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changeset 58:d53281e6edae

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planemo upload
author jpayne
date Mon, 17 Jun 2024 02:57:10 -0400
parents d3095ad12f24
children 49d672730d3e
files 0_index_ref.xml.old 1_map_reads.xml 2_call_sites.xml 3_filter_regions.xml 4_merge_sites.xml 5_call_consensus.xml 6_merge_vcfs.xml 7_smp_matrix.xml CFSAN_SNP_Pipeline.ga Mambaforge-Linux-x86_64.sh snp-filter.py snp-pipeline.xml.old test-data/metrics.tsv test-data/reference/lambda_virus.fasta test-data/reference/lambda_virus.fasta.fai test-data/reference/reference.1.bt2 test-data/reference/reference.2.bt2 test-data/reference/reference.3.bt2 test-data/reference/reference.4.bt2 test-data/reference/reference.rev.1.bt2 test-data/reference/reference.rev.2.bt2 test-data/reference/reference.tar.gz test-data/referenceSNP.fasta test-data/samples/sample1/consensus.fasta test-data/samples/sample1/consensus.vcf test-data/samples/sample1/consensus_preserved.vcf test-data/samples/sample1/duplicate_reads_metrics.txt test-data/samples/sample1/metrics test-data/samples/sample1/reads.sam test-data/samples/sample1/reads.sorted.bam test-data/samples/sample1/reads.sorted.deduped.bam test-data/samples/sample1/reads.unsorted.bam test-data/samples/sample1/sample1_1.fastq test-data/samples/sample1/sample1_1.fastq.gz test-data/samples/sample1/sample1_2.fastq test-data/samples/sample1/sample1_2.fastq.gz test-data/samples/sample1/var.flt.vcf test-data/samples/sample1/var.flt_preserved.vcf test-data/samples/sample1/var.flt_removed.vcf test-data/samples/sample2/consensus.fasta test-data/samples/sample2/consensus.vcf test-data/samples/sample2/consensus_preserved.fasta test-data/samples/sample2/consensus_preserved.vcf test-data/samples/sample2/duplicate_reads_metrics.txt test-data/samples/sample2/metrics test-data/samples/sample2/reads.all.pileup test-data/samples/sample2/reads.sam test-data/samples/sample2/reads.sorted.bam test-data/samples/sample2/reads.sorted.deduped.bam test-data/samples/sample2/reads.unsorted.bam test-data/samples/sample2/sample2_1.fastq test-data/samples/sample2/sample2_2.fastq test-data/samples/sample2/var.flt.vcf test-data/samples/sample2/var.flt_preserved.vcf test-data/samples/sample2/var.flt_removed.vcf test-data/samples/sample3/consensus.fasta test-data/samples/sample3/consensus.vcf test-data/samples/sample3/consensus_preserved.fasta test-data/samples/sample3/consensus_preserved.vcf test-data/samples/sample3/duplicate_reads_metrics.txt test-data/samples/sample3/metrics test-data/samples/sample3/reads.all.pileup test-data/samples/sample3/reads.sam test-data/samples/sample3/reads.sorted.bam test-data/samples/sample3/reads.sorted.deduped.bam test-data/samples/sample3/reads.unsorted.bam test-data/samples/sample3/sample3_1.fastq test-data/samples/sample3/sample3_2.fastq test-data/samples/sample3/var.flt.vcf test-data/samples/sample3/var.flt_preserved.vcf test-data/samples/sample3/var.flt_removed.vcf test-data/samples/sample4/consensus.fasta test-data/samples/sample4/consensus.vcf test-data/samples/sample4/consensus_preserved.fasta test-data/samples/sample4/consensus_preserved.vcf test-data/samples/sample4/duplicate_reads_metrics.txt test-data/samples/sample4/metrics test-data/samples/sample4/reads.all.pileup test-data/samples/sample4/reads.sam test-data/samples/sample4/reads.sorted.bam test-data/samples/sample4/reads.sorted.deduped.bam test-data/samples/sample4/reads.unsorted.bam test-data/samples/sample4/sample4_1.fastq test-data/samples/sample4/sample4_2.fastq test-data/samples/sample4/var.flt.vcf test-data/samples/sample4/var.flt_preserved.vcf test-data/samples/sample4/var.flt_removed.vcf test-data/snp_distance_matrix.tsv test-data/snp_distance_pairwise.tsv test-data/snpma.fasta test-data/snpma.vcf tool-data/all_fasta.loc.sample tool_data_table_conf.xml.sample
diffstat 11 files changed, 98 insertions(+), 30 deletions(-) [+]
line wrap: on
line diff
--- a/1_map_reads.xml	Fri Nov 06 12:50:48 2020 -0500
+++ b/1_map_reads.xml	Mon Jun 17 02:57:10 2024 -0400
@@ -1,10 +1,11 @@
 <tool id="map_reads" name="1. Map Reads" version="1.0.1" profile="16.10">
     <description>to index, or lookup cached alignment</description>
     <requirements>
-        <requirement type="package" version="1.0.6">bzip2</requirement>
-        <requirement type="package" version="2.3.5">bowtie2</requirement>
+        <container type="docker">quay.io/biocontainers/mulled-v2-d736175c8392ecaa2a26c372df9ad15b78f8d5b8:d59a38d618c862df52cf9dae223ed9d93ed7225b-0</container>
+        <requirement type="package" version="1.0.8">bzip2</requirement>
+        <requirement type="package" version="2.4.5">bowtie2</requirement>
         <requirement type="package" version="1.9.134">boto3</requirement>
-        <requirement type="package" version="3.6.8">python</requirement>
+        <!-- <requirement type="package" version="3.6.8">python</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
--- a/2_call_sites.xml	Fri Nov 06 12:50:48 2020 -0500
+++ b/2_call_sites.xml	Mon Jun 17 02:57:10 2024 -0400
@@ -1,13 +1,14 @@
 <tool id="call_sites" name="2. Call Sites" version="1.0.1" profile="16.10">
     <description>of high-confidence SNPs, or lookup cached sitecall</description>
     <requirements>
-        <requirement type="package" version="2.3.5">bowtie2</requirement>
+        <container type="docker">quay.io/biocontainers/mulled-v2-e518cb713b80020daa244e2ce559c37edb42dcde:5cb90165033bd74a97d0a807f439cf4b1aaabb89-0</container>
+        <requirement type="package" version="2.4.5">bowtie2</requirement>
         <requirement type="package" version="1.9">samtools</requirement>
-        <requirement type="package" version="1.0.6">bzip2</requirement>
-        <requirement type="package">picard</requirement>
-        <requirement type="package">varscan</requirement>
+        <requirement type="package" version="1.0.8">bzip2</requirement>
+        <requirement type="package" version="2.27.4">picard</requirement>
+        <requirement type="package" version="2.4.4">varscan</requirement>
         <requirement type="package" version="1.9.134">boto3</requirement>
-        <requirement type="package" version="3.6.8">python</requirement>
+        <!-- <requirement type="package" version="3.6.8">python</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
     export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
--- a/3_filter_regions.xml	Fri Nov 06 12:50:48 2020 -0500
+++ b/3_filter_regions.xml	Mon Jun 17 02:57:10 2024 -0400
@@ -1,11 +1,12 @@
 <tool id="filter_regions" name="3. Filter SNP Regions" version="1.0.1" profile="16.10">
     <description>based on SNP location, or lookup cached filtered sitecall</description>
     <requirements>
+        <container type="docker">quay.io/biocontainers/mulled-v2-b387422e12acd8cf2ba9f5f1b0f12c36f93c00b7:b1c910a35786ca780412af4d314af0670e08604f-0</container>
         <requirement type="package" version="1.9">samtools</requirement>
-        <requirement type="package" version="1.0.6">bzip2</requirement>
-        <requirement type="package" version="2.0.2">snp-pipeline</requirement>
+        <requirement type="package" version="1.0.8">bzip2</requirement>
+        <requirement type="package" version="2.2.1">snp-pipeline</requirement>
         <requirement type="package" version="1.9.134">boto3</requirement>
-        <requirement type="package" version="3.6.8">python</requirement>
+        <!-- <requirement type="package" version="3.6.8">python</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
--- a/4_merge_sites.xml	Fri Nov 06 12:50:48 2020 -0500
+++ b/4_merge_sites.xml	Mon Jun 17 02:57:10 2024 -0400
@@ -1,11 +1,12 @@
 <tool id="merge_sites" name="4. Merge Sites" version="1.0.1" profile="16.10">
     <description>from multiple samples</description>
     <requirements>
-        <requirement type="package" version="2.3.5">bowtie2</requirement>
+        <container type="docker">quay.io/biocontainers/mulled-v2-a9689be5d4f7dc232fcd76f2f32bef2b80afcb49:0560aee94873e022862623c7766c9634a09b9513-0</container>
+        <requirement type="package" version="2.4.5">bowtie2</requirement>
         <requirement type="package" version="1.9">samtools</requirement>
-        <requirement type="package" version="1.0.6">bzip2</requirement>
-        <requirement type="package" version="2.0.2">snp-pipeline</requirement>
-        <requirement type="package" version="3.6.8">python</requirement>
+        <requirement type="package" version="1.0.8">bzip2</requirement>
+        <requirement type="package" version="2.2.1">snp-pipeline</requirement>
+        <!-- <requirement type="package" version="3.6.8">python</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
@@ -32,7 +33,7 @@
                     <element name="sample4" value="samples/sample4/var.flt_preserved.vcf" ftype="fastqsanger" />
                 </collection>
             </param>
-            <!-- <output name="snplist" value="snplist.txt" /> -->
+            <output name="snplist" value="snplist.txt" />
         </test>
     </tests>
     <help><![CDATA[
--- a/5_call_consensus.xml	Fri Nov 06 12:50:48 2020 -0500
+++ b/5_call_consensus.xml	Mon Jun 17 02:57:10 2024 -0400
@@ -1,10 +1,11 @@
 <tool id="call_consensus" name="5. Call consensus SNPs" version="1.0.1" profile="16.10">
     <description>for a sample, or lookup cached consensus SNP calls</description>
     <requirements>
-        <requirement type="package" version="1.0.6">bzip2</requirement>
-        <requirement type="package" version="2.0.2">snp-pipeline</requirement>
+        <container type="docker">quay.io/biocontainers/mulled-v2-fe715cf36e5a6063362b28e50f1f4a1a767770d5:8f94687b7d8826f1473b7e97df0cea2a960b35bf-0</container>
+        <requirement type="package" version="1.0.8">bzip2</requirement>
+        <requirement type="package" version="2.2.1">snp-pipeline</requirement>
         <requirement type="package" version="1.9.134">boto3</requirement>
-        <requirement type="package" version="3.6.8">python</requirement>
+        <!-- <requirement type="package" version="3.6.8">python</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
--- a/6_merge_vcfs.xml	Fri Nov 06 12:50:48 2020 -0500
+++ b/6_merge_vcfs.xml	Mon Jun 17 02:57:10 2024 -0400
@@ -1,12 +1,13 @@
 <tool id="merge_vcfs" name="6. Merge VCFs" version="1.0.1" profile="16.10">
     <description>into a multi-sample VCF with consensus SNPs</description>
     <requirements>
+        <container type="docker">quay.io/biocontainers/mulled-v2-72d480da2f80e0804df2fc75273988c6dba1648d:f354c444b518b0ada8e031aa2984346e2f5d8837-0</container>
         <requirement type="package" version="1.9">bcftools</requirement>
-        <requirement type="package" version="1.0.6">bzip2</requirement>
-        <requirement type="package" version="2.0.2">snp-pipeline</requirement>
-        <requirement type="package" version="0.2.5">tabix</requirement>
+        <requirement type="package" version="1.0.8">bzip2</requirement>
+        <requirement type="package" version="2.2.1">snp-pipeline</requirement>
+        <requirement type="package" version="0.2.6">tabix</requirement>
         <requirement type="package" version="1.9">htslib</requirement>
-        <requirement type="package" version="3.6.8">python</requirement>
+        <!-- <requirement type="package" version="3.6.8">python</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
--- a/7_smp_matrix.xml	Fri Nov 06 12:50:48 2020 -0500
+++ b/7_smp_matrix.xml	Mon Jun 17 02:57:10 2024 -0400
@@ -1,11 +1,12 @@
 <tool id="snp_matrix" name="7. Create a SNP matrix" version="1.0.1" profile="16.10">
     <description>and associated distance metrics</description>
     <requirements>
+        <container type="docker">quay.io/biocontainers/mulled-v2-d2e223d7ac457e81243657cd7ae8336bd1c16e8e:81b350b3fbf165cbf5db53022037a2657a660701-0</container>
         <requirement type="package" version="1.9">bcftools</requirement>
-        <requirement type="package" version="1.0.6">bzip2</requirement>
-        <requirement type="package" version="2.0.2">snp-pipeline</requirement>
-        <requirement type="package" version="0.2.5">tabix</requirement>
-        <requirement type="package" version="3.6.8">python</requirement>
+        <requirement type="package" version="1.0.8">bzip2</requirement>
+        <requirement type="package" version="2.2.1">snp-pipeline</requirement>
+        <requirement type="package" version="0.2.6">tabix</requirement>
+        <!-- <requirement type="package" version="3.6.8">python</requirement> -->
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
         export LD_LIBRARY_PATH="\$CONDA_DEFAULT_ENV/lib" &&
Binary file Mambaforge-Linux-x86_64.sh has changed
--- a/test-data/samples/sample1/reads.sam	Fri Nov 06 12:50:48 2020 -0500
+++ b/test-data/samples/sample1/reads.sam	Mon Jun 17 02:57:10 2024 -0400
@@ -1,6 +1,6 @@
 @HD	VN:1.0	SO:unsorted
 @SQ	SN:gi|9626243|ref|NC_001416.1|	LN:48502
-@PG	ID:bowtie2	PN:bowtie2	VN:2.3.3.1	CL:"/usr/local/bin/bowtie2-align-s --wrapper basic-0 --reorder -X 1000 -p 2 -x reference/lambda_virus -1 samples/sample1/sample1_1.fastq -2 samples/sample1/sample1_2.fastq"
+@PG	ID:bowtie2	PN:bowtie2	VN:2.3.5.1	CL:"/home/chet/miniconda3/envs/mulled-v1-3aaacfa732fb5a9a4edb89d75dc27c600fe12abcc61b59ef7e28f09be834e1ba/bin/bowtie2-align-s --wrapper basic-0 -q -x ./reference -p 1 --reorder -X 1000 -1 ./forward.gz -2 ./reverse.gz"
 r1	83	gi|9626243|ref|NC_001416.1|	16266	42	97M	=	16003	-360	GCAATACAGCGGTATCTGGGACGGAACGTTTAAACCGGCATACAGCAACAACATGGCCTGGCGTCTGTGGGATTTGCTGACCCATCCGCGCTACGGC	*5:441C0)"E,A%72$9-"1%A:8%-0<80-;6H8%7643HB>9*;8BED.D#.2?44:4'5)0<6F6F1*C71A.D;G0G<2<9.6/B:3")?4'	AS:i:-6	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:61T11A23	YS:i:0	YT:Z:CP
 r1	163	gi|9626243|ref|NC_001416.1|	16003	42	58M	=	16266	360	GTGGTGATGGGTAACCTGCCGCCGCGCCCGTTTAATATCCGGATGCGCAGGATGACGC	);A!/,6B:8=(*2GE1FGA>0/,?>),%.,/3+@D(C=<53!$H"HE-$79*HD?4<	AS:i:0	XN:i:0	XM:i:0	XO:i:0	XG:i:0	NM:i:0	MD:Z:58	YS:i:-6	YT:Z:CP
 r2	83	gi|9626243|ref|NC_001416.1|	35315	42	60M	=	35108	-267	CCTGTTTCTCTGCGNGACGTTCGCGGCGGCGTNTTTGTGCATCCATCTGGATTCTCCTGT	E*CD88'0F(71,0A>GA4:@@+CB%@/8369*H2%!"0CE/BE<:4F)3&1BF&:*7#2	AS:i:-2	XN:i:0	XM:i:2	XO:i:0	XG:i:0	NM:i:2	MD:Z:14C17G27	YS:i:-6	YT:Z:CP
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samples/sample1/var.flt_preserved.vcf	Mon Jun 17 02:57:10 2024 -0400
@@ -0,0 +1,61 @@
+##fileformat=VCFv4.1
+##source=VarScan2
+##INFO=<ID=ADP,Number=1,Type=Integer,Description="Average per-sample depth of bases with Phred score >= 15">
+##INFO=<ID=WT,Number=1,Type=Integer,Description="Number of samples called reference (wild-type)">
+##INFO=<ID=HET,Number=1,Type=Integer,Description="Number of samples called heterozygous-variant">
+##INFO=<ID=HOM,Number=1,Type=Integer,Description="Number of samples called homozygous-variant">
+##INFO=<ID=NC,Number=1,Type=Integer,Description="Number of samples not called">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=SDP,Number=1,Type=Integer,Description="Raw Read Depth as reported by SAMtools">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Quality Read Depth of bases with Phred score >= 15">
+##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
+##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
+##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
+##FORMAT=<ID=PVAL,Number=1,Type=String,Description="P-value from Fisher's Exact Test">
+##FORMAT=<ID=RBQ,Number=1,Type=Integer,Description="Average quality of reference-supporting bases (qual1)">
+##FORMAT=<ID=ABQ,Number=1,Type=Integer,Description="Average quality of variant-supporting bases (qual2)">
+##FORMAT=<ID=RDF,Number=1,Type=Integer,Description="Depth of reference-supporting bases on forward strand (reads1plus)">
+##FORMAT=<ID=RDR,Number=1,Type=Integer,Description="Depth of reference-supporting bases on reverse strand (reads1minus)">
+##FORMAT=<ID=ADF,Number=1,Type=Integer,Description="Depth of variant-supporting bases on forward strand (reads2plus)">
+##FORMAT=<ID=ADR,Number=1,Type=Integer,Description="Depth of variant-supporting bases on reverse strand (reads2minus)">
+##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
+##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
+#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Sample1
+gi|9626243|ref|NC_001416.1|	753	.	G	A	.	PASS	ADP=24;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:129:25:24:0:23:100%:1.2146E-13:0:27:0:0:15:8
+gi|9626243|ref|NC_001416.1|	1079	.	T	C	.	PASS	ADP=25;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:135:26:25:0:24:100%:3.101E-14:0:26:0:0:9:15
+gi|9626243|ref|NC_001416.1|	1540	.	A	G	.	PASS	ADP=22;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:123:24:22:0:22:100%:4.7526E-13:0:24:0:0:13:9
+gi|9626243|ref|NC_001416.1|	1804	.	G	C	.	PASS	ADP=23;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:129:23:23:0:23:100%:1.2146E-13:0:28:0:0:11:12
+gi|9626243|ref|NC_001416.1|	2123	.	G	C	.	PASS	ADP=23;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:129:24:23:0:23:100%:1.2146E-13:0:27:0:0:10:13
+gi|9626243|ref|NC_001416.1|	3351	.	C	G	.	PASS	ADP=22;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:123:24:22:0:22:100%:4.7526E-13:0:28:0:0:10:12
+gi|9626243|ref|NC_001416.1|	3656	.	T	G	.	PASS	ADP=23;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:129:25:23:0:23:100%:1.2146E-13:0:25:0:0:12:11
+gi|9626243|ref|NC_001416.1|	6824	.	A	C	.	PASS	ADP=18;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:99:19:18:0:18:100%:1.1019E-10:0:26:0:0:10:8
+gi|9626243|ref|NC_001416.1|	7897	.	G	A	.	PASS	ADP=23;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:129:26:23:0:23:100%:1.2146E-13:0:25:0:0:11:12
+gi|9626243|ref|NC_001416.1|	9175	.	A	G	.	PASS	ADP=22;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:123:22:22:0:22:100%:4.7526E-13:0:28:0:0:8:14
+gi|9626243|ref|NC_001416.1|	12717	.	G	C	.	PASS	ADP=25;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:135:29:25:0:24:100%:3.101E-14:0:28:0:0:10:14
+gi|9626243|ref|NC_001416.1|	12795	.	C	T	.	PASS	ADP=26;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:146:27:26:0:26:100%:2.0165E-15:0:29:0:0:16:10
+gi|9626243|ref|NC_001416.1|	12959	.	T	G	.	PASS	ADP=21;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:117:22:21:0:21:100%:1.8578E-12:0:25:0:0:13:8
+gi|9626243|ref|NC_001416.1|	16654	.	C	G	.	PASS	ADP=23;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:129:24:23:0:23:100%:1.2146E-13:0:26:0:0:14:9
+gi|9626243|ref|NC_001416.1|	16715	.	T	G	.	PASS	ADP=18;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:99:19:18:0:18:100%:1.1019E-10:0:25:0:0:8:10
+gi|9626243|ref|NC_001416.1|	18598	.	C	G	.	PASS	ADP=22;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:123:25:22:0:22:100%:4.7526E-13:0:24:0:0:12:10
+gi|9626243|ref|NC_001416.1|	19469	.	G	T	.	PASS	ADP=18;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:99:21:18:0:18:100%:1.1019E-10:0:28:0:0:11:7
+gi|9626243|ref|NC_001416.1|	20099	.	C	T	.	PASS	ADP=28;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:158:28:28:0:28:100%:1.3074E-16:0:29:0:0:14:14
+gi|9626243|ref|NC_001416.1|	21110	.	T	G	.	PASS	ADP=16;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:87:18:16:0:16:100%:1.6637E-9:0:26:0:0:5:11
+gi|9626243|ref|NC_001416.1|	23362	.	T	A	.	PASS	ADP=11;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:58:14:11:0:11:100%:1.4176E-6:0:26:0:0:3:8
+gi|9626243|ref|NC_001416.1|	24319	.	G	T	.	PASS	ADP=18;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:99:19:18:0:18:100%:1.1019E-10:0:26:0:0:7:11
+gi|9626243|ref|NC_001416.1|	24766	.	G	A	.	PASS	ADP=17;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:93:19:17:0:17:100%:4.2852E-10:0:24:0:0:6:11
+gi|9626243|ref|NC_001416.1|	27790	.	A	C	.	PASS	ADP=18;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:93:20:18:0:17:100%:4.2852E-10:0:26:0:0:6:11
+gi|9626243|ref|NC_001416.1|	29891	.	G	C	.	PASS	ADP=20;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:111:21:20:0:20:100%:7.2544E-12:0:26:0:0:9:11
+gi|9626243|ref|NC_001416.1|	31551	.	A	G	.	PASS	ADP=15;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:81:16:15:0:15:100%:6.4467E-9:0:25:0:0:7:8
+gi|9626243|ref|NC_001416.1|	32086	.	T	A	.	PASS	ADP=15;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:69:17:15:1:14:93.33%:1.0315E-7:33:28:1:0:7:7
+gi|9626243|ref|NC_001416.1|	33000	.	C	T	.	PASS	ADP=17;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:93:18:17:0:17:100%:4.2852E-10:0:26:0:0:7:10
+gi|9626243|ref|NC_001416.1|	33591	.	T	G	.	PASS	ADP=30;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:170:30:30:0:30:100%:8.4556E-18:0:26:0:0:16:14
+gi|9626243|ref|NC_001416.1|	36010	.	C	T	.	PASS	ADP=9;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:46:9:9:0:9:100%:2.0568E-5:0:26:0:0:0:9
+gi|9626243|ref|NC_001416.1|	37208	.	G	C	.	PASS	ADP=19;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:105:19:19:0:19:100%:2.8292E-11:0:29:0:0:8:11
+gi|9626243|ref|NC_001416.1|	38165	.	T	C	.	PASS	ADP=27;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:152:29:27:0:27:100%:5.1363E-16:0:23:0:0:17:10
+gi|9626243|ref|NC_001416.1|	39485	.	A	C	.	PASS	ADP=20;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:111:20:20:0:20:100%:7.2544E-12:0:29:0:0:10:10
+gi|9626243|ref|NC_001416.1|	40457	.	T	C	.	PASS	ADP=27;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:138:28:27:1:26:96.3%:1.4382E-14:24:25:1:0:11:15
+gi|9626243|ref|NC_001416.1|	42439	.	A	C	.	PASS	ADP=24;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:135:28:24:0:24:100%:3.101E-14:0:26:0:0:16:8
+gi|9626243|ref|NC_001416.1|	43306	.	T	G	.	PASS	ADP=32;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:176:33:32:0:31:100%:2.1486E-18:0:27:0:0:11:20
+gi|9626243|ref|NC_001416.1|	46237	.	G	A	.	PASS	ADP=27;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:152:27:27:0:27:100%:5.1363E-16:0:26:0:0:12:15
+gi|9626243|ref|NC_001416.1|	47893	.	G	A	.	PASS	ADP=23;WT=0;HET=0;HOM=1;NC=0	GT:GQ:SDP:DP:RD:AD:FREQ:PVAL:RBQ:ABQ:RDF:RDR:ADF:ADR	1/1:129:28:23:0:23:100%:1.2146E-13:0:25:0:0:12:11
--- a/test-data/snpma.vcf	Fri Nov 06 12:50:48 2020 -0500
+++ b/test-data/snpma.vcf	Mon Jun 17 02:57:10 2024 -0400
@@ -19,8 +19,8 @@
 ##FILTER=<ID=StrBias0,Description="Fraction of variant supporting reads below 0.00 on one strand">
 ##FILTER=<ID=Region,Description="Position is in dense region of snps or near the end of the contig.">
 ##contig=<ID=gi|9626243|ref|NC_001416.1|>
-##bcftools_mergeVersion=1.3.1+htslib-1.3.1
-##bcftools_mergeCommand=merge -o ./snpma.vcf --merge all --info-rules NS:sum ./tmp.vcf.PYaZFQ/sample1.vcf.gz ./tmp.vcf.PYaZFQ/sample2.vcf.gz ./tmp.vcf.PYaZFQ/sample3.vcf.gz ./tmp.vcf.PYaZFQ/sample4.vcf.gz
+##bcftools_mergeVersion=1.9+htslib-1.9
+##bcftools_mergeCommand=merge -o snpma.vcf --merge all --info-rules NS:sum tmp.vcf.3imm9gjk/sample1.vcf.gz tmp.vcf.3imm9gjk/sample2.vcf.gz tmp.vcf.3imm9gjk/sample3.vcf.gz tmp.vcf.3imm9gjk/sample4.vcf.gz; Date=Mon Aug  1 12:20:35 2022
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample1	sample2	sample3	sample4
 gi|9626243|ref|NC_001416.1|	403	.	G	A	.	PASS	NS=4	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	1:27:0:27:0:0:13:14:PASS	0:24:24:0:11:13:0:0:PASS	0:26:26:0:13:13:0:0:PASS	0:15:15:0:11:4:0:0:PASS
 gi|9626243|ref|NC_001416.1|	550	.	G	A	.	PASS	NS=4	GT:SDP:RD:AD:RDF:RDR:ADF:ADR:FT	0:22:21:1:13:8:0:1:PASS	0:26:26:0:14:12:0:0:PASS	0:29:29:0:13:16:0:0:PASS	1:26:0:26:0:0:14:12:PASS