| Next changeset 1:059c552c137a (2018-07-19) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f6dd7c41a45584b478b8af48df5294e3c39f5203 |
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added:
macros.xml racon.xml test-data/consensus_result2.fasta test-data/sample_layout.fasta test-data/sample_overlaps.sam test-data/sample_reads.fasta |
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| diff -r 000000000000 -r 1c2e93f2d7c0 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Jun 11 16:39:36 2018 -0400 |
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| @@ -0,0 +1,14 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="1.3.1">racon</requirement> + <yield/> + </requirements> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1101/gr.214270.116</citation> + <yield /> + </citations> + </xml> +</macros> \ No newline at end of file |
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| diff -r 000000000000 -r 1c2e93f2d7c0 racon.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/racon.xml Mon Jun 11 16:39:36 2018 -0400 |
| [ |
| @@ -0,0 +1,81 @@ +<tool id="racon" name="Racon" version="1.3.1"> + <description>Consensus module for raw de novo DNA assembly of long uncorrected reads.</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <version_command>racon --version</version_command> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$reads' reads.${reads.ext} && + ln -s '$overlaps' overlaps.${overlaps.ext} && + ln -s '$corrected_reads' corrected_reads.${corrected_reads.ext} && + + racon + reads.${reads.ext} + overlaps.${overlaps.ext} + corrected_reads.${corrected_reads.ext} + -t \${GALAXY_SLOTS:-4} + $u + $f + -w $w + -q $q + -e $e + -m $m + -x $x + -g $g + > racon_polished_consensus.fa + ]]></command> + <inputs> + <param type="data" name="reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Sequences"/> + <param type="data" name="overlaps" format="sam" label="Overlaps"/> + <param type="data" name="corrected_reads" format="fasta,fasta.gz,fastq,fastq.gz" label="Target sequences"/> + + <param argument="-u" type="boolean" truevalue="-u" falsevalue="" label="output unpolished target sequences" /> + <param argument="-f" type="boolean" truevalue="-f" falsevalue="" label="perform fragment correction instead of contig polishing" /> + <param argument="-w" type="integer" value="500" label="Size of window on which POA is performed" /> + <param argument="-q" type="float" value="10.0" label="Threshold for average base quality of windows used in poa" /> + <param argument="-e" type="float" value="0.3" label="Maximum allowed error rate used for filtering overlaps" /> + <param argument="-m" type="integer" value="5" label="Score for matching bases" /> + <param argument="-x" type="integer" value="-4" label="Score for mismatching bases" /> + <param argument="-g" type="integer" value="-8" max="0" label="Gap penalty" /> + + </inputs> + <outputs> + <data name="consensus" format="fasta" from_work_dir="racon_polished_consensus.fa" /> + </outputs> + <tests> + <test> + <param name="reads" ftype="fasta" value="sample_reads.fasta"/> + <param name="overlaps" ftype="sam" value="sample_overlaps.sam"/> + <param name="corrected_reads" ftype="fasta" value="sample_layout.fasta"/> + <param name="u" value="true"/> + <param name="f" value="true"/> + <param name="w" value="800"/> + <param name="e" value="0.2"/> + <output name="consensus" ftype="fasta" file="consensus_result2.fasta"/> + </test> + </tests> + <help><![CDATA[ + +**What it does** + +Consensus module for raw de novo DNA assembly of long uncorrected reads. + +Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods +which do not include a consensus step. The goal of Racon is to generate genomic consensus which is of similar +or better quality compared to the output generated by assembly methods which employ both error correction +and consensus steps, while providing a speedup of several times compared to those methods. +It supports data produced by both Pacific Biosciences and Oxford Nanopore Technologies. + +Racon can be used as a polishing tool after the assembly with either Illumina data or data +produced by third generation of sequencing. The type of data inputed is automatically detected. + +Racon takes as input only three files: contigs in FASTA/FASTQ format, reads in FASTA/FASTQ +format and overlaps/alignments between the reads and the contigs in SAM format. Output is a set of polished contigs in FASTA format printed to stdout. + +Racon can also be used as a read error-correction tool. In this scenario, the SAM file needs +to contain pairwise overlaps between reads including dual overlaps. + + ]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r 1c2e93f2d7c0 test-data/consensus_result2.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/consensus_result2.fasta Mon Jun 11 16:39:36 2018 -0400 |
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| b'@@ -0,0 +1,2 @@\n+>utg000001lr LN:i:46960 RC:i:200 XC:f:1.000000\n+ATGATTATCATCTACATATCACAACGTGCGTGGAGGCCATCAAACCACGTCAAATAATCAATTATGACGCAGGTATCGTATTAATTGATCTGCATCAACTTAACGTAAAAACAACTTCAGACAATACAAATCAGCGACACTGAATACGGGGCAACCTCATGTCAACGAAGAACAGAACCCGCAGAACAACAACCCGCAACATCCGCTTTTCTAACCAAATGATTGAACAAATTAACATCGCTCTTGAGCAAAGGGGTCGGGAATTTCTCAGCCTGGGTCATTGAAGCCTGCCGTCGGAGACTAACGTCAGAAAGAGAGCATATACATCAATTAAAGTGATGAAGAATGAACATCCCGCGTTCTTCCCTCCGAACAGGACGATATTGTAAATTCACTTAATTACGAGGGCATTGCAGTAATTGAGTTGCAGTTTTACCACTTTCCTGACAGTGACAGACTGCGTGTTGGCTCTGTCACAGACTAAATAGTTTGAATGATTAGCAGTTATGGTGATCAGTCAACCACCAGGGAATAATCCTTCATATTATTATCGTGCTTCACCAACGCTGCCTCAATTGCTCTGAATGCTTCCAGAGACACCTTATGTTCTATACATGCAATTACAACATCAGGGTAACTCATAGAAATGGTGCTATTAAGCATATTTTTACACGAATCAGATCCACGGAGGGATCATCAGCAGATTGTTCTTTATTCATTTTGTCGCTCCATGCGCTTGCTCTTCATCTAGCGGTTAAAATATTACTTCAAATCTTTCTGTATGAAGATTTGAGCACGTTGGCCTTACATACATCTGTCGGTTGTATTTCCCTCCAGAATGCCAGCAGGACCGCACTTTGTTACGCAACCAATACTATTAAGTGAAAACATTCCTAATATTTGACATAAATCATCAACAAAACACAAGGAGGTCAGACCAGATTGAAACGATAAAACGATAATGCAAACTACGCGCCCTCGTATCACATGGAAGGTTTTACCAATGGCTCAGGTTGCCATTTTAAAGAAATATTCGATCAAGTGCGAAAAGATTTAGACTGTGAATTGTTTTATTCTGAACTAAAACGTCACAACGTCTCACATTATATTTACTATCTAGCCACAGATAATATTCACATCGTGTTAGAAAACGATAACACCGTGTTAATAAAAAGGACTTAAAAAGGTTGTAAATGTTAAATTCTCAAGAAACACGCATCTTATAGAAACGTCCTATGATAGGTTGAAATCAAGAGAAATCACATTTCAGCAATACAGGGAAAATCTTGCTAAAGCAGGAGTTTTCCGATGGGGTTACAAATATCCATGAACATAAAGATATTACTATACCTTTGATAATTCATTACTATTTACTGAGAGCATTCAGAACACTACACAAATCTTTCCACGCTAAATCATAACGTCCGGTTTCTTCCGTGTCAGCACCGGGGCGTTGGCATAATGCAATATACGTGTACGCGCTAAACCCTGTGTGCATCGTTTTAATTATTCCCGGACACTCCCGCAGAGAAGTTCCCCGTCAGGGCTGTGGACATAGTTAATCCGGGAATACAATGACGATTCATCGCACCTGACATACATTAATAAATATTAACAATATGAAATTTCAACTCATTGTTTAGGGTTTGTTTAATTTTCTACACATACGATTCTGCGAACTTCAAAGCATCGGGAATAACACCATGAAAAATGCCTACTCGCTACTGCGCTGGCCCTGCTTATTACAGGATGTGCTCAACAGACGTTTACTGTTCAAACAAAACCGGCAGCAGTAGCACCAAAGGAAACCATCACCCATCATTTCTTCGTTTCTGGAATTGGGCAGAAGAAAACTGTCGATGCAGCCAAATTTGTGGCGGCGCAGAAAATGTTGTTAAAACAGAAACCCAGCAAACATTCGTAAATGGATTGCTCGGTTTTATTACTTTAGGCATTTATACTCCGCTGGAAGCGCGTGTATTGCTCACAATAATTGCATGAGTTGCCCATCGATATGGGCAACTCTATCTGCACTGCTCATTAATATACTTCTGGGTTCCTTCCAGTTGTTTTGCATAGTGATCAGCCTCTCTCTGAGGGTGAAATAATCCCGTTCAGCTCTGTCTGCCAGTCGGGGGAGGCTGCATTATCCACGCCGGAGGCGGTGCTTGGCTTCACGCACTGACTGAGACTGCTTTGATGTGCAACCGACGACGACGACCAGCGGCAACATCATCACGCAGAGCAGAGCATTTTCAGCTTTAGCATCAGCTAACTCCTTCGTGTATTTTGCATCGAGAGCAGCAGCAACATCACGCTGACGCATCTGCATGTCAGTAATTGCCGCGTTCGCCAGCTTCAGTTCTCTGGCATTTTGTCGCGCTGGGCTTTGTAGGTAATGGCGTTATCACGGTAATGATTAACAGCCCATGACAGGCAGACGATGATGCAGATAACCAGAGCGGAGATCGCGGTCGCGGTGACTCTGCTCATACATCAATCTCTCTGACCGTTCCGCCCGCTTCTTTGAATTTGCAATCAGGCTGTCAGCCTTATGCTCGAACTGACCAGACCAGCGCCCGGCAGTGAAGCCCAGATATTGCTGCAACGGTCGATTGCCTGACGGATATCACCACGATCAATCATAGGTAAAGCGCCACGCTCCTTAATCTGCTGCAATGCCACAGCGTCCTGACTTTCGGAGAGAAGTCTTTCAGGCCAAGCTGCTTGCGGTAGGCATCCCACCAACGGGAAAGAAGCTGGTAGCGTCCGGCGCCTGTTGATTTGAGTTTTGGGTTTAGCGTGACAAGTTTGCGAGGGATGATCGGAGTAATCAGTAAATAGCTCTCCGCCTACAATGACGTCATAACCATGATTTCTGGTTTTCTGACGTTATCAGTTCCCTCCGACCACGCCAGCATATCGAGGAACGCCTTACGTTGATTATTGATTTCTACCATCTTCTACTCCGGCTTTTTTAGCAGCGAAGCGTTTGATAAGCGAACCAATCGAGTCAGTACCGATGTAGCCGATAAACACGCTCGTTATAAGCGAGATTGCTACTTAGTCCGGCGAAGTCGAGAAGGTCACGAATGAACTAGGCGATAATGGCGCACATCGTTGCGTCGATTACTGTTTTGTAAACGCACCGCCATTATATCTGCCGCGAAGGTACGCCATTGCAAACGCAAGGATTGCCCCGATGCCTTGTTCCTTTGCCGCGAGAATGGCGGCCAACAGGTCATGTTTTCTGGCATCTTCATGTCTTACCCCCAATAAGGGGATTTGCTCTATTTAATTAGGAATAAGGTCGATTACTGATAGAACAAATCCAGGCTACTGTGTTTAGTAATCAGATTTGTTCGTGACCGATATGCACGGGCAAAACGGCAGGAGGAGTGTTAGCGCGACCTCCTGCCACGCGGATTTCACGAAGGTCATGTGTAAAAGGCCGCAGCGTAACTATTACTAATGAATTCAGGACAGACAGTGGCTACGGCTCAGTTTGGGTTGTGCTGTTGCTGGGCGGCGATGACGCCTGTACGCATTTGGTGATCCGGTTCTGCTTCCGGTATTCGCTTAATTCATTCAGCACAACGGAAAGAGCACGACCTGGCTAACCAGGCTCGCCGACTCTTCACGATTATCGACTCAATGCTCTTACCTGTTGTGCAGATATAAAAATCCCGAAACCGTTATGCAGGCTCTAACTATTACCTGCGAACTGTTTCGGGATTGCATTTTGCAGACCTCTGCCTGCGATGGTTGGAGTTCCAGACGATACGTCGAAGTACCAACTAGGCGGAATCGGTAGTAAGCGCCGCCTCTTTCATCTCACTACACAACGAGCGAATTAACCCATCGTTGAGTCAAATTTACCCAATTTTATTCAATAAGTCAATATCATGCCGTTAATATGTTGCCATCCGTGGCA'..b'GCCCCATAAATGACGCCCACGACTCGTTCGCACTGGCCCGTGCCGTGGAGTAGCTCATCTGGGCGTAATTCCGGGAAAGCTGCTCATACGAGACACCCAGCCCGGCAGCGATATACCGCAGCAGTGACTGCTCAAACACGGAGTAGCCGTTATCCGTATCCTGAGCCGTCTGCAGGTTCAGTGAGAGTACCGGCATCAGGTGCGGTACTTTTGCGCCTCCAGCCGGACCGGCGCTGCTGCGGCGTAATACGCGGCAATTTCACCAATCCAGCCGGTCAGCCTTTCCCGCTGCTCCTGACTGTTCGCGCCCAGAATAAAATCCATCGCTGACTGCGTATCCAGCTCACTCTCAATGGTGGCGGCATACATCGCCTTCACAATGGCGCTCTGCAGCTGCGTGTTTCTGCAGCGTGTCGAGCATCTTCATCTGCTCCATCACGCTGTAAAAACATTTGCACCGCGAGTCTGCCCGTCCTCCACGGTTCAAAACGTGAATGAACGAGGAGGCGCCCGCCGGGTAACTCACGGGGTATCCATGTCCATTTCTGCGGCATCCAGCCAGGATACCCGTCCTCGCTGACGTAATATCCCAGCGCCGCACCGCTGTCATTAATCTGCACACCGGCACGGCAGTTCCGGCTGTCGCCGGTATTGTTCGGGTTGCTGATGCGCTTCGGGCTGACCATCCGGAAGAACTGTGTTTAGAAAAGCCGCGACGAACTGGTATCCCAGGCCTGAACGAACAGTTCACCGTTAAAGGCGTGCATGGCCACACCTTCCCGAATCATCATGGTAAACGTGCGTTTTCGCTCAACGTCAATGCAGCAGCAGTCATCCTCGGCAAACTCTTTCCATGCCGCTTCAACCTCGCGGGAAAGGCACGGGCTTCTTCCTCCCCGATGCCCAGATAGCGCCAGCTTGGGCGATGACTGAGCCGGAAAAGACCCGACGATATGATCCTGATGCAGCTGGATGGCGTTGGCGGCATAGCCGTTATTGCGTACCAGATCGTCTGCGCGGCATTGCCACGGGTAAAGTTGGGCAACAGGGCTGCATCCACACTTTCACTCGGTGGGTTCCACGACCGCAACTGCCCTCCAAATCCGCTGCCACCGCCGCGTGATAACCGGCATATTCGCGCAGCGATGTCATGCCGTCCGGCCCCAGAAGGGTGGGAATGGTGGGCGTTTTCATACATAAATCCTGCAGGTCTCTCCCTGCGTCGCTGTGTCATGCCGGTCTGCACTTCCAGCTCTGCAATATATTTTCAGGTCAGACACGGAAGTGGCCGTAAACTCCACCCTTCGTCCGTCTTTCTGTACTGTTGCCACCCGTTTACCTGTCATCAGGTCATGCAGTGCCGCACGGGCAGCGGCAAGTTCTTCCTGTCGCGTCATTCATCCTCTCCGGATAAGGCACGGCACGGCGTAATCTGCCAGTGTTTTCTTGTTGGTTGCTGCACCATCCTCTTCCTGCAGGCTCGCCAGCAGCGCACTGAGATCCAGCTGCCAGCGGGAAATACTGATGCGCAGCGCCGCCAGCGCATAAACGAAGCAGTCGAGTGCCTCATTGCGTCGCTTTTGCTGTCCACAGTATTTTCCTGCCATCCACCCATTTTCGACCTGCTCTTCAGCAGTCAGCTGCTGCGCTTCGGGTCAGATCAAAATATCCGGGTTATTCGGGAATGAACGGCACCGGGAAGCGGTTCATCCCCTTCCGGCGTCAGTGTGAAGCGGTTATAAATCTGCTCTCTTCGCGGTATCCGTACCGATTTCGGTAAGGTAAACCCCGTTTTGTTTCGCTTACGTGGCATGCTGGCCACCGGCTTTCCGTAGACGGATGCCCCTTTAATGGGGATCACCCGGAACAGCCCATGTTTTTCGAGCGTTCATACACAATGGTCGGGTCAATCCCGCCAGTATCCCAGCAGATACGGGATATCGACATTTCTGCACCATTCGGCGGGTATAGGTTTATTATTGATGGCCTCATCCACGCAGCAGCGTCTGTTCATCGTCGTGGCGGCCCATAATAATCTGCCGGTCAATCAGCCAGCTTTCCTCACCCGGCCCCATCCCCATACGCGCATTTCGTAGCGGTCCAGCTGGGAGTCGATACCGGCGGTCAGGTAAGCCACACGGTCAGGAACGGGCGCTGAATAATGCTCTTCCGCTCTGCCATCACTTCAGCATCCGGACGTTCGCCAATTTTCGCCTCCCACGTCTCACGAGCGTGGTGTTTACGAAGGTTTTACGTTTTCCCGTATCCCTTTCGTTTTCATCCAGTCTTTGACAATCTTGCACCCAGGTGGTGAACGGGCTGTACGCTGTCCAGATGTGAAAGGTCACACTGTCAGGGAGCTCAATCTCTTCACCGGATGACGAAAACCAGAGAATGCCATCACGGGTCCAGATCCCGGTCTTTCGCAGATATAACGGGCATCAGTAAAGTCCAGCTCCTGCTGGCGGATGACGCAGGCATTATGCTCGCAGAGATAAAACACGCTGGAGGGGTCATCCGGCGTCCATTTGAGGCCAAACGGCGTCTCTTTGTCGCCAAATTTAAGATACTGCTCCTCCCCCGCAATGCGGGCAGGCAACATGAAAACGCATAAAATGCGGGGATTCACTGGCTGCACGCTCAATCTGACAGGTGCCTCTCACTTTTGGCGTGGAGCCACGGATGGACTTTGGCCAGACCGAGCCTTCAATACGCTTGTTACCCAGGAACGTCGGAGAGCCTTCCTGTTCAATATCATCATCAAAAGCAGCAAGTTCATCATAACCCGCCACATCCACCGACTTTCACGGTAGTTTTGCCGCTTTACCGCCCAGGCAGCACCAGAAGCCACGCCCATTAGTGAACGCTTCATGGTGAGCGTGTTATCCCGGTGCTTTTGCCATACCACGGGGCCAGCGCCAGCAGCGACGGAATATCACGAATAGTCGGCTCAACGTGGGTTTTCATAAAGTTCTCGGCATCACCATCCGTCGGCAACCAGATAAGGGTGTGCGCTGCTTATGCTCTATAAAGTAGGCATAAACACCCAGCAGCATTTTGGAATAACCGACACGGCAGACTTCACCACATTCACCTCACGGATGTAGTCGCTGCCCATCGCATTCATGATGGCCCGCTGAAAGGGCAGTGTTTCCCAGCGCCCTTCCTGGTATGCGGATTCTTTTCGGGAGATAGTAATTAGCATCCGCCCATTCAACGGCGGTCTGTGGCTCCGGCCTGAACAGGAGCGAAGCCCGGCGCGGACAAAATGCCGCAGCCTGTTAACCTGACTGTTCGATATATTCACTCAGCAACCCCGGTATCAGTTCATCCAGCGCGGCTGCTTTGTTCATGGCTTTGATGATATCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAAAACGCCGCTGCACCGACAGGGGAGCCGTCGAGAATACTGGCAATTTCACCTGCGATTGAGCGACAGCACGAAAGTACAGAATGCGGTTTCCACCACTTCAGCGGAGTCTCTGGCATTCTTCAGTTCCTGTGCGTCGGCCGGCGCACGCGTAAGTCGATGGCGTTCGTACTCAATAGTTCCTGGCTGGAGATCTGCCTCGCTGGCTGCTGCCGCAGTTCTTCAACCTCCCGGCGCAGCTTTTCGTTCTCAATTTCAGCATCCCTTCGGCATACCATTTTATGACGGCGCTGCAGAGTCATAAAGCACCTCATTACCCTGCCACCGCCTCGCAGAACGGGCATTCCCTGTTCCTGCCAGTTCTGAATGGTACGGATACTCGCACCGAAAATGTCAGCCAGCTGCTTTTGTTGACTTCCATTGTTCATTCCACGGACAAAACAGAGAAAGGAACGACAGAGGCCAAAAGCTCGCTTTCAGCAGCCCTGTCGTTTCCTTCTTTCAGAGGGTATTTTAAATAAAAACATTAAGTTATGACGAAGAAGAACGGAAACGCCTTAAACCGGAAAATTTTCATAAATAGCGAAAACCC\n' 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| diff -r 000000000000 -r 1c2e93f2d7c0 test-data/sample_layout.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_layout.fasta Mon Jun 11 16:39:36 2018 -0400 |
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| b'@@ -0,0 +1,2 @@\n+>utg000001l\n+AAAGTGATAATGATTATGATTATCATCTACATATCTACAACGTGCGTGGAGGCCATCAAACCACGTCAAATAATCAATTATGACGCAGGTATCGTATTAATTGATCTGCATCAACTTAACGGTTCAAAACAACTTCAGACAATACAAAGGTCAGCACTGAATACGGGGCAACCTCATGTCAACGAAGAAACCAAAGAACCCGCAGAACAACAACCCGGACCCGCTTTTCCAACCAAATGATTGAACAAATTAACATCGCTGAGCAAAGGGAGTCGGGAATTCTCAGCCTGGGTCATTGAAGCCTGCTGGAGACTAACGTCAGAAAAGAGAGCATATACATCAATTAAAGTGATGAAGAATGAACATCCCGCGTTCTTCCCTCGAGAACAGGACGGTATGTAACCCCACTTAAGTCCCGAAGTCGCAGGAGTGAAGCATCTGAGTTGCAGTTACCACTTTCCTGACAGTGACTTGCGTGTGTGTTGGCTGGTGTCACAGACTAAATAGTTTGAATGATTAGCAGTTATGGTGATCAGTCAACCACTAGGAATAATCCTTCATATTATTATCGTGCTTCACCAACGCTTCCACTTCCTCGCATCCTTCCCCTACACCTTGCTGTTCTACATGCAATTACAACATCAGGGTAACTCATAGAAATGGGTGCTATTAAGCATATTTACACGAATCAGATCACGGAGGAGTAAATCAGCAGATTGTTCTTTATTCATTTTGTCGCTCATGCGCGCTTGCTCTTCATCTAGCGGTTAAAATATTACTTCAAATCTCTTTCTGTATGAAGATTTGAGCACGTTGGCCTTAAGCCATCTGTCGGTTTAGCGTTGTATTTCCCTCCAGAATGCCAGCAGGACGCAATTTTGTTACGCAACCAATACTATTAAGTGAAAACATTCCTAATATTGACATAAATCATCAACAAACACAGGAATAAGACAGATTGAACGATAAAAACGATAATGCAAACTACGTGCCTGCAGTACAGGGGAAGTACCAGCATGGAGCCGAGAGATGCCATTTAAAGAAATATTCCAATCAAGTGCGAAGGATTTAGACTGTGAATTGTTTTTATTCTGAACTAAACGTCACAACGTTCACATTATATTTGTTATCTAGCCCAGACTACTGTCGCCTTCGTGCCACGCTACAGCCGCGTGTTATAACCCGCCAATCTTAAAAAGGTTGTAAATGTTAATTCTCAAGAAACACGCATTATAAGAAACGTCCTATGATAGATTGAAATCAAGAGAAATCACATTTCAGCAATAAGGGAAAAATCTTAAAGCAGGAGTTTTCCGATCGGTTACAAATATCCATGAACATAAAGATATTACTATACCTTTGATAATTCATTACTATTTACTGAGAGCATTCAGAACACTACACAAATCTTTCCACGAAGCTCATAACGTTGCTACGCTTCTTCCGTGCGTGTCAGCACCGGGGCGTTGGCATCAATGCAATACCGTGTACGCGCTAAACCCTGTGTGTGCATCGGTCCTCAATTATTTACGCCGGACACTCCCCGCAGAGAATTCCCGTCAGGGCTGTGGACATAGTTAATCCGGGATCACGACCGATTGCCGCACCGAGAATACAGCAGTAAATATTAAATATGAAATTTCAACTCATTGTTTATAGGGTTTATTAATTTTCTACACATACGATTCTGCGAACTTCAAAAAGCATCGGGAATAACACCATGAAAAATGCCTCGGGCCTCCGCCCCTGCTTATTGGATGTGCTCAACAGACGTTTACTGTTCAAACAAAAGCAGCAGTAGCACCAAGGAAACCATCACCATCATTTCTTCTTTCGTTTCTGGAATTGGGCAGAAGAAAACTGTCGTGATGCAGCCAAATTTGTGGCGGCGCAGAAAATGTTGTCAAACAGAAACCCAGCAAACATTCAAATGGAATTGCTCGGTTTTATTACTTTAGCATTTATACTCATGGAAGCGCGTGTGTATTGCTCAATAATTGCATTCATGCATTACAGTCCGATATGGGCAACTCTATCTGCACTGCTCAGGATATATTTCTGGGTTCCTTCCAGTTGTTTAGCAGTGATGATCAGCCTCTCTCTGAGGGTGAAATAATCCCGTTTAAGCTCCGTCTGCCAGTCGGGGGAGGCTGCATTATCCACGGAGGCGGTGGTGGCTGCATTCACGCAGCACGACCCCGTGGAGTGGCAAATGAGCACGACGAGAAGAGCTTAACATCATCACGCAGAGCATCCTTCAGCTTAGCATCAGCCTACTAACTAATTCGTGCCTTTCCCATTTCGGGCTGCCGGCGATAATACAGCCCGCTGACGCATCTGCAGTGTCAGTAATTGCCGCGTTCTCAGCTTCGTTTTCTCTGAGAGCATTTTGTCGCGCTCCGTTGTAGGCATGGCGTTATCACGGTAATGATTAACAGCCCATGAATAAGCAGACGATGAGGATGCAGATAACCAGAGCGGAGATACTAATCGCGGTGACTGCTCATACGTAATCTCTGACCGTTCTCACGCTTCTTGAATTTGCAATCAGGCTGTCAGCCTTATGCTGAACTGACCAGACAGGGGACGGCAGTGAAGCCCCAGATATGCTGCAACGGTCGATTGCCTGACGGATATCACCACAGATCAATCATAGGTAAAGCGCCACGCGGGCTTAATCTTGCTGCATGCCACAGCGTCTGACTTTCGGAGAGAAGTCTTTTCAGCCAAGCTGCTTGCGGGTAGGCATCCCACCAACGGAAAGAAGCTGGCTCAGTCGGCGCCTGTTGATTTGAGTTTTGGGTTTAGCGTGACATTTTGCTCCTGCAGGGAAGCTCCCAGCAGCGCACACCGCCTCCGAGACACAATAGTCCATAACCATGATTTCTGGTTGGTAGTCGTTATCAGTTCCCTCCGACCACGTCAGCATATCGAGGAACGCCTACGTTGATTATTGATTTCTACCATCTTCTACTCCGGCTTTACAACGGCAGCGAAGCGTTTGATAAGCGAACCAATTCGAGTCAGTACCGATGTAGCCGATAAACACGCTCGTTATAAGCCGAGATTGCTACTTAGAGTCCGTGAAGTCGAGAAGTACAGGAGAATGAACTAGCGGCGATAATGGCGCGCGCACATCGTTGCGGTTCGTCGATTACTGTTTTGTAAACGCACCGGGTTTATATCTGCCTCGAAGGTACGCCATTGCAAACGCATTAAAGCAATGCCTTGTTCCGGCTCCTTTGCCGCGAGAAGCGGCCAACAGGTCATGTTTTTCTCGGCATCTTCATGTCTTACCCCAATAAAGGGATTTGCTCTATTTAATTAGGAATAAGTGATTACTGACGCTAAACAAATCCAGGCTGTGTTTATAATCAGATTTGTTCGTGACCGATATGCACGGGCAAAACGGAGATTTGTCCCCTGGCTCCTGCCTCGCCCGCTTCACGAAGGTCATCCCGAGGGAAGGAGCCCGTACACGTCCCAGCATGAATCCCAGAGAAGACAGTGGCTACGGCTCAGTTTGGGTTGTGCTGTTGCCTGGCGGCGATGACGCCTGATGGATTTGTGATCCGGTTCTGCTTCGGTATTCACTCACGGTGATTCACACAACGCGGAAAGAGCAGATCTGGCTAACCAGGCTCGACTCTTCACGATTATCGACTCAATGCTTATTACCTGTTTGTACCACTACAAAAACCCCGAAATCCATTCATGCAGGCTCACTATTACCTGCGAACTGTTTTCGGGATTGCATTTGCAGACCTCTCTGCCATGCGATGGTTGGAGTTCCAGACGATACGTCGAAGTGACCAACTAGGCGGAATCGGTAGTAAGGCCCCCTCTTTTCATCTCACCCACAACGAGCGAATTAACCCATCGTTGAGTCAAATTTACCCAATTTATTCAATAAGTCAATATCATGCCGTTAATATGTTGCCATCCGTGGCAATCATGCTGCTAACGTGA'..b'TGCCGTGGAGGAGCTCATCTGGGCGTAATTCCGGGAAAGCTGCTCATACGAGACACCCAGCCCGGGCATGCGATATACCGCAGCAGTGACTGCTCAAACACGGAGTAGCCGTTATCCGTATCCTGAGCCGTCTGCAGGTTCAGGTCATCTAGCATCAGGTGCGGTACTTTGCGCCTCCAGCCGGACCGGCGCTGCGATGCGTAATACGGCAATTTCACTCAATCCAGCCGGTCAGCCTTTCCCGCCTGCTCCTGACTGTTCGCGCCCAGAATAAAATCCATCGCTGACTGCGTATCCAGCTCACTCTAATGGTGGCGGCATACATCGCCTTCAATGGCGCTCTGCAGCTGCGTGTTTCTGCCCGTGGTTGCTGAGCATCTTCATCATCTGCTCCATCACGCTGTAAAACATTTGCACCGCGAGTCTGCCCGTCCTCCACGGGGTTCAAACGTGAATGAACGCTGGAGGCGCGCCCTAGTATAACTCACGGGGTATCCATGTCCATTTCTGCGCATCCAGCCAGGATACCCGTCCTCGCTGACGTAATATCCCCAGCGCCGCACCGCTGTCATTAATCTGCACAAGGCACGGCAGTCCCGGCTGTCGCCGGTATTGTTCCTGATGCTGATGCGGTCATGCGTGACCATCCGCCAGAACTGTGTCCGGAAAAGCCGGAGACGAACTGGTATCCCAGGCCTGAACGAACAGTTCACCGTTAAAGGCGTGCAAGGCCACACTTCCCGAATCATCATGGTAAACGTGCGTTAAAACGCTCAACGTCAATGCAGCAGAGCAGTCATCCTCGGCAAACTCTTTCCATGCCGCTTCAACCCGGAAAGCACGGGCTTCTTCCTCCCGATGCCAGATAGCGCCAGCTGCTTGGGCATGACTGAGCCGGAAAAGACCCGACGATGATCCTGATGCAGCTGGATGGCGTTATTGGCGGCATCGTTATTGGGCCAGATCGTCTGCGCCGGCATTGCCACGGGTAAAGTTGGGCAACACAGGGCTGCATCCACTTTCACTCGGTGGGTTCCACGACCGCAACTGCCCTCCAAATCCGCTGCCACCCCGGGTCAACCGGGATATTCATCGATGTCATGCCGTCCGGCCCCAAAGCGGGGAATGGTGGGCGTTTTCATACATAAATCCTGCAGGTCTCCCTGCGTCGCTGTGTCATGCCCCGGTCTGCACTTCCAGCTCTGCAATATGTTTCCAGTACCACGGAAGTGGCCGTCGACTCCACCTTCGTCCGTCTTCTGTACTGTTGCCACCCCGTTTACCTGTCATCAGGTCATGCAGTGCCGCACGGGCAGCGGCAAGTCTTCCTGTCGCGTCATTCATCCTCTCTGGATAAGGCACGGCGTAATCTTGCCAGTGTTTTCTGTGCTTGGTTGCTGGACCCCTTCCTGCAGGCTCGCCAGCAGCGCACTGAGATCCAGCTGCCAGCGGAAATACTGGGTGATGCGCAGCGCCGCCAGCGCATAAACGAAGCAGTCGAGTGCCTCATTGCGTCGCTTTGCTGTCCCACAGTATTTTCCTGCCATCCACCCATTTTTCGACCTGCTCTTCAGCGCAGTCAGCTGCTGCGCTTCGGGTCAGATCAAAATATCCGGGTTATTCGGAAGTGAACGGCACCGGGAAGCGGTTCATCCCCTTCGGGCGTCAGTGTGAAGCCGGTTATATAAATCTGCTCCTTCGCGGTATCCGTACCGATTTCGGTAAGGTAAACCCCGTTTTGTGCTTCGCTTAATGGCGGATGCTGATTCACCGGCTTTCCGGTAGACGCGGGTTGCCCCTTAGCATGGGGATCACCCGGAACAGCCCAGCTTTTCCGGGCGAGTTCATACACAATGGTCCTGGTCAGTCAATCCCGCCAGTATCCCCAGCGCAGGATACGGGATATCGACCTTCTGCTGCACCATTCGGCCGGGTATAGGTATTTTATTGATGGCCTCATCCACGCAGCAGCGTCTGTTCATGGTTTAGTGGCGGCCCATACGTAATAATCTGCCGGTCAATCAGCCGAGCTGTTCCTCTACCAGCCCCGGTACCGCCATACGCATTTCGGGCTGTCCAGCTGGGAGTCGATACCGGCGGTCAGGTACAGCCAATCGTCACGGAAACGGGCGCTGAAGACGAATAATGCTTCCGCCTTGCCATCATTTCAGCATCCGGACGTTCGCCAATTTTCTCCTCCCACGTACCTGACTACGAGCGTGGTGTTTACGAAGGTTTTACGGTTTTCCCCGTATCCCTTCCACTTCATCCAGTCTTTGACAATCTTAAGAGGTGAGGAACGGGCTGTACGCTGTCCAGATGTGAAAGGTCACACTGTCAGGGCGTCCAATCTGTTCACGGATGACGAAAACCAGAGAATGCCATCACGGGTCCAATCCCGGTCTTTCGCAGATATAACGGGCATCAGTACACTGAAGTCCAGTGCTCCTGCTGGCGGATGACGCAGGCATTATGCTCGCAGAGATAAACACGCTGGAGGCGATTCATCCGTCATTTGAGGCCAAACGGCGTCTCTTTGTCCGCCTAAATTTAAGATACTGCTCTCCCCCGCAATGCGAGCAGGGCAACATGAAAACGCATAAAATGCCGGGATTTCACTGGCTGCACTCAATCTGACAGGTGCCTCTCACTTTGGCGTGGAGCCACGGATGGACTTTACAGACCGAGCCTTCAATACGCTTGTTACCCAGGAACGTCGGAGAGCCTTCCTGTTCAATATCATCATCAAAAGCAGCAAGTTCATCATAACCCGCCATCCACCGCTAATCTTCACGCTTAGTTTTGCCGCTTTACCGCCCAGGCAGCCCAGAAGCCACGCCCATTAGTGAACGCTTCATGGGCCGTGTTATCCCGTGCTTTTGCCATACCACGGGGCCAGCGCCAGCAGCGACGGAATATCACGAATAGTCTATCCAACGTGGGTTTTCATAAAGTTCTCGGCATCACCATCCGTCGGCAACCAGATACCGGTGTTGCGCTGCTTATGCTCTATAAAGTAGGCATAAACACCCAGCAGCATTTTGTAGAATAACCGACACGGCAGACTTCACCACATTCACCTCACGGATGTGGTACCTGCTGCCATCGCATTCATGATGGCCCGCCTGAAAGGCAGTGTTTCCCCAGCGCCCTTCCTGGTATGCGGATTCTTTCGGGAGAGATAGTAATTAGCATCCGCCCATTCAAACGGCGGTTCTGTGGCTCCGGCCTGAACAGGTGGGAAGCCCGGCGCGGACAAATGCCGCAGCCTGTTAACCTGACTGTTCGGTTATATTCTGACTGATGAGCAACCCCGGTATCAGTTCATGCAGCGCGGCTGCTTTGTTTGTCATGGCTTTGATGATATTTCCCGTTTCAGGAAATCAACATGTCGGTTTTCCAGTTCCGGAACGCCGCACCGACGGAGAGCCGTCGAGAATACTGAATTCACCTGCGACGTGTGACAGGCACGAAAGTACGAATGCGGTTTCCACCACTTCAGCGGAGTCTGGCATTCTTCAGGTTCCTGTGCGTCGGCCGGGCACGCGAGTTAGATGGCGTTCGTACTCAATAGTTCCCTGGCGTTCGCGATTCTGCCTCGCTGTGCCTGCTTGCCGCAGTTCTTCAACCTCCCGGCGCAGCTTTTCGTTCCAATTTCAGCATCCCTTCGATACCATTTTACTGACGCTGCAGAGTCATAAAGCACCTCATTACCCTGCCACCGCCTCGCAAGAACGGCATCCCTGTTCCTGCCCAGTTCTGAATGGCGGTAACGGGATACTCGCACCGAAAATGTCGAGCCATAGCTGCTTTGTCTTGACTTCCATTGTTCATTCCACGGACAAACAGGAAAGGAACGACAGAGGCCACAAACCCGCTTTCAGCTACCCTGTCGTTTCCTTCTTTCAGAGGGGTATTTGTAAAGTAAAAACATTAAGTTATGACGAAGAAGAACGGAAACGCCTTAACCGGAAAATTTTCAAATAGCGAAAACCCGC\n' |
| b |
| diff -r 000000000000 -r 1c2e93f2d7c0 test-data/sample_overlaps.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_overlaps.sam Mon Jun 11 16:39:36 2018 -0400 |
| b |
| b'@@ -0,0 +1,257 @@\n+@PG\tID:minimap2\tPN:minimap2\tVN:2.1.1-r369-dirty\tCL:minimap2 -Qax map-ont sample_layout.fasta sample_reads.fastq\n+@SQ\tSN:utg000001l\tLN:47564\n+1\t0\tutg000001l\t29076\t60\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\t*\t0\t0\tAGGTAGCCTGTTTTATGAGTGGGGATTACAAAGGATGGTCATCGGTCACGTGACAGTACGGGTACCTGACGGCCGTCACACTGCTTTCACGCTGGCTAGGAAAAGCCGGCCCGCCTTTGTAGGGCCAATGTCCCCGACGATTTTCCGCCCTCAGCGTACCGTTTATCGTACAGTTTCAGCTATCGTCACATTACTGAGCGTCCCGGGGTTCGCATTCACACTGCCACACTGATATCCGCATTTTAGCGGTCATTTCAGTTTGCTGTGTCAGGGAAAGCGGAGGATTGCGCAGGCCTGTAGTAAGCGTGAGCGTCAGGCGGTGCTTCAGGAACACTTCTTCGTTCGCTGAATATCTGGTTGCCCTGCGCCAAACGACCGGCGTTCATTCCCGTTTGCCGTATAATAAATGCATCCCACGATTGGCGGCATGATCCAGAAACTGGGCTCAGTTTGCCTTCCTCCGTGTCCTCCATGCTCAGCGGACCCGCGACATAATGTTTGCCGTCTTTATTCTGCTCAATTTGACGACGCCCGGGCATTCACACTTATCGACTGGCGGCATCCTTCCACTCTGTTCGAAACCCTCCAGTGCTTAGTTATCCTCCGTCATAGCCGGACTTTTCCAGCAGCTCCTGCCGAGGTATGAGGATTGCTTCTTGCCTTTGGAAAATCGAGGTAACCTTCCGCATCATGCCGCCCGACCGACGGCCTCCACGAATGCCGATTTGCCAACGTGTTCCACTGCGAGATAAACATAATCGCTGGCCCGGTTTGATATTGATACTGCGGCTATCCAGTACAGCGCCGTACCAAGATAACGCGTGCTGGTTTCAATGGCTGTCTGATATCCGCAATCTGCTTTTCAGGGGACCAGAACTCAAACTGTACCGTCCGTATAAACGGCAAGATGCGGCGTGGCGGTTATCTGAAGACCCCGGCGTCAGCTCAATCCTCGACGGTGCTGCAGCAATCAGAACGGAATACCATAAGGACCCGCTTAATCGCGCGCCCGCATTTACCGCCCGGTGACTGTCGACCTGTAGTTCCCCAGCGCCAGTGCGTGAAGCGGTATGTGGTTTCCGTCGTCCGCTGCCGTGCTGACCAGCCGCTCACTGCCGTCGTCGTCCGTTACGGTCACGGCCAGCAGGAAACTCACGCCGGTCCCTAGGCTTCGGTGTGTCCCATCGCGCCAGCACCTGATATTCCATGTTGTAGCAGTACTTCTGCGGTCAGGTGCAGTGAGGGGCGGGCGGGATCACCATTCACCGTGCCACTCTGTTCGCCGTTACACTGCACCCGTTATCCACGATGGCCTCTTTTCCGGCACATGCTGCACGCGGGGCGATGGCATACGTGCCGTCGTCGTTCTCACGGATACTCACGCAGCGGAACAGTCACCTCTGGCTGGCGCAGCGAGCGGTTCGGCAAGCTTCAGCTCCCATACGGTGGGTCAGCAACACCGTCAGGAACACGGCTCACTTTACCTTCAGCCGTCGGTGACGACTGAACCTCCACGCTGACCGGATTGCCATTTCCGTCAACCCGAGGGATGACGGGGTCAAGGAGGATGGCAGCGTGATTCAATCCGTCGAGCGTCAGCGTCCGGTATTGGCTGTTCACACAGGCACACGACCACCGGTTAACTGATACCGGCATCATAGTCATCATGGCGCAGATTTCAATAACATCGCCCGGTACCATGGGGCAACGGATTCTGCGCCGACGGTATGAAATCCACGTCCGTTTCCAGCAGTTCTTGTTTTAATCATAGCCACATGCCCGGCGCGGTGCCTGCCCCGGCTGGTACAGCCAAAGGCATCCATCTTCGTAACATTACGACCTGTAACGGGCAATGGCCTGCGTATCTTCAACAAGCTCTGTCGCCGTCTCGAGTAGATAC\t*\ttp:A:P\tcm:i:20\ts1:i:190\ts2:i:0\tNM:i:485\tms:i:968\tAS:i:968\tnn:i:0\n+2\t0\tutg000001l\t26590\t60\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'..b'AATCAATACATGCTTCCCAAATATTCGCGCATGACTCGAACAAGAGCCGGTATCGAATCTTTTAGCTCGTACCATGTCCTGATACAGGGCTTGATAATCAGGATTTCTGAATACATTTCGCGATACCGTCCCAGCGACATTCTTCCTCGGTACATAATCTCCTTTAGCGTTTCCGATGTCCGTCAAAGGCACATGGGATCCCGTGATGACCTCATTAAAACACGCTGCAATCCAATATTCCCTCATCTTTGCAGGCAAGTCCGATTTGCGTTGATTTTAATGCAGAATATGCAGTTACCGAGATGTTCCGGTATTTGCAGCAAATGAATGGTTGTTGCTTCCACCATGCGAGGATATCTTCCTTCTCAAAGTCTGACAGTTCAGCAAGATATCTGATTCCAGGCTTTGGCTTCGGCCATTCGGTTCATCAGCTCTATCCCAATCTCCACGATCTTAATTCCTCACCCGAAATGGTCATCACAGTATTTGGTGAAGGGAACGAGTTGTCAATCTGTCAGTGCAGAACGCGCCGGACGTATGGAGTGCCATATTTTCTTTACCATATCGATAAATGGCTTCGAACAGGCATTCGCGTCTGAATATCCTTTGGTTCCCATACCGTATACCCATTTGGCTGTCCAAGCTCCGGGTTGATATCATCACTGCAATGATACCGGTGAGCCGGTATCCAGAACTTCACAACTTCCCTGACAAACCGATATGTCATTGGATGTTCACAACCTGTATCCATGAAAACGTAATGCGTCTTTACCTGCCGTCGCTTTGCTCCATTAGCCAGAGCAAATAGTTGCTGACGTCTCATGCCACCGGAGAAACTAACGACATTTATCATGCAGCCTGTCTCTCCCCATCGCTTTCCACTCCGAGCCAGTCTCGCTTCGTCTGACCACCTTAACGCCACGCTCTGTACCCGAATTAATGACTGCCTGTATAAGCTCTAATATGCTCCCAAATTCGCCTACACGCATCCTGCTGGTTGACTGGCATAGATCACACAGCCATTCCCGGCAAGGTTAGAATAACATCCTGCTGCTTTAATGCTGCGGTAAACACACTTCCAGCCAGCTTTCTGCATCCAGCCAGCGACCATGCCATTCAACCTGACGGAGACGTCACCTAAGCAGGCCCATAGCTTCCTGTTTGGTCTAAGCTGCGGTTGCGTTTCCTGAAGAATGGGTTACTACGATTGGTTTGGTTGGGTCTGAGAAGGATTTGCTTACTGTGAATAGCGTTTTGCTGATGTGCTGGAGAGTACCGAATTTCAAAGGTTAGTTTTCATGACTTCCCTCTCCCCCAAATAAAGCGCCTGCGATTACCAGCAAGGCCGTTGATCAGTAATGTAGATGGTCATCTTTTAACTCCATATACCGCCAATACCCCGTTTCATCGCGGCACTCTGGCGACATCTCCTTAAAACCAGGTTCGTGCTCATCTTTCCTTCCCGTTCTTCCCTGGAGCAAACCGGTAATACCACCGTTCAGACCTTACTTCGATAACCAGAAGACCTGCCCGTGCCATTTTAGCCGCGGCCTGATTTATGCTGGTTACTCGGTTGCGCCTGTTAGCGCGGCAACGCTTCTAGGGCGCACAGAATAGATTATGGTCGCGTCTCCCCAGGTAATATGAATAGATTGCCTCCTTTGCCCGTCATACATGTGCTCCTTTCAGTCCGAACTTAGGGTTTGATTTCCTGCGATCTTCACAGCCTGTGCACGATTTAGAGGTCTACGCCCATGACAGGAAGTTGTTTTACTGGTTCTCATAGGGATCGCCTCACCACCACGGTTAATTCTCGCAAGTCATATGGACAAGCTCATCTGCGGCCTTATAAAGCGTAATTCACGAATACGGGCACCGCATGCCGCATGTTCTGATACAGGTCGTGATACCGATAGAGTAGTGCGCGTTTGATTTCACTCGATAAGACTCCGCATTGGATGGAGCGCTTCCGGCAATACTCGTAAACCATATCAAACCAGCTCGCTGACGTTTGGCAGTCACGGCGGTAACGATGCTTCTTCCCCGGCACCATGCAACAAACTGCCGGGTGATGCGGCAAGAAATTCGGACGATTCTGATGCGGACGGGCTACCGGAATTCCTGCGTTAACCTGTTCCATCGTGGTGATCCCGTTTCCCGAAAAGCCAGAACCCACTGGCGACGGATTTCGGTTCATGATTCGTTCTGGTCACGCCGTGCCATGAGAGCCGGGAAAGTCCGCCAGTAACTGGGCTGAACACACCGTTGATGATCGCATGCCTGGGTGCTGTATCCTGCGGCTTTCGTCGTTACTGTTCCGGCATGTTGTTGGCGATCCGACGCATCTGCTCACGGTCAAAGTTAACCATCTGTGCGGGGAGTGTTTTCATAATCCACCCCGTAAATCCAGTCTGTTTGTCAGGTCGAGTTTTGGTTTGCTGGCTGGCTGTCACGCCTGCCTGTTGCTTGTTACGGTTGATTCGAGTTGGGTCCACTTATCGCGCGGAGTTTGGCCGGCTCAGCACGTCGTTACCGACCAGGAAGTTTGTCCTGGCATGCCAGCGGAACAGCACAGGGTCTTCTAGGGTGGTTACGTCCGTCTACGTTCACGCATCAGCGTGGATATCGTTAGCCCGCAGCAAGTTAAATCGGTTTTCTGGCTGATGGTGCGTATAGTCTTCTTCACGTCAAACATCCACTCTGCGGCGGTCAGGTCTTCTGCCATGCATGTCCCACTTGCTGCCGCTCTGAATTGCAGCATCCGGTTTCACCACAAGAATAGTCGTTTTCTGGCTGGTCAGGATTCACAGAATTCGTGAATAATCTCTTTCTTTTCTTTTGTAATAGTGTCTTTTTGTCTCCGTTTTGAGGGATAGCAATCCCAGATTGAGGGATGTTTTATCCCTCGTTTAGGGATTTTCCAGCGTTTTGAGGGATGCACCATTCTGAGCAATGTTTTATTTGGTCCAAACATGCCGCCTTGCTGCTTGATAATTCATTCTGACGATTCTAACTTGGCTTCATTGCACCCGTTTGACAGGTAACTTTGTAATCTCGCTAAGTTGAGAATCGGTGAGTCACTCTGTCCATTGGTTTATTCCACCCATTATAGTTTTACGGCAGAATGGCAAGCAGCATAATTTAAAACTGTCGCTTGGTCAGATCTGCGCCCGATGAATAAGCCTCAAGCCGAAGCATATTTGATAGTCTGGCGTAACCATCATGAGATCTGCCATTACGCTCCTGTCCGGCAAAGTCTCCTGCCGAAGTTGAGTATTTTGCTGTATTTGATAATGACTCCTGTTGATAGATCCAGTAATGACCTCAGAACTCCATCTGGATTTGTTCGAACGCTCGGTTGCCGGATGCCGCGTTGATTGGTAGAATCGCAGCAACTTGTCGCGCCAATCGAGCCATGTCAACGTCGATAGATCCCATTCAAGAACAGCAAGCAGCATGCGTGAAAACTTTGGAATCCGGTTCTCCTTCCAAGCCTTGATCTTAGACTTATCAACGCCCACAGCTTCCATGTCTTCTTTGATCGTTTCCAAGCATTGCGATTTTGTTAAGCAACGCACTCTGGATTCTCCGTAGAGCCTCGTTGCGTTTGGCTTTTGCACGAAACCATATGTAAGTATTTCCTTAGATAACAATTGATTGAATGGTCCCAAATAAATGCAAGACGAGGTGGTTTAATTTGATGCCCTTTTCAGGGCTGGAATGGTTGTAAGAGCGGGGTTATTTATGCTGTTGTTTTGTTACTCGGGGAAGGGCAGTTACCTTCTTCCGGCAGAATTCCATCAGGACGCGTTTGAGTCGATGGTTAGTAAAATCCGGCACTTAAATGGCCTTTAATCGAGGATTTGATCGGCCCGCGTATTCTAGCTGTCTTTGGTTTGCCCAAAGCGCATTGGATAAAGAGAGTT\t*\ttp:A:P\tcm:i:196\ts1:i:1832\ts2:i:0\tNM:i:2496\tms:i:6820\tAS:i:6820\tnn:i:0\n' |
| b |
| diff -r 000000000000 -r 1c2e93f2d7c0 test-data/sample_reads.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sample_reads.fasta Mon Jun 11 16:39:36 2018 -0400 |
| b |
| b'@@ -0,0 +1,472 @@\n+>1\n+AGGTAGCCTGTTTTATGAGTGGGGATTACAAAGGATGGTCATCGGTCACGTGACAGTACGGGTACCTGACGGCCGTCACACTGCTTTCACGCTGGCTAGGAAAAGCCGGCCCGCCTTTGTAGGGCCAATGTCCCCGACGATTTTCCGCCCTCAGCGTACCGTTTATCGTACAGTTTCAGCTATCGTCACATTACTGAGCGTCCCGGGGTTCGCATTCACACTGCCACACTGATATCCGCATTTTAGCGGTCATTTCAGTTTGCTGTGTCAGGGAAAGCGGAGGATTGCGCAGGCCTGTAGTAAGCGTGAGCGTCAGGCGGTGCTTCAGGAACACTTCTTCGTTCGCTGAATATCTGGTTGCCCTGCGCCAAACGACCGGCGTTCATTCCCGTTTGCCGTATAATAAATGCATCCCACGATTGGCGGCATGATCCAGAAACTGGGCTCAGTTTGCCTTCCTCCGTGTCCTCCATGCTCAGCGGACCCGCGACATAATGTTTGCCGTCTTTATTCTGCTCAATTTGACGACGCCCGGGCATTCACACTTATCGACTGGCGGCATCCTTCCACTCTGTTCGAAACCCTCCAGTGCTTAGTTATCCTCCGTCATAGCCGGACTTTTCCAGCAGCTCCTGCCGAGGTATGAGGATTGCTTCTTGCCTTTGGAAAATCGAGGTAACCTTCCGCATCATGCCGCCCGACCGACGGCCTCCACGAATGCCGATTTGCCAACGTGTTCCACTGCGAGATAAACATAATCGCTGGCCCGGTTTGATATTGATACTGCGGCTATCCAGTACAGCGCCGTACCAAGATAACGCGTGCTGGTTTCAATGGCTGTCTGATATCCGCAATCTGCTTTTCAGGGGACCAGAACTCAAACTGTACCGTCCGTATAAACGGCAAGATGCGGCGTGGCGGTTATCTGAAGACCCCGGCGTCAGCTCAATCCTCGACGGTGCTGCAGCAATCAGAACGGAATACCATAAGGACCCGCTTAATCGCGCGCCCGCATTTACCGCCCGGTGACTGTCGACCTGTAGTTCCCCAGCGCCAGTGCGTGAAGCGGTATGTGGTTTCCGTCGTCCGCTGCCGTGCTGACCAGCCGCTCACTGCCGTCGTCGTCCGTTACGGTCACGGCCAGCAGGAAACTCACGCCGGTCCCTAGGCTTCGGTGTGTCCCATCGCGCCAGCACCTGATATTCCATGTTGTAGCAGTACTTCTGCGGTCAGGTGCAGTGAGGGGCGGGCGGGATCACCATTCACCGTGCCACTCTGTTCGCCGTTACACTGCACCCGTTATCCACGATGGCCTCTTTTCCGGCACATGCTGCACGCGGGGCGATGGCATACGTGCCGTCGTCGTTCTCACGGATACTCACGCAGCGGAACAGTCACCTCTGGCTGGCGCAGCGAGCGGTTCGGCAAGCTTCAGCTCCCATACGGTGGGTCAGCAACACCGTCAGGAACACGGCTCACTTTACCTTCAGCCGTCGGTGACGACTGAACCTCCACGCTGACCGGATTGCCATTTCCGTCAACCCGAGGGATGACGGGGTCAAGGAGGATGGCAGCGTGATTCAATCCGTCGAGCGTCAGCGTCCGGTATTGGCTGTTCACACAGGCACACGACCACCGGTTAACTGATACCGGCATCATAGTCATCATGGCGCAGATTTCAATAACATCGCCCGGTACCATGGGGCAACGGATTCTGCGCCGACGGTATGAAATCCACGTCCGTTTCCAGCAGTTCTTGTTTTAATCATAGCCACATGCCCGGCGCGGTGCCTGCCCCGGCTGGTACAGCCAAAGGCATCCATCTTCGTAACATTACGACCTGTAACGGGCAATGGCCTGCGTATCTTCAACAAGCTCTGTCGCCGTCTCGAGTAGATAC\n+>2\n+ATCTTGATAGAGATTTCTAGGGGTATGCGTTAATGATCAGAAGCTCCCAATCAGGTTCAGTCAGGCTGGCGGCATCATTTCCGGCAAAATACGGTAATTATTTTCGCCGTGTAGAAAGCCCTGCCACATAGGCTAGAGTCGCAAGCTTCTTCGGTTGTTTACCCGCAAGCGTTAGTCATGGTGGTGGTAGCCAAAATCTGGATCATTCTCCCGAGCGCTGCGGCCAGTTCATTCAGCGTATTCAGTTGCGTCAGGTGACGCGTCGATAACATCTGCTGCAATCGCGGCCAGTACAAAAGCGGTTTCGCAATCTGGGTTTGTTTGTTCCTTGACATCCGGTTGGTGCTGTTGGCGTTCCGGTCAGTGCCGGACTGTTGAGGTTGGCTTTTTCTGTTCGTTTCATCCATTACCACCTTAACCGCCTTTGGCGTTGCAGCAAGCGTTTCAGACGTGCTGTTGGTTGCACTGCTGAGCTGCTATCCGGATTTCTCGTTGTCCGCATCCTCAAGCGCGACAGCTGAAGCTATATCTTCTGCACGTTTTGCCGAATTTGCACGTATTGCCGCCGCTTCTGCCGCGCTCGCATTTGCTCTGCGATGCTGATACCGCACTTCCCGCAGCCTCCCTTCCCTTCGTGATGCCGTTGACGGCACTCCCCGCCGCCGCTGTTTGCGTCGTGCCCCGGCAGGATGAGGGGCGCGTTCCATGCTGTTTCAGATGACCTGGCATTGCGTCTCGGACGTTTTGCCTCACTGGCAGAATTTCTGCCGCCGTTGCCGAGGAAGCTGCACGACTCGGCACTTGATGATGCGTTCGTTTCTGATGATTTTGTGCCTCTTGTTGTACCGGGCATCTCGTGCTGAAGGAGTGGGGGCCTCTGACGCTTTCGTGGCCATGCGGAGGCAGAATTGGCTGATCTTTTAGTCGACTTTGGCTTAGCAGCATTCGTTTCTGTAACGTTTTCGCCGCACCGGCACTGGGCCGCCCGCGTTTTGAGAGAACTCTGCGGCTGCGGCACTTTTCCGCTTCAGTGGCCTTGCTGATGCCGCCTCTTCTGCCGCTACGGGCAGCTTCCTGAGCTGACGGATGCAGCCTGTCCGGCGGACGTGCTGTGGCGGCGCGTCGGGTCAGTTGCATCAGAGTCACAAGCTAGGCCGCGACCTGAGCAGCTGATGCACTGGCATCGCCGGCTGATTTCTTCGCGTCTGCCGTACTCTGTGCCACCACGAAGACGCGTTACGCTGGGAGCTCTTCCACCATGAGTTCGACGAAGCGACGCAGCACCTCCATGGATGGCATCATCCTCGCGTCATGGCACACAGAGAAACCTTCAGCGTCCCCGGTTGTGAATCTTCATACGGTGATGGTCCCGGCGTGCGATGGAAAACCCGTCAACCTGCAGGATATCTGACACTGTACTGACCGTACTCCACATCCATGCTGTAACGCCCGGCTTCATCCGGATTCTCTGAGCCCACCGTGTTTGCCCCACCACCGTGGTGCTGTTAATGTCTGGCTTTCAGCTGAATGGTGCAGTTCTTGACTAGTTTTCCTGTGCCTATCTTTCAGACTCCTGAAATCTTTACTGCCATATTCACCGCAAAAGCCCACCGGTTCCGGCGGGCTGTCATAACACTGTGTTACGCCTGGCTAATCAGAATTTATAACCGACCCCAACGATGAATCCGTTTAGATCGCCAGTCGCCACTGCCGGCCCAGCCTTCATAGACAGCAAGATAATGAACGGACGGACGCTGCCGGATTAATCTGTATACCTGCACTCCACGCCAACCAGGTATGCCGCATTGCATTTCGTCCCTGGCAGTGGTCGTCTCTTATCTTTCAATACCCGGGAGTGATTTCCGTCTTACGGTAATGCGGCTTGTACTGCCGGATAAGCGACTGTGAGCCACTCCATGGCTGAGAAGCCGCACTGATTTACTGATTTGTAAAACCGGTCCGGCCATCACGCCCTAACTAACGTCCACGCAGGCTCTCATAGTGAAGAAACGTATCCTCCCCGGTCATCACTGTGCTTGCTCTTTTCGACGGTGGGGACCCCAGGGAAGC'..b'GGAAGCGGTTATCTTCTTTGCATTCACGCACCGATAACATCTCCGCATCATGCAGCTTCCTCCCGAAGTCGAAATCAATACATGCTTCCCAAATATTCGCGCATGACTCGAACAAGAGCCGGTATCGAATCTTTTAGCTCGTACCATGTCCTGATACAGGGCTTGATAATCAGGATTTCTGAATACATTTCGCGATACCGTCCCAGCGACATTCTTCCTCGGTACATAATCTCCTTTAGCGTTTCCGATGTCCGTCAAAGGCACATGGGATCCCGTGATGACCTCATTAAAACACGCTGCAATCCAATATTCCCTCATCTTTGCAGGCAAGTCCGATTTGCGTTGATTTTAATGCAGAATATGCAGTTACCGAGATGTTCCGGTATTTGCAGCAAATGAATGGTTGTTGCTTCCACCATGCGAGGATATCTTCCTTCTCAAAGTCTGACAGTTCAGCAAGATATCTGATTCCAGGCTTTGGCTTCGGCCATTCGGTTCATCAGCTCTATCCCAATCTCCACGATCTTAATTCCTCACCCGAAATGGTCATCACAGTATTTGGTGAAGGGAACGAGTTGTCAATCTGTCAGTGCAGAACGCGCCGGACGTATGGAGTGCCATATTTTCTTTACCATATCGATAAATGGCTTCGAACAGGCATTCGCGTCTGAATATCCTTTGGTTCCCATACCGTATACCCATTTGGCTGTCCAAGCTCCGGGTTGATATCATCACTGCAATGATACCGGTGAGCCGGTATCCAGAACTTCACAACTTCCCTGACAAACCGATATGTCATTGGATGTTCACAACCTGTATCCATGAAAACGTAATGCGTCTTTACCTGCCGTCGCTTTGCTCCATTAGCCAGAGCAAATAGTTGCTGACGTCTCATGCCACCGGAGAAACTAACGACATTTATCATGCAGCCTGTCTCTCCCCATCGCTTTCCACTCCGAGCCAGTCTCGCTTCGTCTGACCACCTTAACGCCACGCTCTGTACCCGAATTAATGACTGCCTGTATAAGCTCTAATATGCTCCCAAATTCGCCTACACGCATCCTGCTGGTTGACTGGCATAGATCACACAGCCATTCCCGGCAAGGTTAGAATAACATCCTGCTGCTTTAATGCTGCGGTAAACACACTTCCAGCCAGCTTTCTGCATCCAGCCAGCGACCATGCCATTCAACCTGACGGAGACGTCACCTAAGCAGGCCCATAGCTTCCTGTTTGGTCTAAGCTGCGGTTGCGTTTCCTGAAGAATGGGTTACTACGATTGGTTTGGTTGGGTCTGAGAAGGATTTGCTTACTGTGAATAGCGTTTTGCTGATGTGCTGGAGAGTACCGAATTTCAAAGGTTAGTTTTCATGACTTCCCTCTCCCCCAAATAAAGCGCCTGCGATTACCAGCAAGGCCGTTGATCAGTAATGTAGATGGTCATCTTTTAACTCCATATACCGCCAATACCCCGTTTCATCGCGGCACTCTGGCGACATCTCCTTAAAACCAGGTTCGTGCTCATCTTTCCTTCCCGTTCTTCCCTGGAGCAAACCGGTAATACCACCGTTCAGACCTTACTTCGATAACCAGAAGACCTGCCCGTGCCATTTTAGCCGCGGCCTGATTTATGCTGGTTACTCGGTTGCGCCTGTTAGCGCGGCAACGCTTCTAGGGCGCACAGAATAGATTATGGTCGCGTCTCCCCAGGTAATATGAATAGATTGCCTCCTTTGCCCGTCATACATGTGCTCCTTTCAGTCCGAACTTAGGGTTTGATTTCCTGCGATCTTCACAGCCTGTGCACGATTTAGAGGTCTACGCCCATGACAGGAAGTTGTTTTACTGGTTCTCATAGGGATCGCCTCACCACCACGGTTAATTCTCGCAAGTCATATGGACAAGCTCATCTGCGGCCTTATAAAGCGTAATTCACGAATACGGGCACCGCATGCCGCATGTTCTGATACAGGTCGTGATACCGATAGAGTAGTGCGCGTTTGATTTCACTCGATAAGACTCCGCATTGGATGGAGCGCTTCCGGCAATACTCGTAAACCATATCAAACCAGCTCGCTGACGTTTGGCAGTCACGGCGGTAACGATGCTTCTTCCCCGGCACCATGCAACAAACTGCCGGGTGATGCGGCAAGAAATTCGGACGATTCTGATGCGGACGGGCTACCGGAATTCCTGCGTTAACCTGTTCCATCGTGGTGATCCCGTTTCCCGAAAAGCCAGAACCCACTGGCGACGGATTTCGGTTCATGATTCGTTCTGGTCACGCCGTGCCATGAGAGCCGGGAAAGTCCGCCAGTAACTGGGCTGAACACACCGTTGATGATCGCATGCCTGGGTGCTGTATCCTGCGGCTTTCGTCGTTACTGTTCCGGCATGTTGTTGGCGATCCGACGCATCTGCTCACGGTCAAAGTTAACCATCTGTGCGGGGAGTGTTTTCATAATCCACCCCGTAAATCCAGTCTGTTTGTCAGGTCGAGTTTTGGTTTGCTGGCTGGCTGTCACGCCTGCCTGTTGCTTGTTACGGTTGATTCGAGTTGGGTCCACTTATCGCGCGGAGTTTGGCCGGCTCAGCACGTCGTTACCGACCAGGAAGTTTGTCCTGGCATGCCAGCGGAACAGCACAGGGTCTTCTAGGGTGGTTACGTCCGTCTACGTTCACGCATCAGCGTGGATATCGTTAGCCCGCAGCAAGTTAAATCGGTTTTCTGGCTGATGGTGCGTATAGTCTTCTTCACGTCAAACATCCACTCTGCGGCGGTCAGGTCTTCTGCCATGCATGTCCCACTTGCTGCCGCTCTGAATTGCAGCATCCGGTTTCACCACAAGAATAGTCGTTTTCTGGCTGGTCAGGATTCACAGAATTCGTGAATAATCTCTTTCTTTTCTTTTGTAATAGTGTCTTTTTGTCTCCGTTTTGAGGGATAGCAATCCCAGATTGAGGGATGTTTTATCCCTCGTTTAGGGATTTTCCAGCGTTTTGAGGGATGCACCATTCTGAGCAATGTTTTATTTGGTCCAAACATGCCGCCTTGCTGCTTGATAATTCATTCTGACGATTCTAACTTGGCTTCATTGCACCCGTTTGACAGGTAACTTTGTAATCTCGCTAAGTTGAGAATCGGTGAGTCACTCTGTCCATTGGTTTATTCCACCCATTATAGTTTTACGGCAGAATGGCAAGCAGCATAATTTAAAACTGTCGCTTGGTCAGATCTGCGCCCGATGAATAAGCCTCAAGCCGAAGCATATTTGATAGTCTGGCGTAACCATCATGAGATCTGCCATTACGCTCCTGTCCGGCAAAGTCTCCTGCCGAAGTTGAGTATTTTGCTGTATTTGATAATGACTCCTGTTGATAGATCCAGTAATGACCTCAGAACTCCATCTGGATTTGTTCGAACGCTCGGTTGCCGGATGCCGCGTTGATTGGTAGAATCGCAGCAACTTGTCGCGCCAATCGAGCCATGTCAACGTCGATAGATCCCATTCAAGAACAGCAAGCAGCATGCGTGAAAACTTTGGAATCCGGTTCTCCTTCCAAGCCTTGATCTTAGACTTATCAACGCCCACAGCTTCCATGTCTTCTTTGATCGTTTCCAAGCATTGCGATTTTGTTAAGCAACGCACTCTGGATTCTCCGTAGAGCCTCGTTGCGTTTGGCTTTTGCACGAAACCATATGTAAGTATTTCCTTAGATAACAATTGATTGAATGGTCCCAAATAAATGCAAGACGAGGTGGTTTAATTTGATGCCCTTTTCAGGGCTGGAATGGTTGTAAGAGCGGGGTTATTTATGCTGTTGTTTTGTTACTCGGGGAAGGGCAGTTACCTTCTTCCGGCAGAATTCCATCAGGACGCGTTTGAGTCGATGGTTAGTAAAATCCGGCACTTAAATGGCCTTTAATCGAGGATTTGATCGGCCCGCGTATTCTAGCTGTCTTTGGTTTGCCCAAAGCGCATTGGATAAAGAGAGTT\n' 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