGA LN:0 +@SQ SN:AATATTTTTTATCTGCCTCTTCATTCACGTAGGACGCGGCCTCTACTACG LN:0 +@SQ SN:ACAGTTATAGCTACAGCATTCATGGGCTATGTCCTACCATGAGGCCAAAT LN:0 +@SQ SN:ACATCGGTACTACCCTCGTCGAGTGAATCTGAGGTGGATTCTCAGTAGAC LN:0 +@SQ SN:CATCACAGCCCTGGTAGTCGTACATTTACTATTTCTTCACGAAACAGGAT LN:0 +@SQ SN:CCATATTATACAATTAAAGACATCCTAGGACTCCTCCTCCTGATCTTGCT LN:0 +@SQ SN:ACTACACCCCAGCTAACCCTCTCAGCACTCCCCCTCATATTAAACCAGAA LN:0 +@SQ SN:AGGCGGCGTATTAGCCCTAATCCTCTCCATCCTGATCCTAGCACTCATCC LN:0 +@SQ SN:CAATGCGTATTCTGACTCTTAGTGGCAGACTTACTGACACTAACATGAAT LN:0 +@SQ SN:CAATCCTCTACTTCTCCCTAATTCTCATTTTTATACCACTCGCAAGCACC LN:0 +@SQ SN:ACCCTGGTCTTGTAAACCAGAAAAGGGGGAAAACGTTTCCTCCCAAGGAC LN:0 +@SQ SN:TACTTAAACTATTCCTTGATTTCTTCCCCTAAACGACAACAATTTACCCT LN:0 +@SQ SN:CTGACATGCAATATCTTATGAATGGCCTATGTACGTCGTGCATTAAATTG LN:0 +@SQ SN:GTACATTATATTATTGATCGTGCATACCCCATCCAAGTCAAATCATTTCC LN:0 +@SQ SN:GCGGGAAATCAGCAACCCTCCCAACTACGTGTCCCAATCCTCGCTCCGGG LN:0 +@SQ SN:TCTTTCTTCAGGGCCATTCCCACCCAACCTCGCCCATTCTTTCCCCTTAA LN:0 +@SQ SN:CTGTGATTTCATGCATTTGGTATCTTTTTATATTTGGGGATGCTATGACT LN:0 +@SQ SN:CTTAAATTGAACGTTATTCCTCCGCATCAGCAACCATAAGGTGTTATTCA LN:0 +@SQ SN:ctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacct LN:0 +@SQ SN:gcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgc LN:0 +@SQ SN:ctgtgcacctACCCGCGCAGTAAGCAAGTAATATAGCTTTCTTAATCAAA LN:0 +@SQ SN:GCCAAACCCCAAAAACAAGACTAAACAATGCACAATACTTCATGAAGCTT LN:0 +@SQ SN:GAACTTTCCCCCCGCCATTAATACCAACATGCTACTTTAATCAATAAAAT LN:0 +@SQ SN:TTCTTCCCCC LN:0 +HWI-EAS91_1_30788AAXX:1:1:1698:516 16 * 2735 25 36M * 0 0 TTTACACTCAGAGGTTCAACTCCTCTCNNTAACAAC I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1398:854 16 * 3921 25 36M * 0 0 CACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1716:413 0 * 6040 25 36M * 0 0 GATCCAANNCTTTATCAACACCTATTCTGATTCTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1634:211 0 * 9350 25 36M * 0 0 GAAGCAGNNGCTTGATACTGACACTTCGTCGACGTA IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1513:715 16 * 9563 25 36M * 0 0 CTGACTACCACAACTAAACATCTATGCNNAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1310:991 16 * 10002 25 36M * 0 0 CTCCTATGCCTAGAAGGAATAATACTANNACTATTC I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1711:249 16 * 10617 25 36M * 0 0 ACCAAACAGAACGCCTGAACGCAGGCCNNTACTTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1491:637 16 * 10864 25 36M * 0 0 TGTAGAAGCCCCAATTGCCGGATCCATNNTGCTAGC DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1630:59 16 * 12387 25 36M * 0 0 TCATACTCGACCCCAACCTTACCAACCNNCCGCTCC FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27 +HWI-EAS91_1_30788AAXX:1:1:1218:141 16 * 14062 25 36M * 0 0 ACAAAACTAACAACAAAAATAACACTCNNAATAAAC I+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII NM:i:1 X1:i:1 MD:Z:7N0N27
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output.sam Mon Mar 29 14:15:42 2021 +0000 @@ -0,0 +1,178 @@ +@SQ SN:>chrM LN:0 +@SQ SN:GTATTCTTACTCCATAAACACATAGGCTTGGTCCTAGCCTTTTTATTAGT LN:0 +@SQ SN:CTAAATCACGTCTCTACGATTAAAAGGAGCAGGTATCAAGCACACTAGAA LN:0 +@SQ SN:ATAAAAATTAAGCTATGAACGAAAGTTCGACTAAGTCATATTAAATAAGG LN:0 +@SQ SN:ATAAATCTCCGGCGTAAAGCGTGTCAAAGACTAATACCAAAATAAAGTTA LN:0 +@SQ SN:AAGTGACTTTAATACCTCTGACTACACGATAGCTAAGACCCAAACTGGGA LN:0 +@SQ SN:AAGCTATTCGCCAGAGTACTACTAGCAACAGCCTAAAACTCAAAGGACTT LN:0 +@SQ SN:CCGATAAACCCCACCATCCCTTGCTAATTCAGCCTATATACCGCCATCTT LN:0 +@SQ SN:AACGTTAGGTCAAGGTGTAGCCCATGGGATGGAGAGAAATGGGCTACATT LN:0 +@SQ SN:TGGAGACTAAAGGAGGATTTAGCAGTAAATTAAGAATAGAGAGCTTAATT LN:0 +@SQ SN:CACAAATCATAACATAACATAAAACCGTGACCCAAACATATGAAAGGAGA LN:0 +@SQ SN:TGTAGCTTAAACAAAGCATCCAGCTTACACCTAGAAGATTTCACTCAAAA LN:0 +@SQ SN:TTAGTCACTTAACTAAAACATTCACCAAACCATTAAAGTATAGGAGATAG LN:0 +@SQ SN:ATGCATTAAAAGTACTAAACAGCAAAGCTTACCCCTTTTACCTTTTGCAT LN:0 +@SQ SN:CGAAACCAGACGAGCTACCTATGAACAGTTACAAATGAACCAACTCATCT LN:0 +@SQ SN:AGCCTGGTGATAGCTGGTTGTCCAGAAACAGAATTTCAGTTCAAATTTAA LN:0 +@SQ SN:AAAGGTACAGCTTTTTAGATACAGGTTACAACCTTCATTAGAGAGTAAGA LN:0 +@SQ SN:TTCAAGCTCAACGACACATCTATCTTAATCCCAACAATCAACCCAAACTA LN:0 +@SQ SN:TTAATATGAGTAACAAGAATTATTTCTCCTTGCATAAGCTTATATCAGAA LN:0 +@SQ SN:TCATCTATTTAAACCATTGTTAACCCAACACAGGCATGCATCTATAAGGA LN:0 +@SQ SN:ACCAAAAACATCACCTCTAGCATTTCCAGTATTAGAGGCACTGCCTGCCC LN:0 +@SQ SN:taatcacttgttccctaaatagggacttgtatgaatggccacacgagggt LN:0 +@SQ SN:cgggaatgactaaataagacgagaagaccctatggagcttTAATTAACTG LN:0 +@SQ SN:TTGATTGAATCAGCAATTTCGGTTGGGGTGACCTCGGAGAACAAAACAAC LN:0 +@SQ SN:TTGATCCAAACCATTGATCAACGGAACAAGTTACCCTAGGGATAACAGCG LN:0 +@SQ SN:TTGGATCAAGACATCCTAATGGTGCAACCGCTATTAAGGGTTCGTTTGTT LN:0 +@SQ SN:CGGTTTCTATCTATTCTATACTTTTCCCAGTACGAAAGGACAAGAAAAGT LN:0 +@SQ SN:AATCTAACTAATTTATAACTTCTACCGCCCTAGAACAGGGCTCgttaggg LN:0 +@SQ SN:caactcctctccctaacaacaTGTTCATAATTAACGTCCTCCTCCTAATT LN:0 +@SQ SN:CTTAGGCTATATGCAACTTCGCAAAGGACCCAACATCGTAGGCCCCTATG LN:0 +@SQ SN:CTACAACCACTAACATCATCGACATCCATATTCATCATCGCACCAATCCT LN:0 +@SQ SN:CACTAATCAACATAAACCTAGGAATTCTATTCATACTAGCCATGTCCAGC LN:0 +@SQ SN:CGCCCTAATTGGAGCTCTACGAGCAGTAGCACAAACCATCTCATACGAAG LN:0 +@SQ SN:ACATTATCAACACTTATTATTACCCAAGAATACCTCTGATTAATCTTCCC LN:0 +@SQ SN:ACCGAGCTCCATTTGACCTAACAGAAGGAGAATCAGAACTCGTCTCTGGA LN:0 +@SQ SN:ATACGCAAACATCATCATGATAAACATCTTCACAACAACCCTATTTCTAG LN:0 +@SQ SN:ATTAAAGCTCTCCTTCTAACATGTTCCTTCCTATGAATCCGAGCATCCTA LN:0 +@SQ SN:TACCACTCACACTAGCCCTCTGCATATGACACGTCTCACTTCCAATCATA LN:0 +@SQ SN:ACTTTGATAGAGTAAAACATAGAGGCTCAAACCCTCTTATTTctagaact LN:0 +@SQ SN:ttacaccatgtcctaCAAGTAAGGTCAGCTAAATAAGCTATCGGGCCCAT LN:0 +@SQ SN:CTTCACAACTATTCTAATAACAGTTCTTCTAGGAACTATAATCGTTATAA LN:0 +@SQ SN:GCCATTATCCCTATCCTAATAAAAAAGTACAATCCCCGAACCATAGAAGC LN:0 +@SQ SN:TAGCGATCATCATTAACCTCATACACTCAGGCCAATGAACAATCACAAAA LN:0 +@SQ SN:ACTTGGACTCACACCATTCCACTTCTGAGTACCCGAAGTCACACAGGGCA LN:0 +@SQ SN:ATATCAATCCTATATCAAATCTCACCCTCAATTAACCTAAATATCTTATT LN:0 +@SQ SN:AAACCCAACTACGAAAAATCATAGCATACTCGTCAATCGCGCATATAGGA LN:0 +@SQ SN:ATTAATTTACATTATAATAACACTCACAATATTCATACTATTTATCCACA LN:0 +@SQ SN:CTAACCACTACACTAATCTTAATTACCTTACTATCCATAGGAGGCCTCCC LN:0 +@SQ SN:AAAATAGCAGCATCATCCTCCCCACACTAATAGCCATTATAGCACTACTC LN:0 +@SQ SN:CCCATCCACAAACAACATAAAAATAAAATGACAATTCGAAACCAAACGAA LN:0 +@SQ SN:ACCCCCATACTATCAATTTTGGACTAGGAATTTAGGTTAACATCCCAGAC LN:0 +@SQ SN:TAAGGACTGCGAGACTCTATCTCACATCAATTGAACGCAAATCAAACTCT LN:0 +@SQ SN:TTTAGTTAACAGCTAAATACCCTAATCAACTGGCTTCAATCTACTTCTCC LN:0 +@SQ SN:TCCTTTGAATTTGCAATTCAATGTGAAAATTCACCACGGGACTTGATAAG LN:0 +@SQ SN:CCATCTTACCTATGTTCATCAACCGCTGACTATTTTCAACTAACCACAAA LN:0 +@SQ SN:AACTGCCCTAAGCCTCCTAATCCGTGCTGAATTAGGCCAACCTGGGACCC LN:0 +@SQ SN:GTAATAATTTTCTTTATGGTCATACCCATTATAATCGGAGGATTCGGAAA LN:0 +@SQ SN:TAAACAACATAAGCTTCTGATTACTTCCCCCATCATTCCTACTTCTTCTC LN:0 +@SQ SN:TCCTCTAGCTGGAAATCTGGCGCATGCAGGAGCCTCTGTTGACTTAACCA LN:0 +@SQ SN:TTTATTACCACAATCATTAACATAAAACCACCAGCCCTATCCCAATATCA LN:0 +@SQ SN:TAGCCCTCCCGGTCCTAGCAGCAGGCATTACCATGCTTCTCACAGACCGT LN:0 +@SQ SN:TTATCAACACCTATTCTGATTCTTCGGACACCCCGAAGTCTATATTCTTA LN:0 +@SQ SN:AAAAAGGAACCTTTTGGCTACATGGGTATAGTGTGAGCTATAATATCCAT LN:0 +@SQ SN:TAGACGTTGACACACGAGCATACTTCACATCAGCTACCATAATCATCGCT LN:0 +@SQ SN:AAATATCAAATGATCTCCAGCTATACTCTGAGCTCTAGGCTTCATCTTCT LN:0 +@SQ SN:GATATTGTTCTCCACGATACTTATTATGTAGTAGCACATTTCCATTATGT LN:0 +@SQ SN:TCCCTCTATTCTCAGGATACACACTCAACCAAACCTGAGCAAAAATCCAC LN:0 +@SQ SN:CCTTGGCCTCTCAGGAATGCCACGACGCTATTCTGATTATCCAGACGCAT LN:0 +@SQ SN:GCAGTGATACTAATAATTTTCATAATTTGAGAAGCGTTCGCATCCAAACG LN:0 +@SQ SN:GATGCCCCCCACCATACCACACATTTGAAGAACCCACCTACGTAAACCTA LN:0 +@SQ SN:tcataaccactatgtctttctcCATCAATTGAGGTATTAGTAAAAATTAC LN:0 +@SQ SN:GCCTACCCCTTCCAACTAGGATTCCAAGACGCAACATCCCCTATTATAGA LN:0 +@SQ SN:GCTCTCTAGTATTATATATTATCTCATCAATACTAACAACTAAATTAACC LN:0 +@SQ SN:ACCAGCCATCATCCTTATTCTAATCGCCCTCCCATCCCTACGAATTCTAT LN:0 +@SQ SN:CACCAATGATACTGAAGCTACGAGTATACCGATTACGAAGACTTGACCTT LN:0 +@SQ SN:TTCTAGAAGTCGACAATCGAGTGGTTCTCCCCATAGAAATAACCATCCGA LN:0 +@SQ SN:AGGCCTAAAAACAGACGCTATCCCTGGGCGCCTAAATCAGACAACTCTCG LN:0 +@SQ SN:TCAAACCACAGCTTTATACCAATTGTCCTTGAACTAGTTCCACTGAAACA LN:0 +@SQ SN:TAGCATTAACCTTTTAAGTTAAAGATTGAGGGTTCAACCCCCTCCCTAGT LN:0 +@SQ SN:AATCCTAACTCTATTTATTGTATTTCAACTAAAAATCTCAAAGCACTCCT LN:0 +@SQ SN:CCTTGAGAATCAAAATGAACGAAAATCTATTCGCCTCTTTCGCTACCCCA LN:0 +@SQ SN:CCTATTCCCCTCACCCAACCGACTAATCAACAATCGCCTAATCTCAATTC LN:0 +@SQ SN:AGCAAAGGACAAACCTGAACTCTTATACTCATATCACTGATCCTATTCAT LN:0 +@SQ SN:CACAACTATCAATAAACCTAGGCATAGCTATTCCCCTATGGGCAGGGACA LN:0 +@SQ SN:ACCTCAAGGGACGCCCATTTTCCTCATCCCCATACTAGTAATTATCGAGA LN:0 +@SQ SN:AACATTACCGCCGGACACCTCCTAATACACCTCATCGGAGGGGCAACACT LN:0 +@SQ SN:TAATTCTACTAACTATCCTCGAATTCGCAGTAGCTATAATCCAAGCCTAC LN:0 +@SQ SN:CACCAAACCCACGCTTACCACATAGTAAACCCCAGCCCATGACCACTTAC LN:0 +@SQ SN:ACTTTAACTCAACCTTACTTCTAGCTATAGGGCTATTAACTAACATCCTT LN:0 +@SQ SN:CCATCACACATCAATCGTTCAAAAGGGACTCCGATATGGCATAATCCTTT LN:0 +@SQ SN:CACTCAAGCCTAGCCCCCACACCCGAACTAGGCGGCTGCTGACCACCCAC LN:0 +@SQ SN:TGCTCCTAGCATCTGGAGTCTCTATCACCTGAGCCCACCATAGCCTAATA LN:0 +@SQ SN:AGGCGTATACTTCACCCTTCTCCAAGCCTCAGAATACTATGAAGCCTCAT LN:0 +@SQ SN:TTCCACGGACTACACGTAATTATCGGATCTACCTTCCTCATTGTATGTTT LN:0 +@SQ SN:AAGCAGCCGCTTGATACTGACACTTCGTCGACGTAGTCTGACTATTCTTG LN:0 +@SQ SN:CAATTGACTTCCAATCAATCAGCTTCGGTATAACCCGAAAAAGAATAATA LN:0 +@SQ SN:ACTCATCGCATTCTGACTACCACAACTAAACATCTATGCAGAAAAAACCA LN:0 +@SQ SN:TCAATAAAATTTTTCTTAGTGGCCATTACATTTCTGCTATTCGACTTAGA LN:0 +@SQ SN:ACACTATACTTATCATAGCACTAGTCCTAATCTCTCTTCTAGCCATCAGC LN:0 +@SQ SN:TTAGTTTAAACCAAAACAAATGATTTCGACTCATTAAACTATGATTAACT LN:0 +@SQ SN:ACAGTATCCCTCGTAGGCCTACTAATGTACCGATCCCACCTAATATCCTC LN:0 +@SQ SN:TAATAGTCCTAAACACCCACTTCACACTAGCTAGTATAATACCTATCATC LN:0 +@SQ SN:CATAGTCTCCAATACTTATGGAGTAGACCACGTACAAAACCTTAACCTCC LN:0 +@SQ SN:GACTATCAAAAAAGAATATAATCTGAATCAACACTACAACCTATAGTCTA LN:0 +@SQ SN:CCTAAACTTCTCACTAATATTCTTCTCCGATCCCCTATCAGCCCCACTTC LN:0 +@SQ SN:CATCTATCTAAGGAACCACTAATCCGAAAAAAACTCTACATCACCATGCT LN:0 +@SQ SN:TCTCCTTCTACATCCTATTTGAAGCCACATTAGTTCCAACACTAATTATC LN:0 +@SQ SN:CCTATTCTACACACTAATAGGTTCCCTCCCACTCTTAGTTGCACTAATCT LN:0 +@SQ SN:AACCAAGCACTACCCGACTCTTGATCCAATATTTTCCTATGACTAGCATG LN:0 +@SQ SN:TCCCAAAAGCCCATGTAGAAGCCCCAATTGCCGGATCCATAGTGCTAGCA LN:0 +@SQ SN:ACTAAACCCCCAAACTAGCTTTATAGCCTACCCCTTCCTCATACTATCCC LN:0 +@SQ SN:AAATCACTTATTGCATACTCCTCTGTCAGCCACATAGCCCTAGTAATCGT LN:0 +@SQ SN:TAATCGCTCACGGCCTTACATCATCAATACTATTCTGCCTGGCAAACTCA LN:0 +@SQ SN:AACACTTCTTCCCCTTATAGCAGCCTGATGACTATTAGCCAGCCTAACCA LN:0 +@SQ SN:ATATCATCATTCTCATGATCAAATATTACCATTATCCTAATAGGAGCCAA LN:0 +@SQ SN:GAGGGAAATACACACACCATATCAACAGCATTAAACCTTCATTTACACGA LN:0 +@SQ SN:TAACCCTAAAATTATCCTAGGCTTTACGTACTGTAAATATAGTTTAACAA LN:0 +@SQ SN:CGAGAAAGTATGCAAGAACTGCTAATTCATGCCCCCATGTCCAACAAACA LN:0 +@SQ SN:CCAAAAAATTGGTGCAACTCCAAATAAAAGTAATCAACATGTTCTCCTCC LN:0 +@SQ SN:CTTCAATACCTACAAAAACAGCACGTTCCCGCATCATGTAAAAAACACTA LN:0 +@SQ SN:TCTGGACAAGAAACAATTATCTCAAACTGACACTGAATAACCATACAAAC LN:0 +@SQ SN:TACCAGTAGCCCTATTCGTAACATGATCTATTATGGAATTCTCCCTATGA LN:0 +@SQ SN:ATTCCTCATCACTATAATAATTCTAGTCACAGCTAACAACCTTTTCCAAC LN:0 +@SQ SN:TGATGATACGGCCGAACAGATGCCAACACCGCGGCCCTTCAAGCAATCCT LN:0 +@SQ SN:TATTCAACACCAACACATGAGACCTCCAACAAATCTTCATACTCGACCCC LN:0 +@SQ SN:ATCCGCTCAATTTGGACTCCACCCATGACTTCCTTCAGCCATAGAGGGCC LN:0 +@SQ SN:GTCTTCCTGCTAATCCGCTTCCATCCACTAATAGAAAACAACAAAACAAT LN:0 +@SQ SN:TCTGCGCACTCACTCAAAACGATATCAAAAAAATCATTGCTTTCTCCACC LN:0 +@SQ SN:CCTAGCATTCCTCCACATTTGCACTCACGCATTCTTCAAAGCTATACTAT LN:0 +@SQ SN:CGAAAAATAGGCGGACTATTTAATGCAATACCCTTCACCACCACATCTCT LN:0 +@SQ SN:ACTCCAAAGACCTCATCATCGAAACCGCCAACACATCGTACACCAACGCC LN:0 +@SQ SN:TACCCGAATCATCTTCTTTGCACTCCTAGGGCAACCCCGCTTCCTCCCTC LN:0 +@SQ SN:CTCTTAATTGGCAGCATTTTTGCCGGATTCTTCATCTCCAACAATATCTA LN:0 +@SQ SN:CCCTCGCAGTAACCATCCTAGGATTTACACTAGCCCTAGAACTAAGCTTG LN:0 +@SQ SN:CAACCTCCTAGGATACTACCCAACAATTATACACCGACTCCCACCGCTCG LN:0 +@SQ SN:TGACTAGAAAACATCCTGCCAAAATCTATCTCCCAGTTCCAAATAAAAAC LN:0 +@SQ SN:CATTCCTCATCACCCTTACCCTAAGCATACTACTTTTTAATCTCCACGAG LN:0 +@SQ SN:ATCACAACCCAAGCCCCATAACTATACAATGCAGCAGCCCCTATAATTTC LN:0 +@SQ SN:CACCACTAAACTTAAACACTACCCCCACTTCCTCACTCTTCAGAACATAT LN:0 +@SQ SN:AGTCGTATTAGACACCCATACCTCAGGATACTGCTCAGTAGCCATAGCCG LN:0 +@SQ SN:ATCAACCCCAAAAAGGACCCTCCAAAATTCATAATAATACCACAACCTAC LN:0 +@SQ SN:AAGAAAACCCCACAAAACTAACAACAAAAATAACACTCAAAATAAACACA LN:0 +@SQ SN:GAAAAATCATCGTTGTATTTCAACTATAAGAACACCAATGACAAACATCC LN:0 +@SQ SN:CCAGCCCCCTCAAACATTTCATCATGATGAAACTTCGGCTCCCTCCTAGG LN:0 +@SQ SN:ACACATCAGACACGACAACTGCCTTCTCATCCGTCACTCACATCTGCCGA LN:0 +@SQ SN:AATATTTTTTATCTGCCTCTTCATTCACGTAGGACGCGGCCTCTACTACG LN:0 +@SQ SN:ACAGTTATAGCTACAGCATTCATGGGCTATGTCCTACCATGAGGCCAAAT LN:0 +@SQ SN:ACATCGGTACTACCCTCGTCGAGTGAATCTGAGGTGGATTCTCAGTAGAC LN:0 +@SQ SN:CATCACAGCCCTGGTAGTCGTACATTTACTATTTCTTCACGAAACAGGAT LN:0 +@SQ SN:CCATATTATACAATTAAAGACATCCTAGGACTCCTCCTCCTGATCTTGCT LN:0 +@SQ SN:ACTACACCCCAGCTAACCCTCTCAGCACTCCCCCTCATATTAAACCAGAA LN:0 +@SQ SN:AGGCGGCGTATTAGCCCTAATCCTCTCCATCCTGATCCTAGCACTCATCC LN:0 +@SQ SN:CAATGCGTATTCTGACTCTTAGTGGCAGACTTACTGACACTAACATGAAT LN:0 +@SQ SN:CAATCCTCTACTTCTCCCTAATTCTCATTTTTATACCACTCGCAAGCACC LN:0 +@SQ SN:ACCCTGGTCTTGTAAACCAGAAAAGGGGGAAAACGTTTCCTCCCAAGGAC LN:0 +@SQ SN:TACTTAAACTATTCCTTGATTTCTTCCCCTAAACGACAACAATTTACCCT LN:0 +@SQ SN:CTGACATGCAATATCTTATGAATGGCCTATGTACGTCGTGCATTAAATTG LN:0 +@SQ SN:GTACATTATATTATTGATCGTGCATACCCCATCCAAGTCAAATCATTTCC LN:0 +@SQ SN:GCGGGAAATCAGCAACCCTCCCAACTACGTGTCCCAATCCTCGCTCCGGG LN:0 +@SQ SN:TCTTTCTTCAGGGCCATTCCCACCCAACCTCGCCCATTCTTTCCCCTTAA LN:0 +@SQ SN:CTGTGATTTCATGCATTTGGTATCTTTTTATATTTGGGGATGCTATGACT LN:0 +@SQ SN:CTTAAATTGAACGTTATTCCTCCGCATCAGCAACCATAAGGTGTTATTCA LN:0 +@SQ SN:ctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacct LN:0 +@SQ SN:gcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgcacctgtgc LN:0 +@SQ SN:ctgtgcacctACCCGCGCAGTAAGCAAGTAATATAGCTTTCTTAATCAAA LN:0 +@SQ SN:GCCAAACCCCAAAAACAAGACTAAACAATGCACAATACTTCATGAAGCTT LN:0 +@SQ SN:GAACTTTCCCCCCGCCATTAATACCAACATGCTACTTTAATCAATAAAAT LN:0 +@SQ SN:TTCTTCCCCC LN:0 +HWI-EAS91_1_30788AAXX:1:1:1698:516 16 * 2735 25 36M * 0 0 TTTACACTCAGAGGTTCAACTCCTCTCNNTAACAAC I9IIIII5IIIIIIIIIIIIIIIIIII""IIIIIII MD:Z:7N0N27 NM:i:1 X1:i:1 +HWI-EAS91_1_30788AAXX:1:1:1398:854 16 * 3921 25 36M * 0 0 CACCCTTCCCGTACTAATAAATCCCCTNNTCTTCAC IIIII=AIIIIIIIIIIIIIIBIIIII""IIIIIII MD:Z:7N0N27 NM:i:1 X1:i:1 +HWI-EAS91_1_30788AAXX:1:1:1716:413 0 * 6040 25 36M * 0 0 GATCCAANNCTTTATCAACACCTATTCTGATTCTTC IIIIIII""IIIIIIIIIIIIIIIIIIIIIIIIIII MD:Z:7N0N27 NM:i:1 X1:i:1 +HWI-EAS91_1_30788AAXX:1:1:1634:211 0 * 9350 25 36M * 0 0 GAAGCAGNNGCTTGATACTGACACTTCGTCGACGTA IIIIIII""IIIIIIIIIIIIIIIIIIIIII9IIDF MD:Z:7N0N27 NM:i:1 X1:i:1 +HWI-EAS91_1_30788AAXX:1:1:1513:715 16 * 9563 25 36M * 0 0 CTGACTACCACAACTAAACATCTATGCNNAAAAAAC I+-II?IDIIIIIIIIIIIIIIIIIII""IIIIIII MD:Z:7N0N27 NM:i:1 X1:i:1 +HWI-EAS91_1_30788AAXX:1:1:1310:991 16 * 10002 25 36M * 0 0 CTCCTATGCCTAGAAGGAATAATACTANNACTATTC I:2IEI:IIDIIIIII4IIIIIIIIII""IIIIIII MD:Z:7N0N27 NM:i:1 X1:i:1 +HWI-EAS91_1_30788AAXX:1:1:1711:249 16 * 10617 25 36M * 0 0 ACCAAACAGAACGCCTGAACGCAGGCCNNTACTTCC IIIIIIIIIIIIIIIIIIIIIIIIIII""IIIIIII MD:Z:7N0N27 NM:i:1 X1:i:1 +HWI-EAS91_1_30788AAXX:1:1:1491:637 16 * 10864 25 36M * 0 0 TGTAGAAGCCCCAATTGCCGGATCCATNNTGCTAGC DBAIIIIIIIIIIIFIIIIIIIIIIII""IIIIIII MD:Z:7N0N27 NM:i:1 X1:i:1 +HWI-EAS91_1_30788AAXX:1:1:1630:59 16 * 12387 25 36M * 0 0 TCATACTCGACCCCAACCTTACCAACCNNCCGCTCC FIIHII;IIIIIIIIIIIIIIIIIIII""IIIIIII MD:Z:7N0N27 NM:i:1 X1:i:1 +HWI-EAS91_1_30788AAXX:1:1:1218:141 16 * 14062 25 36M * 0 0 ACAAAACTAACAACAAAAATAACACTCNNAATAAAC I+IIII1IIIIIIIIIIIIIIIIIIII""IIIIIII MD:Z:7N0N27 NM:i:1 X1:i:1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_stats.txt Mon Mar 29 14:15:42 2021 +0000 @@ -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.