| Next changeset 1:709490665bad (2018-06-05) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/nanopolish commit 0e94011a4ea84bf4ae5c2079680a37540e022625 |
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added:
macros.xml nanopolish_methylation.xml test-data/draft.fa test-data/eventalign-summary.txt test-data/fast5_files.tar.gz test-data/methylation_calls.tsv test-data/polished.fa test-data/reads-draft.eventalign.sam test-data/reads.fasta test-data/reads.fasta.index test-data/reads.fasta.index.fai test-data/reads.fasta.index.gzi test-data/reads.fasta.index.readdb test-data/reads.sorted.bam test-data/t2-eventalign-summary.txt test-data/t2-polished.fa test-data/t2-variants.vcf test-data/variants.vcf |
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| diff -r 000000000000 -r f9dadc362197 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Wed May 30 11:55:55 2018 -0400 |
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| @@ -0,0 +1,36 @@ +<macros> + <xml name="requirements"> + <requirements> + <requirement type="package" version="0.9.0">nanopolish</requirement> + <yield/> + </requirements> + </xml> + +<!-- index outputs + <data name="output_index" format="nanopolish_index" from_work_dir="reads.fasta.index" /> + <data name="output_index_fai" format="nanopolish_index_fai" from_work_dir="reads.fasta.index.fai" /> + <data name="output_index_gzi" format="nanopolish_index_gzi" from_work_dir="reads.fasta.index.gzi" /> + <data name="output_index_readdb" format="nanopolish_index_readdb" from_work_dir="reads.fasta.index.readdb" /> + --> +<!-- <output name="output_index" file="reads.fasta.index" /> + <output name="output_index_fai" file="reads.fasta.index.fai" /> + <output name="output_index_gzi" file="reads.fasta.index.gzi" /> + <output name="output_index_readdb" file="reads.fasta.index.readdb" /> + --> + + <xml name="citations"> + <citations> + <citation type="doi">10.1038/nmeth.4184</citation> + <citation type="bibtex"> +@misc{githubnanopolish, + author = {LastTODO, FirstTODO}, + year = {TODO}, + title = {nanopolish}, + publisher = {GitHub}, + journal = {GitHub repository}, + url = {https://github.com/jts/nanopolish}, +}</citation> + <yield /> + </citations> + </xml> +</macros> \ No newline at end of file |
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| diff -r 000000000000 -r f9dadc362197 nanopolish_methylation.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/nanopolish_methylation.xml Wed May 30 11:55:55 2018 -0400 |
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| @@ -0,0 +1,72 @@ +<tool id="nanopolish_methylation" name="Nanopolish methylation" version="0.1.0"> + <description>- Classify nucleotides as methylated or not.</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$input_merged' reads.fasta && + + #if $input_reads_raw.extension == 'fast5': + mkdir fast5_files && ln -s '$input_reads_raw' fast5_files/read1.fast5 && + #else + ln -s '$input_reads_raw' fast5_files.tar.gz && + mkdir fast5_files && tar -xzf fast5_files.tar.gz -C fast5_files && + #end if + + nanopolish index -d fast5_files/ reads.fasta && + ln -s '$b' reads.bam && + ln -s '${b.metadata.bam_index}' reads.bam.bai && + ln -s '$g' genome.fa && + + nanopolish call-methylation + -r reads.fasta + -b reads.bam + -g genome.fa + #if $w and str($w).strip(): + -w "${w}" + #end if + > methylation_calls.tsv + ]]></command> + <inputs> + <!-- index inputs --> + <param type="data" name="input_merged" format="fasta,fastq" label="Basecalled merged reads.fa"/> + <param type="data" name="input_reads_raw" format="h5,fast5.tar.gz" label="Flat archive file of raw fast5 files"/> + + <!-- variants consensus inputs --> + <param type="data" argument="-b" format="bam" label="Reads aligned to the reference genome" /> + <param type="data" argument="-g" format="fasta" label="The reference genome"/> + + <param argument="-w" type="text" optional="true" + label="find variants in window of region chromsome:start-end" /> + + </inputs> + + <outputs> + <!-- variants consensus outputs --> + <data name="output_methylation_calls" format="tabular" from_work_dir="methylation_calls.tsv" label="called methylation sites" /> + </outputs> + <tests> + <test> + <!-- index test --> + <param name="input_merged" ftype="fasta" value="reads.fasta" /> + <param name="input_reads_raw" ftype="fast5.tar.gz" value="fast5_files.tar.gz" /> + + <!-- variants consensus test --> + <param name="b" value="reads.sorted.bam" /> + <param name="g" value="draft.fa" /> + <param name="w" value="tig00000001:200000-202000" /> + + <output name="output_methylation_calls" file="methylation_calls.tsv" /> + </test> + </tests> + <help><![CDATA[ + Usage: nanopolish call-methylation [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa + Classify nucleotides as methylated or not. + + Quickstart tutorial and manual available at: + http://nanopolish.readthedocs.io/en/latest/quickstart_call_methylation.html + + ]]></help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r f9dadc362197 test-data/draft.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/draft.fa Wed May 30 11:55:55 2018 -0400 |
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| b'@@ -0,0 +1,46213 @@\n+>tig00000001 len=4376233 reads=23096 covStat=7751.73 gappedBases=no class=contig suggestRepeat=no suggestCircular=no\n+AGATGCTTTGAAAGAAACGCAGAATAGATCTCTATGTAATGATATGGAATACTCTGGTATTGTCTGTAAAGATACTAATGGAAAATATTTTGCATCTAAG\n+GCAGAAACTGATAATTTAAGAAAGGAGTCATATCCTCTGAAAAGAAAATGTCCCACAGGTACAGATAGAGTTGCTGCTTATCATACTCACGGTGCAGATA\n+GTCATGGCGATTATGTTGATGAATTTTTTCAAGTAGCGATAAAATCTTGTAAGAAGTAAAGATAATAATCTTGAAGCATTTTATCTCGCAACACCTGATG\n+GACGATTTGAGGCGCTTAATAATAAAGGAGAATATATTTTATCAGAAATAGTGTCCCGGGATTGAGTTCAGTATGCATACCGTATCATGATTAATTTTAG\n+TGCTTTTATTAGTGGGGCCTATAGGAGATTCAATGAAATATAGTTCAATATTTTCGATGCTTTCATTTTTATACTATTTGCCTGTAATGAGACAGCTGTT\n+TACGGTTCTGATGAAAACATTATTTTTATGAGGTATGTGGAAAAATTACATTTAGATAAATACTCTGTTAAAAATACGGTAAAACTGAAACAATGGCGAT\n+ACAATTAGCTGAAATATATGTTAGGTATCGCTATGGCGAACGGATTGCAGAAGAAAAACCATATTTAATTACGGAACTACCAGATAGTTGGGTTGTTGAG\n+GGAGCAAAGTTACCTTATGAAGTTGCGGGTGGTGTATTTATTATAGAAATTAATAAGAAAAATGGATGTGTTTTGAATTTCCTACATAGTAAATAATGCT\n+GGCGCTGATGGATGCGGATGGAAACATTGCGTGGAGCGGGGAGTATGATGAGTGGGGCAACCAGCTGAATGAAGAGAACCCGCATCACCTGCACCAGCCG\n+TACCGGCTGCCGGGGCAGCAGTATGATAAGGAGTCGGGGCTGTACTACAACCGGAACCGGTACTACGATCCGTTGCAGGGCGGTATATCACCAGGACCCG\n+ATAGGGCTGAGGGGGATGGAGTCTGTATGCGTATCCGCTGAATCCGGTGAATGGTATTGATCCATTAGGTTAAGTCCCGCAGATGTAGCGCTAATAAGAA\n+GAAAAGATCAACTAAACCATCAAAGAGCATGGGATATATTATCTGATACTTATGAAGATATGAAGAGATTAAATTTAGGTGGGACTGATCAATTTTTCCA\n+TTGTATGGCATTTTGTCGAGTGTCTAAATTAAATGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTA\n+AATCTGTTCGGTATGTACGGCAGAAAAGTAAAGCTATCCCATTCTGAAATGATTGAAGATAATAAAAAGACTTGGCTGTAAATGACCATGGGTTGACATG\n+TCCATCAACAACAGATTGCTCAGATAGATGTAGTGATTATATTAATCCAGCATAAAAAACGATAAAGGCTTTACAAGATGCTGGCTATCTCAAGTAATCT\n+ATCAAAGATGATAATATTTATTTTTGCTATTATAATCATTGTTGTTTTATGCGTAATTACTTATCTTTATTTATACAAAGATGAATCTCTTGTAAGTAAA\n+CATTACATAAACTATATGGCAATACCAGAAAATGATGGAGTTTTTACATGGCTCCCAGATTTTTTCCGCACGTAGCGGTGGATATATCAATATACACAAA\n+TGTAGAAGATGATTATTTTTTCTTATTTTCCCTAACAAATGATGATGGGGTAGGTTTAAGAAAACATTGACAGTGAGGGCCAGGGAACAAGTGGCGAAAA\n+TCGTATCAAAGAATGATCCAGATACAAAAAAGTGTGGTGTAAATATGGTAAGATACCAGGGCAAGGGATGGTGTAAACCTTTTTTGTTGGTGAAATTAAT\n+GTTACGCATTATTTTATAACAAATATTGGAGCTGGATTGCCTGATGCTTGTGCAGAGTAATTGCTTGAATTAAGAGTCTATCCCATATCGAAGTCGTCAA\n+CTTCGTAGTGAGGAAAAGTAAAATTCCTGACTGAGAAAAGACATGTCGGCTATTGTGTAAAGCCATATAGCTCAGACGATGAATATCTACTCGTATTCAG\n+TTGTTTATTGAGGGTGAGTTCCGACCCTGAAACAACAAATAAAATGAACAGTCAGAGAGTTTACATAGAATTGCACTGGTCTTTTACGATATCTGACATT\n+GTGTAATACATATTCAGCCATGCATTAATTAAAATGTTACGTGTTTAATGTGAGTCCCTATCTGAAAATAAATAATCCTTCCGGATTAAAATAAATTCTT\n+GCCGGGAAAGAAAGAGGAAATAAACCATTAGCGGAAAACCAGCGGCACGCCAGGGTGACATGCCCCAGTACGGCGGCCCGATAGTCCAGGGTTCAGCGGG\n+GTACTGATAGTCGCGCCGACTGCATCGAGAACTCCATACAACTTTTACGGAACGTCACCTGATAAAATTTGTTCAGTATCGTCTTTGAGATTCTCAAGGT\n+TATGGAGTAACCAGACAGAACGGACACCACTGTCGGAGATAAAACCCCTGTTTACGCAGCTCGTTGCTGGCCCGGTGCTGACCATGTGTCGGGAAAGCGA\n+CGGCGTAATCAACAACAGCCTGTTCAGTTGCCTCATCGGTACGGTTCTTAAGGTTAGGAGCGCGGCGACTACGATTAATCTGCGCATCCACACCGCCTTC\n+AGCGACCAGTTCGCGGTAACGATAAAACGTATCACGCGAAACGCCCATGATTTTACAGGCTTTTGATACGTTGCTGAGTTCTTCAGCCAGATTGAGCAAA\n+CCGGCTTTGTGTTTGATGACGGGATTGGCAGTATGAAGCATGAGAGTTACCTCTTGTTTTGGATAAGGATTCGACACTCATATCAAAACCGGTAACTCTC\n+AACCTTTCAAGGCCATGTGTCAGATCAAGTCGCGACTAATACAAATACGTCCCTCATTACCGCGCCTTAACCCATTCCGCCACTTCCGCCCACTCACCGC\n+GAAAGACAACTTTTTCCGCTTTTTCTCAAGCTGATAGCGATACATCGGGTCGTAATATTCTTCAAGTAACGGCACCAGCCAGGCCAGATGACCGTCGGTG\n+CTGCCGGTGGTGAGTTGCGTTGTCAGTGCTGCATCCAGCCTTGCAGCCAGTTCGTTATAGCGCTGTAGCCCCAGCCGACGCTTAATCGCCGAAAGTCCGT\n+GATGCAGGTATTCGCAATACTCCTGCCAGCCCTGTTCGTCGCCGTACGCGTGGGTAAAATCATGATGCATACGCAAGAAATACTCTTCGTTCAGGCGCTC\n+AAGACGGATCTCAAACGGATCTTCTACCACCGCAATCGCCGCCTGAGTCATTCGCTCGCGCAGGCATTCCGGCAGGTGATTCGAACCGATCATCCGGCTT\n+TCGTCTTCCAGCACCCACAGGCGCAAATTCTGACGGGCGTCGGTTTTAGCATTTCGGCAGCCAGCAGGTTTTCAAAACTCGCCTGGCTAAGTTGTGGTTG\n+TAACGTGCGACCAAACGCCGAACCGCGATGACGCGCCAACCCTTCCAGATCAACACCGTTCGGCTGTTGCTGCACTAACAGCGTTTTACCGCTGCCGGTA\n+CAACCGCCAATCAGCACTATCGGTTTTGTGCCAGTTCAATAGTCGCCTGAATCGCGGTCTGGCGCAGTGCCTTATAACCGCCTTCCACCAGCGGATAATC\n+AATCCCCGCTGCATGCAACCAGCTTTGCACAATATGTGAGCGCTGACCGCCACGGGCGCAGCAGAGAATACCTTGCGGATTTTGCA'..b'ATTCGATTCGCCTGTAAGCATCAGAATGATGTTCGGCATATAGCGCAAGTCCTTCCAGTTTGGGCAAAG\n+CATCAGCCAGATGTAGGCTATGTGGATCTACCAGGTCCACAACCATTTTGCCATCCTGTTCGGCAAAGAACAGGAAATCGGGACGAACAATCTTGTACTG\n+TTCAGCTTCAACATAAGCGATTCCCAGTGACGACTGCCCTGTGTACTGTGGATTACGATACCAGAAAGCAAATCCTTCACGTTTGGTTTCGATCTCAAAA\n+CCTTGGTTTCCCAATGGTTCAACAGAGCCGGATAGTTCCCGCTTTCGTCACACAACAAATGGTGTTTCCAGACTGGAAGGTCAGCTTCCTTTTCACCTTC\n+ACGCACCCTGGTCATTTCAAACTTGTTCGCCGGCCTGACCAGATCCACATCCTGCGGTTCGGTACTCATTTCGACGATTTGACGATAGGCCTCTTTACGC\n+TCATCTTTCAACGACTTGATTTGCGGTGTGTACTCGGCCAGCCACGCCTTCGCCAGTCTATCGGCCTCGCCATCGAAGTAATCCTGCACCTCCATCACCA\n+GCCCCATGCCAGCAACGGTAACACGAGCCTCCATGATTGCTTCCAGATATTCCTCTGCATCCTCTTCTCGATCCGCAACCTTATCGGCCAGATATTCGAC\n+ATAGGTACGTGAAACATCCGGGCTGAAAATTCGGTGATGCTGCCAACTTACTGATTTAGTGTATGATGGTGTTTTGAGGTGCTCCAGTGGCTTCTGTTTC\n+TATCAGCTGTCCCTCCTGTTCAGCTACTGACGGGGTGGTGCGTAACGGCAAAAGCACTGCCGGACATCAGCGCTATCTCTGCTCACTGCCGTAAAACATG\n+GCAACTGCAGTTCACTTACACCGCTTCTCAACCCGGTACGCACCAGAAAATCATTGATATGGCCATGAATGGCGTTGGATGCCGGGCAACCGCCCGCATT\n+ATGGGCGTTGGCCTCAACACGATTTTCCGCCATTTAAAAACTCAGGCCGCAGTCGGTAACCTCGCGCATACAGCCGGGCAGTGACGTCATCGTCTGCGCG\n+GAAATGGACGAACAGTGGGGATACGTCGGGGCTAAATCGCGCCAGCGCTGGCTGTTTACGCGTATGACAGGCTCCGGAAGACGGTTGTTGCGCACGTATT\n+CGGTGAACGCACTATGGCGACGCTGGGGCGTCTTATGAGCCTGCTGTCACCCTTTGACGTGGTGATATGGATGACGGATGGCTGGCCGCTGTATGAATCC\n+CGCCTGAAGGAAAGCTGCACGTAATCAGCAAGCGATATACGCAGCGAATTGAGCGGCATAACCTGAATCTGAGGCAGCACCTGGCACGGCTGGGACGGAA\n+GTCGCTGTCGTTCTCAAAATCGGTGGAGCAGCATGACAAAGTCATCGGGCATTATCTGAACATAAAACACTATCAATAAGTTGGAGTCATTACCCGGTAA\n+CAGATATATCGCCTCCATCACCGCTGAAGTAATGAAGTAAGGCAGCAAGCCTCGCCATGTTCTCCGCCATTTTAGAAGCATAATCCTTAAAATCATAAAG\n+AAGGCCAATCATTCTCATTTCTGACTCGACCTGGTTGTAGAATTCGATCCAATGTCTTTCTGCTTCTGCAGAGAATCGGAGGCAGATACGATTATTTTCA\n+CACACGGACGGGTTTGCCTCCACCTTTGTAAGAAAGAATTGTGAAATGGGGTTGCAAATGAATAATTACACATATAAAGTGAATTTTAATTCAATAAGTG\n+GCGTTCGCCATGCGAGGATAAAATGTCCGATTTATACAAAAACACTTTCTGAAACTGCTCGACTTTACCCTGCACAGTTCACTTCTCTGCTGACCCTTGC\n+CGCACAGCTCAAAGCCGATAAAAAATGGCAAGGAAGTACAGAAGCTTACCGGTAAAACATCGCGCTCATCTTCGAAAAGACTCGACTCGTACCCGTTGCT\n+CTTTCGAAGTTGCCGCATTTGACCAGGGCGCGCGCGTTACCTATTTAGGGCCGAGCGGCAGCCAGATTGGGCATAAAGAGTCAATTAAGGACACCGCGCG\n+GGTTCTCGGGCGGATGTATGACGGCATTCAGTATCGCGGTCACGGCCAGGAAGTGGTCGAAACGCTGGCGCAGTATGCGGGCGTGCCGGTGTGGAACGGG\n+CTGACCAACGAGTTCCACCCGACCCAGCTGCTGGCGGACCTGATGACCATGCAGGAGCACCTGCCGGGCAAGGCGTTTAACGAGATGACGCTGGTCTACG\n+CGGGCGATGCGCGCAACAACATGGGCAACTCGATGCTGGAAGCGGCGGCGCTGACCGGGCTGGATCTGCGCCTGTTGGCCCCGAAAGCCTGCTGGCCGGA\n+AGAGAGCCTGGTGGCGGAGTGCAGCGCGCTGGCGGAGAAGCACGGCGGGAAAATTACTCTGACGGAAGACGTGGCGGCAGGCGTTAAGGGCGCGGACTTT\n+ATCTATACCGACGTGTGGGTGTCGATGGGCGAGGCCAAAGAGAAGTGGGCAGAGCGGATTGCGCTGCTGCGCGGGTATCAGGTGAACGCGCAGATGATGG\n+CGCTGACCGACAACCCGAACGTGAAGTTCCTGCACTGTCTGCCGGCGTTCCATGACGACCAGACTACGCTCGGCAAGCAGATGGCGAAGGAGTTCGATCT\n+GCACGGCGGGATGGAGGTGACGGACGAGGTGTTTGAGTCGGCGGCGAGCATCGTGTTCGACCAGGCGGAAAACCGGATGCATACGATTAAGGCGGTGATG\n+ATGGCAACGCTTGGGGATTGGGTCCGCTGCGCGTTGGTGCCTCACCCGGCCCTCTCCCACAGGAGAGGGAGAACACCGGCTCCATTTCATTGATTTTTCA\n+TCCCGAAAAGGTACGTTTTCGCCTTAATTCCAGCGTGGACATGCCAGCATTATGCCGATTATTCAGTCTGTTGAACGTGCGTTGCAGATCCTCGACCTGT\n+TCAACGAGCAGGCCACCGAGCTTAAGATCACCGACATCAGCAAACTGATGGGGCTGAGCAAGAGTACCCTCCACTCGCTGCTAAAACCCTGCAGCTTCAC\n+GGCTATATCGATCAGAACCCGGAGAACGGCAAGTATCGCCTCGGCATGAAGCTGGTCGAGCGCGGCCATTTTGTCGTGGGCTCCATCGATATTCGGCAGA\n+AGGCAAAGGCTGGCTGACGGAGCTGTCCCGGCGGACCGGGCAGACCACCCATCTGGGGATCCTGGACGGGCGTGAAGGGTCTATATCGAGAAGATTGAAG\n+GCAAGCTGGCCGCCATCGCCTATTCACGCATCGGCCGCCGCCTGCCGGTGCACGCCACCGCCATCGGCAAGGTGTTGATTGCCTGGCTGGGCGAGGCCGA\n+GCTGAACGCCCTGCTGGAGGGCTATCAGTACACTACCTTTACGCCCGCCACCCTCGCGTCTCGCGAAGCCTTAATGAGCGCCCTGGCGCAGACCCGCGCG\n+CAAGGCTACGCCCTGGACAGCGAAGAGAACGAGCAGGGCGTGCGCTGCGTGGCGGTGCCGGTGTGGAACCACGAGTCCCGCGTCATCGCCGCCCTGAGCC\n+TGTCGACGCTGACCTCCCGCGTGGACGACGCGGGCTGGCTAATTTCCGCGAGCAGCTTCAGCAGGCCGGGCTCGCGCTCTCGCGCGCTGGGCTACCGGCC\n+TGAGCCGTTAGACCGGCTCGTAGGTGAAGTAGTCGAAGTCCGCGTAGCAGCCGTCGCTGATGTCCTCGGTGCAGGCCCACAAACGCGCCGGTGAAGAAGC\n+CGCGCCCGCCGATGTAGTCGTCCGACAGCTTCCACGCCTCATACGTCACCGGCACGGTGTGCCACGTCTCGCCATCAAACGAGTAGCTGTAGCGGTAGAC\n+CAGCGTATCCACGTCCACCCGCAGCCAGACGCTCTCCGCATGTTCCGGCAC\n' 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| diff -r 000000000000 -r f9dadc362197 test-data/eventalign-summary.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/eventalign-summary.txt Wed May 30 11:55:55 2018 -0400 |
| b |
| b'@@ -0,0 +1,144 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t0d624d4b-671f-40b8-9798-84f2ccc4d7fc\tfast5_files//odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch391_read2287_strand.fast5\t\ttemplate\t3795\t2002\t49\t1743\t4.94\t39.434\t1.022\t0.000\t1.273\n+128\t2a021335-d1c5-4881-93fc-a673d8960075\tfast5_files//odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch280_read913_strand.fast5\t\ttemplate\t4119\t559\t138\t3421\t5.31\t-2.195\t0.987\t0.000\t1.713\n+129\t67ee25a0-86c1-44be-9b64-5a0db853eaf2\tfast5_files//odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch477_read112_strand.fast5\t\ttemplate\t3853\t1225\t316\t2311\t4.83\t-11.350\t0.988\t0.000\t1.224\n+130\tb1594985-30ce-4f59-9230-dff6ec966710\tfast5_files//odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch139_read6216_strand.fast5\t\ttemplate\t9663\t5042\t96\t4524\t12.22\t-0.918\t1.005\t0.000\t1.729\n+131\t56b8515b-fc38-4531-bb1e-757449205298\tfast5_files//odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch505_read3234_strand.fast5\t\ttemplate\t3127\t1700\t69\t1357\t3.92\t-9.257\t0.992\t0.000\t1.198\n+132\t723b3ed8-ede7-42bd-89c3-d269619eea3d\tfast5_files//odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch54_read3907_strand.fast5\t\ttemplate\t11113\t5507\t148\t5457\t14.20\t13.753\t1.030\t0.000\t1.168\n+133\t2a021335-d1c5-4881-93fc-a673d8960075\tfast5_files//odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch280_read913_strand.fast5\t\ttemplate\t10196\t2710\t19\t7466\t13.22\t-2.195\t0.987\t0.000\t1.713\n+134\t8b55f8dd-3fcb-478c-8384-6df32ed6400b\tfast5_files//odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch196_read2318_strand.fast5\t\ttemplate\t7053\t3675\t100\t3277\t8.91\t-11.473\t1.050\t0.000\t1.143\n+135\t9b070b44-f197-4952-8863-7e27e04ff558\tfast5_files//odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch471_read263_strand.fast5\t\ttemplate\t4914\t2737\t88\t2088\t6.09\t-13.551\t1.004\t0.000\t1.191\n+136\tbd76fe67-db4b-4d72-95df-e23f07aea51a\tfast5_files//odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch378_read4280_strand.fast5\t\ttemplate\t13728\t7760\t338\t5629\t16.91\t-3.697\t0.949\t0.000\t1.523\n+137\t8a553dac-a603-4a38-ab2b-4c9cc41bd7ac\tfast5_files//odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch378_read4310_strand.fast5\t\ttemplate\t5732\t2918\t114\t2699\t7.19\t-9.107\t1.017\t0.000\t1.208\n+138\ta46ed4fe-5181-4a9d-ad1a-9e7ac83a0f95\tfast5_files//odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch54_read3215_strand.fast5\t\ttemplate\t5566\t3148\t133\t2284\t6.96\t19.881\t0.975\t0.000\t1.375\n+139\tfa9ad683-35c5-4dad-a3af-de7a86b1ffa8\tfast5_files//odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch85_read2098_strand.fast5\t\ttemplate\t3058\t1454\t49\t1554\t3.85\t3.181\t0.984\t0.000\t1.404\n+140\t0a238451-b9ed-446d-a152-badd074006c4\tfast5_files//odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch281_read4019_strand.fast5\t\ttemplate\t3989\t1295\t347\t2346\t4.92\t-1.768\t1.038\t0.000\t1.397\n+141\t280af896-8e53-4427-89d3-a554c87269fd\tfast5_files//odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch292_read1173_strand.fast5\t\ttemplate\t1318\t727\t23\t567\t1.64\t-4.813\t0.973\t0.000\t1.282\n+142\tb1594985-30ce-4f59-9230-dff6ec966710\tfast5_files//odw_genlab4209_20161213_FN_MN16303_sequencing_run_sample_id_32395_ch139_read6216_strand.fast5\t\ttemplate\t506\t169\t35\t301\t0.62\t-0.918\t1.005\t0.000\t1.729\n' |
| b |
| diff -r 000000000000 -r f9dadc362197 test-data/fast5_files.tar.gz |
| b |
| Binary file test-data/fast5_files.tar.gz has changed |
| b |
| diff -r 000000000000 -r f9dadc362197 test-data/methylation_calls.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/methylation_calls.tsv Wed May 30 11:55:55 2018 -0400 |
| b |
| b'@@ -0,0 +1,16999 @@\n+chromosome\tstart\tend\tread_name\tlog_lik_ratio\tlog_lik_methylated\tlog_lik_unmethylated\tnum_calling_strands\tnum_cpgs\tsequence\n+tig00000001\t191153\t191157\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-6.31\t-130.59\t-124.28\t1\t2\tTATTACGACCGCTGA\n+tig00000001\t191181\t191181\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-0.75\t-101.63\t-100.88\t1\t1\tTTTGGCGTTGA\n+tig00000001\t191196\t191215\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-11.45\t-223.51\t-212.05\t1\t3\tCAGTGCGGCAAACAGCGGATAGAACGGGCT\n+tig00000001\t191229\t191229\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-5.42\t-101.51\t-96.09\t1\t1\tGGAGGCGTGCA\n+tig00000001\t191244\t191244\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-2.28\t-82.87\t-80.59\t1\t1\tAAAGGCGTTGT\n+tig00000001\t191255\t191273\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-9.25\t-167.61\t-158.35\t1\t3\tTCATGCGTTTGTGCGGTACATAACGCTGT\n+tig00000001\t191354\t191354\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-4.06\t-98.18\t-94.12\t1\t1\tGATTGCGTAAC\n+tig00000001\t191369\t191374\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-1.70\t-119.73\t-118.02\t1\t2\tATACCCGGATCGTTCT\n+tig00000001\t191399\t191420\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-14.84\t-212.15\t-197.31\t1\t4\tAACAGCGGCGAACAGTCCGCCATCATCGGAAT\n+tig00000001\t191440\t191440\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-2.39\t-97.48\t-95.10\t1\t1\tATAGCCGACCC\n+tig00000001\t191502\t191524\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-7.13\t-196.90\t-189.78\t1\t5\tCTTGGCGGGCGTTATAAATCGTACCGTCGTAGG\n+tig00000001\t191548\t191562\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t2.03\t-164.90\t-166.93\t1\t3\tCACAGCGAGGCGGAAAGGACGAGCC\n+tig00000001\t191576\t191595\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-16.47\t-198.51\t-182.04\t1\t5\tTTGCCCGCTGCGGTGCGACTTCCGCGATCA\n+tig00000001\t191606\t191606\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-0.43\t-106.24\t-105.81\t1\t1\tGCTCACGCAGG\n+tig00000001\t191632\t191632\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-5.03\t-101.77\t-96.74\t1\t1\tCAGTGCGCATC\n+tig00000001\t191646\t191646\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-0.52\t-102.26\t-101.75\t1\t1\tGCCACCGATAA\n+tig00000001\t191659\t191671\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-6.16\t-155.98\t-149.82\t1\t3\tCCATACGGGTTACGTGCCGTTTC\n+tig00000001\t191686\t191686\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-1.12\t-84.86\t-83.73\t1\t1\tTAAACCGGTGT\n+tig00000001\t191710\t191715\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-1.66\t-141.17\t-139.51\t1\t2\tAGCAACGCTCCGTGGT\n+tig00000001\t191741\t191741\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-2.49\t-76.49\t-74.01\t1\t1\tTATTGCGATCA\n+tig00000001\t191764\t191764\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-2.28\t-106.49\t-104.21\t1\t1\tTCACCCGGTGT\n+tig00000001\t191778\t191778\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-8.95\t-111.16\t-102.21\t1\t1\tCAGGGCGTTTA\n+tig00000001\t191820\t191820\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-1.97\t-129.21\t-127.24\t1\t1\tTAAAACGAAGT\n+tig00000001\t191835\t191835\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-0.83\t-101.24\t-100.41\t1\t1\tTTTATCGGCAT\n+tig00000001\t191854\t191854\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-3.07\t-94.72\t-91.65\t1\t1\tTTTGCCGCATG\n+tig00000001\t191878\t191886\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-11.48\t-176.19\t-164.71\t1\t3\tCATGGCGCGCCTTCGTGAA\n+tig00000001\t191901\t191919\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-5.54\t-179.90\t-174.37\t1\t5\tCAGATCGCCCATCGCTACGTCGGCGTTGC\n+tig00000001\t191931\t191944\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-19.26\t-177.78\t-158.53\t1\t3\tCAAGTCGGCACGGAACAGCGCCTC\n+tig00000001\t191977\t192002\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-8.41\t-244.04\t-235.63\t1\t6\tTTCCCCGCCGGATGGCGACGGAAAATTCGCCGCCCT\n+tig00000001\t192027\t192029\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-0.80\t-105.66\t-104.86\t1\t2\tTCAAACGCGCTGT\n+tig00000001\t192053\t192064\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-2.40\t-160.39\t-157.99\t1\t3\tATAATCGACCAGTGCGCGGAAG\n+tig00000001\t192079\t192079\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-7.16\t-99.97\t-92.81\t1\t1\tGTGGGCGCAGT\n+tig00000001\t192107\t192107\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-0.87\t-96.22\t-95.35\t1\t1\tGGCAGCGGTTT\n+tig00000001\t192121\t192121\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-0.94\t-100.94\t-100.00\t1\t1\tACTGGCGACCA\n+tig00000001\t192136\t192146\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-4.34\t-143.10\t-138.77\t1\t4\tATTCTCGTCGCGATTCGCAAT\n+tig00000001\t192165\t192172\td57afb7d-903e-46cf-a43d-0e17fb0949d8\t-7.29\t-14'..b'98\t1\t1\tGGTGACGGGCC\n+tig00000001\t202821\t202836\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-1.02\t-218.40\t-217.38\t1\t4\tCATCACGCGCATCACCACGCCGGATG\n+tig00000001\t202851\t202854\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-0.97\t-151.89\t-150.93\t1\t2\tGGCATCGGCGTTTT\n+tig00000001\t202884\t202903\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-3.39\t-239.50\t-236.10\t1\t3\tGTTAACGTCAGCCACCGGGCCTGACGGGCT\n+tig00000001\t202916\t202919\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-5.57\t-158.84\t-153.27\t1\t2\tAAATACGCCGGGAA\n+tig00000001\t202940\t202940\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-0.01\t-137.40\t-137.40\t1\t1\tGGGGCCGTCTG\n+tig00000001\t202966\t202985\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-0.70\t-224.43\t-223.73\t1\t4\tCCTGACGGCGATATCACCCGCTACCGTTAT\n+tig00000001\t203017\t203022\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t0.16\t-138.31\t-138.47\t1\t2\tCCCTGCGCAACGGAAG\n+tig00000001\t203035\t203042\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-0.21\t-179.23\t-179.03\t1\t2\tGCCACCGGCAGCCGGAAA\n+tig00000001\t203055\t203068\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t3.76\t-206.83\t-210.60\t1\t3\tCATGACGTGGAGCCGTTACGGTCA\n+tig00000001\t203098\t203098\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t1.17\t-125.07\t-126.23\t1\t1\tTGTTCCGGTTA\n+tig00000001\t203111\t203111\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-0.97\t-148.33\t-147.36\t1\t1\tTAACCCGCTAT\n+tig00000001\t203126\t203126\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-7.02\t-103.83\t-96.81\t1\t1\tATGACCGTTTT\n+tig00000001\t203142\t203155\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-6.70\t-214.24\t-207.54\t1\t4\tGGTGACGGCGGTGCACCGCGAGGA\n+tig00000001\t203177\t203192\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-0.92\t-216.14\t-215.23\t1\t4\tAGTACCGCGCATACGACAGCCGTGGA\n+tig00000001\t203209\t203209\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-2.79\t-123.73\t-120.94\t1\t1\tATTGCCGTGAA\n+tig00000001\t203220\t203220\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-1.36\t-114.22\t-112.86\t1\t1\tAGACACGCAGG\n+tig00000001\t203235\t203237\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-4.35\t-124.77\t-120.42\t1\t2\tTGAAACGCGGTAT\n+tig00000001\t203251\t203257\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-5.88\t-153.96\t-148.09\t1\t3\tTACAACGCCGCCGGTGA\n+tig00000001\t203272\t203272\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-1.72\t-105.43\t-103.71\t1\t1\tACCACCGTCAT\n+tig00000001\t203283\t203287\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t0.27\t-130.94\t-131.20\t1\t2\tTGCCCCGGACGGCAG\n+tig00000001\t203299\t203299\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-0.22\t-118.31\t-118.09\t1\t1\tAGAAACGGGAC\n+tig00000001\t203311\t203316\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-10.31\t-125.90\t-115.59\t1\t2\tCAGTACGATGCGTGGG\n+tig00000001\t203340\t203357\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-11.70\t-169.31\t-157.61\t1\t4\tTACCACGCAGGGCGGTCTGACGCGCAGT\n+tig00000001\t203371\t203393\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-0.98\t-246.59\t-245.61\t1\t4\tGAATACGATGCTGCCGGACGGGTCATCCGCCTG\n+tig00000001\t203410\t203410\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t3.62\t-109.90\t-113.52\t1\t1\tGAAAACGGCAG\n+tig00000001\t203429\t203447\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-12.27\t-220.57\t-208.29\t1\t4\tCCTTCCGTTACGATGTACTCGACCGGCTG\n+tig00000001\t203464\t203486\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-2.89\t-240.35\t-237.45\t1\t4\tGAAACCGGCTTTGACGGCCGCACACAGCGTTAT\n+tig00000001\t203497\t203506\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-3.73\t-154.07\t-150.34\t1\t2\tCACCACGACCTGACCGGCAA\n+tig00000001\t203519\t203524\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-7.21\t-149.81\t-142.60\t1\t2\tTTATCCGCAGCGAGGA\n+tig00000001\t203560\t203609\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-7.10\t-430.95\t-423.84\t1\t8\tTATGACGAAGCAGACCGCCTCACGCACCGCACCGTGAATGGCGAAACCGCAGAGCGGTGG\n+tig00000001\t203623\t203629\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-1.64\t-163.12\t-161.49\t1\t3\tTATGACGAACGCGGCTG\n+tig00000001\t203659\t203676\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-0.40\t-230.02\t-229.62\t1\t3\tATCAGCGAAGGGCACCGGGTGACGGTGC\n+tig00000001\t203705\t203710\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-7.62\t-166.05\t-158.43\t1\t2\tAAGGCCGCCTCGCCAG\n+tig00000001\t203727\t203727\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-0.50\t-190.77\t-190.27\t1\t1\tCCTGACGGTGC\n+tig00000001\t203739\t203745\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t-0.18\t-205.41\t-205.23\t1\t2\tTCATCCGCAGACGAATG\n+tig00000001\t203781\t203788\t0eb7ac67-e215-4aa1-958a-7cd320d229a4\t0.12\t-163.10\t-163.22\t1\t2\tACATGCGTACAACGCACA\n' |
| b |
| diff -r 000000000000 -r f9dadc362197 test-data/polished.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/polished.fa Wed May 30 11:55:55 2018 -0400 |
| b |
| @@ -0,0 +1,2 @@ +>tig00000001:199960-202040 +TCCTGAGAAGCTACAGGCCCCATGGGTAACAGCTGTTGCGCTCCTTCAACGGTATTCACAGCCTGATAAGGCAGAAAGTTTTGCAGCGCACCTTGTTGAATAAAAAACAGTGCAATCAACAACGCCACAGGGACTAGCACCCATAACGTGATGCGTAGCAGATCGACCCAGGCATTCCCGAGCGTGCTCATGCTCTGGCGGGTAAACGCACGGATGAGGGCAAAAATCACCGCAATCCCGCTGGCGGCAGAAAGAAAGTTTTGCACCGTTAAGCCCGCCATCTGGCTGAAATAGCTCAACGTGGTTTCACCGCTATAAGATTGCCAGTTGGTATTGGTGACAAAGCTGACGGCGGTATTCAGCGCCAGATCCCACGACAGCCCTGGCAACTGCTGTGGATTAAGCGGCAGATAGTGCTGACCGAGCAACATAAAAACAGCACCGCCAGCCCCAGCATGTTCAGGCCGAGAATGGCACAAAGATATTGCTTCCAGTTCATCTCACGGTCAGAGACGCCAAGTGCGCGAAAAAGTACGCGCTCAACGCCCGTTGTACCGGGAAGAGGAATGTCATTAATCAGCCGCGCCAGCCCGCTGCCTAAAGGACGCGCCAGCACCATTAACACCAGTAAAAACGTGGCGATCAGTAAGAACCCTTGCGCAGCCATCAGAACGCCTCCGCATTGATCAGGGCATAAACCAGATAACCCAGTAATAAAAACACCAGCAATACGCCGGTTATCACGCCTGCACTCACAGTGCACCTCCAGTGGCCTAAAAGTGATACCGGAAGGGTAGAATTCTGGCTGCAAAGATTTCGCAAAAATCTGCGGGCGGGGTGTAAAAAAGTATAAAAATGGCAAAAGCCATGATTTAACTAATGTTTAGTATTAATTTAACTTTTGTGTAACTTAATTACAGGATGAATGTAAATAAACCATCAATAAGCAAAAATAAGTGGTCGGATGAGTAGTAAAATTACACAAAAGGCGGTACTATTTTCATCAGATAAACAAATTCATTTTTCCGGTGCCATTCACCGGGTAGATACAAAAGGGGGAGAAAAGTATGGAACTCTACAGAGAATATCCTGCATGGCTTATCTTTTTACGCCGTACTTATGCGGTTGCAGCGGGCGTTCTGGCGCTGCCTTTCATGCTTTTCTGGAAAGACCGCGCCCGCTTTTACAGCTACCTGCATCGCGTCTGGTCGAAAACCAGCGATAAACCGGTGTGGATGGATCAGGCCGAAAAGGCAACTGGTGATTTTTATTGATTGCTGAGTTTTGAATACATTGAAAACCGCCAGCGGAAACGCTGGCGGTTTTTTGTATCAGGAAGATGTTCAGAGGAATATTTAGACATCGTTATACCAATCGAAACATATATTCATGAAATATATATAAATATTTTCCTAATTGTTCTTATCTGACAGATATCTCACTTAAGGCTTTCTTATAAATCTGTAGGGTTTCGCCTGTCAGCAGACAAATAACCCGATAAAACAAGGATGAGCAGATGAGCGGAAAACCGGCGGCGCGTCAGGGCGACATGACGCAGTATGGCGGTAGCATTGTCCAGGGTTCAGCCGGGGTACGCATCGGTGCCCCCACCGGCGTGGCCTGTTCGGTGTGCCCCGGCGGGGTGACGTCCGGCCATCCGGTCAATCCGCTGCTCGGTGCAAAGGTCCTTCCCGGTGAAACCGACATCGCCCTGCCCGGCCCGCTGCCGTTCATTCTCTCCCGCACCTACAGCAGTTACCGGACAAAAACGCCCGCGCCGGTGGGGAGCCTCGGCCCCGGCTGGAAAATGCCTGCGGATATCCGCTTACAGCTGCGCGATAACACACTGATACTCAGTGATAACGGCGGCAGAAGCCTGTATTTTGAGCACCTGTTTCCCGGTGAGGACGGTTACAGCCGCAGCGAGTCACTGTGGCTGGTGCGCGGCGGCGTGGCGAAACTGGATGAAGGTCACCGGCTGGCCGCACTCTGGCAGGCGCTGCCGGAAGAACTCCGCTTAAGTCCGCATCGTTATCTGGCGACAAACAGTCCGCAGGGGCCGTGGTGGCTGCTCGGCTGGTGTGAGCGGGTGCC |
| b |
| diff -r 000000000000 -r f9dadc362197 test-data/reads-draft.eventalign.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads-draft.eventalign.sam Wed May 30 11:55:55 2018 -0400 |
| b |
| b'@@ -0,0 +1,148 @@\n+@HD\tVN:1.5\tSO:coordinate\n+@SQ\tSN:tig00000001\tLN:4376233\n+@SQ\tSN:tig00000005\tLN:10541\n+@SQ\tSN:tig00000118\tLN:234051\n+@PG\tID:minimap2\tPN:minimap2\tVN:2.10-r761\tCL:minimap2 -ax map-ont -t 8 draft.fa reads.fasta\n+0a238451-b9ed-446d-a152-badd074006c4.template\t0\ttig00000001\t16\t60\t10711S1M1I1M3I1M1I1M2I2M2I2M19I1M20I2D4M70I5M2I6D3M1I3D2M1I1M153I2M6I1M1I1M13I1M2I1M6I1M2I3M1I1M1I5M1I3M3I3M2I2M1I2M2I2M1I1M1I1M1I2M1I5M3I3M1I1M1D2M1I5M1I4D3M2I2M1I5M2I9M1I4M2I1M1I1D2M2I2M2I3M1I1M1I10M1I1M1I1D2M1I3M1I2M1I1M1I1M1I2M1I1M1I2M2I1M2I4M1I3M1I1M1I7M1I4M1I2M2I1M1I1M4I2M1I1M2I5M2I1M2I3D1M1I1M4I3M1I4M1I2M2I2M2I1M2I2M1I6M1I1D1M2I5M1I2M3I3M1I1M1I2M1I1D4M2I1M1I1D1M1I1M1I1M2I3M1I7M1I4M1I3M1I2D1M1I1M1I2M3I1M2I9M1I6M2I3M1I1M3I2M1I1M3I2M1I1M2I1M2I1M1I1M1I2M2I4M1I6M3I4M1I1M2I2M2I1M3I2M2I1M1I7M1I3M1I1M1I1D4M4I1M1I1M1I3M1I4M1I2M1I5M2I1M2I1M3I2M1I3M1I1M1I3M1I2D4M1I1M2I4M1I1M3I5M1I2M1I2M1I1M1I3M1I2M1I1M1I2D3M1I2M1I2M3I2M3I1M3I1M1I1M1I5M2I1M1I1M1I2M1I1M1I3M1I2M2I2M1I2M1I2M2I1M2I2M1I3M1I4M1I4M1I1D2M1I2M1I3M1I5M1I1M1I1D3M1I1M1I1D6M4I6M2I1M1I3M2I4M2I1M2I2M1I1M2I1M2I1M1I1D3M1I3M1I3M1I2M3I2M2I3M1I2M2I1M2I2M1I1D2M3I1M1I3D3M2I3M1I3M2I2M1I6M2I1M1I3M1I4M1I1D3M1I2M2I2M2I2M2I4M1I3M2I4M1I2M1I1D5M1I1M3I1M1I3M1I6M2I1M2I2M1I2D3M1I1M5I9M1I3D5M1I2M1I3M3I1M1I1M2I3M1I2M1I1D2M2I1M2I2M2I1M3I3M1I1D5M1I2M1I3M1I2M1I4M1I4M1I1M5I1M1I1M1I3M1I1M1I2M1I2M1I5M1I7M1I1D2M1I3M1I1D2M1D2M1I1M1I2M4I4M1I4M1D5M1I1M1I1M1I2D3M1I1D2M1I1M1I2M1I5M1I1M1I4M2I4M1I6M1I4M1I1M1I3M6I1M2I4M4I1M1I1M1I1M1I2M1I2M1I2M2I1M1I1M2I1M2I2M1I2M2I1M1I1M1I2D3M1I2M1I9M1I2M1I1M1I3M3I1M2I5M3I4M1I2M3I1M1I1M1I1M2I4M1I1M2I3M2I2M3I2M1I4M1I2M2I1D1M3I1M2I2M1I1M1I4M1I1M3I3M2I2M2I1M1I4M2I5M1I2M1I4M1I5M2I2M3I4M1I2M1I1M1I1M2I7M1I2D8M1I1M1I2D4M1I3M1I3M1I1D1M1I1M5I3M1I1M1I6M1I1M1I2M2I1M2I1M1I2M1I2M3I1M1I1M1I1M1I1M3I2M1D2M1I5M1I2M1I11M1I3M1I4M2I3M2I4M2I4M1I2M2I2M2I8M1I1M1I1M1I2M1I1M1I3M2I1M1I2M2I1M2I1D2M1I2M2I1M1I2M1I1M1I1M3I2M2I1M1D2M1I1M1I2M1I1D1M1I2M3I2M1I3M2I2M3I1M1I2M2I4M2I3M1I3M1I5M1I2M1I1M1I2M2I1M1I3M1I4M1I2D1M1I6M1I3M1I1M1I2M1I1M2I1M1I4M2I1M1I3M2I2M1I1M1I2M1I3M1I2M1I2M1I4M1I2M1I4M1I8M1I5M4I2M1I5M4I2M1I1M2I1M1I2M2I2M1I3M1I2M1I1M1I1M2I15M1I2M1I1D8M2I2M1I1M1I4M4I3D2M1I2M3I1M1I1M1I1M1I1D3M1I4M1I3M2I3M1D4M1I5M3I8M1I2M1I2M3I2M3I5M1I7M1I2M1I1M1I2M1I1M2I2M2I1M2I3M1I5M2I5M3I3M1I2M2I1M1I1M2I2M1D4M1I2M1I3M1I1M1I2D3M1I2M1I7M1I3M1I4M1I1M1I3M1I1M1I2M1I4M1I2M1I2M1I1M1I1M1I1M1I3M1I1M1I1M1I5M1I1M1I1M1I10M1I1M1I4M1I3M1I2M1I3D4M1I2M2I2M3I1M2I1M1I1D3M2I10M3I7M1I2M1I3M1I1M2I4M1I1M1I2M1I2M2I1D1M1I2M1I6M1I2D3M1I2M1I1D3M1I3M4I1M1I3D2M2I3M3I2M1I2M1I2M1I2M1I1M1I1M1I9M1I1M3I3M2I5M1I6M1I1M6I1M1I1M2I3M1I3M1I2M2I3M1I1M3I1M4I1M1I5M1I1D6M1I2M1I6M1I1M1I8M1I3M1I6M2I6M1I4M1I1M1I1M1I2M1I1M2I3M1I1M2I2M1I2M1I2M1I2D3M2I6M1I3M1I1M1I3M3I2D5M2I1M1I3D7M1I4D2M2I1M1I1M1I1M1I4M1I2D3M3I1M1I6M1I2M3I1M1I2M2I3M1I2M4I1M1I1M2I2M2I5M1I1M2I1M1I2M1I4M2I1M2I2M2I4M1I2M1I3M2I4M9I7M1I2M1I1M1I5M1I2M1I3M1I4M5I2M1I1M1I1D1M2I1M1I1M1I1M1I2M3I1M1I1M2I3M1I2D1M1I4M1I1M1I1M1I2M1I2M2I4M1I4M1I2M1I6M3I1M1I2D1M1I2M1I10M1I1D1M1I1M1I5M2I1M2I2M4I2M8I1M2I5M5I1M1I3M1I4M1I1D3M1I1D3M1I1D6M2I6M6I2M2I2M1D3M1I1M1I1M4I1D3M2I1M2I4M1I3M1I6M1I2M1I3M1I2M1I5M1I2D2M1I4M1I2D2M2I3M1I1M6I1M1I1M1I4M1I1M1I1M1I3M1I1D9M8I1M1I1M2I5M1I1M2I2M2I2M1I2M1I3M1I1M2I1M1I1D4M1I1M1I5M1I1M3I3M7I3M2I2M3I1M1I1M1I1M2I5M1I1D3M1I1M1I1M1I5M3I1M2I2M1I1D2M1I1M1I3M1I4M4I1D3M1I3M1I1M1I2M1I1M1I2M6I1M1I3M1I1M2I1M1I2M1I1M4I4M1I2M2I4M1I1M1I1M2I2M1I2M1I2M1I5M1I1M2I4M1I4M1I1M1I1M4I1M1I2M1I4M2I1M1I1M1I1M2I1M1I6M2I2M3I1M1I2D1M6I8M2I1M2I3D6M2I3M2I1M2I1M1I1M3I1M1I1M3I4M3I2M2I2M1I4M2I3M2I2M1I1M2I4M1I1M1I1M1I10M6I6M1I3M1I1M2I15M1I3M2I6M1I2M4I4M1I1M3I3M2I1M1I8M2I1M3I3M1I4M1I2M1I1M1I4M1I1M1I2D3M1I4M3I1M1I3M1I2M1I2M2I2D2M5I3M1I2M1I3M2I1M1I1M2I1M3I2M3I1M2I1M2I2M2I2D3M1I1D5M1I12D4M1I1M2I2D1M1I3M3I1D1M2I5M4I1M3I1M10I5M1I1M1I1D3M1I1M3I1M1I3M2I2M2I1M2I1M1I3D2M3I2M2I1M1I2M1I1M2I2M1I4M1I1D2M1I1M1I1M1I3M1I1M1I4M1I4M1I10M1I3M1I1M1I2M1I1M3I1M1I2M1I2M1I3M1I3M1I2M1I1M1I1M5I1M3I2M1I1M1I1M2I3M2I1M1I3M1I4M1I3M2I2M2I5M1I1M3I3M1I2M1I2M1I3M8I2M1I1M1I4M1I3M1I2M2I1M1I1M3I5M2I1M1I3M3I3M1I1M1I2M2I1M1I1M4I2M3I9M1I1M1I2M1I1D3M1I1M2I3M3I4M1I1M1I1M3I2M1I2M1I1M1I3M2I2M1I2M2'..b'4D2M1I1M11I1M2I2D1M4I6D1M1I2M1I4M1I1D3M9I1M1I13D4M1I1M3I1D1M2I3D1M1I1M3I7D1M1I1M1I2D1M1I3D1M1I2D1M2I2D3M1I3D2M2I1D4M2I2D2M3I1M1I1D1M2I4M4I4M4I6M1I5D6M1I1M1I2M2I2M2I16D2M2I1M1I3M1I1M1I1M1I2M1I1M2I1M3I8D1M4I2M1I1M1I4M3I2D2M2I3D1M3I2D2M1I2M2I1M2I2M1I2M7I1M2I1M3I1D1M5I1D3M2I2D4M1I1M1I4D2M1I1M1I1M1I1M3I3M1I1D1M2I3M1I1M5I1D2M1I3M1I1M3I1M1I1M6I1M6I2M3I2M1I1D4M1I2D1M2I2D1M3I2M1I1M1I1M4I2M1I3M3I3M1I3D2M2I4D3M1I3D3M3I1M2I2D1M4I1M3I1M1I1M1I1M3I3M2I5M1I10D3M2I1M2I1D3M3I1M1I2M1I1D3M2I1M2I1M6I2M3I1M1I2M2I2M3I1D2M4I1M4I1M1I2D3M4I1D2M2I1M1I2D2M1I2D2M1I9D2M1I2M1I2M5D3M1I1D3M1I1D6M1I3D1M6I1D2M2I4M1I1M5I1M4I1D1M1I3M1I1M1I1D3M2I2D1M5I3M2I2D1M4I1M4I1M2I1M1I2M1I3M1I4M4I1M2I1M8I1D2M4I1M2I3D1M2I1M1I1M2I1M1I1M1I1M11I1M1I1M4I1M1I2M5I1M1I1M2I1M1I1D1M1I1D3M1I7D4M1I2D1M1I1D6M1I1M7I11D4M2I2D1M5I1M3I2M1I1M3I1M2I1M4I1M1I5D4M6I2D2M2I1M1I1M3I2D4M1I2M6I1M1I1M1I2M1I2D1M2I1D3M2I1M3I4D1M2I6M1I1D3M2I1M2I1D1M1I2M2I3M1I1M4I1D2M1I1M3I2M1I2M2I1M2I1D2M4I1M1I14D4M1I2D1M2I2M2I2D3M2I1M2I4M1I1M2I2D3M2I3M1I1D1M4I2M1I4D2M1I1D1M1I1M1I1M3I3D2M2I1M1I1D2M4I2D1M14I1M3I3M3I1M3I1M1I4D1M1I1M2I2D1M1I1M1I3M2I2D3M7I1M2I3M7I1M1I1M1I3D2M7I1M8I3M1I1M1I3M2I1M4I1D2M2I7D1M2I2M1I2D3M1I1M2I1M2I1M3I1M1I2D2M2I1M2I1D2M3I5D1M2I2D3M1I1M3I2M6I2M2I1M2I1M7I1D2M1I1M1I1M1I13D1M3I6M1I1M2I1M3I3D1M2I1D1M2I1M3I1M3I1M8I5M1I1M1I1D2M1I1M1I4D2M1I1D1M1I1M15D7M1I3D4M1I2M2I1M1I1M1I1M3I1D1M1I2M1I1M5I1M7I3D2M7I1D1M2I1D4M4I2M2I1M4I3D5M1I2D5M1I2D1M10I1M8I2D2M1I1M2I1D4M2I4D4M1I1D8M1I1M4I3D2M2I3M1I4M1I2D1M3I1M4I1M4I1D2M2I1M1I2M5I2D1M1I1D1M1I4M7I2M9I1D1M6I2M3I1D1M4I2M4I2M4I1M2I3M1I3M1I1M1I11D3M1I1M3I4M1I1D1M4I1D1M1I1M1I2D3M1I4D4M1I5D2M1I2M1I3D2M1I1M3I1M5I1M5I1M1I2D2M2I1M5I1D2M9I1D3M1I1M2I2M2I3M2I1M3I1D1M5I1M2I2M1I1D1M3I1M1I8D2M1I2M1I4D4M5I1M5I1M1I2M1I1M1I1D1M1I1M1I7D4M1I3M1I2D1M1I2M1I2D1M1I4D1M1I1M1I1M4I1M2I2D1M6I1D1M2I2M1I1M5I4M5I1M2I2D1M1I3D4M1I2D1M2I1M10I1D1M2I1D2M1I1M3I3M6I1M1I1M2I1M1I3M1I2D3M1I2D1M7I1M2I1M1I2M7I1D1M2I1M2I1M10I1D2M1I3D4M4I6D2M2I2D2M3I1M1I1M1I3D3M1I9D1M1I2D1M1I1M5I1D1M\t*\t0\t0\t*\t*\tES:i:-1\n+280af896-8e53-4427-89d3-a554c87269fd.template\t0\ttig00000118\t21\t60\t1587S1M1I4M1I1M1I1M1I2D1M2I3M1I2M2I1M2I1D1M6I2M2I4M1I2M1I1D4M3I5M1I3M6I4M1I2D4M2I1M1I3M1I1M1I1M3I2M3I4M4I5M1I1M3I3M1I3M1D3M1I6M1I4M2I2M1I1M2I1M1I1M3I1M1I1M1I1M1I1M1I1M2I2M1I2M3I5M2I1M1I1D1M1I1M3I1M1I2D3M2I1M1I1M1I1M1I1M6I2M2I1M1I6M1I1M1I4M1I1M2I1M1I6M2I1M1I1M1I2M1I3M2I11M1I1M2I1M4I3M3I2M1I1M2I6M1I3M1I2M1I1M2I2M1I5M2I1D4M3I12M2I1M1I2D1M1I2M2I2M4I1M1D7M2I1M1I1M2I3M3I1M4I1M1I3M4I3M1I1M2I1M1I1M5I2M1I2M2I5M1I2M2I1M10I5M3I3M1I2M1I13M2I1M2I2M1I4M2I2M1I4M4I2M2I2M1I1M1I1M1I2M1I1M1I1M2I1M1I3M2I2M1I1M1I5M2I2M1I5M1I3M1I2M1I3M1I2M2I3M1I1M1I1M1I3M1I2M2I1M1D3M1I1M3I1M1I2M5I2M1I2M2I5M1I3M4I1M1I2M1I4M4I1M1I4M4I2M1I1M6I2M2I5M1I2M2I4M1I2M1I4M1I3M1I1D1M1I3M1I1M1I2M1I6M1I1M3I1M4I3M2I1M2I5M1I1M1I2M1I2M1I4M1I1M1I1M1I2M3I1M3I2M3I3M3I2M1I2D2M1I3M2I1D3M2I1M1I1M1I2D8M2I2M1I2M5I2M1I2M1I2M1D2M2I4M1I2M1I1M1I6M2I3M1I2M1I3M1I2M3I1D3M1I2M2I1M2I3M2I2M1I2M5I1M2I1M1I1D5M2I7M3I2M6I1M1I1M3I1M1I4M1I3D1M1I2M1I2M3I1M2I1M2I6M3I1M2I1M1I1D2M3I4M3I2M3I5M1I1M1I5M1I2M1I2M1I1M1I1M1I1M1I6M2I4M1I3M2I1M2I1M1I1M2I1M1I2M1I3M1I1D5M1I2M1I1M1I1M3I2M1I1M1I1M1I2D2M1I1M1I1M1I1M2I1M3I1M1I1M4I1M4I3M1I2M1I2M1I6M1I4M1I2M12I1M1I3M1I2M2I1M1I2M1I1M2I3M1I8M1I1M2I3M1I2M2I1M2I2M1I2M1I4M1I2M1I3M1I2M1I2M2I5M1I2M1I2M2I2M1I2M2I1M1I1M1I2M1I1M3I1M1I1M2I3M1I1M1I3M1I2M1I1M1I5M1I3M7I1M1I2M1I1M1I1M1I1M2I3M1I2M1I1M1I1D3M3I2M1I1M2I1M1I2M3I1M1I2M3I1M2I6M1I1M1I1M1I3M3I1M2I4M2I3M1I2M3I2M1I1M1I2M3I2M7I\t*\t0\t0\t*\t*\tES:i:1\n+b1594985-30ce-4f59-9230-dff6ec966710.template\t16\ttig00000118\t4962\t60\t21118S1M1I1M1I6D1M9I1M5I1M1I1M1I3D1M1I1M1I1M1I2M1I1D1M1I2M1I2M1I1D2M1I2M6I2M2I2M3I1M1I1D2M5I2D1M1I3M1I3D5M1I1M1I3D1M1I1M1I2M1I2D2M2I3D3M2I1M1I5M1I2M1I3M1I7D1M1I2M5I1D3M14I1M1I2M3I3M2I2M2I1D1M1I2D1M1I2M2I1M14I1M5I1M1I1D3M1I2M2I1M2I3M1I1D3M11I2M6I1M2I1M1I1M1I1D4M2I1M1I1D1M1I1M2I2M1I1M2I2D1M2I1D1M4I2M2I1D6M3I1M3I1M2I1M9I1M3I1M1I2M5I1M4I1D2M3I7M1I1M1I1D2M3I1M3I2M9I1M1I2M4I3M2I1D1M2I1M1I3M3I1M2I2M5I2D1M1I1M2I1M1I1M2I1M1I1D1M10I5M1I1M1I1M3I1M1I1D2M3I2D1M4I1M2I2M2I1M3I1M6I2M5I1M1I2D1M6I6M1I4M1I7D1M1I2M3I2D3M1I5D2M4I1D2M1I5D4M7I1M1I1M1I2D1M1I\t*\t0\t0\t*\t*\tES:i:-1\n' |
| b |
| diff -r 000000000000 -r f9dadc362197 test-data/reads.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.fasta Wed May 30 11:55:55 2018 -0400 |
| b |
| b'@@ -0,0 +1,224 @@\n+>fa9ad683-35c5-4dad-a3af-de7a86b1ffa8\n+TTGGTATGCTTCGTTCCAGTTACGTATTACTTTCTGTTGGTGCTGATGTTGCGTCTGCTGATTGTTTAACCTGGCTGGATCGCTGCTGAATAACTTCGCCGCATGGCCGCTGAAATCTTTCACCCTCTGCGCCTGGCGGTTAGCCGCCTGTTACGTCAGCCGTGGTCAACGTTAAGTCAGCTTTTCGGCATTTCGCTCCGCTATGCTGGCACTGCTGCGGTGTGCATAGCGATCTGCTCGACCGCTGGCAGCAGCATCTCAAGCGAACTACTTGCATTCATCGCCACAGAACAGGTAACCATCGAGGCGTTCCTCGGAACATCAGATAGTCAGAATCGTTTTGTATCCGAGTGGGTACAGGCGCGGCTGACGGCGATTAACGATAAGCAACAAAAGGTAAATAGAAGATGCGGCGCTTAACCGCGAGCTCAATCTTACCTGGCAAAATACGCGGCTTGATCATGATCGATTGTAATGCCCGGTAACTGGCCGCCAAAGCCGATGAAGTGTCGATGGAAGGGGCTGGCCGAAACGCTTAAACGATTGCCCTCGGTGATACCGTGGCTTTGCGGGGCGATGCGCAGGAGTTTCCGCGCTAAAGTAGCCAGCCTGCGCAAGTGGACTGGAAAGTCACGGCCTAATTTCTATTTTATTTTTCCCTGAAGGGCATTCGTTAAGGCAACCGCAGAGCAACCACCCAGTTTCCGCTGGGAGAATGGCAACGGCATGATGACACCGGCTCTTCGCCAGTTCCCGACCATCAGCCTGATAGATATTGGCGCGATTTTTAAAACCGTCGGTCAGGTGCTGGAGCAGATGGGGTCGGGCGCTGGAAGTGATAAATTGGTACTGGTCACCGCCTGCGGTATATTTGCTGTTGCTAGCACAGGGGTACGGGCGAGACATCCAGCGTCATCAAGGCTAATTGGGTGTGGCGCACTCGGTGCGGAAAAAGGCTTTGCTGCGTACCACGTTGGCAAGTGTAGAGTTCGCCATACTTGGGTTTTGTTTTGTACCAAGTGGCCGCAAAATTAGTGCACAGAAACAGCGCTGGCGGCGGTGTGCAGGCGAAAGTGAACGATTTTCAAAGTAGGAGCCAAGACTGGCGATTGTGGATTATTCTACCGTGCAGCGGGCGGCTGCTGCTGTCGCTTTCCGGCGGCTGGCTGGGTGCGGTTGGGTAGGCGCTGTTCGAGGCAGTTTGCAGAAATGCGCAAGGTAAATAGGGGGCGTTCTGGTTTAGAATGAACGCGCCCAGCAATTTCGATGAATTCTACAATATGTTTCATTGATGATGTTATTGAATTGGTGATTTTATCTTTCTGTTGCTGTCGCTAATCACAAGATCGAGGTGGGTTTGTTGATTTTTAAATGTAGCCTACAATACTCCGTTCGTGAAATCATAAAAAGCCATATGCGTTGAATGGATGTCATCCTATGGTAATTTGTTGATGATGAATTCATCCTGTGTAAAAATGTTAGTTTAATAAAATATTAGTGACCTGTAACTAACGGTTTGTTTGTTGATTGAGAACCGTGGTTATATTGAAAAATATATAAATACATTGGCTGGTCTTGTATGTCGGTTTTATTTTTTGTTGCCTAAACACAGGGATATCGAACTAATAACTAAAGGGCACTTTATAGGCAGAAAAACCAACGCGTCGGGAGATATGAGCTCAAGTATGGCGGATCCCATTGTCCGGGGCTCGGCAGGTGTAAAATTGGCGCGCCCACCAGCGTGGCATGCTCGTTGTCGGGCGGGATGACTTCGGGCAACCCGGTAAATCCGCTGCTGGGGGCAGGTACGCTTGGCCGAGACGGACTTGCCGCTGCCCGTACGCTGCGTTCATTCTCTCCCGCACCTAAAAAGCCTTCTGGACGAAGACGCCTGCCGGTGGGCGTTTTCGGCCCCGGCACAAACGCTGATATCCGCTTACAACTGCGTGATGACGGACTGATACTCCAGCAACAACGGCAGACGAACATTCCGCTGAGCCGCTGCTGCCACATGAGGAGAGCGAAATTAATACAACCGCAGGGTACGAGTCAATGTGGCTGGTGCGGTAAGGCAGCGCAACTGGACGGCCATACTGCTAGCGCGCGGCTGTGGGGGCTATACCGCCGGATATCAGTTAAGCCCGCATCTTTACCTGGCGACCAACGCGCACAGGGGCCGTGGTGGATGCTGGGTGGTCTGAGCGGGTGCCGGGTGCTGAGGACGCTTGCTGCCAGCGCCGCTGCCGTACCAGGTGCCACCAGGATAGCGGACCGCTTCAGGCGGACGCTGACGCCTGCGGCGTAGAACATGGTGACCCTGGCCAGAAATCACCAGCGTGACGGACGGTGCCGGGCGGGGTTATTCTGATTTTGTCACGCAGGCGCGAGCGTTGCGGAAAAGGCCACTTACCTCTTCGCTATCTTAATACGACGTTCCCCGCCCTATATAGCCTCAGCGTTCCCCAACCTACCCAGTACCGAATACGGCCCCGTGGTGGCTGATCACGACCGGCATGCCAGAGAAACCCTGCCGCTGCGCCACTAGATTGCGGTACGTCTCTGGAAACCGAGTGAACTGCGGCGGTATATGAGCCGCAGCAATACGCAGGTGCGCTTTCATTATGACGCGCTTACCCGGGCAGATGTGGCGCACCGTTACACTTAGGAAAGGCCGGAGATGCGCTACCACTTCGACGATACAGGGCGGGTGGTGGAGCAACGACCAGCAGGGGTTAAGCTACACTATCTTTATAGGCAAGGACCATATCGTCACCGACGGCCTGAACCGGCGTGGGAGTGCTGCATACAGAAGGCAGGGCCGGGCTAAAACAAATTGGTGAAAAAGAACGAGCGGACGGCACAGAAGCGTTCCGCGCTGAAATTGCATCGACCGCGAAGCAGGAAGGCTCACGGCATGAACGGACGCGGCAGGGCAGGAGGATAAGTACGGTCTGAATGTGGTGTCCAGCGATATCGAATACCACCGGACGGGCGGGAGACGAAATTCCTATAACGACGGGAGCCAGCTGACGGCGGTGGTAATGCCGGACGAACTGGAGAAACCGCCAGGAATATGATGAACCGGGCAGGCTGGTGTCAGAACATCGCGCAGCGGGGACAGTACGCTACCGCTACGTGGCCGCCTGATAGTTACCGGCGACGACAACGGATGCGACGGGCGCTTACCAACAGATAATATAGACACGCTACGGGCGTTGCTGGCGTTCTGGCTTTTCGACACGGAGCCATTATGAATACGACCGCTTCGGCCAGATGACGGCGAAGTCCACCGCGAAGGCATCAAACGCTACCGCTATAATAACGTGGCGGTTAACCTCGATGAAAACCGCACAGGGCGATGAAACGCGACATGAGCCACAACGCCGCAGAGCAACCTATTTCGCCAATTATCTGCCCCGGACGCGGCCGGAGCGGAAGACACGAGGTACGATGCGTGGGGAAAGGCGGGTCAGCACCACACCAGGGCGGCTGACGCGCAGTATCATTACGGTGCTGCCGGATGTCATCGCCCTGACCAACGAGAACACGGCAGCCACGGCGTCTTCTGGTTACGATGCGCTGGACCGGCTGGTGGGACAAACACCAAGCAGACGCCGAAGATGAGAACGATGAGCAGTATACCCGTAATGACGCTTCCTC\n+>a403a23e-20e7-43f7-a5fa-dae8ebc59a01\n+TTGACTGTGCTTCGTTCGGTTACGTATTGCTTTTTCTGTTGGTGCTGATATTGCGGCGTCTGTAGGTGTTTAACCTGCCAGCATCACACGAGATTGGTCAAGTGCGGTTGGGTTTTTCAAACGGATGCGACAGCAGTTGGCATTAAAGAAGCCACCGCCGTTAGGCGCCGAGCATCTTGATGCTTCCACGAAGCTACGATACCGCCGGGTAACAGCTGTTGCGCTCCTTCAACGGTATTC'..b'CCGGGGCTGAGGCTCCCCACCGGCGCGGGCGTTTTGTCCGGTAACTGCTGTAGGTGCGGGAGAGAATGAAAGACGGCAGCAGGCCGGGGCAGGGGGCGTCAGTTTCACCAGGAAGGACCTTTACCGAGCAGCGGATTGACCGGATGGCCGGACGTCACCCGCGGGGCACCGAACAGGCCACGCCGGTGGGGCACCGATGCGTACCCCGGCTGAACCCTGGACAATGCTGCCGCCATACCGTCATGTCGCCCTGACGCCGCCGGTTTTCCGCTCATCTGCTCATCCTTGTTTTATCGGGTTATTTGTCTGCTGACAGGCGAAACCCTACAGATTTATAAGAAACTAAGTGAGATATCTGTCAGATAAGAACAATTAGGAAAATATTTATATATATTTCCTTGAATATATGTTTCGATTGGTATAACGATGTCACAAATATTCCTCTGAACATCTTCCTGTTAAAAAACCGCCAGCGTTTCCCGCTGGCGGTTTCAATAATATTCAAACTCAGCAATCAATAAAATCACCAGTTGCCTTTTCGGCCTGATCCATCCGCACCGGTTTATCATGGTTTCGATGGAGCGCGATGCAAGGTAGCTGTAAAGCGGGCGCGGTCTTTCCAGAAAAGCATAAGAAAAGAGCCAGCGCCAGAACGCCCGCTGCAACCGCATAAGTACAGCGTAAAGATAAAGCCATGCAGGATATTCTCTGTAGAGTTCCATACTTTTCTCCCCTTTTATCTACCCGATTATGAATGGCACCGGAAAAATGAATTGTTTATCTGATGAAAATAGTACCGCCAGCACGTAGTTTTACTACTCATCCGACCACTTATTTTGCTTATTGATGGTTTATTTACATTCATCCGCAATTAAGTTACACAAAGTTAAATTAATACTAAACATTAGTTAAATCATGGCTTTTGCCATTTTTATACTTTACACCCCGCCCGCAGATTTTGCGAAATCTTTGCAGCCAGGTCTACCTTCGGTATCACTTTTAGGCCACTGGAGGTGCACTGTGAGTGCAGGCGTGATAACCGGCATTATTGCTGGTGTTTTATTACTGGGTTATCTGGTTTGTAACCTGATCCAAATGCGGAGCGTTCTGATGGCTGCGCAAAGGGTTCTTACTGATCGCCACGTTTTTACTGGTGTTATGGGTGCTGGCGCGTCCTTTAGGCAGCGGGCTGGCGCAGCTGATTAATGACATTCCCTTCCCGGTACAACGGGCGTTGAGCGCGTACTTTTTCCTTTGCCCAGCGTCTCTGACCGTGAGAGATGAACTGGAAGCAATATCTTTGTGCCATTCTCGGCCTGAACATGCTGGGGCTGGCGGTGCTGTTTTATGTTATCAGTCAGCACTATCTGCCGCCAATCCACAGCAGTTGCCAGGGCTGTCATTGGGATCTGGCGCTGAATACCGTCAGCTTTGTCACCAATACCAACTGGCAATCTTATAGCGGTGAAACCACGTTGACTTCTTCAGCCAGATGGCGGGCTTAACGGTGCAAACTTTCTTTCTGCCGCCAGCGGGATTGCGGTGATTTTGCCTCATCCGTGCAGTTTACCCGCCAGGTATGAGCACGCTCAAGAATGCCTGGGTCGATCTGCTACGCATCACGTTATGATTGCTAGTCCTGTGGCGTTGTTGATTGCGCTGTTTTTATTCAGCAAGGTGCGCTGCAAACTTTCTGCCTTATCGGGCTGTGAATACCGTTGAAGAGGCGCAACAGCTGTTACCATGGGGCCTGCTGCTTCTCAGGAAGCAGTCAAGATGCTCAGTACTAGCGAAGGCGGTGGCCTAACAATGCCAGCTCAAAATCGCATCCGTTTGAAAACAACCGCGCGGCAACTTCGTGCAGATGCTGGCGATCTTCTTGATCCCAACGGCGCTGGTAATACTTTGCCTTTGGTGAAGTGATGGGCGATCGCCGCCGAGAGCATGTTGCTTATGTGGGCGATGTCGGTAATTTTTTGTGTCATCTCTGCGTAGGCGTGGTGATGTGGGCAGAAGTTCAGGGTAATCCTCATCTGCTGGCACTGGGCACGGACGCTTGTATCAATATGGAAGGTAAAGAGAGCCGTTTCGGCGTGCTGGTCAGTAACCTGTTTGCGGTCGACGGCTGACGGCTTCCTGTGTTGCAGTGATTACGCGATGCATGATTCGTTTACCGCTCTCGGTGGCATGGTGCCGATGTGGCTGATGCTAAATTGGTGGTGGTAATTTCGGCGGTGTCGGTTCTGGTCTTTGGCATGATGCTGTTTGTCCTGCTGGCGGTGTTTTGTGCCGGGCTGATGATTGGGGTCGTACACCGGAATATCTGGGTAAAAAAATCGACGTACGCGAGATGAAGCTGACTGCGCACAGCAGTCTGGTTACCCCGACGCTGGTGCTGATGGGCGCGGCGTTGTGATATTGACCGACGCCGGACGTAGCGCCATGCTCAACCCCTGGCCCGCATGGTTTTAGCGAAGTGCTGCTACGCCATGTCATCACCGCCGCTAACAACAACGGCAGCGCCTTTGCCAGTTCGCGCCAACTCCGTTCTGGAACTGTTTACTGGCGTTCTGCATGTTTTGTCGGTCCTTCGGGGTGATTATCCCGGTGATGGCAGTGCCGGTTCGCTGGTGATAAAAAGAGCCAAACCGCCAGCTCGGCACGCTGCCAGCACACGGCCCGCTGTTTGTTGGCCTGTTAATCGCTGCTGTGTTGCTGGTTGGCACTGAAGCCTTTATCTGCTGGCGGTCAGTGGCGGGAATATCTCTCCTGATGATGTTGGTGAGCACTGGATATGAGTCGTAAACAAACTTCCGGCTATTCAAGACCAACACTTGTCGTTCAGGCGCTGAAAGAAGCGGTGAAAAATTAAACCCGCAGGCGCAATGGCGCAATCCGGTGATGTTATCGTCTGGATCGGCAGTCTGCTGACCACCTGTATTAGCATCGCGATGGCAAAAGCAGGTGCGATGCCCGGCAATGCTGTTTAGCGCGGCCATTAGCGGTTGGCTGTGGGATCACCGTACTGTTCCTTCAATTTCGCCGAGGCGCTGGCAGAAGGCCGCAGTAAGCCTGGGTAACAGTCTGAAGGTGAAAAAACTGCGCTTTGCCCACCAAGCTGCGTGAGCCGAAATATGGCGCTGCGGCAGACCAAAGTTCCTGCGACCAACTTCGTAAAGGCGATATCATGCTGGTAGAAGCTGGCGATATTATCCCCTGCGATGGTGAAGTTATTGAAGGAAATTGCATCGGTCGATAAACTATGCATCACTGCGAGAATCGGCACCGGTGATCCGTGAATCCGGCGGCGTTTTGCCTCGATCACCGGCGGCGCATATTCTTTCTGACTGGCTGGTGATTGGGTGTAGCGTTAACTTGGCAGACATTTCTGGATCGGATGATCGCGATGGTGGAAAGGCGCACAGCGGCGCAAAACGCCGAACGAAATTGCCCTGACCATTCTGCTGATTGCCCTGACTATCGTCACTGCTGGCAACCGCCGCACGCTGTAACCGTTTTCGCGTAGGGCGGTAATGCAGTCAGCGTAACGGTACTGGTGGCGCTGCTGGTCTGTCTGATCCCAAAAGCCACTATTGGCGGCCTGTTGTCAGCAGTCGTCGCCGGGATGAGCCGGATGCTAGGCGCCGAATGTGATTGCCACCAGCGGACGATGCAGTTGAAGCGGCAGGTGACGTTGACGTTCTGCTACTGGATAAAACCAGCACCATCACACTCGGTAACCGTCAGGCGTCGAGTTTATCCCACGCAGAGGGCGTGGATGAAAAAACGCTGGCTGACGCCGCTGGCAGCTTCGCTGGCTGATGAAACGCGGAAGGCCGCAGTATTGATCCTCGCCAAGCAGCGTTTTAACCTGCGCGAGCGCGATGTGCAGTCATCATGCCACCCTTTGTACCGTTTGCAAGCCGGATGAAGCCAGGATCAGCATCGACAACCGCAGGTTAAACACCCAAGCAGACGCCGAAGATGGGGAAACCGTA\n' |
| b |
| diff -r 000000000000 -r f9dadc362197 test-data/reads.fasta.index |
| b |
| Binary file test-data/reads.fasta.index has changed |
| b |
| diff -r 000000000000 -r f9dadc362197 test-data/reads.fasta.index.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.fasta.index.fai Wed May 30 11:55:55 2018 -0400 |
| b |
| @@ -0,0 +1,112 @@ +fa9ad683-35c5-4dad-a3af-de7a86b1ffa8 3660 38 3660 3661 +a403a23e-20e7-43f7-a5fa-dae8ebc59a01 2365 3737 2365 2366 +ae3ab29f-07ae-4476-85eb-b212d69ce732 4941 6141 4941 4942 +88b1797f-3a41-442f-bab4-cdfedf7ec597 8486 11121 8486 8487 +c2cfeb47-1930-4486-ba44-fb1f43519806 2045 19646 2045 2046 +1c935ec4-4503-44ea-be57-7201fc03eeb6 10879 21730 10879 10880 +756abc44-d69f-46e2-8464-2f309b147a27 4303 32648 4303 4304 +6ffbbdea-7881-4ec3-b14a-e5a0c37c056d 4674 36990 4674 4675 +adeedf44-dbc5-401b-8b3c-07c944e12deb 6345 41703 6345 6346 +c75c8f96-eb4b-4465-9d43-024209a6a35a 1237 48087 1237 1238 +40aac17d-56a6-44db-934d-c0dbb853e2cd 5023 49363 5023 5024 +1d5ccec9-296a-4afd-ad74-010ebd3732ec 7297 54425 7297 7298 +690186f5-a384-40a4-8aae-9a99ad2322f5 3813 61761 3813 3814 +c7937d7b-d85f-433b-9327-7eb293974905 6626 65613 6626 6627 +c65d1bb9-c11b-4d4e-bba5-c821e0eb7758 1607 72278 1607 1608 +0d624d4b-671f-40b8-9798-84f2ccc4d7fc 3748 73924 3748 3749 +d4402dd6-1f80-4d82-9ce1-f4e7326e5054 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| b |
| diff -r 000000000000 -r f9dadc362197 test-data/reads.fasta.index.gzi |
| b |
| Binary file test-data/reads.fasta.index.gzi has changed |
| b |
| diff -r 000000000000 -r f9dadc362197 test-data/reads.fasta.index.readdb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/reads.fasta.index.readdb Wed May 30 11:55:55 2018 -0400 |
| b |
| b'@@ -0,0 +1,112 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|
| b |
| diff -r 000000000000 -r f9dadc362197 test-data/reads.sorted.bam |
| b |
| Binary file test-data/reads.sorted.bam has changed |
| b |
| diff -r 000000000000 -r f9dadc362197 test-data/t2-variants.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/t2-variants.vcf Wed May 30 11:55:55 2018 -0400 |
| b |
| @@ -0,0 +1,19 @@ +##fileformat=VCFv4.2 +##INFO=<ID=TotalReads,Number=1,Type=Integer,Description="The number of event-space reads used to call the variant"> +##INFO=<ID=SupportFraction,Number=1,Type=Float,Description="The fraction of event-space reads that support the variant"> +##INFO=<ID=BaseCalledReadsWithVariant,Number=1,Type=Integer,Description="The number of base-space reads that support the variant"> +##INFO=<ID=BaseCalledFraction,Number=1,Type=Float,Description="The fraction of base-space reads that support the variant"> +##INFO=<ID=AlleleCount,Number=1,Type=Integer,Description="The inferred number of copies of the allele"> +##INFO=<ID=SupportFractionByBase,Number=4,Type=Integer,Description="The fraction of reads supporting A,C,G,T at this position"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample +tig00000001 200180 . C CA 30.6 PASS BaseCalledReadsWithVariant=18;BaseCalledFraction=0.268657;TotalReads=66;AlleleCount=2;SupportFraction=0.596279;SupportFractionByBase=0.042,0.831,0.008,0.119 GT 1/1 +tig00000001 200208 . GA G 28.2 PASS BaseCalledReadsWithVariant=15;BaseCalledFraction=0.223881;TotalReads=66;AlleleCount=1;SupportFraction=0.392611;SupportFractionByBase=0.180,0.007,0.780,0.034 GT 0/1 +tig00000001 200484 . G GA 37.7 PASS BaseCalledReadsWithVariant=17;BaseCalledFraction=0.261538;TotalReads=63;AlleleCount=1;SupportFraction=0.569915;SupportFractionByBase=0.049,0.009,0.928,0.014 GT 0/1 +tig00000001 200776 . C CA 82.3 PASS BaseCalledReadsWithVariant=24;BaseCalledFraction=0.358209;TotalReads=67;AlleleCount=2;SupportFraction=0.71125;SupportFractionByBase=0.039,0.883,0.046,0.032 GT 1/1 +tig00000001 200796 . T TA 82.1 PASS BaseCalledReadsWithVariant=17;BaseCalledFraction=0.253731;TotalReads=66;AlleleCount=2;SupportFraction=0.697381;SupportFractionByBase=0.037,0.148,0.018,0.797 GT 1/1 +tig00000001 200804 . TA T 82.1 PASS BaseCalledReadsWithVariant=20;BaseCalledFraction=0.298507;TotalReads=66;AlleleCount=1;SupportFraction=0.405017;SupportFractionByBase=0.100,0.185,0.006,0.709 GT 0/1 +tig00000001 200966 . CA C 45.5 PASS BaseCalledReadsWithVariant=16;BaseCalledFraction=0.242424;TotalReads=64;AlleleCount=1;SupportFraction=0.383448;SupportFractionByBase=0.039,0.740,0.061,0.159 GT 0/1 +tig00000001 201216 . A AT 85.8 PASS BaseCalledReadsWithVariant=24;BaseCalledFraction=0.352941;TotalReads=67;AlleleCount=2;SupportFraction=0.715932;SupportFractionByBase=0.908,0.004,0.026,0.061 GT 1/1 +tig00000001 201554 . G GC 50.2 PASS BaseCalledReadsWithVariant=20;BaseCalledFraction=0.263158;TotalReads=76;AlleleCount=2;SupportFraction=0.632478;SupportFractionByBase=0.090,0.047,0.821,0.042 GT 1/1 +tig00000001 201712 . C CA 29.7 PASS BaseCalledReadsWithVariant=21;BaseCalledFraction=0.272727;TotalReads=74;AlleleCount=1;SupportFraction=0.57415;SupportFractionByBase=0.046,0.747,0.074,0.133 GT 0/1 |
| b |
| diff -r 000000000000 -r f9dadc362197 test-data/variants.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/variants.vcf Wed May 30 11:55:55 2018 -0400 |
| b |
| @@ -0,0 +1,44 @@ +##fileformat=VCFv4.2 +##INFO=<ID=TotalReads,Number=1,Type=Integer,Description="The number of event-space reads used to call the variant"> +##INFO=<ID=SupportFraction,Number=1,Type=Float,Description="The fraction of event-space reads that support the variant"> +##INFO=<ID=BaseCalledReadsWithVariant,Number=1,Type=Integer,Description="The number of base-space reads that support the variant"> +##INFO=<ID=BaseCalledFraction,Number=1,Type=Float,Description="The fraction of base-space reads that support the variant"> +##INFO=<ID=AlleleCount,Number=1,Type=Integer,Description="The inferred number of copies of the allele"> +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample +tig00000001 200061 . T TA 22.4 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.583757 GT 1 +tig00000001 200180 . C CA 30.6 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.596279 GT 1 +tig00000001 200484 . G GA 25.3 PASS TotalReads=63;AlleleCount=1;SupportFraction=0.569915 GT 1 +tig00000001 200672 . T TA 94.1 PASS TotalReads=65;AlleleCount=1;SupportFraction=0.720712 GT 1 +tig00000001 200776 . C CA 82.3 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.71125 GT 1 +tig00000001 200796 . T TA 75.4 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.698132 GT 1 +tig00000001 201007 . A AG 31.0 PASS TotalReads=65;AlleleCount=1;SupportFraction=0.604821 GT 1 +tig00000001 201216 . A AT 85.8 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.715932 GT 1 +tig00000001 201273 . G GT 25.2 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.588877 GT 1 +tig00000001 201554 . G GC 49.9 PASS TotalReads=76;AlleleCount=1;SupportFraction=0.632029 GT 1 +tig00000001 201588 . C CG 125.4 PASS TotalReads=75;AlleleCount=1;SupportFraction=0.660079 GT 1 +tig00000001 201712 . C CA 21.1 PASS TotalReads=74;AlleleCount=1;SupportFraction=0.57415 GT 1 +tig00000001 200061 . T TA 22.4 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.583757 GT 1 +tig00000001 200180 . C CA 30.6 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.596279 GT 1 +tig00000001 200484 . G GA 25.3 PASS TotalReads=63;AlleleCount=1;SupportFraction=0.569915 GT 1 +tig00000001 200672 . T TA 94.1 PASS TotalReads=65;AlleleCount=1;SupportFraction=0.431464 GT 1 +tig00000001 200776 . C CA 82.3 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.362655 GT 1 +tig00000001 200796 . T TAA 117.1 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.544883 GT 1 +tig00000001 201007 . A AG 31.0 PASS TotalReads=65;AlleleCount=1;SupportFraction=0.604821 GT 1 +tig00000001 201216 . A AT 85.8 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.457699 GT 1 +tig00000001 201273 . G GT 25.2 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.588877 GT 1 +tig00000001 201554 . G GC 49.9 PASS TotalReads=76;AlleleCount=1;SupportFraction=0.632029 GT 1 +tig00000001 201588 . C CG 125.4 PASS TotalReads=75;AlleleCount=1;SupportFraction=0.387616 GT 1 +tig00000001 201712 . C CA 21.1 PASS TotalReads=74;AlleleCount=1;SupportFraction=0.57415 GT 1 +tig00000001 200061 . T TA 22.4 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.583757 GT 1 +tig00000001 200180 . C CA 30.6 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.596279 GT 1 +tig00000001 200484 . G GA 25.3 PASS TotalReads=63;AlleleCount=1;SupportFraction=0.569915 GT 1 +tig00000001 200672 . T TA 94.1 PASS TotalReads=65;AlleleCount=1;SupportFraction=0.431464 GT 1 +tig00000001 200776 . C CA 82.3 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.362655 GT 1 +tig00000001 200796 . T TAA 117.1 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.268565 GT 1 +tig00000001 201007 . A AG 31.0 PASS TotalReads=65;AlleleCount=1;SupportFraction=0.604821 GT 1 +tig00000001 201216 . A AT 85.8 PASS TotalReads=67;AlleleCount=1;SupportFraction=0.457699 GT 1 +tig00000001 201273 . G GT 25.2 PASS TotalReads=66;AlleleCount=1;SupportFraction=0.588877 GT 1 +tig00000001 201554 . G GC 49.9 PASS TotalReads=76;AlleleCount=1;SupportFraction=0.632029 GT 1 +tig00000001 201588 . C CG 125.4 PASS TotalReads=75;AlleleCount=1;SupportFraction=0.387616 GT 1 +tig00000001 201712 . C CA 21.1 PASS TotalReads=74;AlleleCount=1;SupportFraction=0.57415 GT 1 |