| Next changeset 1:1abf6b32ecfd (2017-12-13) |
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Commit message:
planemo upload for repository https://github.com/phac-nml/quasitools commit 8a264400a75945e2e0fdd5a08c007a8b1b7a2f0f |
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added:
aacoverage.xml callaavar.xml callcodonvar.xml callntvar.xml consensus.xml dnds.xml drmutations.xml hydra.xml test-data/align.bam test-data/forward.fastq test-data/hxb2_pol.bed test-data/hxb2_pol.fas test-data/mutant_types.csv test-data/mutation_db.tsv test-data/nt_variants.vcf test-data/test.vcf |
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| diff -r 000000000000 -r 71976cfc9022 aacoverage.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/aacoverage.xml Mon Dec 04 10:25:26 2017 -0500 |
| [ |
| @@ -0,0 +1,49 @@ +<tool id="aacoverage" name="Amino Acid Coverage" version="0.1.0"> + <description>Builds an aa census and returns its coverage</description> + <requirements> + <requirement type="package" version="0.2.2">quasitools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + + ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && + + quasitools aacoverage $input_bam $ref_file $input_genes -o output.csv + + ]]></command> + <inputs> + <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" /> + <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> + <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" /> + </inputs> + <outputs> + <data format="csv" name="output" from_work_dir="output.csv" /> + </outputs> + <tests> + <test> + <param name="input_bam" value="align.bam" /> + <param name="ref_file" value="hxb2_pol.fas" /> + <param name="input_genes" ftype="bed" value="hxb2_pol.bed" /> + <output name="output" > + <assert_contents> + <has_text text="frame: 0" /> + <has_text text="1,0" /> + <has_text text="948,1" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +Amino Acid Coverage +=================== + +Builds an amino acid census and returns its coverage. + +**Output** + +A file with one entry per line with the AA position and the coverage at the position. + + ]]></help> + <citations> + </citations> +</tool> |
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| diff -r 000000000000 -r 71976cfc9022 callaavar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/callaavar.xml Mon Dec 04 10:25:26 2017 -0500 |
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| @@ -0,0 +1,59 @@ +<tool id="aavariants" name="Amino Acid Variants" version="0.1.0"> + <description>Identifies amino acid mutations</description> + <requirements> + <requirement type="package" version="0.2.2">quasitools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + + ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && + quasitools call aavar $input_bam $ref_file $var_file $input_genes + + #if $mutation_db: + $mutation_db + #end if + + -o output.vcf + + ]]></command> + <inputs> + <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" /> + <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> + <param name="var_file" type="data" format="vcf" optional="false" label="Variants file" /> + <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" /> + <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Not required. Defaults to HIV mutation database." /> + <param name="min_freq" type="float" optional="true" min="0" max="1" label="Minimum frequency" value="0.01" help="The minimum required frequency. Defaults to 0.01." /> + </inputs> + <outputs> + <data format="vcf" name="output" from_work_dir="output.vcf" /> + </outputs> + <tests> + <test> + <param name="input_bam" value="align.bam" /> + <param name="ref_file" value="hxb2_pol.fas" /> + <param name="var_file" value="nt_variants.vcf" /> + <param name="input_genes" ftype="bed" value="hxb2_pol.bed" /> + <param name="min_freq" value="0.01" /> + <output name="output" > + <assert_contents> + <has_text_matching expression="#CHROM\sGENE\sTYPE\sWILDTYPE\sPOS\sMUTANT\sFILTER\sMUTANT_FREQ\sCOVERAGE\sINFO"/> + <has_text_matching expression="hxb2_pol\sRT\smutation\sK\s103\sN\sPASS\s0.0779\s154\sWC=aaa;MC=aaC;MCF=0.0779;CAT=.;SRVL=." /> + <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s70\sE\sPASS\s0.0103\s2422\sWC=gga;MC=gAa;MCF=0.0103;CAT=.;SRVL=." /> + <has_text_matching expression="hxb2_pol\sIN\smutation\sE\s96\sG\sPASS\s0.0163\s1959\sWC=gaa;MC=gGa;MCF=0.0163;CAT=.;SRVL=." /> + <has_text_matching expression="hxb2_pol\sIN\smutation\sE\s96\sK\sPASS\s0.0148\s1959\sWC=gaa;MC=Aaa;MCF=0.0148;CAT=.;SRVL=." /> + <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s189\sR\sPASS\s0.0234\s214\sWC=ggg;MC=Agg;MCF=0.0234;CAT=.;SRVL=." /> + <has_text_matching expression="hxb2_pol\sIN\smutation\sG\s192\sW\sPASS\s0.0159\s314\sWC=ggg;MC=Tgg;MCF=0.0159;CAT=.;SRVL=." /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +Amino Acid Variants +=================== + +Identifies amino acid mutations. + + ]]></help> + <citations> + </citations> +</tool> |
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| diff -r 000000000000 -r 71976cfc9022 callcodonvar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/callcodonvar.xml Mon Dec 04 10:25:26 2017 -0500 |
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| @@ -0,0 +1,56 @@ +<tool id="callcodonvar" name="Codon Variants" version="0.1.0"> + <description>Identifies codon variants and non-synonymous/synonymous mutations</description> + <requirements> + <requirement type="package" version="0.2.2">quasitools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + + cat $input_genes && + + ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && + quasitools call codonvar $input_bam $ref_file $offset $input_genes + + #if $error_rate: + -e $error_rate + #end if + + -o output.csv + + ]]></command> + <inputs> + <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" /> + <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> + <param name="offset" type="integer" optional="false" label="Offset" min="0" value="0"/> + <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" /> + <param name="error_rate" type="float" optional="true" min="0" max="1" label="Error rate" value="0.01" help="Estimated sequencing error rate. Defaults to 0.01." /> + </inputs> + <outputs> + <data format="csv" name="output" from_work_dir="output.csv" /> + </outputs> + <tests> + <test> + <param name="input_bam" value="align.bam" /> + <param name="ref_file" value="hxb2_pol.fas" /> + <param name="offset" value="1269"/> + <param name="input_genes" ftype="bed" value="hxb2_pol.bed" /> + <output name="output" > + <assert_contents> + <has_text text="#gene,nt position (gene),nt start position,nt end position,ref codon,mutant codon,ref AA,mutant AA,coverage,mutant frequency,mutant type,NS count,S count" /> + <has_text text="RT,1566-2885,1872,1874,aaa,aaC,K,N,154,7.79,NS,1.0000,0.0000" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +Codon Variants +============== + +Call codon variants for a given BAM. A report is generated that details nucleotide variants within a +codon and the resulting AA variants. The report indicates whether the nucleotide variants correspond to +a synonymous or non-synonymous mutation. + + ]]></help> + <citations> + </citations> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r 71976cfc9022 callntvar.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/callntvar.xml Mon Dec 04 10:25:26 2017 -0500 |
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| @@ -0,0 +1,48 @@ +<tool id="callntvar" name="Nucleotide Variants" version="0.1.0"> + <description>Identifies nucleotide variants</description> + <requirements> + <requirement type="package" version="0.2.2">quasitools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + + ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && + quasitools call ntvar $input_bam $ref_file + + #if $error_rate: + -e $error_rate + #end if + + -o output.vcf + + ]]></command> + <inputs> + <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" /> + <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> + <param name="error_rate" type="float" optional="true" min="0" max="1" value="0.01" label="Error rate" help="Estimated sequencing error rate. Defaults to 0.01."/> + </inputs> + <outputs> + <data format="vcf" name="output" from_work_dir="output.vcf" /> + </outputs> + <tests> + <test> + <param name="input_bam" value="align.bam" ftype="bam" /> + <param name="ref_file" value="hxb2_pol.fas" ftype="fasta" /> + <output name="output" > + <assert_contents> + <has_text_matching expression="#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"/> + <has_text_matching expression="hxb2_pol\s606\s.\sa\sc\s69\sPASS\sDP=157;AC=12;AF=0.0764" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +Nucleotide Variants +=================== + +Call nucleotide variants for a given BAM file and a supplied reference file. + + ]]></help> + <citations> + </citations> +</tool> |
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| diff -r 000000000000 -r 71976cfc9022 consensus.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/consensus.xml Mon Dec 04 10:25:26 2017 -0500 |
| [ |
| b'@@ -0,0 +1,76 @@\n+<tool id="consensus" name="Consensus Sequence" version="0.1.0">\n+ <description>Generate a consensus sequence from a BAM file</description>\n+ <requirements>\n+ <requirement type="package" version="0.2.2">quasitools</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+\n+ ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai &&\n+ quasitools consensus $input_bam $ref_file \n+\n+ #if $base_type.type == \'mixed\':\n+ -p $base_type.percentage \n+ #end if\n+\n+ -o output.fasta\n+\n+ ]]></command>\n+ <inputs>\n+ <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" />\n+ <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" />\n+ <conditional name="base_type">\n+ <param name="type" type="select" label="Specify majority or mixed base consensus" multiple="false" display="radio">\n+ <option value="majority" >Majority base consensus</option>\n+ <option value="mixed">Mixed base consensus</option>\n+ </param>\n+ <when value="majority">\n+ </when>\n+ <when value="mixed">\n+ <param name="percentage" type="integer" min="0" max="100" optional="true" value="100" label="Percentage" help="Percentage to include base in mixture. Defaults to 100."/>\n+ </when>\n+ </conditional>\n+ </inputs>\n+ <outputs>\n+ <data format="fasta" name="output" from_work_dir="output.fasta" />\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="input_bam" value="align.bam" />\n+ <param name="ref_file" value="hxb2_pol.fas" />\n+ <param name="type" value="majority" />\n+ <output name="output" >\n+ <assert_contents>\n+ <has_text text=">blah_100_hxb2_pol" />\n+ <has_text text="AGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGAC'..b'AAAGCAAAGATCATTAGGGAT" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ <test>\n+ <param name="input_bam" value="align.bam" />\n+ <param name="ref_file" value="hxb2_pol.fas" />\n+ <param name="type" value="mixed" />\n+ <param name="percentage" value="5" />\n+ <output name="output" >\n+ <assert_contents>\n+ <has_text text=">blah_5_hxb2_pol" />\n+ <has_text text="AGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAMAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGAT" />\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+Consensus\n+=========\n+\n+Generate a consensus sequence for a given BAM and reference file.\n+\n+Percentage info:\n+When percentage is set to 100, the most frequent base will be incorporated (note: in the case of a tie the base will be chosen in reverse alphabetical order). Insertions that are at least a multiple of 3 will be incorporated (i.e. codon length).\n+When percentage is less than 100, the base that has frequency greater than equal to percentage set will be incorporated, tie breaking same as above.\n+When there is zero coverage or no bases meet the percentage threshold (only when percentage is < 100) a n will be incorporated.\n+\n+ ]]></help>\n+ <citations>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 71976cfc9022 dnds.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dnds.xml Mon Dec 04 10:25:26 2017 -0500 |
| [ |
| @@ -0,0 +1,41 @@ +<tool id="dnds" name="dNdS Report" version="0.1.0"> + <description>Calculate the dN/dS value for each region in a bed file</description> + <requirements> + <requirement type="package" version="0.2.2">quasitools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + + quasitools dnds $csv_file $ref_file $offset -o output.csv + + ]]></command> + <inputs> + <param name="csv_file" type="data" format="csv" optional="false" label="CSV file" /> + <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> + <param name="offset" type="integer" optional="false" label="Offset" min="0" value="0"/> + </inputs> + <outputs> + <data format="csv" name="output" from_work_dir="output.csv" /> + </outputs> + <tests> + <test> + <param name="csv_file" value="mutant_types.csv" /> + <param name="ref_file" value="hxb2_pol.fas" /> + <output name="output" ftype="csv" > + <assert_contents> + <has_text_matching expression="#gene,pn,ps,pn_sites,ps_sites,dn/ds"/> + <has_text text="RT,0.0334,0.0111,1,1,3.0539" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +dNdS Report +=================== + +Determines the dNdS ratio for each codon variant in a supplied csv file (codon variants). + + ]]></help> + <citations> + </citations> +</tool> \ No newline at end of file |
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| diff -r 000000000000 -r 71976cfc9022 drmutations.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/drmutations.xml Mon Dec 04 10:25:26 2017 -0500 |
| [ |
| @@ -0,0 +1,64 @@ +<tool id="drmutations" name="Drug Resistance Mutations" version="0.1.0"> + <description></description> + <requirements> + <requirement type="package" version="0.2.2">quasitools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + + ln -f -s ${input_bam.metadata.bam_index} ${input_bam}.bai && + quasitools drmutations $input_bam $ref_file $var_file $input_genes + + #if $mutation_db: + $mutation_db + #end if + + #if $min_freq: + -f $min_freq + #end if + + #if $reporting_thres: + -t $reporting_thres + #end if + + -o output.csv + + ]]></command> + <inputs> + <param name="input_bam" type="data" format="bam" optional="false" label="Bam file" /> + <param name="ref_file" type="data" format="fasta" optional="false" label="Reference file" /> + <param name="var_file" type="data" format="vcf" optional="false" label="Variants file" /> + <param name="input_genes" type="data" format="bed" optional="false" label="Gene file" /> + <param name="mutation_db" type="data" format="tsv" optional="false" label="Mutation DB" /> + <param name="min_freq" type="float" optional="true" min="0" max="1" label="Minimum frequency" value="0.01" help="The minimum required frequency. Defaults to 0.01." /> + <param name="reporting_thres" type="integer" min="1" max="20" optional="true" label="Reporting threshold" value="1" + help="The minimum percentage required for an entry in the drug resistant report. Defaults to 1."/> + </inputs> + <outputs> + <data format="csv" name="output" from_work_dir="output.csv" /> + </outputs> + <tests> + <test> + <param name="input_bam" value="align.bam" /> + <param name="ref_file" value="hxb2_pol.fas" /> + <param name="var_file" value="nt_variants.vcf" /> + <param name="input_genes" ftype="bed" value="hxb2_pol.bed" /> + <param name="mutation_db" value="mutation_db.tsv" /> + <output name="output" > + <assert_contents> + <has_text text="Chromosome,Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage" /> + <has_text text="hxb2_pol,RT,NNRTI,Yes,K,103,N,7.79,154" /> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +Drug Resistance Mutations +========================= + +Generates a report detailing the drug resistant mutations found, above the reporting threshold (default: 1%). + + ]]></help> + <citations> + </citations> +</tool> |
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| diff -r 000000000000 -r 71976cfc9022 hydra.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/hydra.xml Mon Dec 04 10:25:26 2017 -0500 |
| [ |
| b'@@ -0,0 +1,223 @@\n+<tool id="hydra" name="Hydra pipeline" version="0.1.0">\n+ <description>Identifies drug resistance within an NGS dataset</description>\n+ <requirements>\n+ <requirement type="package" version="0.2.2">quasitools</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+\n+ quasitools hydra \'$forward\' \n+\n+ #if $reverse:\n+ \'$reverse\' \n+ #end if\n+\n+ #if $mutation_db:\n+ -m \'$mutation_db\' \n+ #end if\n+\n+ #if $reporting_threshold:\n+ -rt \'$reporting_threshold\' \n+ #end if\n+\n+ #if $consensus_pct:\n+ -cp \'$consensus_pct\' \n+ #end if\n+\n+ #if $length_cutoff:\n+ -lc \'$length_cutoff\' \n+ #end if\n+\n+ #if $score_cutoff:\n+ -sc \'$score_cutoff\' \n+ #end if\n+\n+ #if $error_rate:\n+ -e \'$error_rate\' \n+ #end if\n+\n+ #if $min_qual:\n+ -mq \'$min_qual\' \n+ #end if\n+\n+ #if $min_depth:\n+ -md \'$min_depth\' \n+ #end if\n+\n+ #if $min_ac:\n+ -ma \'$min_ac\' \n+ #end if\n+\n+ #if $min_freq:\n+ -mf \'$min_freq\' \n+ #end if\n+\n+ #if $generate_consensus:\n+ --generate_consensus \n+ #end if\n+\n+ #if $filter_ns:\n+ --ns \n+ #end if\n+\n+ -o output\n+\n+ ]]></command>\n+ <inputs>\n+ <param name="forward" type="data" format="fastq" optional="false" label="Forward read" />\n+ <param name="reverse" type="data" format="fastq" optional="true" label="Reverse read" help="Not required."/>\n+ <param name="mutation_db" type="data" format="tsv" optional="true" label="Mutation DB" help="Defaults to HIV mutation database." />\n+ <param name="reporting_threshold" type="integer" optional="true" min="1" max="100" value="1" label="Reporting threshold. Defaults to 1." help="Minimum mutation frequency to report." />\n+ <param name="consensus_pct" type="integer" optional="true" min="1" max="20" value="20" label="Reporting threshold" help="Minimum mutation frequency to report. Defaults to 20." />\n+ <param name="length_cutoff" type="integer" optional="true" min="0" max="1000" label="Length cutoff" value="100" help="Reads which fall short of the specified length will be filtered out. Defaults to 100." />\n+ <param name="score_cutoff" type="integer" optional="true" min="0" max="40" label="Score cutoff" value="30" help="Reads whose average quality score is less than the specified score will be filtered out. Defaults to 30." />\n+ <param name="error_rate" type="float" optional="true" min="0" max="1" label="Error rate" value="0.0021" help="Estimated sequencing error rate. Defaults to 0.0021."/>\n+ <param name="min_qual" type="integer" optional="true" min="1" max="100" label="Minimum quality" value="30" help="Minimum required quality for variant to be considered later on in the pipeline. Defaults to 30." />\n+ <param name="min_depth" type="integer" optional="true" min="0" max="5000" label="Minimum depth" value="100" help="Minimum required depth for variant to be considered later on in the pipeline. Defaults to 100." />\n+ <param name="min_ac" type="integer" optional="true" min="0" max="5000" label="Minimum allele count" value="5" help="Minimum required allele count for variant to be considered later on in the pipeline. Defaults to 5." />\n+ <param name="min_freq" type="float" optional="true" min="0" max="1" label="Minimum frequency" value="0.01" help="Minimum required frequency for variant to be considered later on in the pipeline. Defaults to 0.01." />\n+ <param name="generate_consensus" type="boolean" truevalue="--generate_consensus" falsevalue="" checked="False" label="Generate consensus" />\n+ <param name="filter_ns" type="boolean" truevalue="--ns" falsevalue="" checked="False" label="Filter out n\'s" />\n+ </inputs>\n+ <outputs>\n+ '..b' <has_text text="Input Size: 25000"/>\n+ <has_text text="Number of reads filtered due to length: 15074"/>\n+ <has_text text="Number of reads filtered due to average quality score: 501"/>\n+ <has_text text="Number of reads filtered due to presence of Ns: 0"/>\n+ <has_text text="Number of reads filtered due to excess coverage: 0"/>\n+ <has_text text="Number of reads filtered due to poor mapping: 12"/>\n+ <has_text text="Percentage of reads filtered: 62.35"/>\n+ </assert_contents>\n+ </output>\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+\n+HyDRA - HIV Drug Resistance Analyzer\n+====================================\n+\n+The HyDRA pipeline provides a pipeline for identifying drug resistance within a Next Generation Sequencing dataset. The pipeline takes as input the raw reads produced by a Next Generation Sequencer and produces a report detailing found drug resistance per sample.\n+\n+Authors\n+-------\n+\n+The HyDRA pipeline was developed by Eric Enns and David Peddle.\n+\n+Stages\n+------\n+\n+The HyDRA pipleine proceeds through the following stages:\n+\n+1. Quality Control/Filtering\n+2. Reference mapping using bowtie2.\n+3. Variant Calling and filtering using a Poisson distribution.\n+4. AA Mutation Calling and filtering.\n+5. Drug Resistance report generation.\n+\n+Details\n+-------\n+\n+The following is an example for running the pipeline, using our included test dataset:\n+ * Output directory name: "/tmp/hydra_out"\n+ * Forward reads: "reads_w_K103N.fastq"\n+\n+### Output ###\n+\n+The detailed output directory tree looks as follows:\n+\n+ /tmp/hydra_out/\n+ * align.bam\n+ * align.bam.bai\n+ * coverage_file.csv\n+ * dr_report.csv\n+ * filtered.fastq\n+ * hydra.vcf\n+ * mutation_report.hmcf\n+ * stats.txt\n+\n+The description of each of these directories/files are as follows:\n+\n+* __run.conf__: The configuration used when this output was produced.\n+* __reads_w_K103N/__: The results directory for the input file reads_w_K103N.fastq\n+ * __align.bam__: The alignment file in bam format.\n+ * __align.bam.bai__: The index to the alignment file.\n+ * __coverage_file.csv__: A file with one entry per line with the AA position and the coverage at the position.\n+ * __dr_report.csv__: A report detailing the drug resistant mutations found, above the reporting threshold (default: 1%).\n+ * __filtered.fastq__: The reads remaining after the filtering stage.\n+ * __hydra.vcf__: The variants found by the pipeline.\n+ * __mutation_report.hmcf__: The AA mutations found by the pipeline.\n+ * __stats.txt__: A log file detailing size after filtering and major stages.\n+\n+The __dr_report.csv__ file lists all found drug resistant mutations (mutations included in the mutation database) which have frequency greater than the reporting threshold. An example of this file is given below.\n+\n+Example: __dr_report.csv__\n+\n+ Gene,Category,Surveillance,Wildtype,Position,Mutation,Mutation Frequency,Coverage\n+ RT,NNRTI,Yes,K,103,N,9.03,155\n+\n+The __mutation_report.hmcf__ files is our custom VCF like file which details all of the AA mutations found by the pipeline. An example if this file is given below.\n+\n+Example: __mutation_report.hmcf__\n+\n+ ##fileformat=HMCFv1\n+ ##fileDate=20150008\n+ ##source=HyDRA\n+ ##reference=/home/ericenns/hydra/var/hxb2_pol.fas\n+ ##INFO=<ID=MC,Number=.,Description="String">\n+ ##INFO=<ID=MCF,Number=.,Description="String">\n+ ##INFO=<ID=WC,Number=.,Description="String">\n+ ##FILTER=<ID=mf0.01,Description="Mutant freq below 0.01">\n+ #GENE CATEGORY SURVEILLANCE TYPE WILDTYPE POS MUTANT FILTER MUTANT_FREQ COVERAGE INFO\n+ RT NNRTI Yes mutation K 103 N PASS 0.0903 155 WC=aaa;MC=aaC;MCF=0.0903\n+\n+ ]]></help>\n+ <citations>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 71976cfc9022 test-data/forward.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/forward.fastq Mon Dec 04 10:25:26 2017 -0500 |
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| b'@@ -0,0 +1,100000 @@\n+@M01647:10:000000000-ACPHB:1:1101:18589:1580 1:N:0:86\n+TAGGGATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAATATACTGCATTTACCATACCT\n++\n+8-89,-EEGG@ECCECE;C7+:+CE8,,,,+;,<,C87FE,<C99E9<F,EF98,C8E997FC7FAE<F9EFFGGGFEFFFEFGG8@,C@<<A9FGGGAD98,,C?FAFGCFCFGGGFF9E9?=F\n+@M01647:10:000000000-ACPHB:1:1101:8590:1626 1:N:0:86\n+NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n++\n+###################################\n+@M01647:10:000000000-ACPHB:1:1101:16780:1629 1:N:0:86\n+TTAACTATGTCTGGATTTTGTTTTCTAAAAGGCTCTAAGATTTTTGTCATGCTACTTTGGAATAGGGCAGCATAGAACAAAAAT\n++\n+-8<ABDCE9ECCEC9C@FGCGFGDEG99EAE7<AFFAEE,EFEGG7FFFFFF<AC@FF,,<CF9CFCFC,@E<FCCFG@E8,CF\n+@M01647:10:000000000-ACPHB:1:1101:21332:1630 1:N:0:86\n+TTACAAATCATCCATGTATTGACAGATAACTATGTCTGGATTTTGTTTTCTTAAAGGCTCTAAGATTTTTGTCATGCTACTTTGGAATATTGCTGGTTATCCTTTCCATCCCTGTGGAAGCACATTGTACTGATATCTAATCCCTGGTGTCTCAT\n++\n+-8,<6;@EFAFFG8E<E9EE99EFD8FDGGFDEEFGGGG9EE@E9CFFGFC,,,,,66CEF,,C,CCEFF:FE,C,<CACEEFC8,,C,CA,CEACE,6EAFGGGGGCFF<EF@F8,,,,?,B<FE995:?,<5?<,?,,CA<EF87E:FEC@,A\n+@M01647:10:000000000-ACPHB:1:1101:20276:1631 1:N:0:86\n+CAGTAACAGTACTGGATGTGGGTTATGAACTCCATCCTGA\n++\n+6-6A@9FDAFAFFA@8C<F9C,@F<F9<FGG<FCFFCF<,\n+@M01647:10:000000000-ACPHB:1:1101:10550:1662 1:N:0:86\n+GTATATTTCCTGAAGTCTTCATCTAAGGGAACTGAAAAATATGCATCACCCACATCCAGTACTGTTACTGATTTGTTC\n++\n+-ABCCGGGFFGGFFGGGGGGAFGGACFDF8FGGGDCEGFGGGFGFGGGGGGGGGGGG?FGGGGGGGGGGGDGFG9FGD\n+@M01647:10:000000000-ACPHB:1:1101:13990:1665 1:N:0:86\n+TTTCATAACCCATCCAAAGGAATGGAGGTTCTTTCTGATGTTTTTTGTCTGGTGTGGTACGTCCCCACCTCAACAGATGTTGTCTCAGCTCCTCTATTTTTGTTCTATGCTGCCCTATTTCTAAGTCAGATCCTACATACACATCATCCATGTATTGAACGATAATTATGTCTTGTTTTTGTTTTCTAAAAGGCTCTAAGATTTTTGACATGCTACTTTGTATTATTGCTGGTGATCCTTTCCTTCC\n++\n+-8CCCF9EFEEBFFFGC9,<,,C,;,;,FFFGGGGGF,C,C@FGGG+EEGAFF?F:,E<,@F@C@FFEFEFGFGG8<FEFGGGFGCC,@FE@FGF9EGGGG:FGFGDGGGGCFFGG,EFFFG,,5ED?,?FAGG<A<FFCF,CE=FGGCFF9E,CA@CD,>:B8@,:,@6EFG,,,>DEF6>@EGDFA9A,,+D==D==,,@@FGG6=FA==8D,+C9C@,++5,?C++<2+=+2B@2BFF1++1+3\n+@M01647:10:000000000-ACPHB:1:1101:19446:1671 1:N:0:86\n+ATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAG\n++\n+-ACCCGGGGGGG9CFFCGFCFEEFGGGF9AEGG,,EFFFGFEFEGCGGGGGFGC8CFEE\n+@M01647:10:000000000-ACPHB:1:1101:10485:1674 1:N:0:86\n+ATTGACAGATAACTATGTCTGGATTTTGTTTTCTAAAAGGCTCTAAGATTTTTGTCATGCTACTTTGGAATATTGCTGGTGATCCTTTCCATCCCTGTGGAAGCACATTGTAC\n++\n+-CCCCGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGCGGGGGGGFGGGGGGGGGGGGGGGGGGGF@FFGGGAFGFGGGCGGGGGGGGGGFEGGGGGGG9FGGDFGG9FGG\n+@M01647:10:000000000-ACPHB:1:1101:18082:1680 1:N:0:86\n+TAGGGATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAATATAC\n++\n+C@CCCFGGGGGGGFGGGGGEGGGGGGGGGGGGFGGGFGGGGGGCGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG8BFFFGGG\n+@M01647:10:000000000-ACPHB:1:1101:11858:1681 1:N:0:86\n+AAATAGAGGAGCTGAGACAACATCTGTTGAGGTAGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGAC\n++\n+-86CBDEGG?EGGGFGGGGGFFGGGGGGFGGGG9C8CGCFFDDFFGFGDFGGGGFGGF:FGGGDGFAFGFFGGGGGGGGGGGGGCCFFGGFFGGGGCFGGGGGGGGGGGGGGFFF9FFGFGGEFFFGGGGGGGGGGGGGGGFGGGGEGGFFGGDGGGGFGGGGGGGG\n+@M01647:10:000000000-ACPHB:1:1101:22194:1685 1:N:0:86\n+ATGTTGTCTCAGCTCCTCTATTTTTGTTCTATGCTGCCCTATTTCTAAGTCAGATCCTACATAC\n++\n+-ACCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFECGGGGGGGGFFGGGGG\n+@M01647:10:000000000-ACPHB:1:1101:13885:1694 1:N:0:86\n+TTTGAACGATAACTATGTCTGGATTTTGTTTTCTAAAAGGCTCTAAGATTTTTGTCATGCTACTTTGGAATATTGCTGGTGATCCTTTCCATCCCTGTGGAAGCACATTGTACTGATATCTAATCCCTGGTGTCTCATTGTTTATACT\n++\n+-ACCCEFFEG7CGGGGGGGGGGGGFGGCFEGCFGGGFE9FGC<FE<<@FGGGGGGGGGGCCGCACFG@<,CCFF,EAFFG@DFGGGGGGGDFGFGGGGGG,EAFFEFGGGGGAF@FE<FFFFECFFGG<FFEF,CFFFGGGGGGGGGG\n+@M01647:10:000000000-ACPHB:1:1101:14208:1697 1:N:0:86\n+CTCTAAGATTTTTGTCATGCTACTTTGGAATATTGCTGGTGTTCCTTTCCATCCCTGTGGAAGCACTTTGTACTGATATCTAATCC\n++\n+@@CCCEE9F@DFFGGCEFECFCGFGGGCGGGGGG9EACFFD,BFFFGC@6FCGFEFFFGFDFC<<F,CEAFFFE9,C<EFGCGGGG\n+@M01647:10:000000000-ACPHB:1:1101:23453:1699 1:N:0:86\n+TTTGGAATACCACATCCCGCAGGGTTAAAAAAGAA'..b'13906 1:N:0:86\n+CTATTTTTGTTCTATGCTGCCCTATTTCTAAGTCAGATCCTACATACAAATC\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGG\n+@M01647:10:000000000-ACPHB:1:1102:20180:13906 1:N:0:86\n+CATCCAGTACTGTTACTGATTTTTTCTTTTTTAACCC\n++\n+BCCCCGGGGAFGGFFFFGGGGGGGGFGGGGGGGFFEE\n+@M01647:10:000000000-ACPHB:1:1102:18169:13911 1:N:0:86\n+TAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATAC\n++\n+CCCCCGGGGGGGFGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n+@M01647:10:000000000-ACPHB:1:1102:12854:13911 1:N:0:86\n+GAGACAACATCTGTTGAGGCGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATG\n++\n+CCCCCFA@@<;FFGC9CFG,+@+@+6CFD@8EEFG:ECF,C@A8FCFFEACE9CFGEGGD8C6<<<EAFGGGCG<8C<FF4CE<FFF9=EFF=FAFGFFC@<\n+@M01647:10:000000000-ACPHB:1:1102:26240:13912 1:N:0:86\n+AGCATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCATTCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCAT\n++\n+CCCCCGGGGGFGGGGFGGGGGGGGFFGGGGGGGGGEGGGFGFGGGFGGGGGGGGGGGGFGGGGGGGFGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n+@M01647:10:000000000-ACPHB:1:1102:18865:13912 1:N:0:86\n+CTATAGGCTGTACTGTCCATTTATCAGGATGGAGTTCATAACCCATCCAAAGGAATGGAGGTTCTTTCTGATGTTTTTTGTCTGGTGTGGTAAGTCCCCACCTCAACAGATGTTGTCTCAGCTCCTCTATTTTTGTTCTATGCTGCCCTATTTCTAAGTCAGATCCTACATACAAATC\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGGGGGGGGGG\n+@M01647:10:000000000-ACPHB:1:1102:12418:13915 1:N:0:86\n+ATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCATTCAA\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG\n+@M01647:10:000000000-ACPHB:1:1102:8600:13917 1:N:0:86\n+AAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAATATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCGTTCAAT\n++\n+CCC<BFGGGGFDFGFFGGGGGGGG@FDGGFEFFGGGGGGGGGGGGGGFGGFFGGGGGFAFFGGGGGGADFGGFFADGGGGGGGGGGGGGGDGGGGGGGGGGGGGGGGGGGGGGGGGGGEGGGGGGGGGFGGGGGGGGGGGGGGGGGFFGFGGGGGGGGGGGGGGGCFBFGGGGGGGDGE,CEEFGGGGGGGGGDGGGG9=FGGGGGGGGFFFF@FFGGGFGFGFGGGGGGGG9=C@CC@?7DF7\n+@M01647:10:000000000-ACPHB:1:1102:14512:13918 1:N:0:86\n+GTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAATATAC\n++\n+CCCCCGGFEEFGGGFGGGGGGGGGGGGFFFFFFGGFFGGGGGGGGGGGGGGGGGCFGGGGGG\n+@M01647:10:000000000-ACPHB:1:1102:11362:13918 1:N:0:86\n+TAGTTATCTATCAATACATGGATGATTTGTATGTAGGATC\n++\n+CCCCCFGGGGGGCFGFFFGGGGGGFFGGGGGGGGGGGGGG\n+@M01647:10:000000000-ACPHB:1:1102:16891:13919 1:N:0:86\n+AGGCTGTACTGTCCATTTATCAGGATGGAGTTCATAACCCATCCAAAGGAATGGAGGTTCTTTCTGATGTTTTTTGTCTGGTGTGGTAAGTCCCCACC\n++\n+CCCCCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFGGGGGGGGGGGGGF@FGGGGGGGGGGGGGGGGGGGGFFFGGG\n+@M01647:10:000000000-ACPHB:1:1102:8085:13920 1:N:0:86\n+GTTACCAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATAC\n++\n+CCCCCGGFGGGFGGGGGCGFEFGGGFGGDFEGCEFFGGGFG@FGGFGFGGGGGEGGEGGGGFGFFFGGGGGGGGFGGGGGGGGGGGG\n+@M01647:10:000000000-ACPHB:1:1102:27057:13923 1:N:0:86\n+TTGACAGATAACTATGTCTGGATTTTGTTTTCTAAAAGGCTCTAAGATTTTTGTCATGCTACTTTGGAATATTGCTGGGGATCCTTTCAATCCCTGTGGAAGAACATGGTACTGATATCTAATCCCTGGTGTCTCATTGTTTATACTAGGTATGGTAAATGC\n++\n+CCCCCGGGGGGGGGCFGGFGGGGGGGGGDGGGGGGGGGGGEGFGGGGGGGGC7C@<C,@6EFGG9EEGC9@F,CE9CA,+86CFFGCF<,,:EC,C,C<C@<,,C,E,B,<,,6C,6,9AF,AFGE,FEFC4A,5,C5<FF,,@,9,9C@,A5A,5AE9;;F\n+@M01647:10:000000000-ACPHB:1:1102:9313:13925 1:N:0:86\n+TCTCAGCTCCTCTATTTTTGTTCTATGCTGCCCTATTTCTAAGTCAGATCCTACATACAAATCATCCATGTATTGAATGATAACTATGTCTGGATTTTGTTTTCTAAAAGGCTCTAAGATTTTTGTC\n++\n+CCCCCGG@FFGGGGGGGGGGGGCGGGGGGGGDGFFFGGGGGDEGCFGCFFFGGGGGGGGGGGGGGGGFGGGGGGGGGGFCFCGGGGCGFGGGGFGEGGGGGGGGGGGGGGGGGGGGGFEFGGGGGGF\n+@M01647:10:000000000-ACPHB:1:1102:12646:13925 1:N:0:86\n+GTATATTTCCTGAAGTCTTCATCTAAGGGAACTGAAAAATATGCATCACC\n++\n+CCCCCGGGGGGGFGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGF\n' |
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| diff -r 000000000000 -r 71976cfc9022 test-data/hxb2_pol.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hxb2_pol.bed Mon Dec 04 10:25:26 2017 -0500 |
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| @@ -0,0 +1,3 @@ +hxb2_pol 0 296 PR +hxb2_pol 297 1616 RT +hxb2_pol 1977 2843 IN |
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| diff -r 000000000000 -r 71976cfc9022 test-data/hxb2_pol.fas --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/hxb2_pol.fas Mon Dec 04 10:25:26 2017 -0500 |
| b |
| @@ -0,0 +1,2 @@ +>hxb2_pol +CCTCAGGTCACTCTTTGGCAACGACCCCTCGTCACAATAAAGATAGGGGGGCAACTAAAGGAAGCTCTATTAGATACAGGAGCAGATGATACAGTATTAGAAGAAATGAGTTTGCCAGGAAGATGGAAACCAAAAATGATAGGGGGAATTGGAGGTTTTATCAAAGTAAGACAGTATGATCAGATACTCATAGAAATCTGTGGACATAAAGCTATAGGTACAGTATTAGTAGGACCTACACCTGTCAACATAATTGGAAGAAATCTGTTGACTCAGATTGGTTGCACTTTAAATTTTCCCATTAGCCCTATTGAGACTGTACCAGTAAAATTAAAGCCAGGAATGGATGGCCCAAAAGTTAAACAATGGCCATTGACAGAAGAAAAAATAAAAGCATTAGTAGAAATTTGTACAGAGATGGAAAAGGAAGGGAAAATTTCAAAAATTGGGCCTGAAAATCCATACAATACTCCAGTATTTGCCATAAAGAAAAAAGACAGTACTAAATGGAGAAAATTAGTAGATTTCAGAGAACTTAATAAGAGAACTCAAGACTTCTGGGAAGTTCAATTAGGAATACCACATCCCGCAGGGTTAAAAAAGAAAAAATCAGTAACAGTACTGGATGTGGGTGATGCATATTTTTCAGTTCCCTTAGATGAAGACTTCAGGAAGTATACTGCATTTACCATACCTAGTATAAACAATGAGACACCAGGGATTAGATATCAGTACAATGTGCTTCCACAGGGATGGAAAGGATCACCAGCAATATTCCAAAGTAGCATGACAAAAATCTTAGAGCCTTTTAGAAAACAAAATCCAGACATAGTTATCTATCAATACATGGATGATTTGTATGTAGGATCTGACTTAGAAATAGGGCAGCATAGAACAAAAATAGAGGAGCTGAGACAACATCTGTTGAGGTGGGGACTTACCACACCAGACAAAAAACATCAGAAAGAACCTCCATTCCTTTGGATGGGTTATGAACTCCATCCTGATAAATGGACAGTACAGCCTATAGTGCTGCCAGAAAAAGACAGCTGGACTGTCAATGACATACAGAAGTTAGTGGGGAAATTGAATTGGGCAAGTCAGATTTACCCAGGGATTAAAGTAAGGCAATTATGTAAACTCCTTAGAGGAACCAAAGCACTAACAGAAGTAATACCACTAACAGAAGAAGCAGAGCTAGAACTGGCAGAAAACAGAGAGATTCTAAAAGAACCAGTACATGGAGTGTATTATGACCCATCAAAAGACTTAATAGCAGAAATACAGAAGCAGGGGCAAGGCCAATGGACATATCAAATTTATCAAGAGCCATTTAAAAATCTGAAAACAGGAAAATATGCAAGAATGAGGGGTGCCCACACTAATGATGTAAAACAATTAACAGAGGCAGTGCAAAAAATAACCACAGAAAGCATAGTAATATGGGGAAAGACTCCTAAATTTAAACTGCCCATACAAAAGGAAACATGGGAAACATGGTGGACAGAGTATTGGCAAGCCACCTGGATTCCTGAGTGGGAGTTTGTTAATACCCCTCCCTTAGTGAAATTATGGTACCAGTTAGAGAAAGAACCCATAGTAGGAGCAGAAACCTTCTATGTAGATGGGGCAGCTAACAGGGAGACTAAATTAGGAAAAGCAGGATATGTTACTAATAGAGGAAGACAAAAAGTTGTCACCCTAACTGACACAACAAATCAGAAGACTGAGTTACAAGCAATTTATCTAGCTTTGCAGGATTCGGGATTAGAAGTAAACATAGTAACAGACTCACAATATGCATTAGGAATCATTCAAGCACAACCAGATCAAAGTGAATCAGAGTTAGTCAATCAAATAATAGAGCAGTTAATAAAAAAGGAAAAGGTCTATCTGGCATGGGTACCAGCACACAAAGGAATTGGAGGAAATGAACAAGTAGATAAATTAGTCAGTGCTGGAATCAGGAAAGTACTATTTTTAGATGGAATAGATAAGGCCCAAGATGAACATGAGAAATATCACAGTAATTGGAGAGCAATGGCTAGTGATTTTAACCTGCCACCTGTAGTAGCAAAAGAAATAGTAGCCAGCTGTGATAAATGTCAGCTAAAAGGAGAAGCCATGCATGGACAAGTAGACTGTAGTCCAGGAATATGGCAACTAGATTGTACACATTTAGAAGGAAAAGTTATCCTGGTAGCAGTTCATGTAGCCAGTGGATATATAGAAGCAGAAGTTATTCCAGCAGAAACAGGGCAGGAAACAGCATATTTTCTTTTAAAATTAGCAGGAAGATGGCCAGTAAAAACAATACATACTGACAATGGCAGCAATTTCACCGGTGCTACGGTTAGGGCCGCCTGTTGGTGGGCGGGAATCAAGCAGGAATTTGGAATTCCCTACAATCCCCAAAGTCAAGGAGTAGTAGAATCTATGAATAAAGAATTAAAGAAAATTATAGGACAGGTAAGAGATCAGGCTGAACATCTTAAGACAGCAGTACAAATGGCAGTATTCATCCACAATTTTAAAAGAAAAGGGGGGATTGGGGGGTACAGTGCAGGGGAAAGAATAGTAGACATAATAGCAACAGACATACAAACTAAAGAATTACAAAAACAAATTACAAAAATTCAAAATTTTCGGGTTTATTACAGGGACAGCAGAAATCCACTTTGGAAAGGACCAGCAAAGCTCCTCTGGAAAGGTGAAGGGGCAGTAGTAATACAAGATAATAGTGACATAAAAGTAGTGCCAAGAAGAAAAGCAAAGATCATTAGGGATTATGGAAAACAGATGGCAGGTGATGATTGTGTGGCAAGTAGACAGGATGAGGATTAG |
| b |
| diff -r 000000000000 -r 71976cfc9022 test-data/mutant_types.csv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mutant_types.csv Mon Dec 04 10:25:26 2017 -0500 |
| b |
| @@ -0,0 +1,25 @@ +#gene,nt position (gene),nt start position,nt end position,ref codon,mutant codon,ref AA,mutant AA,coverage,mutant frequency,mutant type,NS count,S count +IN,3246-4112,3384,3386,gga,ggG,G,G,2647,0.08,S,0.0000,1.0000 +IN,3246-4112,3387,3389,gaa,Aaa,E,K,2646,0.30,NS,1.0000,0.0000 +IN,3246-4112,3450,3452,gaa,Aaa,E,K,2455,0.08,NS,1.0000,0.0000 +IN,3246-4112,3450,3452,gaa,AGa,E,R,2455,0.81,NS,2.0000,0.0000 +IN,3246-4112,3450,3452,gaa,gGa,E,G,2455,0.08,NS,1.0000,0.0000 +IN,3246-4112,3453,3455,gga,Aga,G,R,2422,0.21,NS,1.0000,0.0000 +IN,3246-4112,3453,3455,gga,AgG,G,R,2422,0.74,NS,1.5000,0.5000 +IN,3246-4112,3453,3455,gga,gAa,G,E,2422,1.03,NS,1.0000,0.0000 +IN,3246-4112,3453,3455,gga,ggG,G,G,2422,0.21,S,0.0000,1.0000 +IN,3246-4112,3456,3458,aaa,aaG,K,K,2411,0.91,S,0.0000,1.0000 +IN,3246-4112,3459,3461,gtt,Ttt,V,F,2406,0.33,NS,1.0000,0.0000 +IN,3246-4112,3462,3464,atc,Ttc,I,F,2408,0.17,NS,1.0000,0.0000 +IN,3246-4112,3504,3506,gaa,Aaa,E,K,2319,0.39,NS,1.0000,0.0000 +IN,3246-4112,3507,3509,gtt,gGt,V,G,2297,0.09,NS,1.0000,0.0000 +IN,3246-4112,3510,3512,att,Ttt,I,F,2281,0.44,NS,1.0000,0.0000 +IN,3246-4112,3519,3521,gaa,Aaa,E,K,2140,0.51,NS,1.0000,0.0000 +IN,3246-4112,3519,3521,gaa,AGa,E,R,2140,0.56,NS,2.0000,0.0000 +IN,3246-4112,3519,3521,gaa,gGa,E,G,2140,0.33,NS,1.0000,0.0000 +IN,3246-4112,3522,3524,aca,aAa,T,K,2093,0.10,NS,1.0000,0.0000 +IN,3246-4112,3531,3533,gaa,Aaa,E,K,1959,1.48,NS,1.0000,0.0000 +IN,3246-4112,3531,3533,gaa,gGa,E,G,1959,1.63,NS,1.0000,0.0000 +IN,3246-4112,3546,3548,ctt,Ttt,L,F,530,0.94,NS,1.0000,0.0000 +RT,1566-2885,1872,1874,aaa,aaC,K,N,154,7.79,NS,1.0000,0.0000 +RT,1566-2885,2823,2825,cct,ccC,P,P,1362,0.37,S,0.0000,1.0000 |
| b |
| diff -r 000000000000 -r 71976cfc9022 test-data/mutation_db.tsv --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mutation_db.tsv Mon Dec 04 10:25:26 2017 -0500 |
| b |
| b'@@ -0,0 +1,269 @@\n+#Gene\tWildtype\tPosition\tMutation\tCategory\tSurveillance\tComment\n+PR\tL\t10\tF\tPIMinor\tNo\tL10F is a common nonpolymorphic, PI-selected accessory mutation associated with reduced susceptibility to each of the PIs except ATV, SQV, and TPV.\n+PR\tL\t10\tI\tPIMinor\tNo\tL10I/V are polymorphic, PI-selected accessory mutations that reduce PI susceptibility or increase the replication of viruses with other PI-resistance mutations. \n+PR\tL\t10\tV\tPIMinor\tNo\tL10I/V are polymorphic, PI-selected accessory mutations that reduce PI susceptibility or increase the replication of viruses with other PI-resistance mutations. \n+PR\tL\t10\tR\tPIMinor\tNo\tL10R/Y are rare, nonpolymorphic PI-selected accessory mutations. Their effects on PI susceptibility have not been well studied. \n+PR\tL\t10\tY\tPIMinor\tNo\tL10R/Y are rare, nonpolymorphic PI-selected accessory mutations. Their effects on PI susceptibility have not been well studied. \n+PR\tV\t11\tI\tPIMinor\tNo\tV11I is a minimally polymorphic PI-resistance accessory mutation that is often selected in patients receiving DRV. It is associated with minimal reductions in DRV and FPV susceptibility. It is included in the Tibotec GSS for DRV. V11L is a nonpolymorphic accessory PI-resistance mutation that is also associated with minimal reductions in DRV and FPV susceptibility. \n+PR\tV\t11\tL\tPIMinor\tNo\tV11I is a minimally polymorphic PI-resistance accessory mutation that is often selected in patients receiving DRV. It is associated with minimal reductions in DRV and FPV susceptibility. It is included in the Tibotec GSS for DRV. V11L is a nonpolymorphic accessory PI-resistance mutation that is also associated with minimal reductions in DRV and FPV susceptibility. \n+PR\tK\t20\tR\tOther\tNo\tK20R is a highly polymorphic, PI-selected accessory mutation that improves HIV-1 replication fitness in viruses with other PI-resistance mutations. \n+PR\tK\t20\tI\tPIMinor\tNo\tK20I is the consensus amino acid in subtype G and CRF02_AG. In subtypes B and C, K20I is a PI-selected mutation that appears to reduce NFV susceptibility. \n+PR\tK\t20\tT\tPIMinor\tNo\tK20T is a nonpolymorphic accessory PI-selected mutation that is associated with reduced susceptibility to each of the PIs except SQV and TPV. \n+PR\tK\t20\tM\tPIMinor\tNo\tK20M/V are rare, relatively nonpolymorphic PI-selected mutations that have not been well studied.\n+PR\tK\t20\tV\tPIMinor\tNo\tK20M/V are rare, relatively nonpolymorphic PI-selected mutations that have not been well studied.\n+PR\tL\t23\tI\tPIMinor\tYes\tL23I is an uncommon nonpolymorphic mutation selected primarily by NFV. It causes low/intermediate-level resistance to NFV.\n+PR\tL\t24\tI\tPIMinor\tYes\tL24I is a nonpolymorphic mutation selected by IDV and, less often, LPV. It reduces susceptibility to FPV, IDV, LPV, SQV, ATV and NFV. It increases susceptibility to TPV.\n+PR\tL\t24\tF\tPIMinor\tNo\tL24F is an uncommon nonpolymorphic PI-selected mutation that appears to have a susceptibility profile similar to L24I. L24M is a rare nonpolymorphic PI-selected mutation that has not been well studied.\n+PR\tL\t24\tM\tPIMinor\tNo\tL24F is an uncommon nonpolymorphic PI-selected mutation that appears to have a susceptibility profile similar to L24I. L24M is a rare nonpolymorphic PI-selected mutation that has not been well studied.\n+PR\tD\t30\tN\tPIMajor\tYes\tD30N is a nonpolymorphic substrate-cleft mutation that causes high-level resistance to NFV.\n+PR\tV\t32\tI\tPIMajor\tYes\tV32I is a nonpolymorphic substrate-cleft mutation associated with reduced susceptibility to each PI except SQV. It is included in the Tibotec DRV GSS.\n+PR\tL\t33\tF\tPIMinor\tNo\tL33F is a relatively nonpolymorphic accessory mutation selected by DRV, FPV, LPV, NFV and TPV. In combination with other PI-resistance mutations, L33F is associated with reduced susceptibility to these PIs. It is included in the Tibotec DRV GSS.\n+PR\tL\t33\tI\tPIMinor\tNo\tL33I is a relatively nonpolymorphic PI-selected mutation that appears to have minimal, if any, effects on PI susceptibility.\n+PR\tL\t33\tV\tOther\tNo\tL33V is a polymorphism that does '..b'/K/R have minimal effects on DTG susceptibility. In combination with E138K/A +/- G140S/A/C they cause >10-fold reduced susceptibility to DTG. \n+IN\tV\t151\tA\tAccessory\tNo\tV151A is an extremely rare nonpolymorphic mutation selected in vitro by an investigational INI. It has been reported to reduce susceptibility to RAL by 4-fold and to EVG by 12-fold. \n+IN\tV\t151\tI\tAccessory\tNo\tV151I is a polymorphic mutation selected in patients receiving RAL and in vitro by EVG. It appears to have little or no effect on INI susceptibility. \n+IN\tV\t151\tL\tMajor\tNo\tV151L is an extremely rare nonpolymorphic mutation selected in vitro by early investigational INIs but not in patients receiving current INIs. It reduces susceptibility to RAL, EVG, and DTG by ~10, ~40, and 3-fold, respectively. \n+IN\tS\t153\tY\tAccessory\tNo\tS153Y/F are extremely rare nonpolymorphic mutations selected in vitro by EVG (S153Y) and DTG (S153Y/F). S153Y/F reduce RAL and DTG susceptibility by ~2-fold and EVG susceptibility by ~4-fold. \n+IN\tS\t153\tF\tAccessory\tNo\tS153Y/F are extremely rare nonpolymorphic mutations selected in vitro by EVG (S153Y) and DTG (S153Y/F). S153Y/F reduce RAL and DTG susceptibility by ~2-fold and EVG susceptibility by ~4-fold. \n+IN\tN\t155\tH\tMajor\tYes\tN155H is a nonpolymorphic mutation selected in patients receiving RAL and EVG. Alone, it reduces RAL susceptibility ~15-fold and EVG susceptibility ~30-fold. Susceptibility is further reduced when N155H occurs in combination with E92Q and other primary or accessory INI-resistance mutations. N155H has been selected by DTG in RAL-experienced patients but does not reduce DTG susceptibility by itself.\n+IN\tN\t155\tS\tMajor\tYes\tN155H is a nonpolymorphic mutation selected in patients receiving RAL and EVG. Alone, it reduces RAL susceptibility ~15-fold and EVG susceptibility ~30-fold. Susceptibility is further reduced when N155H occurs in combination with E92Q and other primary or accessory INI-resistance mutations. N155H has been selected by DTG in RAL-experienced patients but does not reduce DTG susceptibility by itself. N155S/T are rare nonpolymorphic mutations selected in vitro by investigational INIs. N155S/T reduce RAL and EVG susceptibility somewhat less effectively than N155H \n+IN\tN\t155\tT\tMajor\tNo\tN155H is a nonpolymorphic mutation selected in patients receiving RAL and EVG. Alone, it reduces RAL susceptibility ~15-fold and EVG susceptibility ~30-fold. Susceptibility is further reduced when N155H occurs in combination with E92Q and other primary or accessory INI-resistance mutations. N155H has been selected by DTG in RAL-experienced patients but does not reduce DTG susceptibility by itself. N155S/T are rare nonpolymorphic mutations selected in vitro by investigational INIs. N155S/T reduce RAL and EVG susceptibility somewhat less effectively than N155H \n+IN\tE\t157\tQ\tAccessory\tNo\tE157Q is a polymorphic accessory mutation that is weakly selected in patients receiving RAL. It is selected in vitro by EVG. E157Q reduces RAL susceptibility by about 5-fold and EVG susceptibility by about 2-fold.\n+IN\tG\t163\tR\tAccessory\tNo\tG163R/K are nonpolymorphic mutations in all subtypes except subtype F. They are commonly selected in patients receiving RAL. Their effect on INI susceptibility has not been well studied.\n+IN\tG\t163\tK\tAccessory\tNo\tG163R/K are nonpolymorphic mutations in all subtypes except subtype F. They are commonly selected in patients receiving RAL. Their effect on INI susceptibility has not been well studied.\n+IN\tS\t230\tR\tAccessory\tNo\tS230R is a nonpolymorphic accessory mutation selected in vitro and in vivo by RAL and in vitro by EVG. It appears to have minimal, if any, effect on INI susceptibility.\n+IN\tS\t230\tN\tOther\tNo\tS230N is a polymorphism that is not associated with reduced INI susceptibility.\n+IN\tR\t263\tK\tAccessory\tNo\tR263K is a nonpolymorphic mutation selected in patients receiving RAL and DTG and in vitro by EVG and DTG. It reduces RAL, DTG, and EVG susceptibility about 2-fold, 2-fold, and 3 to 5-fold, respectively.\n' |
| b |
| diff -r 000000000000 -r 71976cfc9022 test-data/nt_variants.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/nt_variants.vcf Mon Dec 04 10:25:26 2017 -0500 |
| b |
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|
| b |
| diff -r 000000000000 -r 71976cfc9022 test-data/test.vcf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.vcf Mon Dec 04 10:25:26 2017 -0500 |
| b |
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