| Next changeset 1:c5c9f02b6167 (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_variants.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 12d66d0d05ac ivar_variants.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ivar_variants.xml Mon Mar 30 07:45:57 2020 -0400 |
| [ |
| @@ -0,0 +1,48 @@ +<tool id="ivar_variants" name="ivar variants" version="@VERSION@+galaxy0"> + <description>Call variants from aligned BAM file</description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="requirements" /> + <expand macro="version_command" /> + <command detect_errors="exit_code"><![CDATA[ + ln -s '$ref' ref.fa && + ln -s '$input_bam' sorted.bam && + samtools mpileup -A -d 0 --reference ref.fa -B -Q 0 sorted.bam | ivar variants + -p variants + -q $min_qual + -t $min_freq + ]]> </command> + <inputs> + <param name="input_bam" type="data" format="bam" label="Bam file" help="Aligned reads, to trim primers and quality"/> + <param name="ref" type="data" format="fasta" label="Reference"/> + <param name="min_qual" argument="-q" type="integer" min="1" value="20" label="Minimum quality score threshold to count base"/> + <param name="min_freq" argument="-t" type="float" min="0" max="1" value="0.03" label="Minimum frequency threshold"/> + </inputs> + <outputs> + <data name="output_variants" format="tabular" label="${tool.name} on ${on_string}" from_work_dir="variants.tsv"/> + </outputs> + <tests> + <test> + <param name="input_bam" value="zika/Z52_a.masked.sorted.bam" /> + <param name="ref" value="zika/db/PRV.fa" /> + <output name="output_variants" file="zika/Z52_a.tsv" lines_diff="10"/> + </test> + </tests> + <help><![CDATA[ + iVar uses the output of the samtools mpileup command to call variants - + single nucleotide variants(SNVs) and indels. In order to call variants + correctly, the reference file used for alignment must be passed to iVar + using the -r flag. The output of samtools pileup is piped into ivar variants + to generate a .tsv file with the variants. There are two parameters that can + be set for variant calling using iVar - minimum quality(Default: 20) and + minimum frequency(Default: 0.03). Minimum quality is the minimum quality for + a base to be counted towards the ungapped depth to canculate iSNV frequency + at a given position. For insertions, the quality metric is discarded and the + mpileup depth is used directly. Minimum frequency is the minimum frequency + required for a SNV or indel to be reported. + + Documentation can be found at `<https://andersen-lab.github.io/ivar/html/manualpage.html>`_. + ]]> </help> + <expand macro="citations" /> +</tool> |
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| diff -r 000000000000 -r 12d66d0d05ac macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/macros.xml Mon Mar 30 07:45:57 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 12d66d0d05ac 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 07:45:57 2020 -0400 |
| b |
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| b |
| diff -r 000000000000 -r 12d66d0d05ac 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 07:45:57 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 12d66d0d05ac 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 07:45:57 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +29903 1 0 |
| b |
| diff -r 000000000000 -r 12d66d0d05ac 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 07:45:57 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 12d66d0d05ac test-data/covid19/NC_045512.fa.bwt |
| b |
| Binary file test-data/covid19/NC_045512.fa.bwt has changed |
| b |
| diff -r 000000000000 -r 12d66d0d05ac 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 07:45:57 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +NC_045512.2 29903 97 70 71 |
| b |
| diff -r 000000000000 -r 12d66d0d05ac test-data/covid19/NC_045512.fa.pac |
| b |
| Binary file test-data/covid19/NC_045512.fa.pac has changed |
| b |
| diff -r 000000000000 -r 12d66d0d05ac test-data/covid19/NC_045512.fa.sa |
| b |
| Binary file test-data/covid19/NC_045512.fa.sa has changed |
| b |
| diff -r 000000000000 -r 12d66d0d05ac 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 07:45:57 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 12d66d0d05ac 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 07:45:57 2020 -0400 |
| [ |
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| diff -r 000000000000 -r 12d66d0d05ac 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 12d66d0d05ac 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 12d66d0d05ac 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 12d66d0d05ac 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 12d66d0d05ac test-data/covid19/PC00101P_sub.trimmed.sorted.bam.bai |
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| Binary file test-data/covid19/PC00101P_sub.trimmed.sorted.bam.bai has changed |
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| diff -r 000000000000 -r 12d66d0d05ac 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 07:45:57 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 12d66d0d05ac 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 07:45:57 2020 -0400 |
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|
| b |
| diff -r 000000000000 -r 12d66d0d05ac 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 07:45:57 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 12d66d0d05ac test-data/covid19/zika_primers.bam |
| b |
| Binary file test-data/covid19/zika_primers.bam has changed |
| b |
| diff -r 000000000000 -r 12d66d0d05ac 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 07:45:57 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 12d66d0d05ac 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 07:45:57 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 12d66d0d05ac test-data/covid19/zika_primers_consensus.bam |
| b |
| Binary file test-data/covid19/zika_primers_consensus.bam has changed |
| b |
| diff -r 000000000000 -r 12d66d0d05ac 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 07:45:57 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 12d66d0d05ac 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 07:45:57 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +Consensus_Z52.consensus_threshold_0_quality_20 10139 48 10139 10140 |
| b |
| diff -r 000000000000 -r 12d66d0d05ac 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 07:45:57 2020 -0400 |
| [ |
| b'@@ -0,0 +1,1 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| b |
| diff -r 000000000000 -r 12d66d0d05ac 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 07:45:57 2020 -0400 |
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| diff -r 000000000000 -r 12d66d0d05ac 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 12d66d0d05ac 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 07:45:57 2020 -0400 |
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| diff -r 000000000000 -r 12d66d0d05ac 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 07:45:57 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 12d66d0d05ac test-data/zika/Z52.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/zika/Z52.tsv Mon Mar 30 07:45:57 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 12d66d0d05ac 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 12d66d0d05ac 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 12d66d0d05ac 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 12d66d0d05ac 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 12d66d0d05ac 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 12d66d0d05ac 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 12d66d0d05ac 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 12d66d0d05ac 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 07:45:57 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 12d66d0d05ac test-data/zika/Z52_b.masked.bam |
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| Binary file test-data/zika/Z52_b.masked.bam has changed |
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| diff -r 000000000000 -r 12d66d0d05ac 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 12d66d0d05ac 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 12d66d0d05ac 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 12d66d0d05ac 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 12d66d0d05ac 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 12d66d0d05ac 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 12d66d0d05ac 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 07:45:57 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 12d66d0d05ac 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 07:45:57 2020 -0400 |
| b |
| b'@@ -0,0 +1,2 @@\n+>PRV\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAGCTAGCAACAGTATCAACAGGTTTTATTTTGGATTTGGAAACGAGAGTTTCTGGTCATGAAAAACCCAAAAAAGAAATCCGGAGGATTCCGGATTGTCAATATGCTAAAACGCGGAGTAGCCCGTGTGAGCCCCTTTGGGGGCTTGAAGAGGCTGCCAGCCGGACTTCTGCTGGGTCATGGGCCCATCAGGATGGTCTTGGCGATTCTAGCCTTTTTGAGATTCACGGCAATCAAGCCATCACTGGGTCTCATCAATAGATGGGGTTCAGTGGGGAAAAAAGAGGCTATGGAAACAATAAAGAAGTTCAAGAAAGATCTGGCTGCCATGCTGAGAATAATCAATGCTAGGAAGGAGAAGAAGAGACGAGGCGCAGATACTAGTGTCGGAATTGTTGGCCTCCTGCTGACCACAGCTATGGCAGCGGAGGTCACTAGACGTGGGAGTGCATACTATATGTACTTGGACAGAAACGATGCTGGGGAGGCCATATCTTTTCCAACCACATTGGGGATGAATAAGTGTTATATACAGATCATGGATCTTGGACACATGTGTGATGCCACCATGAGCTATGAATGCCCTATGCTGGATGAGGGGGTGGAACCAGATGACGTCGATTGTTGGTGCAACACGACGTCAACTTGGGTTGTGTACGGAACCTGCCATCACAAAAAAGGTGAAGCACGGAGATCTAGAAGAGCTGTGACGCTCCCCTCCCATTCCACCAGGAAGCTGCAAACGCGGTCGCAAACCTGGTTGGAATCAAGAGAATACACAAAGCACTTGATTAGAGTCGAAAATTGGATATTCAGGAACCCTGGCTTCGCGTTAGCAGCAGCTGCCATCGCTTGGCTTTTGGGAAGCTCAACGAGCCAAAAAGTCATATACTTGGTCATGATACTGCTGATTGCCCCGGCATACAGCATCAGGTGCATAGGAGTCAGCAATAGGGACTTTGTGGAAGGTATGTCAGGTGGGACTTGGGTTGATGTTGTCTTGGAACATGGAGGTTGTGTCACCGTAATGGCACAGGACAAACCGACTGTCGACATAGAGCTGGTTACAACAACAGTCAGCAACATGGCGGAGGTAAGATCCTACTGCTATGAGGCATCAATATCAGACATGGCTTCTGACAGCCGCTGCCCAACACAAGGTGAAGCCTACCTTGACAAGCAATCAGACACTCAATATGTCTGCAAAAGAACGTTAGTGGACAGAGGCTGGGGAAATGGATGTGGACTTTTTGGCAAAGGGAGCCTGGTGACATGCGCTAAGTTTGCATGCTCCAAGAAAATGACCGGGAAGAGCATCCAGCCAGAGAATCTGGAGTACCGGATAATGCTGTCAGTTCATGGCTCCCAGCACAGTGGGATGATCGTTAATGACACAGGACATGAAACTGATGAGAATAGAGCGAAAGTTGAGATAACGCCCAATTCACCGAGAGCCGAAGCCACCCTGGGGGGTTTTGGAAGCCTAGGACTTGATTGTGAACCGAGGACAGGCCTTGACTTTTCAGATTTGTATTACTTGACTATGAATAACAAGCACTGGTTGGTTCACAAGGAGTGGTTCCACGACATTCCATTACCTTGGCACGCTGGGGCAGACACCGGAACTCCACACTGGAACAACAAAGAAGCACTGGTAGAGTTCAAGGACGCACATGCCAAAAGGCAAACTGTCGTGGTTCTAGGGAGTCAAGAAGGAGCAGTTCACACGGCCCTTGCTGGAGCTCTGGAGGCTGAGATGGATGGTGCAAAGGGAAGGCTGTCCTCTGGCCACTTGAAATGTCGCCTGAAAATGGATAAACTTAGATTGAAGGGCGTGTCATACTCCTTGTGTACTGCAGCGTTCACATTCACCAAGATCCCGGCTGAAACACTGCACGGGACAGTCACAGTGGAGTTACAGTACGCAGGGACAGATGGACCTTGCAAGGTTCCAGCTCAGATGGCGGTGGACATGCAAACTCTGACCCCAGTTGGGAGGTTGATAACCGCTAACCCCGTAATCACTGAAAGCACTGAGAACTCTAAGATGATGCTGGAACTTGATCCACCATTTGGGGACTCTTACATTGTCATAGGAGTCGGGGAGAAGAAGATCACCCACCACTGGCACAGGAGTGGCAGCACCATTGGAAAAGCATTTGAAGCCACTGTGAGAGGTGCCAAGAGAATGGCAGTCTTGGGAGACACAGCCTGGGACTTTGGATCAGTTGGAGGCGCTCTCAACTCATTGGGCAAGGGCATCCATCAAATTTTTGGAGCAGCTTTCAAATCATTGTTTGGAGGAATGTCCTGGTTCTCACAAATTCTCATTGGAACGTTGCTGATGTGGTTGGGTCTGAACACAAAGAATGGATCTATTTCCCTTATGTGCTTGGCCTTAGGGGGAGTGTTGATCTTCTTATCCACAGCCGTCTCTGCTGATGTGGGGTGCTCGGTGGACTTCTCAAAGAAGGAGACGAGATGCGGTACAGGGGTGTTCGTCTATAACGACGTTGAAGCCTGGAGGGACAGGTACAAGTACCATCCTGACTCCCCCCGTAGATTGGCAGCAGCAGTCAAGCAAGCCTGGGAAGATGGTATCTGCGGGATCTCCTCTGTTTCAAGAATGGAAAACATCATGTGGAGATCAGTAGAAGGGGAGCTCAACGCAATCCTGGAAGAGAATGGAGTTCAACTGACGGTCGTTGTGGGATCTGTAAAAAACCCCATGTGGAGAGGTCCACAGAGATTGCCCGTGCCTGTGAACGAGCTGCCCCACGGCTGGAAGGCTTGGGGGAAATCGTATTTCGTCAGAGCAGCAAAGACAAATAACAGCTTTGTCGTGGATGGTGACACACTGAAGGAATGCCCACTCAAACATAGAGCATGGAACAGCTTTCTTGTGGAGGATCATGGGTTCGGGGTATTTCACACTAGTGTCTGGCTCAAGGTTAGAGAAGATTATTCATTAGAGTGTGATCCAGCCGTTATTGGAACAGCTGTTAAGGGAAAGGAGGCTGTACACAGTGATCTAGGCTACTGGATTGAGAGTGAGAAGAATGACACATGGAGGCTGAAGAGGGCCCATCTGATCGAGAYGAAAACATGTGAATGGCCAAAGTCCCACACATTGTGGACAGATGGAATAGAAGAGAGTGATCTGATCATACCCAAGTCTTTAGCTGGGCCACTCAGCCATCACAATACCAGAGAGGGCTACAGGACCCAAATGAAAGGGCCATGGCACAGTGAAGAGCTTGAAATTCGGTTTGAGGAATGCCCAGGCACTAAGGTCCACGTGGAGGAAACATGTGGAACAAGAGGACCATCTCTGAGATCAACCACTGCAAGCGGAAGGGTGATCGAGGAATGGTGCTGCAGGGAGTGCACAATGCCCCCACTGTCGTTCCGGGCTAAAGATGGCTGTTGGTATGGAATGGAGATAAGGCCCAGGAAAGAACCAGAAAGCAACTTAGTAAGGTCAATGGTGACTGCAGGATCAACTGATCACATGGACCACTTCTCCCTTGGAGTGCTTGTGATCCTGCTCATGGTGCAGGAAGGGCTGAAGAAGAGAATGACCACAAAGATCATCATAAGCACATCAATGGCAGTGCTGGTAGCTATGATCCTGGGAGGATTTTCAATGAGTGACCTGGCTAAGCTTGCAATTTTGATGGGTGCCACCTTCGCGGAAATGAACACTGGAGGAGATGTAGCTCATCTGGCGCTGATAGCGGCATTCAAAGTCAGACCAGCGTTGCTGGTATCTTTCATCTTCAGAGCTAATTGGACACCCCGTGAAAGCATGCTGCTGGCCTTGGCCTCGTGTCTTTTGCAAACTGCGATCTCCGCCTTGGAAGGCGACCTGATGGTTCTCATCAATGGTTTTGCTTTGGCCTGGTTGGCAATACGAGCGATGGTTGT'..b'CTGGTGGTGCTCATACCTGAGCCAGAAAAGCAAAGATCTCCCCAGGACAACCAAATGGCAATCATCATCATGGTAGCAGTAGGTCTTCTGGGCTTGATTACCGCCAATGAACTCGGATGGTTGGAGAGAACAAAGAGTGACCTAAGCCATCTAATGGGAAGGAGAGAGGAGGGGGCAACCATAGGATTCTCAATGGACATTGACCTGCGGCCAGCCTCAGCTTGGGCCATCTATGCTGCCTTGACAACTTTCATTACCCCAGCCGTCCAACATGCAGTGACCACCTCATACAACAACTACTCCTTAATGGCGATGGCCACGCAAGCTGGAGTGTTGTTTGGCATGGGCAAAGGGATGCCATTCTACGCATGGGACTTTGGAGTCCCGCTGCTAATGATAGGTTGCTACTCACAATTAACACCCCTGACCCTAATAGTGGCCATCATTTTGCTCGTGGCGCACTACATGTACTTGATCCCAGGGCTGCAGGCAGCAGCTGCGCGTGCTGCCCAGAAGAGAACGGCAGCTGGCATCATGAAGAACCCTGTTGTGGATGGAATAGTGGTGACTGACATTGACACAATGACAATTGACCCCCAAGTGGAGAAAAAGATGGGACAGGTGCTACTCATAGCAGTAGCCGTCTCCAGCGCCATACTGTCGCGGACCGCCTGGGGGTGGGGGGAGGCTGGGGCTCTGATCACAGCCGCAACTTCCACTTTGTGGGAAGGCTCTCCGAACAAGTACTGGAACTCCTCTACAGCCACTTCACTGTGTAACATTTTTAGGGGAAGTTACTTGGCTGGAGCTTCTCTAATCTACACAGTAACAAGAAACGCTGGCTTGGTCAAGAGACGTGGGGGTGGAACAGGAGAGACCCTGGGAGAGAAATGGAAGGCCCGCTTGAACCAGATGTCGGCCCTGGAGTTCTACTCCTACAAAAAGTCAGGCATCACCGAGGTGTGCAGAGAAGAGGCCCGCCGCGCCCTCAAGGACGGTGTGGCAACGGGAGGCCATGCTGTGTCCCGAGGAAGTGCAAAGCTGAGATGGTTGGTGGAGCGGGGATACCTGCAGCCCTATGGAAAGGTCATTGATCTTGGATGTGGCAGAGGGGGCTGGAGTTACTACGTCGCCACCATCCGCAAAGTTCAAGAAGTGAAAGGATACACAAAAGGAGGCCCTGGTCATGAAGAACCCGTGTTGGTGCAAAGCTATGGGTGGAACATAGTCCGTCTTAAGAGTGGGGTGGACGTCTTTCATATGGCGGCTGAGCCGTGTGACACGTTGCTGTGTGACATAGGTGAGTCATCATCTAGTCCTGAAGTGGAAGAAGCACGGACGCTCAGAGTCCTCTCCATGGTGGGGGATTGGCTTGAAAAAAGACCAGGAGCCTTTTGTATAAAAGTGTTGTGCCCATACACCAGCACTATGATGGAAACCCTGGAGCGACTGCAGCGTAGGTATGGGGGAGGACTGGTCAGAGTGCCACTCTCCCGCAACTCTACACATGAGATGTACTGGGTCTCTGGAGCGAAAAGCAACACCATAAAAAGTGTGTCCACCACGAGCCAGCTCCTCTTGGGGCGCATGGACGGGCCTAGGAGGCCAGTGAAATATGAGGAGGATGTGAATCTCGGCTCTGGCACGCGGGCTGTGGTAAGCTGCGCTGAAGCTCCCAACATGAAGATCATTGGTAACCGCATTGAAAGGATCCGCAGTGAGCACGCGGAAACGTGGTTCTTTGACGAGAACCACCCATATAGGACATGGGCTTACCATGGAAGCTATGAGGCCCCCACACAAGGGTCAGCGTCCTCTCTAATAAACGGGGTTGTCAGGCTCCTGTCAAAACCCTGGGATGTGGTGACTGGAGTCACAGGAATAGCCATGACCGACACCACACCGTATGGTCAGCAAAGAGTTTTCAAGGAAAAAGTGGACACTAGGGTGCCAGACCCCCAAGAAGGCACTCGTCAGGTTATGAGCATGGTCTCTTCCTGGTTGTGGAAAGAGCTAGGCAAACACAAACGGCCACGAGTCTGCACCAAAGAAGAGTTCATCAACAAGGTTCGTAGCAATGCAGCATTAGGGGCAATATTTGAAGAGGAAAAAGAGTGGAAGACTGCAGTGGAAGCTGTGAACGATCCAAGGTTCTGGGCTCTAGTGGACAAGGAAAGAGAGCACCACCTGAGAGGAGAGTGCCAGAGCTGTGTGTACAACATGATGGGAAAAAGAGAAAAGAAACAAGGGGAATTTGGAAAGGCCAAGGGCAGCCGCGCCATCTGGTATATGTGGCTAGGGGCTAGATTTCTAGAGTTCGAAGCCCTTGGATTCTTGAACGAGGATCACTGGATGGGGAGAGAGAACTCAGGAGGTGGTGTTGAAGGGCTGGGATTACAAAGACTCGGATATGTCCTAGAAGAGATGAGTCGTATACCAGGAGGAAGGATGTATGCAGATGACACTGCTGGCTGGGACACCCGCATTAGCAGGTTTGATCTGGAGAATGAAGCTCTAATCACCAACCAAATGGAGAAAGGGCACAGGGCCTTGGCATTGGCCATAATCAAGTACACATACCAAAACAAAGTGGTAAAGGTCCTTAGACCAGCTGAAAAAGGGAAAACAGTTATGGACATTATTTCGAGACAAGACCAAAGGGGGAGCGGACAAGTTGTCACTTACGCTCTTAACACATTTACCAACCTAGTGGTGCAACTCATTCGGAATATGGAGGCTGAGGAAGTTCTAGAGATGCAAGACTTGTGGCTGCTGCGGAGGTCAGAGAAAGTGACCAACTGGTTGCAGAGCAACGGATGGGATAGGCTCAAACGAATGGCAGTCAGTGGAGATGATTGCGTTGTGAAGCCAATTGATGATAGGTTTGCACATGCCCTCAGGTTCTTGAATGATATGGGAAAAGTTAGGAAGGACACACAAGAGTGGAAACCCTCAACTGGATGGGACAACTGGGAAGAAGTTCCGTTTTGCTCCCACCACTTCAACAAGCTCCATCTCAAGGACGGGAGGTCCATTGTGGTTCCCTGCCGCCACCAAGATGAACTGATTGGCCGGGCCCGCGTCTCTCCAGGGGCGGGATGGAGCATCCGGGAGACTGCTTGCCTAGCAAAATCATATGCGCAAATGTGGCAGCTCCTTTATTTCCACAGAAGGGACCTCCGACTGATGGCCAATGCCATTTGTTCATCTGTGCCAGTTGACTGGGTTCCAACTGGGAGAACTACCTGGTCAATCCATGGAAAGGGAGAATGGATGACCACTGAAGACATGCTTGTGGTGTGGAACAGAGTGTGGATTGAGGAGAACGACCACATGGAAGACAAGACCCCAGTTACGAAATGGACAGACATTCCCTATTTGGGAAAAAGGGAAGACTTGTGGTGTGGATCTCTCATAGGGCACAGACCGCGCACCACCTGGGCTGAGAACATTAAAAACACAGTCAACATGGTGCGCAGGATCATAGGTGATGAAGAAAAGTACATGGACTACCTATCCACCCAAGTTCGCTACTTGGGTGAAGAAGGGTCTACACCTGGAGTGCTGTAAGCACCAATCTTAATGTTGTCAGGCCTGCTAGTCANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n' |
| b |
| diff -r 000000000000 -r 12d66d0d05ac 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 07:45:57 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 12d66d0d05ac 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 07:45:57 2020 -0400 |
| b |
| @@ -0,0 +1,3 @@ +10807 1 11 +0 PRV (null) +0 10807 4 |
| b |
| diff -r 000000000000 -r 12d66d0d05ac test-data/zika/db/PRV.fa.bwt |
| b |
| Binary file test-data/zika/db/PRV.fa.bwt has changed |
| b |
| diff -r 000000000000 -r 12d66d0d05ac 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 07:45:57 2020 -0400 |
| b |
| @@ -0,0 +1,1 @@ +PRV 10807 5 10807 10808 |
| b |
| diff -r 000000000000 -r 12d66d0d05ac test-data/zika/db/PRV.fa.pac |
| b |
| Binary file test-data/zika/db/PRV.fa.pac has changed |
| b |
| diff -r 000000000000 -r 12d66d0d05ac test-data/zika/db/PRV.fa.sa |
| b |
| Binary file test-data/zika/db/PRV.fa.sa has changed |
| b |
| diff -r 000000000000 -r 12d66d0d05ac 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 07:45:57 2020 -0400 |
| b |
| @@ -0,0 +1,2 @@ +10139 1 1 +6345 48 - |
| b |
| diff -r 000000000000 -r 12d66d0d05ac 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 07:45:57 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 12d66d0d05ac test-data/zika/db/Z52.consensus.bwt |
| b |
| Binary file test-data/zika/db/Z52.consensus.bwt has changed |
| b |
| diff -r 000000000000 -r 12d66d0d05ac test-data/zika/db/Z52.consensus.pac |
| b |
| Binary file test-data/zika/db/Z52.consensus.pac has changed |
| b |
| diff -r 000000000000 -r 12d66d0d05ac test-data/zika/db/Z52.consensus.sa |
| b |
| Binary file test-data/zika/db/Z52.consensus.sa has changed |
| b |
| diff -r 000000000000 -r 12d66d0d05ac 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 07:45:57 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 12d66d0d05ac test-data/zika/db/zika_primers.bam |
| b |
| Binary file test-data/zika/db/zika_primers.bam has changed |
| b |
| diff -r 000000000000 -r 12d66d0d05ac 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 07:45:57 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 12d66d0d05ac 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 07:45:57 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 12d66d0d05ac 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 12d66d0d05ac 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 07:45:57 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 - +Consensus_Z52.consensus_threshold_0_quality_20 2192 2214 400_9_out_L* 60 + +Consensus_Z52.consensus_threshold_0_quality_20 2355 2377 400_8_out_R* 60 - +Consensus_Z52.consensus_threshold_0_quality_20 2495 2517 400_10_out_L 60 + +Consensus_Z52.consensus_threshold_0_quality_20 2650 2672 400_9_out_R* 60 - +Consensus_Z52.consensus_threshold_0_quality_20 2778 2800 400_11_out_L 60 + +Consensus_Z52.consensus_threshold_0_quality_20 2902 2924 400_10_out_R 60 - +Consensus_Z52.consensus_threshold_0_quality_20 3082 3104 400_12_out_L 60 + +Consensus_Z52.consensus_threshold_0_quality_20 3229 3251 400_11_out_R 60 - +Consensus_Z52.consensus_threshold_0_quality_20 3405 3427 400_13_out_L 60 + +Consensus_Z52.consensus_threshold_0_quality_20 3511 3533 400_12_out_R 60 - +Consensus_Z52.consensus_threshold_0_quality_20 3679 3701 400_14_out_L* 60 + +Consensus_Z52.consensus_threshold_0_quality_20 3825 3847 400_13_out_R 60 - +Consensus_Z52.consensus_threshold_0_quality_20 3979 4001 400_15_out_L 60 + +Consensus_Z52.consensus_threshold_0_quality_20 4136 4158 400_14_out_R* 60 - +Consensus_Z52.consensus_threshold_0_quality_20 4290 4312 400_16_out_L* 60 + +Consensus_Z52.consensus_threshold_0_quality_20 4407 4429 400_15_out_R 60 - +Consensus_Z52.consensus_threshold_0_quality_20 4599 4621 400_17_out_L** 60 + +Consensus_Z52.consensus_threshold_0_quality_20 4713 4735 400_16_out_R* 60 - +Consensus_Z52.consensus_threshold_0_quality_20 4884 4906 400_18_out_L** 60 + +Consensus_Z52.consensus_threshold_0_quality_20 5052 5074 400_17_out_R** 60 - +Consensus_Z52.consensus_threshold_0_quality_20 5209 5231 400_19_out_L 60 + +Consensus_Z52.consensus_threshold_0_quality_20 5335 5357 400_18_out_R** 60 - +Consensus_Z52.consensus_threshold_0_quality_20 5494 5516 400_20_out_L* 60 + +Consensus_Z52.consensus_threshold_0_quality_20 5650 5672 400_19_out_R 60 - +Consensus_Z52.consensus_threshold_0_quality_20 5794 5816 400_21_out_L* 60 + +Consensus_Z52.consensus_threshold_0_quality_20 5926 5948 400_20_out_R* 60 - +Consensus_Z52.consensus_threshold_0_quality_20 6101 6123 400_22_out_L** 60 + +Consensus_Z52.consensus_threshold_0_quality_20 6206 6228 400_21_out_R* 60 - +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 12d66d0d05ac 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 07:45:57 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 12d66d0d05ac 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 07:45:57 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 |