| Next changeset 1:a38934e303b9 (2020-04-04) |
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Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 4b0b7fb6c79dcd437392a496a99301d124c9f1dd" |
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added:
ivar_consensus.xml macros.xml test-data/covid19/ARTIC-V1.bed test-data/covid19/NC_045512.fa test-data/covid19/NC_045512.fa.amb test-data/covid19/NC_045512.fa.ann test-data/covid19/NC_045512.fa.bwt test-data/covid19/NC_045512.fa.fai test-data/covid19/NC_045512.fa.pac test-data/covid19/NC_045512.fa.sa test-data/covid19/PC00101P_sub.fa test-data/covid19/PC00101P_sub.qual.txt test-data/covid19/PC00101P_sub.sorted.bam test-data/covid19/PC00101P_sub.sorted.bam.bai test-data/covid19/PC00101P_sub.trimmed.bam test-data/covid19/PC00101P_sub.trimmed.sorted.bam test-data/covid19/PC00101P_sub.trimmed.sorted.bam.bai test-data/covid19/PC00101P_variants.tsv test-data/covid19/nCoV-2019.scheme.bed test-data/covid19/primers_consensus.tsv test-data/covid19/zika_primers.bam test-data/covid19/zika_primers.bed test-data/covid19/zika_primers.fa test-data/covid19/zika_primers_consensus.bam test-data/covid19/zika_primers_consensus.bed test-data/zika/Z52.consensus.fa test-data/zika/Z52.consensus.fa.fai test-data/zika/Z52.consensus.qual.txt test-data/zika/Z52.masked.sorted.depth test-data/zika/Z52.merged.bam test-data/zika/Z52.sorted.depth test-data/zika/Z52.trimmed.sorted.depth test-data/zika/Z52.tsv test-data/zika/Z52_a.masked.bam test-data/zika/Z52_a.masked.sorted.bam test-data/zika/Z52_a.sorted.bam test-data/zika/Z52_a.sorted.bam.bai test-data/zika/Z52_a.trimmed.bam test-data/zika/Z52_a.trimmed.sorted.bam test-data/zika/Z52_a.trimmed.sorted.bam.bai test-data/zika/Z52_a.tsv test-data/zika/Z52_b.masked.bam test-data/zika/Z52_b.masked.sorted.bam test-data/zika/Z52_b.sorted.bam test-data/zika/Z52_b.sorted.bam.bai test-data/zika/Z52_b.trimmed.bam test-data/zika/Z52_b.trimmed.sorted.bam test-data/zika/Z52_b.trimmed.sorted.bam.bai test-data/zika/Z52_b.tsv test-data/zika/db/PRV.fa test-data/zika/db/PRV.fa.amb test-data/zika/db/PRV.fa.ann test-data/zika/db/PRV.fa.bwt test-data/zika/db/PRV.fa.fai test-data/zika/db/PRV.fa.pac test-data/zika/db/PRV.fa.sa test-data/zika/db/Z52.consensus.amb test-data/zika/db/Z52.consensus.ann test-data/zika/db/Z52.consensus.bwt test-data/zika/db/Z52.consensus.pac test-data/zika/db/Z52.consensus.sa test-data/zika/db/pair_information.tsv test-data/zika/db/zika_primers.bam test-data/zika/db/zika_primers.bed test-data/zika/db/zika_primers.fa test-data/zika/db/zika_primers_consensus.bam test-data/zika/db/zika_primers_consensus.bed test-data/zika/primer_mismatchers_indices.txt test-data/zika/primers_Z52_consensus.tsv |
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| diff -r 000000000000 -r f362150bef41 ivar_consensus.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ivar_consensus.xml Mon Mar 30 06:37:01 2020 -0400 |
| [ |
| @@ -0,0 +1,74 @@ +<tool id="ivar_consensus" name="ivar consensus" version="@VERSION@+galaxy0"> + <description>Call consensus from aligned BAM file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"><![CDATA[ + #import re + #set $clean_name = re.sub('[^\w\-]', '_', str($input_bam.element_identifier)) + ln -s '$input_bam' sorted.bam && + samtools mpileup -A -d 0 -Q 0 sorted.bam | ivar consensus + -p consensus + -q $min_qual + -t $min_freq + -m $min_depth + $filter_depth + #if $gap + -n N + #end if + && + sed -i "s|consensus|$clean_name|" consensus.fa + ]]> </command> + <inputs> + <param name="input_bam" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/> + <param name="min_qual" argument="-q" type="integer" min="0" value="20" label="Minimum quality score threshold to count base"/> + <param name="min_freq" argument="-t" type="float" min="0" max="1" value="0.0" label="Minimum frequency threshold"> + <help> + <![CDATA[ + 0 - Majority or most common base <br/> + 0.2 - Bases that make up atleast 20% of the depth at a position <br/> + 0.5 - Strict or bases that make up atleast 50% of the depth at a position <br/> + 0.9 - Strict or bases that make up atleast 90% of the depth at a position <br/> + 1 - Identical or bases that make up 100% of the depth at a position. Will have highest ambiguities + ]]> + </help> + </param> + <param name="min_depth" argument="-m" type="integer" min="1" value="10" label="Minimum depth to call consensus"/> + <param name="filter_depth" argument="-k" type="boolean" truevalue="-k" falsevalue="" checked="false" label="Exclude regions with smaller depth than the minimum threshold"/> + <param name="gap" argument="-n" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Use N instead of - for regions with less than minimum coverage"/> + </inputs> + <outputs> + <data name="consensus" format="fasta" label="${tool.name} on ${on_string} Consensus" from_work_dir="consensus.fa"/> + </outputs> + <tests> + <test> + <param name="input_bam" value="covid19/PC00101P_sub.trimmed.sorted.bam" /> + <param name="gap" value="true" /> + <output name="consensus" file="covid19/PC00101P_sub.fa" ftype="fasta" compare="contains" lines_diff="1"/> + </test> + </tests> + <help><![CDATA[ + .. class:: infomark + + To generate a consensus sequence iVar uses the output of samtools mpileup + command. The mpileup output must be piped into ivar consensus + + The command for this wrapper is from https://github.com/andersen-lab/ivar/blob/master/pipeline_consensus/Snakefile : + + samtools mpileup -A -d 0 -Q 0 sorted.bam | ivar consensus [options] + + There are five parameters that can be set: + + - Minimum quality (Default: 20): the minimum quality of a base to be considered in calculations of variant frequencies at a given position + + - Minimum frequency threshold (Default: 0): the minimum frequency that a base must match to be called as the consensus base at a position. + + - Minimum depth to call a consensus (Default: 1): the minimum required depth to call a consensus + + - Filter depth is a flag to exclude nucleotides from regions with depth less than the minimum depth and a character to call in regions with coverage lower than the speicifed minimum depth(Default: '-'). If this flag is set then these regions are not included in the consensus sequence. If it is not set then by default, a '-' is called in these regions. + - You can also specfy which character you want to add to the consensus to cover regions with depth less than the minimum depth. This can be done using gap option. It takes of two values: '-' or 'N'. + ]]> </help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r f362150bef41 macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Mar 30 06:37:01 2020 -0400 |
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| @@ -0,0 +1,18 @@ +<macros> + <token name="@VERSION@">1.0.1</token> + <xml name="requirements"> + <requirements> + <requirement type="package" version="@VERSION@">ivar</requirement> + <requirement type="package" version="1.9">samtools</requirement> + <yield /> + </requirements> + </xml> + <xml name="version_command"> + <version_command>ivar version | grep version</version_command> + </xml> + <xml name="citations"> + <citations> + <citation type="doi">10.1186/s13059-018-1618-7</citation> + </citations> + </xml> +</macros> |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/covid19/ARTIC-V1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/covid19/ARTIC-V1.bed Mon Mar 30 06:37:01 2020 -0400 |
| b |
| b'@@ -0,0 +1,196 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| b |
| diff -r 000000000000 -r f362150bef41 test-data/covid19/NC_045512.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/covid19/NC_045512.fa Mon Mar 30 06:37:01 2020 -0400 |
| b |
| b'@@ -0,0 +1,430 @@\n+>NC_045512.2 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome\n+ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAA\n+CGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAAC\n+TAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTG\n+TTGCAGCCGATCATCAGCACATCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTC\n+CCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTAC\n+GTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGG\n+CTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGAT\n+GCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTC\n+GTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCT\n+TCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTA\n+GGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTG\n+TTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGG\n+CCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTG\n+TCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTG\n+CTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAA\n+ATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAA\n+CCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCAC\n+CAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCA\n+GACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACT\n+ACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAG\n+GACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCG\n+CACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCA\n+CGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACA\n+ACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGA\n+GATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGAT\n+TATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAG\n+GTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCG\n+TGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCC\n+GCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTG\n+ATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTG\n+GCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTT\n+AAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAA\n+TTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGT\n+AAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTA\n+GGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCC\n+TACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTT\n+AACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAA\n+GCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGT\n+ACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAA\n+GGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTT\n+GATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAA\n+ATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACC\n+ACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAA\n+TTGGCTTCACATATGTATTGTTCTTTCTACCCTCCAGATGAGGATGAAGAAGAAGGTGATTGTGAAGAAG\n+AAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATT\n+TGGTGCCACTTCTGCTGCTCTTCAACCTGAAGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAA\n+CAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTC\n+AACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTT\n+AAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACA\n+GTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATAAGGCTA\n+CTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAG\n+TTGTGTTTTAAGCGGACACAATCTTGCTAAACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGT\n+GAAGACATTCAACTTCTTAAGAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTAT\n+TATCAGCTGGTATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCA'..b'GACTATTACCAGCTGTACTCA\n+ACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGC\n+CTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAAT\n+TTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTAC\n+TCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTAT\n+TCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGT\n+GAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGAT\n+CTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCCATGGCAGA\n+TTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAATGGAACCTAGTAATAGGTTTC\n+CTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTA\n+AGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAAT\n+AAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTC\n+ATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTC\n+TCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAATCGGAGCTGT\n+GATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTGACATCAAGGACCTGCCTAAA\n+GAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTG\n+ACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAG\n+CAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTAC\n+TATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATA\n+AACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAAC\n+CAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGA\n+GCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAACA\n+TACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAAT\n+TTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACT\n+GTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTT\n+ATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTG\n+CTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAA\n+GATCATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTG\n+TAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCC\n+GTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAA\n+TTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCT\n+GTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGA\n+AGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTG\n+ATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAG\n+TAACCAGAATGGAGAACGCAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACT\n+GCGTCTTGGTTCACCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTC\n+CAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGG\n+TGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCT\n+GGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAA\n+AAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAAC\n+ATTGCCAAAAGGCTTCTACGCAGAAGGGAGCAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGT\n+AGTCGCAACAGTTCAAGAAATTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCA\n+ATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGG\n+TAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGG\n+CAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAGACGTGGTCCAGAACAAACCC\n+AAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAACTGATTACAAACATTGGCCGCAAATTGCACA\n+ATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACG\n+TGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGC\n+TGAATAAGCATATTGACGCATACAAAACATTCCCACCAACAGAGCCTAAAAAGGACAAAAAGAAGAAGGC\n+TGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCCTGCTGCAGAT\n+TTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATG\n+CAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTT\n+GTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATCTCACATAGCAATCT\n+TTAATCAGTGTGTAACATTAGGGAGGACTTGAAAGAGCCACCACATTTTCACCGAGGCCACGCGGAGTAC\n+GATCGAGTGTACAGTGAACAATGCTAGGGAGAGCTGCCTATATGGAAGAGCCCTAATGTGTAAAATTAAT\n+TTTAGTAGTGCTATCCCCATGTGATTTTAATAGCTTCTTAGGAGAATGACAAAAAAAAAAAAAAAAAAAA\n+AAAAAAAAAAAAA\n+\n' |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/covid19/NC_045512.fa.amb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/covid19/NC_045512.fa.amb Mon Mar 30 06:37:01 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +29903 1 0 |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/covid19/NC_045512.fa.ann --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/covid19/NC_045512.fa.ann Mon Mar 30 06:37:01 2020 -0400 |
| b |
| @@ -0,0 +1,3 @@ +29903 1 11 +0 NC_045512.2 Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1, complete genome +0 29903 0 |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/covid19/NC_045512.fa.bwt |
| b |
| Binary file test-data/covid19/NC_045512.fa.bwt has changed |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/covid19/NC_045512.fa.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/covid19/NC_045512.fa.fai Mon Mar 30 06:37:01 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +NC_045512.2 29903 97 70 71 |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/covid19/NC_045512.fa.pac |
| b |
| Binary file test-data/covid19/NC_045512.fa.pac has changed |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/covid19/NC_045512.fa.sa |
| b |
| Binary file test-data/covid19/NC_045512.fa.sa has changed |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/covid19/PC00101P_sub.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/covid19/PC00101P_sub.fa Mon Mar 30 06:37:01 2020 -0400 |
| b |
| b'@@ -0,0 +1,2 @@\n+>Consensus_PC00101P_sub_threshold_0.6_quality_20\n+NNNNNNNNNNNNNNNNNCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGGACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTTTGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGCCTGTTTTACAGGTTCGCGACGTGCTCGTACGTGGCTTTGGAGACTCCGTGGAGGAGGTCTTATCAGAGGCACGTCAACATCTTAAAGATGGCACTTGTGGCTTAGTAGAAGTTGAAAAAGGCGTTTTGCCTCAACTTGAACAGCCCTATGTGTTCATCAAACGTTCGGATGCTCGAACTGCACCTCATGGTCATGTTATGGTTGAGCTGGTAGCAGAACTCGAAGGCATTCAGTACGGTCGTAGTGGTGAGACACTTGGTGTCCTTGTCCCTCATGTGGGCGAAATACCAGTGGCTTACCGCAAGGTTCTTCTTCGTAAGAACGGTAATAAAGGAGCTGGTGGCCATAGTTACGGCGCCGATCTAAAGTCATTTGACTTAGGCGACGAGCTTGGCACTGATCCTTATGAAGATTTTCAAGAAAACTGGAACACTAAACATAGCAGTGGTGTTACCCGTGAACTCATGCGTGAGCTTAACGGAGGGGCATACACTCGCTATGTCGATAACAACTTCTGTGGCCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTAAAGCTTCATGCACTTTGTCCGAACAACTGGACTTTATTGACACTAAGAGGGGTGTATACTGCTGCCGTGAACATGAGCATGAAATTGCTTGGTACACGGAACGTTCTGAAAAGAGCTATGAATTGCAGACACCTTTTGAAATTAAATTGGCAAAGAAATTTGACACCTTCAATGGGGAATGTCCAAATTTTGTATTTCCCTTAAATTCCATAATCAAGACTATTCAACCAAGGGTTGAAAAGAAAAAGCTTGATGGCTTTATGGGTAGAATTCGATCTGTCTATCCAGTTGCGTCACCAAATGAATGCAACCAAATGTGCCTTTCAACTCTCATGAAGTGTGATCATTGTGGTGAAACTTCATGGCAGACGGGCGATTTTGTTAAAGCCACTTGCGAATTTTGTGGCACTGAGAATTTGACTAAAGAAGGTGCCACTACTTGTGGTTACTTACCCCAAAATGCTGTTGTTAAAATTTATTGTCCAGCATGTCACAATTCAGAAGTAGGACCTGAGCATAGTCTTGCCGAATACCATAATGAATCTGGCTTGAAAACCATTCTTCGTAAGGGTGGTCGCACTATTGCCTTTGGAGGCTGTGTGTTCTCTTATGTTGGTTGCCATAACAAGTGTGCCTATTGGGTTCCACGTGCTAGCGCTAACATAGGTTGTAACCATACAGGTGTTGTTGGAGAAGGTTCCGAAGGTCTTAATGACAACCTTCTTGAAATACTCCAAAAAGAGAAAGTCAACATCAATATTGTTGGTGACTTTAAACTTAATGAAGAGATCGCCATTATTTTGGCATCTTTTTCTGCTTCCACAAGTGCTTTTGTGGAAACTGTGAAAGGTTTGGATTATAAAGCATTCAAACAAATTGTTGAATCCTGTGGTAATTTTAAAGTTACAAAAGGAAAAGCTAAAAAAGGTGCCTGGAATATTGGTGAACAGAAATCAATACTGAGTCCTCTTTATGCATTTGCATCAGAGGCTGCTCGTGTTGTACGATCAATTTTCTCCCGCACTCTTGAAACTGCTCAAAATTCTGTGCGTGTTTTACAGAAGGCCGCTATAACAATACTAGATGGAATTTCACAGTATTCACTGAGACTCATTGATGCTATGATGTTCACATCTGATTTGGCTACTAACAATCTAGTTGTAATGGCCTACATTACAGGTGGTGTTGTTCAGTTGACTTCGCAGTGGCTAACTAACATCTTTGGCACTGTTTATGAAAAACTCAAACCCGTCCTTGATTGGCTTGAAGAGAAGTTTAAGGAAGGTGTAGAGTTTCTTAGAGACGGTTGGGAAATTGTTAAATTTATCTCAACCTGTGCTTGTGAAATTGTCGGTGGACAAATTGTCACCTGTGCAAAGGAAATTAAGGAGAGTGTTCAGACATTCTTTAAGCTTGTAAATAAATTTTTGGCTTTGTGTGCTGACTCTATCATTATTGGTGGAGCTAAACTTAAAGCCTTGAATTTAGGTGAAACATTTGTCACGCACTCAAAGGGATTGTACAGAAAGTGTGTTAAATCCAGAGAAGAAACTGGCCTACTCATGCCTCTAAAAGCCCCAAAAGAAATTATCTTCTTAGAGGGAGAAACACTTCCCACAGAAGTGTTAACAGAGGAAGTTGTCTTGAAAACTGGTGATTTACAACCATTAGAACAACCTACTAGTGAAGCTGTTGAAGCTCCATTGGTTGGTACACCAGTTTGTATTAACGGGCTTATGTTGCTCGAAATCAAAGACACAGAAAAGTACTGTGCCCTTGCACCTAATATGATGGTAACAAACAATACCTTCACACTCAAAGGCGGTGCACCAACAAAGGTTACTTTTGGTGATGACACTGTGATAGAAGTGCAAGGTTACAAGAGTGTGAATATCACTTTTGAACTTGATGAAAGGATTGATAAAGTACTTAATGAGAAGTGCTCTGCCTATACAGTTGAACTCGGTACAGAAGTAAATGAGTTCGCCTGTGTTGTGGCAGATGCTGTCATAAAAACTTTGCAACCAGTATCTGAATTACTTACACCACTGGGCATTGATTTAGATGAGTGGAGTATGGCTACATACTACTTATTTGATGAGTCTGGTGAGTTTAAATTGGCTTCACATATGTATTGTTCTTTTTACCCTCCAGATGAGGATGAAGAAGAAGGTGATTGTGAAGAAGAAGAGTTTGAGCCATCAACTCAATATGAGTATGGTACTGAAGATGATTACCAAGGTAAACCTTTGGAATTTGGTGCCACTTCTGCTGCTCTTCAACCTGAAGAAGAGCAAGAAGAAGATTGGTTAGATGATGATAGTCAACAAACTGTTGGTCAACAAGACGGCAGTGAGGACAATCAGACAACTACTATTCAAACAATTGTTGAGGTTCAACCTCAATTAGAGATGGAACTTACACCAGTTGTTCAGACTATTGAAGTGAATAGTTTTAGTGGTTATTTAAAACTTACTGACAATGTATACATTAAAAATGCAGACATTGTGGAAGAAGCTAAAAAGGTAAAACCAACAGTGGTTGTTAATGCAGCCAATGTTTACCTTAAACATGGAGGAGGTGTTGCAGGAGCCTTAAATAAGGCTACTAACAATGCCATGCAAGTTGAATCTGATGATTACATAGCTACTAATGGACCACTTAAAGTGGGTGGTAGTTGTGTTTTAAGCGGACACAATCTTGCTAAACACTGTCTTCATGTTGTCGGCCCAAATGTTAACAAAGGTGAAGACATTCAACTTCTTAAGAGTGCTTATGAAAATTTTAATCAGCACGAAGTTCTACTTGCACCATTATTATCAGCTGGTATTTTTGGTGCTGACCCTATACATTCTTTAAGAGTTTGTGTAGATACTGTTCGCACAAATGTCTACTTAGCTGTCTTTGATAAAAATCTCTATGACAAACTTGTTTCAAGCTTTTTGGAAATGAAGAGTGAAAAGCAAGTTGAACAAAAGATCGCTGAGATTCCTAAAGAGGAAGTTAAGCCATTTATAACTGAAAGTAAACCTTCAGTTGAACAGAGAAAACAAGATGATAAGAAAATCAAA'..b'TAATTGTTACGACTATTGTATACCTTACAATAGTGTAACTTCTTCAATTGTCATTACTTCAGGTGATGGCACAACAAGTCCTATTTCTGAACATGACTACCAGATTGGTGGTTATACTGAAAAATGGGAATCTGGAGTAAAAGACTGTGTTGTATTACACAGTTACTTCACTTCAGACTATTACCAGCTGTACTCAACTCAATTGAGTACAGACACTGGTGTTGAACATGTTACCTTCTTCATCTACAATAAAATTGTTGATGAGCCTGAAGAACATGTCCAAATTCACACAATCGACGGTTCATCCGGAGTTGTTAATCCAGTAATGGAACCAATTTATGATGAACCGACGACGACTACTAGCGTGCCTTTGTAAGCACAAGCTGATGAGTACGAACTTATGTACTCATTCGTTTCGGAAGAGACAGGTACGTTAATAGTTAATAGCGTACTTCTTTTTCTTGCTTTCGTGGTATTCTTGCTAGTTACACTAGCCATCCTTACTGCGCTTCGATTGTGTGCGTACTGCTGCAATATTGTTAACGTGAGTCTTGTAAAACCTTCTTTTTACGTTTACTCTCGTGTTAAAAATCTGAATTCTTCTAGAGTTCCTGATCTTCTGGTCTAAACGAACTAAATATTATATTAGTTTTTCTGTTTGGAACTTTAATTTTAGCCATGGCAGATTCCAACGGTACTATTACCGTTGAAGAGCTTAAAAAGCTCCTTGAACAATGGAACCTAGTAATAGGTTTCCTATTCCTTACATGGATTTGTCTTCTACAATTTGCCTATGCCAACAGGAATAGGTTTTTGTATATAATTAAGTTAATTTTCCTCTGGCTGTTATGGCCAGTAACTTTAGCTTGTTTTGTGCTTGCTGCTGTTTACAGAATAAATTGGATCACCGGTGGAATTGCTATCGCAATGGCTTGTCTTGTAGGCTTGATGTGGCTCAGCTACTTCATTGCTTCTTTCAGACTGTTTGCGCGTACGCGTTCCATGTGGTCATTCAATCCAGAAACTAACATTCTTCTCAACGTGCCACTCCATGGCACTATTCTGACCAGACCGCTTCTAGAAAGTGAACTCGTAATCGGAGCTGTGATCCTTCGTGGACATCTTCGTATTGCTGGACACCATCTAGGACGCTGTGACATCAAGGACCTGCCTAAAGAAATCACTGTTGCTACATCACGAACGCTTTCTTATTACAAATTGGGAGCTTCGCAGCGTGTAGCAGGTGACTCAGGTTTTGCTGCATACAGTCGCTACAGGATTGGCAACTATAAATTAAACACAGACCATTCCAGTAGCAGTGACAATATTGCTTTGCTTGTACAGTAAGTGACAACAGATGTTTCATCTCGTTGACTTTCAGGTTACTATAGCAGAGATATTACTAATTATTATGAGGACTTTTAAAGTTTCCATTTGGAATCTTGATTACATCATAAACCTCATAATTAAAAATTTATCTAAGTCACTAACTGAGAATAAATATTCTCAATTAGATGAAGAGCAACCAATGGAGATTGATTAAACGAACATGAAAATTATTCTTTTCTTGGCACTGATAACACTCGCTACTTGTGAGCTTTATCACTACCAAGAGTGTGTTAGAGGTACAACAGTACTTTTAAAAGAACCTTGCTCTTCTGGAACATACGAGGGCAATTCACCATTTCATCCTCTAGCTGATAACAAATTTGCACTGACTTGCTTTAGCACTCAATTTGCTTTTGCTTGTCCTGACGGCGTAAAACACGTCTATCAGTTACGTGCCAGATCAGTTTCACCTAAACTGTTCATCAGACAAGAGGAAGTTCAAGAACTTTACTCTCCAATTTTTCTTATTGTTGCGGCAATAGTGTTTATAACACTTTGCTTCACACTCAAAAGAAAGACAGAATGATTGAACTTTCATTAATTGACTTCTATTTGTGCTTTTTAGCCTTTCTGCTATTCCTTGTTTTAATTATGCTTATTATCTTTTGGTTCTCACTTGAACTGCAAGATCATAATGAAACTTGTCACGCCTAAACGAACATGAAATTTCTTGTTTTCTTAGGAATCATCACAACTGTAGCTGCATTTCACCAAGAATGTAGTTTACAGTCATGTACTCAACATCAACCATATGTAGTTGATGACCCGTGTCCTATTCACTTCTATTCTAAATGGTATATTAGAGTAGGAGCTAGAAAATCAGCACCTTTAATTGAATTGTGCGTGGATGAGGCTGGTTCTAAATCACCCATTCAGTACATCGATATCGGTAATTATACAGTTTCCTGTTTACCTTTTACAATTAATTGCCAGGAACCTAAATTGGGTAGTCTTGTAGTGCGTTGTTCGTTCTATGAAGACTTTTTAGAGTATCATGACGTTCGTGTTGTTTTAGATTTCATCTAAACGAACAAACTAAAATGTCTGATAATGGACCCCAAAATCAGCGAAATGCACCCCGCATTACGTTTGGTGGACCCTCAGATTCAACTGGCAGTAACCAGAATGGAGAACGCAGTGGGGCGCGATCAAAACAACGTCGGCCCCAAGGTTTACCCAATAATACTGCGTCTTGGTTCACCGCTCTCACTCAACATGGCAAGGAAGACCTTAAATTCCCTCGAGGACAAGGCGTTCCAATTAACACCAATAGCAGTCCAGATGACCAAATTGGCTACTACCGAAGAGCTACCAGACGAATTCGTGGTGGTGACGGTAAAATGAAAGATCTCAGTCCAAGATGGTATTTCTACTACCTAGGAACTGGGCCAGAAGCTGGACTTCCCTATGGTGCTAACAAAGACGGCATCATATGGGTTGCAACTGAGGGAGCCTTGAATACACCAAAAGATCACATTGGCACCCGCAATCCTGCTAACAATGCTGCAATCGTGCTACAACTTCCTCAAGGAACAACATTGCCAAAAGGCTTCTACGCAGAAGGGAGCAGAGGCGGCAGTCAAGCCTCTTCTCGTTCCTCATCACGTAGTCGCAACAGTTCAAGAAATTCAACTCCAGGCAGCAGTAGGGGAACTTCTCCTGCTAGAATGGCTGGCAATGGCGGTGATGCTGCTCTTGCTTTGCTGCTGCTTGACAGATTGAACCAGCTTGAGAGCAAAATGTCTGGTAAAGGCCAACAACAACAAGGCCAAACTGTCACTAAGAAATCTGCTGCTGAGGCTTCTAAGAAGCCTCGGCAAAAACGTACTGCCACTAAAGCATACAATGTAACACAAGCTTTCGGCAGACGTGGTCCAGAACAAACCCAAGGAAATTTTGGGGACCAGGAACTAATCAGACAAGGAACTGATTACAAACATTGGCCGCAAATTGCACAATTTGCCCCCAGCGCTTCAGCGTTCTTCGGAATGTCGCGCATTGGCATGGAAGTCACACCTTCGGGAACGTGGTTGACCTACACAGGTGCCATCAAATTGGATGACAAAGATCCAAATTTCAAAGATCAAGTCATTTTGCTGAATAAGCATATTGACGCATACAAAACATNNNNNNNNNNNGAGCCTAAAAANNACAAAAAGAAGAAGGCTGATGAAACTCAAGCCTTACCGCAGAGACAGAAGAAACAGCAAACTGTGACTCTTCTTCCTGCTGCAGATTTGGATGATTTCTCCAAACAATTGCAACAATCCATGAGCAGTGCTGACTCAACTCAGGCCTAAACTCATGCAGACCACACAAGGCAGATGGGCTATATAAACGTTTTCGCTTTTCCGTTTACGATATATAGTCTACTCTTGTGCAGAATGAATTCTCGTAACTACATAGCACAAGTAGATGTAGTTAACTTTAATNTCACATNNNNNNNNNNNNNNNNNNNNNAACATTAGGGAGGACTTGAAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n' |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/covid19/PC00101P_sub.qual.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/covid19/PC00101P_sub.qual.txt Mon Mar 30 06:37:01 2020 -0400 |
| [ |
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| diff -r 000000000000 -r f362150bef41 test-data/covid19/PC00101P_sub.sorted.bam |
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| Binary file test-data/covid19/PC00101P_sub.sorted.bam has changed |
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| diff -r 000000000000 -r f362150bef41 test-data/covid19/PC00101P_sub.sorted.bam.bai |
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| Binary file test-data/covid19/PC00101P_sub.sorted.bam.bai has changed |
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| diff -r 000000000000 -r f362150bef41 test-data/covid19/PC00101P_sub.trimmed.bam |
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| Binary file test-data/covid19/PC00101P_sub.trimmed.bam has changed |
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| diff -r 000000000000 -r f362150bef41 test-data/covid19/PC00101P_sub.trimmed.sorted.bam |
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| Binary file test-data/covid19/PC00101P_sub.trimmed.sorted.bam has changed |
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| diff -r 000000000000 -r f362150bef41 test-data/covid19/PC00101P_sub.trimmed.sorted.bam.bai |
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| diff -r 000000000000 -r f362150bef41 test-data/covid19/PC00101P_variants.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/covid19/PC00101P_variants.tsv Mon Mar 30 06:37:01 2020 -0400 |
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| @@ -0,0 +1,35 @@ +REGION POS REF ALT REF_DP REF_RV REF_QUAL ALT_DP ALT_RV ALT_QUAL ALT_FREQ TOTAL_DP PVAL PASS +NC_045512.2 241 C T 0 0 0 89 89 37 1 89 4.3706e-53 TRUE +NC_045512.2 693 T C 15 1 39 1 0 37 0.0625 16 0.516129 FALSE +NC_045512.2 968 G T 13 13 38 1 1 39 0.0714286 14 0.518519 FALSE +NC_045512.2 2661 A +C 90 20 37 6 0 20 0.0645161 93 0.0163863 FALSE +NC_045512.2 2880 C A 23 23 37 1 1 38 0.0416667 24 0.5 FALSE +NC_045512.2 3037 C T 0 0 0 71 62 40 1 71 7.05539e-45 TRUE +NC_045512.2 4432 G +C 284 0 38 12 0 20 0.041958 286 0.00725964 TRUE +NC_045512.2 7165 C T 62 0 37 2 0 38 0.03125 64 0.251969 FALSE +NC_045512.2 14408 C T 0 0 0 163 163 38 1 163 1.65662e-97 TRUE +NC_045512.2 14844 A G 56 13 37 3 3 27 0.0508475 59 0.118724 FALSE +NC_045512.2 16501 G +T 10 0 37 1 0 20 0.1 10 0.55 FALSE +NC_045512.2 17429 A G 20 0 38 1 0 39 0.047619 21 0.512195 FALSE +NC_045512.2 18154 T G 32 0 38 1 0 20 0.030303 33 0.5 FALSE +NC_045512.2 18156 T A 32 0 37 1 0 20 0.030303 33 0.5 FALSE +NC_045512.2 18162 C A 32 0 38 1 0 20 0.030303 33 0.5 FALSE +NC_045512.2 18191 A G 22 0 37 1 0 39 0.0434783 23 0.5 FALSE +NC_045512.2 18814 C T 0 0 0 266 216 39 1 266 4.36601e-162 TRUE +NC_045512.2 19867 A +C 100 0 37 5 0 20 0.0490196 102 0.11521 FALSE +NC_045512.2 20087 G A 27 0 36 1 0 33 0.0357143 28 0.509091 FALSE +NC_045512.2 20475 A G 10 10 38 1 1 38 0.0909091 11 0.52381 FALSE +NC_045512.2 20842 C A 19 0 38 1 0 20 0.05 20 0.512821 FALSE +NC_045512.2 20843 C A 19 0 37 1 0 20 0.05 20 0.512821 FALSE +NC_045512.2 20863 C A 18 0 38 1 0 20 0.0526316 19 0.513514 FALSE +NC_045512.2 21109 A G 9 9 38 1 1 39 0.1 10 0.526316 FALSE +NC_045512.2 21174 A G 15 15 38 1 1 20 0.0625 16 0.5 FALSE +NC_045512.2 22692 T A 30 0 38 1 0 39 0.0322581 31 0.508197 FALSE +NC_045512.2 23403 A G 0 0 0 118 0 37 1 118 3.49082e-70 TRUE +NC_045512.2 24012 T C 9 9 36 1 1 39 0.1 10 0.526316 FALSE +NC_045512.2 26834 G A 23 23 37 1 1 37 0.0416667 24 0.5 FALSE +NC_045512.2 28424 T C 23 0 36 1 0 38 0.0416667 24 0.5 FALSE +NC_045512.2 29377 T -A 14 13 38 1 0 20 0.0714286 14 0.535714 FALSE +NC_045512.2 29447 G T 20 20 37 1 1 20 0.047619 21 0.512195 FALSE +NC_045512.2 29449 G T 18 18 36 1 1 20 0.0526316 19 0.487179 FALSE +NC_045512.2 29547 A G 27 2 38 1 0 38 0.0357143 28 0.5 FALSE |
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| diff -r 000000000000 -r f362150bef41 test-data/covid19/nCoV-2019.scheme.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/covid19/nCoV-2019.scheme.bed Mon Mar 30 06:37:01 2020 -0400 |
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|
| b |
| diff -r 000000000000 -r f362150bef41 test-data/covid19/primers_consensus.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/covid19/primers_consensus.tsv Mon Mar 30 06:37:01 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +REGION POS REF ALT REF_DP REF_RV REF_QUAL ALT_DP ALT_RV ALT_QUAL ALT_FREQ TOTAL_DP PVAL PASS |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/covid19/zika_primers.bam |
| b |
| Binary file test-data/covid19/zika_primers.bam has changed |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/covid19/zika_primers.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/covid19/zika_primers.bed Mon Mar 30 06:37:01 2020 -0400 |
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+NC_045512.2 22565 22576 400_32_out_L 0 - +NC_045512.2 14948 14958 400_32_out_L 0 - +NC_045512.2 10089 10101 400_32_out_R 0 + +NC_045512.2 26251 26261 400_33_out_L* 0 - +NC_045512.2 9642 9650 400_33_out_L* 0 + +NC_045512.2 28807 28815 400_33_out_L* 0 + +NC_045512.2 11383 11394 400_33_out_R* 0 - +NC_045512.2 8948 8962 400_33_out_R* 0 + +NC_045512.2 2507 2516 400_34_out_L* 0 + +NC_045512.2 11229 11239 400_34_out_R* 0 - +NC_045512.2 3611 3619 400_34_out_R* 0 - +NC_045512.2 17081 17090 400_35_out_L 1 + +NC_045512.2 27497 27508 400_35_out_R 0 + +NC_045512.2 21585 21595 400_35_out_R 0 + |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/covid19/zika_primers.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/covid19/zika_primers.fa Mon Mar 30 06:37:01 2020 -0400 |
| b |
| @@ -0,0 +1,140 @@ +>400_1_out_L +GACAGTTCGAGTTTGAAGCGAAAG +>400_1_out_R +AGTATGCACTCCCACGTCTAGT +>400_2_out_L +AAGAAAGATCTGGCTGCCATGC +>400_2_out_R +TGATTCCAACCAGGTTTGCGAC +>400_3_out_L* +AGATGACGTCGATTGTTGGTGC +>400_3_out_R* +TACGGTGACACAACCTCCATGT +>400_4_out_L +TCAGGTGCATAGGAGTCAGCAA +>400_4_out_R +GGAGCCATGAACTGACAGCATT +>400_5_out_L +AGAACGTTAGTGGACAGAGGCT +>400_5_out_R +TGTGCGTCCTTGAACTCTACCA +>400_6_out_L +TTGATTGTGAACCGAGGACAGG +>400_6_out_R +CCATCTGTCCCTGCGTACTGTA +>400_7_out_L +TGAAGGGCGTGTCATACTCCTT +>400_7_out_R +CGCCTCCAACTGATCCAAAGTC +>400_8_out_L* +GGGAGAAGAAGATCACCCACCA +>400_8_out_R* +TTGACTGCTGCTGCCAATCTAC +>400_9_out_L* +GCCTTAGGGGGAGTGTTGATCT +>400_9_out_R* +GAGTGGGCATTCCTTCAGTGTG +>400_10_out_L +ACGGTCGTTGTGGGATCTGTAA +>400_10_out_R +GTGGGACTTTGGCCATTCACAT +>400_11_out_L +CAGCCGTTATTGGAACAGCTGT +>400_11_out_R +CCTGGGCCTTATCTCCATTCCA +>400_12_out_L +CACTAAGGTCCACGTGGAGGAA +>400_12_out_R +TATCAGCGCCAGATGAGCTACA +>400_13_out_L +TGGCAGTGCTGGTAGCTATGAT +>400_13_out_R +AGAGAGAGGAGCATAAACCCCC +>400_14_out_L* +CAATGGTTTTGCTTTGGCCTGG +>400_14_out_R* +TTTCCCATGTGATGTCACCTGC +>400_15_out_L +CCCTAGCGAAGTACTCACAGCT +>400_15_out_R +TACACTCCATCTGTGGTCTCCC +>400_16_out_L* +GTGGCATGAACCCAATAGCCAT +>400_16_out_R* +GCTCCAATGTCCCCATCCTTTG +>400_17_out_L** +GTGGTCCATGGAAGCTAGATGC +>400_17_out_R** +CCTCTAAGGGCCTCCTCCATTT +>400_18_out_L** +CTGTTGAGTGCTTCGAGCCTTC +>400_18_out_R** +TGGTGAGTTGGAGTCCGGAAAT +>400_19_out_L +TATGGATGAGGCCCACTTCACA +>400_19_out_R +GCCATCAAGTATGACCGGCTTT +>400_20_out_L* +GGCTGGAAAACGGGTCATACAG +>400_20_out_R* +CCTTTGCTCCGTCCTAAGCTTG +>400_21_out_L* +AGAGACTGACGAAGACCATGCA +>400_21_out_R* +CTCCAAAAGCCGCTCCTCTTTT +>400_22_out_L** +TGGACCAGACACGGAGAGAAAA +>400_22_out_R** +ATTCTGGCTGGCTCAATTTCCG +>400_23_out_L +CGTCTTGATGAGGAACAAGGGC +>400_23_out_R +AAGTGGTCACTGCATGTTGGAC +>400_24_out_L** +TAATGGGAAGGAGAGAGGAGGG +>400_24_out_R** +TCTCCACTTGGGGGTCAATTGT +>400_25_out_L** +CCCTGACCCTAATAGTGGCCAT +>400_25_out_R** +CCTTCCATTTCTCTCCCAGGGT +>400_26_out_L +ACTGGAACTCCTCTACAGCCAC +>400_26_out_R +ACCAGGGCCTCCTTTTGTGTAT +>400_27_out_L +AGTGCAAAGCTGAGATGGTTGG +>400_27_out_R +ATGTGTAGAGTTGCGGGAGAGT +>400_28_out_L +GGTGGGGGATTGGCTTGAAAAA +>400_28_out_R +GGGCCTCATAGCTTCCATGGTA +>400_29_out_L +AGGATGTGAATCTCGGCTCTGG +>400_29_out_R +ATGCTGCATTGCTACGAACCTT +>400_30_out_L +AAAAGTGGACACTAGGGTGCCA +>400_30_out_R +TAATCCCAGCCCTTCAACACCA +>400_31_out_L +ACAAGGGGAATTTGGAAAGGCC +>400_31_out_R +CGTAAGTGACAACTTGTCCGCT +>400_32_out_L +AAATGGAAAAAGGGCACAGGGC +>400_32_out_R +TGTCCCATCCAGTTGAGGGTTT +>400_33_out_L* +CAAACGAATGGCAGTCAGTGGA +>400_33_out_R* +ATCCACACTCTGTTCCACACCA +>400_34_out_L* +ATTTCCACAGAAGGGACCTCCG +>400_34_out_R* +TGACTAGCAGGCCTGACAACAT +>400_35_out_L +ACCACCTGGGCTGAGAACATTA +>400_35_out_R +ACCACTAGTCCCTCTTCTGGAG |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/covid19/zika_primers_consensus.bam |
| b |
| Binary file test-data/covid19/zika_primers_consensus.bam has changed |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52.consensus.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/Z52.consensus.fa Mon Mar 30 06:37:01 2020 -0400 |
| b |
| b'@@ -0,0 +1,2 @@\n+>Consensus_Z52.consensus_threshold_0_quality_20\n+CGATTCTAGCCTTTTTGAGATTCACGGCAATCAAGCCATCACTGGGTCTCATCAATAGATGGGGTTCAGTGGGGAAAAAAGAGGCTATGGAAACAATAAAGAAGTTCAAGAAAGATCTGGCTGCCATGCTGAGAATAATCAATGCTAGGAAGGAGAAGAAGAGACGAGGCGCAGATACTAGTGTCGGAATTGTTGGCCTCCTGCTGACCACAGCTATGGCAGCGGAGGTCACTAGACGTGGGAGTGCATACTATATGTACTTGGACAGAAACGATGCTGGGGAGGCCATATCTTTTCCAACCACATTGGGGATGAATAAGTGTTATATACAGATCATGGATCTTGGACACATGTGTGATGCCACCATGAGCTATGAATGCCCTATGCTGGATGAGGGGGTGGAACCAGATGACGTCGATTGTTGGTGCAACACGACGTCAACTTGGGTTGTGTACGGAACCTGCCATCACAAAAAAGGTGAAGCACGGAGATCTAGAAGAGCTGTGACGCTCCCCTCCCATTCCACCAGGAAGCTGCAAACGCGGTCGCAAACCTGGTTGGAATCAAGAGAATACACAAAGCACTTGATTAGAGTCGAAAATTGGATATTCAGGAACCCTGGCTTCGCGTTAGCAGCAGCTGCCATCGCTTGGCTTTTGGGAAGCTCAACGAGCCAAAAAGTCATATACTTGGTCATGATACTGCTGATTGCCCCGGCATACAGCATCAGGTGCATAGGAGTCAGCAATAGGGACTTTGTGGAAGGTATGTCAGGTGGGACTTGGGTTGATGTTGTCTTGGAACATGGAGGTTGTGTCACCGTAATGGCACAGGACAAACCGACTGTCGACATAGAGCTGGTTACAACAACAGTCAGCAACATGGCGGAGGTAAGATCCTACTGCTATGAGGCATCAATATCAGACATGGCTTCTGACAGCCGCTGCCCAACACAAGGTGAAGCCTACCTTGACAAGCAATCAGACACTCAATATGTCTGCAAAAGAACGTTAGTGGACAGAGGCTGGGGAAATGGATGTGGACTTTTTGGCAAAGGGAGCCTGGTGACATGCGCTAAGTTTGCATGCTCCAAGAAAATGACCGGGAAGAGCATCCAGCCAGAGAATCTGGAGTACCGGATAATGCTGTCAGTTCATGGCTCCCAGCACAGTGGGATGATCGTTAATGACACAGGACATGAAACTGATGAGAATAGAGCGAAAGTTGAGATAACGCCCAATTCACCGAGAGCCGAAGCCACCCTGGGGGGTTTTGGAAGCCTAGGACTTGATTGTGAACCGAGGACAGGCCTTGACTTTTCAGATTTGTATTACTTGACTATGAATAACAAGCACTGGTTGGTTCACAAGGAGTGGTTCCACGACATTCCATTACCTTGGCACGCTGGGGCAGACACCGGAACTCCACACTGGAACAACAAAGAAGCACTGGTAGAGTTCAAGGACGCACATGCCAAAAGGCAAACTGTCGTGGTTCTAGGGAGTCAAGAAGGAGCAGTTCACACGGCCCTTGCTGGAGCTCTGGAGGCTGAGATGGATGGTGCAAAGGGAAGGCTGTCCTCTGGCCACTTGAAATGTCGCCTGAAAATGGATAAACTTAGATTGAAGGGCGTGTCATACTCCTTGTGTACTGCAGCGTTCACATTCACCAAGATCCCGGCTGAAACACTGCACGGGACAGTCACAGTGGAGTTACAGTACGCAGGGACAGATGGACCTTGCAAGGTTCCAGCTCAGATGGCGGTGGACATGCAAACTCTGACCCCAGTTGGGAGGTTGATAACCGCTAACCCCGTAATCACTGAAAGCACTGAGAACTCTAAGATGATGCTGGAACTTGATCCACCATTTGGGGACTCTTACATTGTCATAGGAGTCGGGGAGAAGAAGATCACCCACCACTGGCACAGGAGTGGCAGCACCATTGGAAAAGCATTTGAAGCCACTGTGAGAGGTGCCAAGAGAATGGCAGTCTTGGGAGACACAGCCTGGGACTTTGGATCAGTTGGAGGCGCTCTCAACTCATTGGGCAAGGGCATCCATCAAATTTTTGGAGCAGCTTTCAAATCATTGTTTGGAGGAATGTCCTGGTTCTCACAAATTCTCATTGGAACGTTGCTGATGTGGTTGGGTCTGAACACAAAGAATGGATCTATTTCCCTTATGTGCTTGGCCTTAGGGGGAGTGTTGATCTTCTTATCCACAGCCGTCTCTGCTGATGTGGGGTGCTCGGTGGACTTCTCAAAGAAGGAGACGAGATGCGGTACAGGGGTGTTCGTCTATAACGACGTTGAAGCCTGGAGGGACAGGTACAAGTACCATCCTGACTCCCCCCGTAGATTGGCAGCAGCAGTCAAGCAAGCCTGGGAAGATGGTATCTGCGGGATCTCCTCTGTTTCAAGAATGGAAAACATCATGTGGAGATCAGTAGAAGGGGAGCTCAACGCAATCCTGGAAGAGAATGGAGTTCAACTGACGGTCGTTGTGGGATCTGTAAAAAACCCCATGTGGAGAGGTCCACAGAGATTGCCCGTGCCTGTGAACGAGCTGCCCCACGGCTGGAAGGCTTGGGGGAAATCGTATTTCGTCAGAGCAGCAAAGACAAATAACAGCTTTGTCGTGGATGGTGACACACTGAAGGAATGCCCACTCAAACATAGAGCATGGAACAGCTTTCTTGTGGAGGATCATGGGTTCGGGGTATTTCACACTAGTGTCTGGCTCAAGGTTAGAGAAGATTATTCATTAGAGTGTGATCCAGCCGTTATTGGAACAGCTGTTAAGGGAAAGGAGGCTGTACACAGTGATCTAGGCTACTGGATTGAGAGTGAGAAGAATGACACATGGAGGCTGAAGAGGGCCCATCTGATCGAGATGAAAACATGTGAATGGCCAAAGTCCCACACATTGTGGACAGATGGAATAGAAGAGAGTGATCTGATCATACCCAAGTCTTTAGCTGGGCCACTCAGCCATCACAATACCAGAGAGGGCTACAGGACCCAAATGAAAGGGCCATGGCACAGTGAAGAGCTTGAAATTCGGTTTGAGGAATGCCCAGGCACTAAGGTCCACGTGGAGGAAACATGTGGAACAAGAGGACCATCTCTGAGATCAACCACTGCAAGCGGAAGGGTGATCGAGGAATGGTGCTGCAGGGAGTGCACAATGCCCCCACTGTCGTTCCGGGCTAAAGATGGCTGTTGGTATGGAATGGAGATAAGGCCCAGGAAAGAACCAGAAAGCAACTTAGTAAGGTCAATGGTGACTGCAGGATCAACTGATCACATGGACCACTTCTCCCTTGGAGTGCTTGTGATCCTGCTCATGGTGCAGGAAGGGCTGAAGAAGAGAATGACCACAAAGATCATCATAAGCACATCAATGGCAGTGCTGGTAGCTATGATCCTGGGAGGATTTTCAATGAGTGACCTGGCTAAGCTTGCAATTTTGATGGGTGCCACCTTCGCGGAAATGAACACTGGAGGAGATGTAGCTCATCTGGCGCTGATAGCGGCATTCAAAGTCAGACCAGCGTTGCTGGTATCTTTCATCTTCAGAGCTAATTGGACACCCCGTGAAAGCATGCTGCTGGCCTTGGCCTCGTGTCTTTTGCAAACTGCGATCTCCGCCTTGGAAGGCGACCTGATGGTTCTCATCAATGGTTTTGCTTTGGCCTGGTTGGCAATACGAGCGATGGTTGTTCCACGCACTGATAACATCACCTTGGCAATCCTGGCTGCTCTGACACCACTGGCCCGGGGCACACTGCTTGTGGCGTGGAGAGCAGGCCTTGCTACTTGCGGGGGGTTTATGCTCCTCTCTCTGAAGGGAAAAGGCAGTGTGAAGAAGAACTTACCATTTGTCATGGCCCTGGGACTAACCGCTGTGAGGCTGGTCGACCCCATCAACG'..b'GGATGGACGCCAGAGTTTGTTCAGATCATGCGGCCCTGAAGTCATTCAAGGAGTTTGCCGCTGGGAAAAGAGGAGCGGCTTTTGGAGTGATGGAAGCCCTGGGAACACTGCCAGGACACATGACAGAGAGATTCCAGGAAGCCATTGACAACCTCGCTGTGCTCATGCGGGCAGAGACTGGAAGCAGGCCTTACAAAGCCGCGG------------------------------------------------TGGGAACAGTCTCGCTGGGAATCTTCTTCGTCTTGATGAGGAACAAGGGCATAGGGAAGATGGGCTTTGGAATGGTGACTCTTGGGGCCAGCGCATGGCTCATGTGGCTCTCGGAAATTGAGCCAGCCAGAATTGCATGTGTCCTCATTGTTGTGTTCCTATTGCTGGTGGTGCTCATACCTGAGCCAGAAAAGCAAAGATCTCCCCAGGACAACCAAATGGCAATCATCATCATGGTAGCAGTAGGTCTTCTGGGCTTGATTACCGCCAATGAACTCGGATGGTTGGAGAGAACAAAGAGTGACCTAAGCCATCTAATGGGAAGGAGAGAGGAGGGGGCAACCATAGGATTCTCAATGGACATTGACCTGCGGCCAGCCTCAGCTTGGGCCATCTATGCTGCCTTGACAACTTTCATTACCCCAGCCGTCCAACATGCAGTGACCACCTCATACAACAACTACTCCTTAATGGCGATGGCCACGCAAGCTGGAGTGTTGTTTGGCATGGGCAAAGGGATGCCATTCTACGCATGGGACTTTGGAGTCCCGCTGCTAATGATAGGTTGCTACTCACAATTAACACCCCTGACCCTAATAGTGGCCATCATTTTGCTCGTGGCGCACTACATGTACTTGATCCCAGGGCTGCAGGCAGCAGCTGCGCGTGCTGCCCAGAAGAGAACGGCAGCTGGCATCATGAAGAACCCTGTTGTGGATGGAATAGTGGTGACTGACATTGACACAATGACAATTGACCCCCAAGTGGAGAAAAAGATGGGACAGGTGCTACTCATAGCAGTAGCCGTCTCCAGCGCCATACTGTCGCGGACCGCCTGGGGGTGGGGGGAGGCTGGGGCTCTGATCACAGCCGCAACTTCCACTTTGTGGGAAGGCTCTCCGAACAAGTACTGGAACTCCTCTACAGCCACTTCACTGTGTAACATTTTTAGGGGAAGTTACTTGGCTGGAGCTTCTCTAATCTACACAGTAACAAGAAACGCTGGCTTGGTCAAGAGACGTGGGGGTGGAACAGGAGAGACCCTGGGAGAGAAATGGAAGGCCCGCTTGAACCAGATGTCGGCCCTGGAGTTCTACTCCTACAAAAAGTCAGGCATCACCGAGGTGTGCAGAGAAGAGGCCCGCCGCGCCCTCAAGGACGGTGTGGCAACGGGAGGCCATGCTGTGTCCCGAGGAAGTGCAAAGCTGAGATGGTTGGTGGAGCGGGGATACCTGCAGCCCTATGGAAAGGTCATTGATCTTGGATGTGGCAGAGGGGGCTGGAGTTACTACGTCGCCACCATCCGCAAAGTTCAAGAAGTGAAAGGATACACAAAAGGAGGCCCTGGTCATGAAGAACCCGTGTTGGTGCAAAGCTATGGGTGGAACATAGTCCGTCTTAAGAGTGGGGTGGACGTCTTTCATATGGCGGCTGAGCCGTGTGACACGTTGCTGTGTGACATAGGTGAGTCATCATCTAGTCCTGAAGTGGAAGAAGCACGGACGCTCAGAGTCCTCTCCATGGTGGGGGATTGGCTTGAAAAAAGACCAGGAGCCTTTTGTATAAAAGTGTTGTGCCCATACACCAGCACTATGATGGAAACCCTGGAGCGACTGCAGCGTAGGTATGGGGGAGGACTGGTCAGAGTGCCACTCTCCCGCAACTCTACACATGAGATGTACTGGGTCTCTGGAGCGAAAAGCAACACCATAAAAAGTGTGTCCACCACGAGCCAGCTCCTCTTGGGGCGCATGGACGGGCCTAGGAGGCCAGTGAAATATGAGGAGGATGTGAATCTCGGCTCTGGCACGCGGGCTGTGGTAAGCTGCGCTGAAGCTCCCAACATGAAGATCATTGGTAACCGCATTGAAAGGATCCGCAGTGAGCACGCGGAAACGTGGTTCTTTGACGAGAACCACCCATATAGGACATGGGCTTACCATGGAAGCTATGAGGCCCCCACACAAGGGTCAGCGTCCTCTCTAATAAACGGGGTTGTCAGGCTCCTGTCAAAACCCTGGGATGTGGTGACTGGAGTCACAGGAATAGCCATGACCGACACCACACCGTATGGTCAGCAAAGAGTTTTCAAGGAAAAAGTGGACACTAGGGTGCCAGACCCCCAAGAAGGCACTCGTCAGGTTATGAGCATGGTCTCTTCCTGGTTGTGGAAAGAGCTAGGCAAACACAAACGGCCACGAGTCTGCACCAAAGAAGAGTTCATCAACAAGGTTCGTAGCAATGCAGCATTAGGGGCAATATTTGAAGAGGAAAAAGAGTGGAAGACTGCAGTGGAAGCTGTGAACGATCCAAGGTTCTGGGCTCTAGTGGACAAGGAAAGAGAGCACCACCTGAGAGGAGAGTGCCAGAGCTGTGTGTACAACATGATGGGAAAAAGAGAAAAGAAACAAGGGGAATTTGGAAAGGCCAAGGGCAGCCGCGCCATCTGGTATATGTGGCTAGGGGCTAGATTTCTAGAGTTCGAAGCCCTTGGATTCTTGAACGAGGATCACTGGATGGGGAGAGAGAACTCAGGAGGTGGTGTTGAAGGGCTGGGATTACAAAGACTCGGATATGTCCTAGAAGAGATGAGTCGTATACCAGGAGGAAGGATGTATGCAGATGACACTGCTGGCTGGGACACCCGCATTAGCAGGTTTGATCTGGAGAATGAAGCTCTAATCACCAACCAAATGGAGAAAGGGCACAGGGCCTTGGCATTGGCCATAATCAAGTACACATACCAAAACAAAGTGGTAAAGGTCCTTAGACCAGCTGAAAAAGGGAAAACAGTTATGGACATTATTTCGAGACAAGACCAAAGGGGGAGCGGACAAGTTGTCACTTACGCTCTTAACACATTTACCAACCTAGTGGTGCAACTCATTCGGAATATGGAGGCTGAGGAAGTTCTAGAGATGCAAGACTTGTGGCTGCTGCGGAGGTCAGAGAAAGTGACCAACTGGTTGCAGAGCAACGGATGGGATAGGCTCAAACGAATGGCAGTCAGTGGAGATGATTGCGTTGTGAAGCCAATTGATGATAGGTTTGCACATGCCCTCAGGTTCTTGAATGATATGGGAAAAGTTAGGAAGGACACACAAGAGTGGAAACCCTCAACTGGATGGGACAACTGGGAAGAAGTTCCGTTTTGCTCCCACCACTTCAACAAGCTCCATCTCAAGGACGGGAGGTCCATTGTGGTTCCCTGCCGCCACCAAGATGAACTGATTGGCCGGGCCCGCGTCTCTCCAGGGGCGGGATGGAGCATCCGGGAGACTGCTTGCCTAGCAAAATCATATGCGCAAATGTGGCAGCTCCTTTATTTCCACAGAAGGGACCTCCGACTGATGGCCAATGCCATTTGTTCATCTGTGCCAGTTGACTGGGTTCCAACTGGGAGAACTACCTGGTCAATCCATGGAAAGGGAGAATGGATGACCACTGAAGACATGCTTGTGGTGTGGAACAGAGTGTGGATTGAGGAGAACGACCACATGGAAGACAAGACCCCAGTTACGAAATGGACAGACATTCCCTATTTGGGAAAAAGGGAAGACTTGTGGTGTGGATCTCTCATAGGGCACAGACCGCGCACCACCTGGGCTGAGAACATTAAAAACACAGTCAACATGGTGCGCAGGATCATAGGTGATGAAGAAAAGTACATGGACTACCTATCCACCCAAGTTCGCTACTTGGGTGAAGAAGGGTCTACACCTGGAGTGCTGTAAGCACCAATCTTA\n' |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52.consensus.fa.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/Z52.consensus.fa.fai Mon Mar 30 06:37:01 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +Consensus_Z52.consensus_threshold_0_quality_20 10139 48 10139 10140 |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52.consensus.qual.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/Z52.consensus.qual.txt Mon Mar 30 06:37:01 2020 -0400 |
| [ |
| b'@@ -0,0 +1,1 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|
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52.masked.sorted.depth --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/Z52.masked.sorted.depth Mon Mar 30 06:37:01 2020 -0400 |
| b |
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| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52.merged.bam |
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| Binary file test-data/zika/Z52.merged.bam has changed |
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| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52.sorted.depth --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/Z52.sorted.depth Mon Mar 30 06:37:01 2020 -0400 |
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| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52.trimmed.sorted.depth --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/Z52.trimmed.sorted.depth Mon Mar 30 06:37:01 2020 -0400 |
| b |
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t0\t0\n+PRV\t10794\t0\t0\n+PRV\t10795\t0\t0\n+PRV\t10796\t0\t0\n+PRV\t10797\t0\t0\n+PRV\t10798\t0\t0\n+PRV\t10799\t0\t0\n+PRV\t10800\t0\t0\n+PRV\t10801\t0\t0\n+PRV\t10802\t0\t0\n+PRV\t10803\t0\t0\n+PRV\t10804\t0\t0\n+PRV\t10805\t0\t0\n+PRV\t10806\t0\t0\n+PRV\t10807\t0\t0\n' 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| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/Z52.tsv Mon Mar 30 06:37:01 2020 -0400 |
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| @@ -0,0 +1,11 @@ +REGION POS REF ALT REF_DP_Z52_a.tsv REF_RV_Z52_a.tsv REF_QUAL_Z52_a.tsv ALT_DP_Z52_a.tsv ALT_RV_Z52_a.tsv ALT_QUAL_Z52_a.tsv ALT_FREQ_Z52_a.tsv TOTAL_DP_Z52_a.tsv PVAL_Z52_a.tsv PASS_Z52_a.tsv REF_DP_Z52_b.tsv REF_RV_Z52_b.tsv REF_QUAL_Z52_b.tsv ALT_DP_Z52_b.tsv ALT_RV_Z52_b.tsv ALT_QUAL_Z52_b.tsv ALT_FREQ_Z52_b.tsv TOTAL_DP_Z52_b.tsv PVAL_Z52_b.tsv PASS_Z52_b.tsv +PRV 1682 C T 1097 984 37 34 33 37 0.0300088 1133 7.79053e-10 TRUE 1505 1475 37 50 50 37 0.0321543 1555 1.59703e-14 TRUE +PRV 1965 T G 302 113 37 41 3 35 0.119534 343 2.81419e-14 TRUE 469 28 36 71 1 36 0.131481 540 1.31011e-23 TRUE +PRV 2781 T G 353 70 37 48 8 36 0.117936 407 4.05758e-16 TRUE 404 75 37 35 7 36 0.0788288 444 1.12705e-11 TRUE +PRV 2922 C T 263 0 36 11 0 36 0.040146 274 0.000431954 TRUE 277 0 36 19 0 34 0.0641892 296 1.46245e-06 TRUE +PRV 3148 Y C 0 0 0 381 75 36 0.223199 1707 0 TRUE 0 0 0 679 99 37 0.258765 2624 0 TRUE +PRV 3148 Y T 0 0 0 1324 264 36 0.77563 1707 0 TRUE 0 0 0 1943 271 36 0.740473 2624 0 TRUE +PRV 3295 A G 1002 1002 35 38 38 33 0.0365385 1040 4.30837e-11 TRUE 1806 1806 36 69 69 34 0.0368 1875 2.28815e-20 TRUE +PRV 5680 C T 27 5 44 8 2 45 0.228571 35 0.000596701 TRUE 38 5 50 7 1 49 0.155556 45 0.00133612 TRUE +PRV 7916 C T 351 289 36 81 78 37 0.1875 432 5.39655e-27 TRUE 286 227 36 45 38 37 0.135952 331 4.31473e-15 TRUE +PRV 9713 C T 374 0 37 13 0 35 0.0335917 387 0.00010474 TRUE 475 0 37 27 0 36 0.0537849 502 4.66646e-09 TRUE |
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| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52_a.masked.bam |
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| Binary file test-data/zika/Z52_a.masked.bam has changed |
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| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52_a.masked.sorted.bam |
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| Binary file test-data/zika/Z52_a.masked.sorted.bam has changed |
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| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52_a.sorted.bam |
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| Binary file test-data/zika/Z52_a.sorted.bam has changed |
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| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52_a.sorted.bam.bai |
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| Binary file test-data/zika/Z52_a.sorted.bam.bai has changed |
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| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52_a.trimmed.bam |
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| Binary file test-data/zika/Z52_a.trimmed.bam has changed |
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| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52_a.trimmed.sorted.bam |
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| Binary file test-data/zika/Z52_a.trimmed.sorted.bam has changed |
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| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52_a.trimmed.sorted.bam.bai |
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| Binary file test-data/zika/Z52_a.trimmed.sorted.bam.bai has changed |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52_a.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/Z52_a.tsv Mon Mar 30 06:37:01 2020 -0400 |
| b |
| @@ -0,0 +1,17 @@ +REGION POS REF ALT REF_DP REF_RV REF_QUAL ALT_DP ALT_RV ALT_QUAL ALT_FREQ TOTAL_DP PVAL PASS +PRV 350 A T 101 101 36 5 5 35 0.0471698 106 0.0304989 FALSE +PRV 722 C +A 280 234 36 9 0 20 0.0319149 282 0.0349042 FALSE +PRV 1682 C T 1097 984 37 34 33 37 0.0300088 1133 7.79053e-10 TRUE +PRV 1965 T G 302 113 37 41 3 35 0.119534 343 2.81419e-14 TRUE +PRV 2702 A G 31 31 36 1 1 23 0.03125 32 0.507937 FALSE +PRV 2781 T G 353 70 37 48 8 36 0.117936 407 4.05758e-16 TRUE +PRV 2922 C T 263 0 36 11 0 36 0.040146 274 0.000431954 TRUE +PRV 3148 Y T 0 0 0 1324 264 36 0.77563 1707 0 TRUE +PRV 3148 Y C 0 0 0 381 75 36 0.223199 1707 0 TRUE +PRV 3295 A G 1002 1002 35 38 38 33 0.0365385 1040 4.30837e-11 TRUE +PRV 5680 C T 27 5 44 8 2 45 0.228571 35 0.000596701 TRUE +PRV 5723 T G 31 31 35 1 1 21 0.03125 32 0.507937 FALSE +PRV 6201 A G 10 0 35 2 0 25 0.166667 12 0.26087 FALSE +PRV 6211 T C 8 0 36 1 0 35 0.111111 9 0.5 FALSE +PRV 7916 C T 351 289 36 81 78 37 0.1875 432 5.39655e-27 TRUE +PRV 9713 C T 374 0 37 13 0 35 0.0335917 387 0.00010474 TRUE |
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| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52_b.masked.bam |
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| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52_b.masked.sorted.bam |
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| Binary file test-data/zika/Z52_b.masked.sorted.bam has changed |
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| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52_b.sorted.bam |
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| Binary file test-data/zika/Z52_b.sorted.bam has changed |
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| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52_b.sorted.bam.bai |
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| Binary file test-data/zika/Z52_b.sorted.bam.bai has changed |
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| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52_b.trimmed.bam |
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| Binary file test-data/zika/Z52_b.trimmed.bam has changed |
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| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52_b.trimmed.sorted.bam |
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| Binary file test-data/zika/Z52_b.trimmed.sorted.bam has changed |
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| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52_b.trimmed.sorted.bam.bai |
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| Binary file test-data/zika/Z52_b.trimmed.sorted.bam.bai has changed |
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| diff -r 000000000000 -r f362150bef41 test-data/zika/Z52_b.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/Z52_b.tsv Mon Mar 30 06:37:01 2020 -0400 |
| b |
| @@ -0,0 +1,24 @@ +REGION POS REF ALT REF_DP REF_RV REF_QUAL ALT_DP ALT_RV ALT_QUAL ALT_FREQ TOTAL_DP PVAL PASS +PRV 685 C T 268 203 36 10 0 37 0.0359712 278 0.000867393 TRUE +PRV 1682 C T 1505 1475 37 50 50 37 0.0321543 1555 1.59703e-14 TRUE +PRV 1721 A T 27 0 36 1 0 38 0.0357143 28 0.509091 FALSE +PRV 1818 A T 31 31 37 1 1 37 0.03125 32 0.507937 FALSE +PRV 1848 T C 31 31 36 1 1 36 0.03125 32 0.5 FALSE +PRV 1965 T G 469 28 36 71 1 36 0.131481 540 1.31011e-23 TRUE +PRV 2781 T G 404 75 37 35 7 36 0.0788288 444 1.12705e-11 TRUE +PRV 2922 C T 277 0 36 19 0 34 0.0641892 296 1.46245e-06 TRUE +PRV 3148 Y T 0 0 0 1943 271 36 0.740473 2624 0 TRUE +PRV 3148 Y C 0 0 0 679 99 37 0.258765 2624 0 TRUE +PRV 3295 A G 1806 1806 36 69 69 34 0.0368 1875 2.28815e-20 TRUE +PRV 3827 C T 248 0 37 14 0 36 0.0534351 262 5.10688e-05 TRUE +PRV 5680 C T 38 5 50 7 1 49 0.155556 45 0.00133612 TRUE +PRV 5683 G -A 45 8 53 2 0 20 0.0444444 45 0.159299 FALSE +PRV 6301 T G 10 10 37 1 1 24 0.0909091 11 0.52381 FALSE +PRV 6374 A -AGAGTGCTCAAACCGAGGTGGATGGACGCC 12 12 37 1 0 20 0.0833333 12 0.52 FALSE +PRV 6390 A G 26 12 37 1 0 38 0.037037 27 0.5 FALSE +PRV 6439 T A 27 12 36 1 1 38 0.0357143 28 0.509091 FALSE +PRV 6479 A T 14 0 36 1 0 37 0.0666667 15 0.517241 FALSE +PRV 7916 C T 286 227 36 45 38 37 0.135952 331 4.31473e-15 TRUE +PRV 8074 C T 18 2 39 1 0 76 0.0526316 19 0.463415 FALSE +PRV 9713 C T 475 0 37 27 0 36 0.0537849 502 4.66646e-09 TRUE +PRV 10227 G T 533 528 37 18 18 37 0.0326087 552 2.31457e-06 TRUE |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/db/PRV.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/db/PRV.fa Mon Mar 30 06:37:01 2020 -0400 |
| b |
| b'@@ -0,0 +1,2 @@\n+>PRV\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGCTAGCAACAGTATCAACAGGTTTTATTTTGGATTTGGAAACGAGAGTTTCTGGTCATGAAAAACCCAAAAAAGAAATCCGGAGGATTCCGGATTGTCAATATGCTAAAACGCGGAGTAGCCCGTGTGAGCCCCTTTGGGGGCTTGAAGAGGCTGCCAGCCGGACTTCTGCTGGGTCATGGGCCCATCAGGATGGTCTTGGCGATTCTAGCCTTTTTGAGATTCACGGCAATCAAGCCATCACTGGGTCTCATCAATAGATGGGGTTCAGTGGGGAAAAAAGAGGCTATGGAAACAATAAAGAAGTTCAAGAAAGATCTGGCTGCCATGCTGAGAATAATCAATGCTAGGAAGGAGAAGAAGAGACGAGGCGCAGATACTAGTGTCGGAATTGTTGGCCTCCTGCTGACCACAGCTATGGCAGCGGAGGTCACTAGACGTGGGAGTGCATACTATATGTACTTGGACAGAAACGATGCTGGGGAGGCCATATCTTTTCCAACCACATTGGGGATGAATAAGTGTTATATACAGATCATGGATCTTGGACACATGTGTGATGCCACCATGAGCTATGAATGCCCTATGCTGGATGAGGGGGTGGAACCAGATGACGTCGATTGTTGGTGCAACACGACGTCAACTTGGGTTGTGTACGGAACCTGCCATCACAAAAAAGGTGAAGCACGGAGATCTAGAAGAGCTGTGACGCTCCCCTCCCATTCCACCAGGAAGCTGCAAACGCGGTCGCAAACCTGGTTGGAATCAAGAGAATACACAAAGCACTTGATTAGAGTCGAAAATTGGATATTCAGGAACCCTGGCTTCGCGTTAGCAGCAGCTGCCATCGCTTGGCTTTTGGGAAGCTCAACGAGCCAAAAAGTCATATACTTGGTCATGATACTGCTGATTGCCCCGGCATACAGCATCAGGTGCATAGGAGTCAGCAATAGGGACTTTGTGGAAGGTATGTCAGGTGGGACTTGGGTTGATGTTGTCTTGGAACATGGAGGTTGTGTCACCGTAATGGCACAGGACAAACCGACTGTCGACATAGAGCTGGTTACAACAACAGTCAGCAACATGGCGGAGGTAAGATCCTACTGCTATGAGGCATCAATATCAGACATGGCTTCTGACAGCCGCTGCCCAACACAAGGTGAAGCCTACCTTGACAAGCAATCAGACACTCAATATGTCTGCAAAAGAACGTTAGTGGACAGAGGCTGGGGAAATGGATGTGGACTTTTTGGCAAAGGGAGCCTGGTGACATGCGCTAAGTTTGCATGCTCCAAGAAAATGACCGGGAAGAGCATCCAGCCAGAGAATCTGGAGTACCGGATAATGCTGTCAGTTCATGGCTCCCAGCACAGTGGGATGATCGTTAATGACACAGGACATGAAACTGATGAGAATAGAGCGAAAGTTGAGATAACGCCCAATTCACCGAGAGCCGAAGCCACCCTGGGGGGTTTTGGAAGCCTAGGACTTGATTGTGAACCGAGGACAGGCCTTGACTTTTCAGATTTGTATTACTTGACTATGAATAACAAGCACTGGTTGGTTCACAAGGAGTGGTTCCACGACATTCCATTACCTTGGCACGCTGGGGCAGACACCGGAACTCCACACTGGAACAACAAAGAAGCACTGGTAGAGTTCAAGGACGCACATGCCAAAAGGCAAACTGTCGTGGTTCTAGGGAGTCAAGAAGGAGCAGTTCACACGGCCCTTGCTGGAGCTCTGGAGGCTGAGATGGATGGTGCAAAGGGAAGGCTGTCCTCTGGCCACTTGAAATGTCGCCTGAAAATGGATAAACTTAGATTGAAGGGCGTGTCATACTCCTTGTGTACTGCAGCGTTCACATTCACCAAGATCCCGGCTGAAACACTGCACGGGACAGTCACAGTGGAGTTACAGTACGCAGGGACAGATGGACCTTGCAAGGTTCCAGCTCAGATGGCGGTGGACATGCAAACTCTGACCCCAGTTGGGAGGTTGATAACCGCTAACCCCGTAATCACTGAAAGCACTGAGAACTCTAAGATGATGCTGGAACTTGATCCACCATTTGGGGACTCTTACATTGTCATAGGAGTCGGGGAGAAGAAGATCACCCACCACTGGCACAGGAGTGGCAGCACCATTGGAAAAGCATTTGAAGCCACTGTGAGAGGTGCCAAGAGAATGGCAGTCTTGGGAGACACAGCCTGGGACTTTGGATCAGTTGGAGGCGCTCTCAACTCATTGGGCAAGGGCATCCATCAAATTTTTGGAGCAGCTTTCAAATCATTGTTTGGAGGAATGTCCTGGTTCTCACAAATTCTCATTGGAACGTTGCTGATGTGGTTGGGTCTGAACACAAAGAATGGATCTATTTCCCTTATGTGCTTGGCCTTAGGGGGAGTGTTGATCTTCTTATCCACAGCCGTCTCTGCTGATGTGGGGTGCTCGGTGGACTTCTCAAAGAAGGAGACGAGATGCGGTACAGGGGTGTTCGTCTATAACGACGTTGAAGCCTGGAGGGACAGGTACAAGTACCATCCTGACTCCCCCCGTAGATTGGCAGCAGCAGTCAAGCAAGCCTGGGAAGATGGTATCTGCGGGATCTCCTCTGTTTCAAGAATGGAAAACATCATGTGGAGATCAGTAGAAGGGGAGCTCAACGCAATCCTGGAAGAGAATGGAGTTCAACTGACGGTCGTTGTGGGATCTGTAAAAAACCCCATGTGGAGAGGTCCACAGAGATTGCCCGTGCCTGTGAACGAGCTGCCCCACGGCTGGAAGGCTTGGGGGAAATCGTATTTCGTCAGAGCAGCAAAGACAAATAACAGCTTTGTCGTGGATGGTGACACACTGAAGGAATGCCCACTCAAACATAGAGCATGGAACAGCTTTCTTGTGGAGGATCATGGGTTCGGGGTATTTCACACTAGTGTCTGGCTCAAGGTTAGAGAAGATTATTCATTAGAGTGTGATCCAGCCGTTATTGGAACAGCTGTTAAGGGAAAGGAGGCTGTACACAGTGATCTAGGCTACTGGATTGAGAGTGAGAAGAATGACACATGGAGGCTGAAGAGGGCCCATCTGATCGAGAYGAAAACATGTGAATGGCCAAAGTCCCACACATTGTGGACAGATGGAATAGAAGAGAGTGATCTGATCATACCCAAGTCTTTAGCTGGGCCACTCAGCCATCACAATACCAGAGAGGGCTACAGGACCCAAATGAAAGGGCCATGGCACAGTGAAGAGCTTGAAATTCGGTTTGAGGAATGCCCAGGCACTAAGGTCCACGTGGAGGAAACATGTGGAACAAGAGGACCATCTCTGAGATCAACCACTGCAAGCGGAAGGGTGATCGAGGAATGGTGCTGCAGGGAGTGCACAATGCCCCCACTGTCGTTCCGGGCTAAAGATGGCTGTTGGTATGGAATGGAGATAAGGCCCAGGAAAGAACCAGAAAGCAACTTAGTAAGGTCAATGGTGACTGCAGGATCAACTGATCACATGGACCACTTCTCCCTTGGAGTGCTTGTGATCCTGCTCATGGTGCAGGAAGGGCTGAAGAAGAGAATGACCACAAAGATCATCATAAGCACATCAATGGCAGTGCTGGTAGCTATGATCCTGGGAGGATTTTCAATGAGTGACCTGGCTAAGCTTGCAATTTTGATGGGTGCCACCTTCGCGGAAATGAACACTGGAGGAGATGTAGCTCATCTGGCGCTGATAGCGGCATTCAAAGTCAGACCAGCGTTGCTGGTATCTTTCATCTTCAGAGCTAATTGGACACCCCGTGAAAGCATGCTGCTGGCCTTGGCCTCGTGTCTTTTGCAAACTGCGATCTCCGCCTTGGAAGGCGACCTGATGGTTCTCATCAATGGTTTTGCTTTGGCCTGGTTGGCAATACGAGCGATGGTTGT'..b'CTGGTGGTGCTCATACCTGAGCCAGAAAAGCAAAGATCTCCCCAGGACAACCAAATGGCAATCATCATCATGGTAGCAGTAGGTCTTCTGGGCTTGATTACCGCCAATGAACTCGGATGGTTGGAGAGAACAAAGAGTGACCTAAGCCATCTAATGGGAAGGAGAGAGGAGGGGGCAACCATAGGATTCTCAATGGACATTGACCTGCGGCCAGCCTCAGCTTGGGCCATCTATGCTGCCTTGACAACTTTCATTACCCCAGCCGTCCAACATGCAGTGACCACCTCATACAACAACTACTCCTTAATGGCGATGGCCACGCAAGCTGGAGTGTTGTTTGGCATGGGCAAAGGGATGCCATTCTACGCATGGGACTTTGGAGTCCCGCTGCTAATGATAGGTTGCTACTCACAATTAACACCCCTGACCCTAATAGTGGCCATCATTTTGCTCGTGGCGCACTACATGTACTTGATCCCAGGGCTGCAGGCAGCAGCTGCGCGTGCTGCCCAGAAGAGAACGGCAGCTGGCATCATGAAGAACCCTGTTGTGGATGGAATAGTGGTGACTGACATTGACACAATGACAATTGACCCCCAAGTGGAGAAAAAGATGGGACAGGTGCTACTCATAGCAGTAGCCGTCTCCAGCGCCATACTGTCGCGGACCGCCTGGGGGTGGGGGGAGGCTGGGGCTCTGATCACAGCCGCAACTTCCACTTTGTGGGAAGGCTCTCCGAACAAGTACTGGAACTCCTCTACAGCCACTTCACTGTGTAACATTTTTAGGGGAAGTTACTTGGCTGGAGCTTCTCTAATCTACACAGTAACAAGAAACGCTGGCTTGGTCAAGAGACGTGGGGGTGGAACAGGAGAGACCCTGGGAGAGAAATGGAAGGCCCGCTTGAACCAGATGTCGGCCCTGGAGTTCTACTCCTACAAAAAGTCAGGCATCACCGAGGTGTGCAGAGAAGAGGCCCGCCGCGCCCTCAAGGACGGTGTGGCAACGGGAGGCCATGCTGTGTCCCGAGGAAGTGCAAAGCTGAGATGGTTGGTGGAGCGGGGATACCTGCAGCCCTATGGAAAGGTCATTGATCTTGGATGTGGCAGAGGGGGCTGGAGTTACTACGTCGCCACCATCCGCAAAGTTCAAGAAGTGAAAGGATACACAAAAGGAGGCCCTGGTCATGAAGAACCCGTGTTGGTGCAAAGCTATGGGTGGAACATAGTCCGTCTTAAGAGTGGGGTGGACGTCTTTCATATGGCGGCTGAGCCGTGTGACACGTTGCTGTGTGACATAGGTGAGTCATCATCTAGTCCTGAAGTGGAAGAAGCACGGACGCTCAGAGTCCTCTCCATGGTGGGGGATTGGCTTGAAAAAAGACCAGGAGCCTTTTGTATAAAAGTGTTGTGCCCATACACCAGCACTATGATGGAAACCCTGGAGCGACTGCAGCGTAGGTATGGGGGAGGACTGGTCAGAGTGCCACTCTCCCGCAACTCTACACATGAGATGTACTGGGTCTCTGGAGCGAAAAGCAACACCATAAAAAGTGTGTCCACCACGAGCCAGCTCCTCTTGGGGCGCATGGACGGGCCTAGGAGGCCAGTGAAATATGAGGAGGATGTGAATCTCGGCTCTGGCACGCGGGCTGTGGTAAGCTGCGCTGAAGCTCCCAACATGAAGATCATTGGTAACCGCATTGAAAGGATCCGCAGTGAGCACGCGGAAACGTGGTTCTTTGACGAGAACCACCCATATAGGACATGGGCTTACCATGGAAGCTATGAGGCCCCCACACAAGGGTCAGCGTCCTCTCTAATAAACGGGGTTGTCAGGCTCCTGTCAAAACCCTGGGATGTGGTGACTGGAGTCACAGGAATAGCCATGACCGACACCACACCGTATGGTCAGCAAAGAGTTTTCAAGGAAAAAGTGGACACTAGGGTGCCAGACCCCCAAGAAGGCACTCGTCAGGTTATGAGCATGGTCTCTTCCTGGTTGTGGAAAGAGCTAGGCAAACACAAACGGCCACGAGTCTGCACCAAAGAAGAGTTCATCAACAAGGTTCGTAGCAATGCAGCATTAGGGGCAATATTTGAAGAGGAAAAAGAGTGGAAGACTGCAGTGGAAGCTGTGAACGATCCAAGGTTCTGGGCTCTAGTGGACAAGGAAAGAGAGCACCACCTGAGAGGAGAGTGCCAGAGCTGTGTGTACAACATGATGGGAAAAAGAGAAAAGAAACAAGGGGAATTTGGAAAGGCCAAGGGCAGCCGCGCCATCTGGTATATGTGGCTAGGGGCTAGATTTCTAGAGTTCGAAGCCCTTGGATTCTTGAACGAGGATCACTGGATGGGGAGAGAGAACTCAGGAGGTGGTGTTGAAGGGCTGGGATTACAAAGACTCGGATATGTCCTAGAAGAGATGAGTCGTATACCAGGAGGAAGGATGTATGCAGATGACACTGCTGGCTGGGACACCCGCATTAGCAGGTTTGATCTGGAGAATGAAGCTCTAATCACCAACCAAATGGAGAAAGGGCACAGGGCCTTGGCATTGGCCATAATCAAGTACACATACCAAAACAAAGTGGTAAAGGTCCTTAGACCAGCTGAAAAAGGGAAAACAGTTATGGACATTATTTCGAGACAAGACCAAAGGGGGAGCGGACAAGTTGTCACTTACGCTCTTAACACATTTACCAACCTAGTGGTGCAACTCATTCGGAATATGGAGGCTGAGGAAGTTCTAGAGATGCAAGACTTGTGGCTGCTGCGGAGGTCAGAGAAAGTGACCAACTGGTTGCAGAGCAACGGATGGGATAGGCTCAAACGAATGGCAGTCAGTGGAGATGATTGCGTTGTGAAGCCAATTGATGATAGGTTTGCACATGCCCTCAGGTTCTTGAATGATATGGGAAAAGTTAGGAAGGACACACAAGAGTGGAAACCCTCAACTGGATGGGACAACTGGGAAGAAGTTCCGTTTTGCTCCCACCACTTCAACAAGCTCCATCTCAAGGACGGGAGGTCCATTGTGGTTCCCTGCCGCCACCAAGATGAACTGATTGGCCGGGCCCGCGTCTCTCCAGGGGCGGGATGGAGCATCCGGGAGACTGCTTGCCTAGCAAAATCATATGCGCAAATGTGGCAGCTCCTTTATTTCCACAGAAGGGACCTCCGACTGATGGCCAATGCCATTTGTTCATCTGTGCCAGTTGACTGGGTTCCAACTGGGAGAACTACCTGGTCAATCCATGGAAAGGGAGAATGGATGACCACTGAAGACATGCTTGTGGTGTGGAACAGAGTGTGGATTGAGGAGAACGACCACATGGAAGACAAGACCCCAGTTACGAAATGGACAGACATTCCCTATTTGGGAAAAAGGGAAGACTTGTGGTGTGGATCTCTCATAGGGCACAGACCGCGCACCACCTGGGCTGAGAACATTAAAAACACAGTCAACATGGTGCGCAGGATCATAGGTGATGAAGAAAAGTACATGGACTACCTATCCACCCAAGTTCGCTACTTGGGTGAAGAAGGGTCTACACCTGGAGTGCTGTAAGCACCAATCTTAATGTTGTCAGGCCTGCTAGTCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n' |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/db/PRV.fa.amb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/db/PRV.fa.amb Mon Mar 30 06:37:01 2020 -0400 |
| b |
| @@ -0,0 +1,5 @@ +10807 1 4 +0 49 N +3147 1 Y +6597 48 N +10413 394 N |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/db/PRV.fa.ann --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/db/PRV.fa.ann Mon Mar 30 06:37:01 2020 -0400 |
| b |
| @@ -0,0 +1,3 @@ +10807 1 11 +0 PRV (null) +0 10807 4 |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/db/PRV.fa.bwt |
| b |
| Binary file test-data/zika/db/PRV.fa.bwt has changed |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/db/PRV.fa.fai --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/db/PRV.fa.fai Mon Mar 30 06:37:01 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +PRV 10807 5 10807 10808 |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/db/PRV.fa.pac |
| b |
| Binary file test-data/zika/db/PRV.fa.pac has changed |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/db/PRV.fa.sa |
| b |
| Binary file test-data/zika/db/PRV.fa.sa has changed |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/db/Z52.consensus.amb --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/db/Z52.consensus.amb Mon Mar 30 06:37:01 2020 -0400 |
| b |
| @@ -0,0 +1,2 @@ +10139 1 1 +6345 48 - |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/db/Z52.consensus.ann --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/db/Z52.consensus.ann Mon Mar 30 06:37:01 2020 -0400 |
| b |
| @@ -0,0 +1,3 @@ +10139 1 11 +0 Consensus_Z52.consensus_threshold_0_quality_20 (null) +0 10139 1 |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/db/Z52.consensus.bwt |
| b |
| Binary file test-data/zika/db/Z52.consensus.bwt has changed |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/db/Z52.consensus.pac |
| b |
| Binary file test-data/zika/db/Z52.consensus.pac has changed |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/db/Z52.consensus.sa |
| b |
| Binary file test-data/zika/db/Z52.consensus.sa has changed |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/db/pair_information.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/db/pair_information.tsv Mon Mar 30 06:37:01 2020 -0400 |
| b |
| @@ -0,0 +1,35 @@ +400_1_out_L 400_1_out_R +400_2_out_L 400_2_out_R +400_3_out_L* 400_3_out_R* +400_4_out_L 400_4_out_R +400_5_out_L 400_5_out_R +400_6_out_L 400_6_out_R +400_7_out_L 400_7_out_R +400_8_out_L* 400_8_out_R* +400_9_out_L* 400_9_out_R* +400_10_out_L 400_10_out_R +400_11_out_L 400_11_out_R +400_12_out_L 400_12_out_R +400_13_out_L 400_13_out_R +400_14_out_L* 400_14_out_R* +400_15_out_L 400_15_out_R +400_16_out_L* 400_16_out_R* +400_17_out_L** 400_17_out_R** +400_18_out_L** 400_18_out_R** +400_19_out_L 400_19_out_R +400_20_out_L* 400_20_out_R* +400_21_out_L* 400_21_out_R* +400_22_out_L** 400_22_out_R** +400_23_out_L 400_23_out_R +400_24_out_L** 400_24_out_R** +400_25_out_L** 400_25_out_R** +400_26_out_L 400_26_out_R +400_27_out_L 400_27_out_R +400_28_out_L 400_28_out_R +400_29_out_L 400_29_out_R +400_30_out_L 400_30_out_R +400_31_out_L 400_31_out_R +400_32_out_L 400_32_out_R +400_33_out_L* 400_33_out_R* +400_34_out_L* 400_34_out_R* +400_35_out_L 400_35_out_R |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/db/zika_primers.bam |
| b |
| Binary file test-data/zika/db/zika_primers.bam has changed |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/db/zika_primers.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/db/zika_primers.bed Mon Mar 30 06:37:01 2020 -0400 |
| b |
| @@ -0,0 +1,68 @@ +PRV 482 504 400_1_out_R 60 - +PRV 359 381 400_2_out_L 60 + +PRV 796 818 400_2_out_R 60 - +PRV 658 680 400_3_out_L* 60 + +PRV 1054 1076 400_3_out_R* 60 - +PRV 978 1000 400_4_out_L 60 + +PRV 1393 1415 400_4_out_R 60 - +PRV 1256 1278 400_5_out_L 60 + +PRV 1701 1723 400_5_out_R 60 - +PRV 1539 1561 400_6_out_L 60 + +PRV 1965 1987 400_6_out_R 60 - +PRV 1875 1897 400_7_out_L 60 + +PRV 2264 2286 400_7_out_R 60 - +PRV 2151 2173 400_8_out_L* 60 + +PRV 2607 2629 400_8_out_R* 60 - +PRV 2444 2466 400_9_out_L* 60 + +PRV 2902 2924 400_9_out_R* 60 - +PRV 2747 2769 400_10_out_L 60 + +PRV 3154 3176 400_10_out_R 60 - +PRV 3030 3052 400_11_out_L 60 + +PRV 3481 3503 400_11_out_R 60 - +PRV 3334 3356 400_12_out_L 60 + +PRV 3763 3785 400_12_out_R 60 - +PRV 3657 3679 400_13_out_L 60 + +PRV 4077 4099 400_13_out_R 60 - +PRV 3931 3953 400_14_out_L* 60 + +PRV 4388 4410 400_14_out_R* 60 - +PRV 4231 4253 400_15_out_L 60 + +PRV 4659 4681 400_15_out_R 60 - +PRV 4542 4564 400_16_out_L* 60 + +PRV 4965 4987 400_16_out_R* 60 - +PRV 4851 4873 400_17_out_L** 60 + +PRV 5304 5326 400_17_out_R** 60 - +PRV 5136 5158 400_18_out_L** 60 + +PRV 5587 5609 400_18_out_R** 60 - +PRV 5461 5483 400_19_out_L 60 + +PRV 5902 5924 400_19_out_R 60 - +PRV 5746 5768 400_20_out_L* 60 + +PRV 6178 6200 400_20_out_R* 60 - +PRV 6046 6068 400_21_out_L* 60 + +PRV 6458 6480 400_21_out_R* 60 - +PRV 6353 6375 400_22_out_L** 60 + +PRV 6756 6778 400_22_out_R** 60 - +PRV 6673 6695 400_23_out_L 60 + +PRV 7073 7095 400_23_out_R 60 - +PRV 6960 6982 400_24_out_L** 60 + +PRV 7394 7416 400_24_out_R** 60 - +PRV 7230 7252 400_25_out_L** 60 + +PRV 7685 7707 400_25_out_R** 60 - +PRV 7554 7576 400_26_out_L 60 + +PRV 7972 7994 400_26_out_R 60 - +PRV 7841 7863 400_27_out_L 60 + +PRV 8296 8318 400_27_out_R 60 - +PRV 8167 8189 400_28_out_L 60 + +PRV 8582 8604 400_28_out_R 60 - +PRV 8430 8452 400_29_out_L 60 + +PRV 8873 8895 400_29_out_R 60 - +PRV 8740 8762 400_30_out_L 60 + +PRV 9184 9206 400_30_out_R 60 - +PRV 9052 9074 400_31_out_L 60 + +PRV 9473 9495 400_31_out_R 60 - +PRV 9336 9358 400_32_out_L 30 + +PRV 9755 9777 400_32_out_R 60 - +PRV 9637 9659 400_33_out_L* 60 + +PRV 10104 10126 400_33_out_R* 60 - +PRV 9969 9991 400_34_out_L* 60 + +PRV 10391 10413 400_34_out_R* 60 - +PRV 10241 10263 400_35_out_L 60 + |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/db/zika_primers.fa --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/db/zika_primers.fa Mon Mar 30 06:37:01 2020 -0400 |
| b |
| @@ -0,0 +1,140 @@ +>400_1_out_L +GACAGTTCGAGTTTGAAGCGAAAG +>400_1_out_R +AGTATGCACTCCCACGTCTAGT +>400_2_out_L +AAGAAAGATCTGGCTGCCATGC +>400_2_out_R +TGATTCCAACCAGGTTTGCGAC +>400_3_out_L* +AGATGACGTCGATTGTTGGTGC +>400_3_out_R* +TACGGTGACACAACCTCCATGT +>400_4_out_L +TCAGGTGCATAGGAGTCAGCAA +>400_4_out_R +GGAGCCATGAACTGACAGCATT +>400_5_out_L +AGAACGTTAGTGGACAGAGGCT +>400_5_out_R +TGTGCGTCCTTGAACTCTACCA +>400_6_out_L +TTGATTGTGAACCGAGGACAGG +>400_6_out_R +CCATCTGTCCCTGCGTACTGTA +>400_7_out_L +TGAAGGGCGTGTCATACTCCTT +>400_7_out_R +CGCCTCCAACTGATCCAAAGTC +>400_8_out_L* +GGGAGAAGAAGATCACCCACCA +>400_8_out_R* +TTGACTGCTGCTGCCAATCTAC +>400_9_out_L* +GCCTTAGGGGGAGTGTTGATCT +>400_9_out_R* +GAGTGGGCATTCCTTCAGTGTG +>400_10_out_L +ACGGTCGTTGTGGGATCTGTAA +>400_10_out_R +GTGGGACTTTGGCCATTCACAT +>400_11_out_L +CAGCCGTTATTGGAACAGCTGT +>400_11_out_R +CCTGGGCCTTATCTCCATTCCA +>400_12_out_L +CACTAAGGTCCACGTGGAGGAA +>400_12_out_R +TATCAGCGCCAGATGAGCTACA +>400_13_out_L +TGGCAGTGCTGGTAGCTATGAT +>400_13_out_R +AGAGAGAGGAGCATAAACCCCC +>400_14_out_L* +CAATGGTTTTGCTTTGGCCTGG +>400_14_out_R* +TTTCCCATGTGATGTCACCTGC +>400_15_out_L +CCCTAGCGAAGTACTCACAGCT +>400_15_out_R +TACACTCCATCTGTGGTCTCCC +>400_16_out_L* +GTGGCATGAACCCAATAGCCAT +>400_16_out_R* +GCTCCAATGTCCCCATCCTTTG +>400_17_out_L** +GTGGTCCATGGAAGCTAGATGC +>400_17_out_R** +CCTCTAAGGGCCTCCTCCATTT +>400_18_out_L** +CTGTTGAGTGCTTCGAGCCTTC +>400_18_out_R** +TGGTGAGTTGGAGTCCGGAAAT +>400_19_out_L +TATGGATGAGGCCCACTTCACA +>400_19_out_R +GCCATCAAGTATGACCGGCTTT +>400_20_out_L* +GGCTGGAAAACGGGTCATACAG +>400_20_out_R* +CCTTTGCTCCGTCCTAAGCTTG +>400_21_out_L* +AGAGACTGACGAAGACCATGCA +>400_21_out_R* +CTCCAAAAGCCGCTCCTCTTTT +>400_22_out_L** +TGGACCAGACACGGAGAGAAAA +>400_22_out_R** +ATTCTGGCTGGCTCAATTTCCG +>400_23_out_L +CGTCTTGATGAGGAACAAGGGC +>400_23_out_R +AAGTGGTCACTGCATGTTGGAC +>400_24_out_L** +TAATGGGAAGGAGAGAGGAGGG +>400_24_out_R** +TCTCCACTTGGGGGTCAATTGT +>400_25_out_L** +CCCTGACCCTAATAGTGGCCAT +>400_25_out_R** +CCTTCCATTTCTCTCCCAGGGT +>400_26_out_L +ACTGGAACTCCTCTACAGCCAC +>400_26_out_R +ACCAGGGCCTCCTTTTGTGTAT +>400_27_out_L +AGTGCAAAGCTGAGATGGTTGG +>400_27_out_R +ATGTGTAGAGTTGCGGGAGAGT +>400_28_out_L +GGTGGGGGATTGGCTTGAAAAA +>400_28_out_R +GGGCCTCATAGCTTCCATGGTA +>400_29_out_L +AGGATGTGAATCTCGGCTCTGG +>400_29_out_R +ATGCTGCATTGCTACGAACCTT +>400_30_out_L +AAAAGTGGACACTAGGGTGCCA +>400_30_out_R +TAATCCCAGCCCTTCAACACCA +>400_31_out_L +ACAAGGGGAATTTGGAAAGGCC +>400_31_out_R +CGTAAGTGACAACTTGTCCGCT +>400_32_out_L +AAATGGAAAAAGGGCACAGGGC +>400_32_out_R +TGTCCCATCCAGTTGAGGGTTT +>400_33_out_L* +CAAACGAATGGCAGTCAGTGGA +>400_33_out_R* +ATCCACACTCTGTTCCACACCA +>400_34_out_L* +ATTTCCACAGAAGGGACCTCCG +>400_34_out_R* +TGACTAGCAGGCCTGACAACAT +>400_35_out_L +ACCACCTGGGCTGAGAACATTA +>400_35_out_R +ACCACTAGTCCCTCTTCTGGAG |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/db/zika_primers_consensus.bam |
| b |
| Binary file test-data/zika/db/zika_primers_consensus.bam has changed |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/db/zika_primers_consensus.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/db/zika_primers_consensus.bed Mon Mar 30 06:37:01 2020 -0400 |
| b |
| @@ -0,0 +1,67 @@ +Consensus_Z52.consensus_threshold_0_quality_20 107 129 400_2_out_L 60 + +Consensus_Z52.consensus_threshold_0_quality_20 230 252 400_1_out_R 60 - +Consensus_Z52.consensus_threshold_0_quality_20 406 428 400_3_out_L* 60 + +Consensus_Z52.consensus_threshold_0_quality_20 544 566 400_2_out_R 60 - +Consensus_Z52.consensus_threshold_0_quality_20 726 748 400_4_out_L 60 + +Consensus_Z52.consensus_threshold_0_quality_20 802 824 400_3_out_R* 60 - +Consensus_Z52.consensus_threshold_0_quality_20 1004 1026 400_5_out_L 60 + +Consensus_Z52.consensus_threshold_0_quality_20 1141 1163 400_4_out_R 60 - +Consensus_Z52.consensus_threshold_0_quality_20 1287 1309 400_6_out_L 60 + +Consensus_Z52.consensus_threshold_0_quality_20 1449 1471 400_5_out_R 60 - +Consensus_Z52.consensus_threshold_0_quality_20 1623 1645 400_7_out_L 60 + +Consensus_Z52.consensus_threshold_0_quality_20 1713 1735 400_6_out_R 60 - +Consensus_Z52.consensus_threshold_0_quality_20 1899 1921 400_8_out_L* 60 + +Consensus_Z52.consensus_threshold_0_quality_20 2012 2034 400_7_out_R 60 - 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+Consensus_Z52.consensus_threshold_0_quality_20 6421 6443 400_23_out_L 60 + +Consensus_Z52.consensus_threshold_0_quality_20 6504 6526 400_22_out_R** 60 - +Consensus_Z52.consensus_threshold_0_quality_20 6708 6730 400_24_out_L** 60 + +Consensus_Z52.consensus_threshold_0_quality_20 6821 6843 400_23_out_R 60 - +Consensus_Z52.consensus_threshold_0_quality_20 6978 7000 400_25_out_L** 60 + +Consensus_Z52.consensus_threshold_0_quality_20 7142 7164 400_24_out_R** 60 - +Consensus_Z52.consensus_threshold_0_quality_20 7302 7324 400_26_out_L 60 + +Consensus_Z52.consensus_threshold_0_quality_20 7433 7455 400_25_out_R** 60 - +Consensus_Z52.consensus_threshold_0_quality_20 7589 7611 400_27_out_L 60 + +Consensus_Z52.consensus_threshold_0_quality_20 7720 7742 400_26_out_R 60 - +Consensus_Z52.consensus_threshold_0_quality_20 7915 7937 400_28_out_L 60 + +Consensus_Z52.consensus_threshold_0_quality_20 8044 8066 400_27_out_R 60 - +Consensus_Z52.consensus_threshold_0_quality_20 8178 8200 400_29_out_L 60 + +Consensus_Z52.consensus_threshold_0_quality_20 8330 8352 400_28_out_R 60 - +Consensus_Z52.consensus_threshold_0_quality_20 8488 8510 400_30_out_L 60 + +Consensus_Z52.consensus_threshold_0_quality_20 8621 8643 400_29_out_R 60 - +Consensus_Z52.consensus_threshold_0_quality_20 8800 8822 400_31_out_L 60 + +Consensus_Z52.consensus_threshold_0_quality_20 8932 8954 400_30_out_R 60 - +Consensus_Z52.consensus_threshold_0_quality_20 9084 9106 400_32_out_L 30 + +Consensus_Z52.consensus_threshold_0_quality_20 9221 9243 400_31_out_R 60 - +Consensus_Z52.consensus_threshold_0_quality_20 9385 9407 400_33_out_L* 60 + +Consensus_Z52.consensus_threshold_0_quality_20 9503 9525 400_32_out_R 60 - +Consensus_Z52.consensus_threshold_0_quality_20 9717 9739 400_34_out_L* 60 + +Consensus_Z52.consensus_threshold_0_quality_20 9852 9874 400_33_out_R* 60 - +Consensus_Z52.consensus_threshold_0_quality_20 9989 10011 400_35_out_L 60 + |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/primer_mismatchers_indices.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/primer_mismatchers_indices.txt Mon Mar 30 06:37:01 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +400_18_out_L** 400_18_out_R** 400_23_out_R 400_23_out_L 400_32_out_L 400_32_out_R \ No newline at end of file |
| b |
| diff -r 000000000000 -r f362150bef41 test-data/zika/primers_Z52_consensus.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/primers_Z52_consensus.tsv Mon Mar 30 06:37:01 2020 -0400 |
| b |
| @@ -0,0 +1,4 @@ +REGION POS REF ALT REF_DP REF_RV REF_QUAL ALT_DP ALT_RV ALT_QUAL ALT_FREQ TOTAL_DP PVAL PASS +Consensus_Z52.consensus_threshold_0_quality_20 4904 C T 0 0 0 1 0 93 1 1 1 FALSE +Consensus_Z52.consensus_threshold_0_quality_20 6842 C T 0 0 0 1 1 93 1 1 1 FALSE +Consensus_Z52.consensus_threshold_0_quality_20 9092 G A 0 0 0 1 0 93 1 1 1 FALSE |