# HG changeset patch
# User dfornika
# Date 1560804159 14400
# Node ID 0bf16c8aca732bcca348cc78a1c48d7a8d345581
# Parent 0e733df972b56009fe9cbb614b6f72fcc3fe2b5c
planemo upload commit 60e2302cfac90d0c909ef61815aaaafaaad5816a-dirty
diff -r 0e733df972b5 -r 0bf16c8aca73 snippy-core.xml
--- a/snippy-core.xml Tue Mar 12 17:37:29 2019 -0400
+++ b/snippy-core.xml Mon Jun 17 16:42:39 2019 -0400
@@ -1,3 +1,4 @@
+
Combine multiple Snippy outputs into a core SNP alignment
@@ -7,15 +8,16 @@
-
+
@@ -43,10 +45,10 @@
-
+
-
+
@@ -71,6 +73,5 @@
snippy **must** have been run with --cleanup False
]]>
-
diff -r 0e733df972b5 -r 0bf16c8aca73 snippy.xml
--- a/snippy.xml Tue Mar 12 17:37:29 2019 -0400
+++ b/snippy.xml Mon Jun 17 16:42:39 2019 -0400
@@ -1,4 +1,4 @@
-
+
Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
@@ -18,7 +18,8 @@
#end if
snippy
--outdir 'out'
- --cpus "\${GALAXY_SLOTS:-1}"
+ --cpus \${GALAXY_SLOTS:-1}
+ --ram \$((\${GALAXY_MEMORY_MB:-4096}/1024))
#if $ref.is_of_type("fasta")
--ref 'ref.fna'
#end if
@@ -33,22 +34,19 @@
--rgid '$adv.rgid'
#end if
#if $adv.bwaopt
- --bwaopt '$advanced.bwaopt'
+ --bwaopt '$adv.bwaopt'
#end if
#if str( $fastq_input.fastq_input_selector ) == "paired"
--R1 '$fastq_input.fastq_input1'
--R2 '$fastq_input.fastq_input2'
- #end if
- #if str( $fastq_input.fastq_input_selector ) == "paired_collection"
+ #elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
--R1 '$fastq_input.fastq_input.forward'
--R2 '$fastq_input.fastq_input.reverse'
- #end if
- #if str( $fastq_input.fastq_input_selector ) == "single"
- --se '$fastq_input.fastq_input'
- #end if
- #if str( $fastq_input.fastq_input_selector ) == "paired_iv"
- --peil '$fastq_input.fastq_input'
+ #elif str( $fastq_input.fastq_input_selector ) == "single"
+ --se '$fastq_input.fastq_input_single'
+ #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
+ --peil '$fastq_input.fastq_input_interleaved'
#end if
&&
@@ -58,8 +56,10 @@
#set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
#elif str( $fastq_input.fastq_input_selector ) == "paired_collection"
#set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.name)
- #else
- #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input.element_identifier)
+ #elif str( $fastq_input.fastq_input_selector ) == "single"
+ #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_single.element_identifier)
+ #elif str( $fastq_input.fastq_input_selector ) == "paired_iv"
+ #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input_interleaved.element_identifier)
#end if
mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ &&
@@ -87,13 +87,13 @@
-
+
-
+
@@ -101,10 +101,10 @@
-
+
-
+
@@ -167,8 +167,8 @@
-
-
+
+
@@ -179,8 +179,8 @@
-
-
+
+
@@ -195,10 +195,20 @@
-
-
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 0e733df972b5 -r 0bf16c8aca73 snippy_core_wrapper.pl
--- a/snippy_core_wrapper.pl Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,82 +0,0 @@
-#!/usr/bin/env perl
-
-#--------------------------------------
-#
-# snippy_core_wrapper.pl
-#
-# This is an intermediary script between snippy-core.xml and snippy-core
-# It:
-# - Copys the supplied zipped snippy output files to the working dir
-# - Untars them to their datafile name
-# - Builds the snippy-core command
-# - Runs the snippy-core command
-#
-#--------------------------------------
-
-use warnings;
-use strict;
-use File::Copy;
-use File::Basename;
-
-my(@Options, $indirs, $ref);
-setOptions();
-
-my @list_of_dirs = split /\s+/, $indirs;
-
-#The list of final directories to be passed to snippy-core will be stored here.
-my @snippy_outs;
-
-foreach my $d (@list_of_dirs){
- print STDERR "$d\n";
- my $bn = basename($d);
- my ($name, $dir, $ext) = fileparse($d, '\..*');
- copy($d, $bn);
- print STDERR "$d, $bn, $name, $dir, $ext\n";
- `tar -xf $bn`;
-}
-
-my $test_list = `ls -d */`;
-$test_list =~ s/\///g;
-print STDERR "$test_list\n";
-
-@snippy_outs = split /\s+/, $test_list;
-
-
-my $commandline = "snippy-core ";
-
-$commandline .= " --ref $ref " if $ref;
-$commandline .= join(" ", @snippy_outs);
-print STDERR "snippy-core commandline: $commandline\n";
-
-my $ok = system($commandline);
-
-#----------------------------------------------------------------------
-# Option setting routines
-
-sub setOptions {
- use Getopt::Long;
-
- @Options = (
- {OPT=>"help", VAR=>\&usage, DESC=>"This help"},
- {OPT=>"ref=s", VAR=>\$ref, DEFAULT=>"", DESC=>"Reference genome."},
- {OPT=>"indirs=s", VAR=>\$indirs, DEFAULT=>"", DESC=>"A whitespace delimited list of the snippy output zipped dirs."},
- );
-
- &GetOptions(map {$_->{OPT}, $_->{VAR}} @Options) || usage();
-
- # Now setup default values.
- foreach (@Options) {
- if (defined($_->{DEFAULT}) && !defined(${$_->{VAR}})) {
- ${$_->{VAR}} = $_->{DEFAULT};
- }
- }
-}
-
-sub usage {
- print "Usage: $0 [options] -i inputfile > ... \n";
- foreach (@Options) {
- printf " --%-13s %s%s.\n",$_->{OPT},$_->{DESC},
- defined($_->{DEFAULT}) ? " (default '$_->{DEFAULT}')" : "";
- }
- exit(1);
-}
diff -r 0e733df972b5 -r 0bf16c8aca73 snippy_core_wrapper.py
--- a/snippy_core_wrapper.py Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,44 +0,0 @@
-#!/usr/bin/env python
-
-# --------------------------------------
-#
-# snippy_core_wrapper.py
-#
-# This is an intermediary script between snippy-core.xml and snippy-core
-# It:
-# - Copys the supplied zipped snippy output files to the working dir
-# - Untars them to their datafile name
-# - Builds the snippy-core command
-# - Runs the snippy-core command
-#
-# --------------------------------------
-
-import argparse
-import os
-import subprocess
-from shutil import copyfile
-
-
-def main():
-
- parser = argparse.ArgumentParser()
- parser.add_argument('-r', '--ref', help='Reference fasta', required=True)
- parser.add_argument('-i', '--indirs', help='Comma-separated list of input datasets')
- args = parser.parse_args()
-
- snippy_core_command_line = ['snippy-core', '--ref', args.ref]
-
- for input_dataset in args.indirs.split(','):
- base_name = os.path.basename(input_dataset)
- copyfile(input_dataset, base_name)
- subprocess.Popen(['tar', '-xf', base_name]).wait()
-
- extracted_dirs = [f for f in os.listdir('.') if os.path.isdir(f) ]
- for extracted_dir in extracted_dirs:
- snippy_core_command_line.append(extracted_dir)
-
- subprocess.Popen(snippy_core_command_line).wait()
-
-
-if __name__ == '__main__':
- main()
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/a.dat
Binary file test-data/a.dat has changed
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/a.tgz
Binary file test-data/a.tgz has changed
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/a_b_c.core.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/a_b_c.core.txt Mon Jun 17 16:42:39 2019 -0400
@@ -0,0 +1,5 @@
+ID LENGTH ALIGNED UNALIGNED VARIANT HET MASKED LOWCOV
+a 700 51 649 0 0 0 0
+b 700 51 649 1 0 0 0
+c 700 51 649 1 0 0 0
+Reference 700 700 0 0 0 0 0
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/a_fna_ref_mincov_2_minqual_60.snps.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/a_fna_ref_mincov_2_minqual_60.snps.gff Mon Jun 17 16:42:39 2019 -0400
@@ -0,0 +1,1 @@
+##gff-version 3
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/a_fna_ref_mincov_2_minqual_60.snps.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/a_fna_ref_mincov_2_minqual_60.snps.txt Mon Jun 17 16:42:39 2019 -0400
@@ -0,0 +1,6 @@
+DateTime 1970-01-01T00:00:00
+ReadFiles a_1.fastq a_2.fastq
+Reference reference.fasta
+ReferenceSize 700
+Software snippy 4.3.6
+VariantTotal 0
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b.dat
Binary file test-data/b.dat has changed
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b.tgz
Binary file test-data/b.tgz has changed
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_2_fna_ref_mincov_2_minqual_60.snps.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_2_fna_ref_mincov_2_minqual_60.snps.gff Mon Jun 17 16:42:39 2019 -0400
@@ -0,0 +1,2 @@
+##gff-version 3
+reference snippy:4.3.6 variation 4 4 . . 0 note=snp A=>T T:5 A:0
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_fna_ref_mincov_2_minqual_60.snps.gff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_fna_ref_mincov_2_minqual_60.snps.gff Mon Jun 17 16:42:39 2019 -0400
@@ -0,0 +1,2 @@
+##gff-version 3
+reference snippy:4.3.6 variation 4 4 . . 0 note=snp A=>T T:10 A:0
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_fna_ref_mincov_2_minqual_60.snps.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_fna_ref_mincov_2_minqual_60.snps.txt Mon Jun 17 16:42:39 2019 -0400
@@ -0,0 +1,7 @@
+DateTime 1970-01-01T00:00:00
+ReadFiles b_1.fastq b_2.fastq
+Reference reference.fasta
+ReferenceSize 700
+Software snippy 4.3.6
+Variant-SNP 1
+VariantTotal 1
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/ref.fa
--- a/test-data/b_out_dev/ref.fa Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
->reference
-TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA
-GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT
-CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT
-GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT
-ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC
-AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC
-AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA
-AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT
-TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA
-ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG
-TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT
-TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/ref.fa.fai
--- a/test-data/b_out_dev/ref.fa.fai Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference 700 11 60 61
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/reference/genomes/ref.fa
--- a/test-data/b_out_dev/reference/genomes/ref.fa Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
->reference
-TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA
-GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT
-CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT
-GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT
-ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC
-AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC
-AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA
-AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT
-TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA
-ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG
-TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT
-TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/reference/ref.fa
--- a/test-data/b_out_dev/reference/ref.fa Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
->reference
-TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA
-GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT
-CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT
-GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT
-ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC
-AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC
-AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA
-AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT
-TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA
-ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG
-TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT
-TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/reference/ref.fa.amb
--- a/test-data/b_out_dev/reference/ref.fa.amb Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-700 1 0
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/reference/ref.fa.ann
--- a/test-data/b_out_dev/reference/ref.fa.ann Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-700 1 11
-0 reference (null)
-0 700 0
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/reference/ref.fa.bwt
Binary file test-data/b_out_dev/reference/ref.fa.bwt has changed
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/reference/ref.fa.fai
--- a/test-data/b_out_dev/reference/ref.fa.fai Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference 700 11 60 61
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/reference/ref.fa.pac
Binary file test-data/b_out_dev/reference/ref.fa.pac has changed
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/reference/ref.fa.sa
Binary file test-data/b_out_dev/reference/ref.fa.sa has changed
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/reference/ref.gff
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/reference/ref.txt
--- a/test-data/b_out_dev/reference/ref.txt Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference:0-700
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/reference/ref/genes.gff.gz
Binary file test-data/b_out_dev/reference/ref/genes.gff.gz has changed
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/snps.aligned.fa
--- a/test-data/b_out_dev/snps.aligned.fa Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
->reference
-TCCTCAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACT---------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-----------------------------------------
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/snps.bam
Binary file test-data/b_out_dev/snps.bam has changed
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/snps.bam.bai
Binary file test-data/b_out_dev/snps.bam.bai has changed
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/snps.bed
--- a/test-data/b_out_dev/snps.bed Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference 3 4
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/snps.consensus.fa
--- a/test-data/b_out_dev/snps.consensus.fa Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
->reference
-TCCTCAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA
-GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT
-CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT
-GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT
-ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC
-AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC
-AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA
-AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT
-TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA
-ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG
-TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT
-TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/snps.consensus.subs.fa
--- a/test-data/b_out_dev/snps.consensus.subs.fa Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
->reference
-TCCTCAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA
-GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT
-CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT
-GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT
-ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC
-AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC
-AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA
-AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT
-TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA
-ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG
-TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT
-TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/snps.csv
--- a/test-data/b_out_dev/snps.csv Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-CHROM,POS,TYPE,REF,ALT,EVIDENCE,FTYPE,STRAND,NT_POS,AA_POS,EFFECT,LOCUS_TAG,GENE,PRODUCT
-reference,4,snp,A,T,T:10 A:0
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/snps.filt.vcf
--- a/test-data/b_out_dev/snps.filt.vcf Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-##fileformat=VCFv4.2
-##FILTER=
-##fileDate=20190312
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=
-##phasing=none
-##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700"
-##INFO=
-##INFO=
-##INFO=
-##INFO=
-##INFO=
-##INFO=
-##INFO=
-##FORMAT=
-##FORMAT=
-##FORMAT=
-##FORMAT=
-##FORMAT=
-##FORMAT=
-##FORMAT=
-##bcftools_viewVersion=1.9+htslib-1.9
-##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Tue Mar 12 14:35:28 2019
-##bcftools_annotateVersion=1.9+htslib-1.9
-##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Tue Mar 12 14:35:28 2019
-#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT b
-reference 4 . A T 321.326 . AB=0;AO=10;DP=10;QA=400;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:10:0:0:10:400:-36.3607,-3.0103,0
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/snps.gff
--- a/test-data/b_out_dev/snps.gff Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-##gff-version 3
-reference snippy:4.3.6 variation 4 4 . . 0 note=snp A=>T T:10 A:0
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/snps.html
--- a/test-data/b_out_dev/snps.html Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-
-
-| CHROM
- | POS
- | TYPE
- | REF
- | ALT
- | EVIDENCE
- | FTYPE
- | STRAND
- | NT_POS
- | AA_POS
- | EFFECT
- | LOCUS_TAG
- | GENE
- | PRODUCT
- |
-| reference
- | 4
- | snp
- | A
- | T
- | T:10 A:0
- |
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/snps.log
--- a/test-data/b_out_dev/snps.log Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,261 +0,0 @@
-### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
-
-### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --outdir b_out_dev --ref ref.fna --mapqual 60 --mincov 2 --minfrac 0.9 --minqual 60.0 --R1 b_1.fastq --R2 b_2.fastq
-
-### samtools faidx reference/ref.fa
-
-
-### bwa index reference/ref.fa
-
-[bwa_index] Pack FASTA... 0.00 sec
-[bwa_index] Construct BWT for the packed sequence...
-[bwa_index] 0.00 seconds elapse.
-[bwa_index] Update BWT... 0.00 sec
-[bwa_index] Pack forward-only FASTA... 0.00 sec
-[bwa_index] Construct SA from BWT and Occ... 0.00 sec
-[main] Version: 0.7.17-r1188
-[main] CMD: bwa index reference/ref.fa
-[main] Real time: 0.009 sec; CPU: 0.003 sec
-
-### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa
-
-
-### ln -sf reference/ref.fa .
-
-
-### ln -sf reference/ref.fa.fai .
-
-
-### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz
-
-
-### bwa mem -Y -M -R '@RG\tID:b_out_dev\tSM:b_out_dev' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.9396. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.9396. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.9396. -r -s - - > snps.bam
-
-READ 10 WRITTEN 10
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 0 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 0
-
-### samtools index snps.bam
-
-
-### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt
-
-
-### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf
-
-
-### bcftools view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf
-
-
-### cp snps.filt.vcf snps.vcf
-
-
-### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab
-
-Loading reference: reference/ref.fa
-Loaded 1 sequences.
-Loading features: reference/ref.gff
-Parsing variants: snps.vcf
-Converted 1 SNPs to TAB format.
-
-### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf
-
-
-### bcftools convert -Oz -o snps.vcf.gz snps.vcf
-
-
-### bcftools index -f snps.vcf.gz
-
-
-### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz
-
-Note: the --sample option not given, applying all records regardless of the genotype
-
-### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf
-
-
-### bcftools index -f snps.subs.vcf.gz
-
-
-### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz
-
-Note: the --sample option not given, applying all records regardless of the genotype
-
-### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi
-
-### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
-
-### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --force --outdir b_out_dev --rgid b --ref ref.fna --mapqual 60 --mincov 2 --minfrac 0.9 --minqual 60.0 --R1 b_1.fastq --R2 b_2.fastq
-
-### samtools faidx reference/ref.fa
-
-
-### bwa index reference/ref.fa
-
-[bwa_index] Pack FASTA... 0.00 sec
-[bwa_index] Construct BWT for the packed sequence...
-[bwa_index] 0.00 seconds elapse.
-[bwa_index] Update BWT... 0.00 sec
-[bwa_index] Pack forward-only FASTA... 0.00 sec
-[bwa_index] Construct SA from BWT and Occ... 0.00 sec
-[main] Version: 0.7.17-r1188
-[main] CMD: bwa index reference/ref.fa
-[main] Real time: 0.008 sec; CPU: 0.002 sec
-
-### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa
-
-
-### ln -sf reference/ref.fa .
-
-
-### ln -sf reference/ref.fa.fai .
-
-
-### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz
-
-
-### bwa mem -Y -M -R '@RG\tID:b\tSM:b' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.10001. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.10001. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.10001. -r -s - - > snps.bam
-
-READ 10 WRITTEN 10
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 0 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 0
-
-### samtools index snps.bam
-
-
-### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt
-
-
-### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf
-
-
-### bcftools view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf
-
-
-### cp snps.filt.vcf snps.vcf
-
-
-### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab
-
-Loading reference: reference/ref.fa
-Loaded 1 sequences.
-Loading features: reference/ref.gff
-Parsing variants: snps.vcf
-Converted 1 SNPs to TAB format.
-
-### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf
-
-
-### bcftools convert -Oz -o snps.vcf.gz snps.vcf
-
-
-### bcftools index -f snps.vcf.gz
-
-
-### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz
-
-Note: the --sample option not given, applying all records regardless of the genotype
-
-### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf
-
-
-### bcftools index -f snps.subs.vcf.gz
-
-
-### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz
-
-Note: the --sample option not given, applying all records regardless of the genotype
-
-### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi
-
-### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
-
-### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --force --outdir b_out_dev --rgid b --ref ref.fna --mapqual 60 --mincov 2 --minfrac 0.9 --minqual 60.0 --R1 b_1.fastq --R2 b_2.fastq
-
-### samtools faidx reference/ref.fa
-
-
-### bwa index reference/ref.fa
-
-[bwa_index] Pack FASTA... 0.00 sec
-[bwa_index] Construct BWT for the packed sequence...
-[bwa_index] 0.00 seconds elapse.
-[bwa_index] Update BWT... 0.00 sec
-[bwa_index] Pack forward-only FASTA... 0.00 sec
-[bwa_index] Construct SA from BWT and Occ... 0.00 sec
-[main] Version: 0.7.17-r1188
-[main] CMD: bwa index reference/ref.fa
-[main] Real time: 0.009 sec; CPU: 0.003 sec
-
-### mkdir -p reference/genomes && cp -f reference/ref.fa reference/genomes/ref.fa
-
-
-### ln -sf reference/ref.fa .
-
-
-### ln -sf reference/ref.fa.fai .
-
-
-### mkdir -p reference/ref && gzip -c reference/ref.gff > reference/ref/genes.gff.gz
-
-
-### bwa mem -Y -M -R '@RG\tID:b\tSM:b' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.22109. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.22109. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.22109. -r -s - - > snps.bam
-
-READ 10 WRITTEN 10
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 0 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 0
-
-### samtools index snps.bam
-
-
-### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt
-
-
-### freebayes-parallel reference/ref.txt 8 -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam > snps.raw.vcf
-
-
-### bcftools view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf | vt normalize -r reference/ref.fa - | bcftools annotate --remove '^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL' > snps.filt.vcf
-
-
-### cp snps.filt.vcf snps.vcf
-
-
-### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_to_tab --gff reference/ref.gff --ref reference/ref.fa --vcf snps.vcf > snps.tab
-
-Loading reference: reference/ref.fa
-Loaded 1 sequences.
-Loading features: reference/ref.gff
-Parsing variants: snps.vcf
-Converted 1 SNPs to TAB format.
-
-### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy-vcf_extract_subs snps.filt.vcf > snps.subs.vcf
-
-
-### bcftools convert -Oz -o snps.vcf.gz snps.vcf
-
-
-### bcftools index -f snps.vcf.gz
-
-
-### bcftools consensus -f reference/ref.fa -o snps.consensus.fa snps.vcf.gz
-
-Note: the --sample option not given, applying all records regardless of the genotype
-
-### bcftools convert -Oz -o snps.subs.vcf.gz snps.subs.vcf
-
-
-### bcftools index -f snps.subs.vcf.gz
-
-
-### bcftools consensus -f reference/ref.fa -o snps.consensus.subs.fa snps.subs.vcf.gz
-
-Note: the --sample option not given, applying all records regardless of the genotype
-
-### rm -f snps.subs.vcf.gz snps.subs.vcf.gz.csi snps.subs.vcf.gz.tbi
-
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/snps.raw.vcf
--- a/test-data/b_out_dev/snps.raw.vcf Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,62 +0,0 @@
-##fileformat=VCFv4.2
-##fileDate=20190312
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=
-##phasing=none
-##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700"
-##INFO=
-##INFO=
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-##INFO=
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-##INFO=
-##INFO=
-##INFO=
-##INFO=
-##INFO=
-##INFO=
-##INFO=
-##INFO=
-##INFO=
-##INFO=
-##INFO=
-##INFO=
-##INFO=
-##INFO=
-##INFO=
-##INFO=
-##FORMAT=
-##FORMAT=
-##FORMAT=
-##FORMAT=
-##FORMAT=
-##FORMAT=
-##FORMAT=
-##FORMAT=
-##FORMAT=
-##FORMAT=
-#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT b
-reference 4 . A T 321.326 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=10;CIGAR=1X;DP=10;DPB=10;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=18.4681;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=400;QR=0;RO=0;RPL=0;RPP=24.725;RPPR=0;RPR=10;RUN=1;SAF=5;SAP=3.0103;SAR=5;SRF=0;SRP=0;SRR=0;TYPE=snp GT:DP:AD:RO:QR:AO:QA:GL 1/1:10:0,10:0:0:10:400:-36.3607,-3.0103,0
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/snps.subs.vcf
--- a/test-data/b_out_dev/snps.subs.vcf Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-##fileformat=VCFv4.2
-##snippy="snippy-vcf_extract_subs snps.filt.vcf"
-##fileformat=VCFv4.2
-##FILTER=
-##fileDate=20190312
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=
-##phasing=none
-##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700"
-##INFO=
-##INFO=
-##INFO=
-##INFO=
-##FORMAT=
-##FORMAT=
-##FORMAT=
-##FORMAT=
-##FORMAT=
-##FORMAT=
-##bcftools_viewVersion=1.9+htslib-1.9
-##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Tue Mar 12 14:35:28 2019
-##bcftools_annotateVersion=1.9+htslib-1.9
-##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Tue Mar 12 14:35:28 2019
-##INFO=
-#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT b
-reference 4 . A T 321.326 . TYPE=snp;DP=10;RO=0;AO=10 GT:DP:RO:AO:QR:QA 1/1:10:0:10:0:400
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/snps.tab
--- a/test-data/b_out_dev/snps.tab Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-CHROM POS TYPE REF ALT EVIDENCE FTYPE STRAND NT_POS AA_POS EFFECT LOCUS_TAG GENE PRODUCT
-reference 4 snp A T T:10 A:0
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/snps.txt
--- a/test-data/b_out_dev/snps.txt Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-DateTime 2019-03-12T14:35:28
-ReadFiles /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/b_2.fastq
-Reference /home/dfornika/Code/tools-iuc/tools/snippy/test-data/ref.fna
-ReferenceSize 700
-Software snippy 4.3.6
-Variant-SNP 1
-VariantTotal 1
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/snps.vcf
--- a/test-data/b_out_dev/snps.vcf Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-##fileformat=VCFv4.2
-##FILTER=
-##fileDate=20190312
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=
-##phasing=none
-##commandline="freebayes -p 2 -P 0 -C 2 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 2 -F 0.05 -f reference/ref.fa snps.bam --region reference:0-700"
-##INFO=
-##INFO=
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-##INFO=
-##INFO=
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-##FORMAT=
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-##FORMAT=
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-##bcftools_viewVersion=1.9+htslib-1.9
-##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60.0 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0.9' snps.raw.vcf; Date=Tue Mar 12 14:35:28 2019
-##bcftools_annotateVersion=1.9+htslib-1.9
-##bcftools_annotateCommand=annotate --remove ^INFO/TYPE,^INFO/DP,^INFO/RO,^INFO/AO,^INFO/AB,^FORMAT/GT,^FORMAT/DP,^FORMAT/RO,^FORMAT/AO,^FORMAT/QR,^FORMAT/QA,^FORMAT/GL; Date=Tue Mar 12 14:35:28 2019
-#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT b
-reference 4 . A T 321.326 . AB=0;AO=10;DP=10;QA=400;QR=0;RO=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 1/1:10:0:0:10:400:-36.3607,-3.0103,0
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/snps.vcf.gz
Binary file test-data/b_out_dev/snps.vcf.gz has changed
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/b_out_dev/snps.vcf.gz.csi
Binary file test-data/b_out_dev/snps.vcf.gz.csi has changed
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/c.dat
Binary file test-data/c.dat has changed
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/c.tgz
Binary file test-data/c.tgz has changed
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/core/core.txt
--- a/test-data/core/core.txt Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
-ID LENGTH ALIGNED UNALIGNED VARIANT HET MASKED LOWCOV
-a 700 51 649 0 0 0 0
-b 700 51 649 1 0 0 0
-c 700 51 649 1 0 0 0
-Reference 700 700 0 0 0 0 0
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/fna_ref_a/snps.gff
--- a/test-data/fna_ref_a/snps.gff Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-##gff-version 3
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/fna_ref_a/snps.txt
--- a/test-data/fna_ref_a/snps.txt Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-DateTime 1970-01-01T00:00:00
-ReadFiles a_1.fastq a_2.fastq
-Reference reference.fasta
-ReferenceSize 700
-Software snippy 4.3.6
-VariantTotal 0
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/fna_ref_b/snps.gff
--- a/test-data/fna_ref_b/snps.gff Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-##gff-version 3
-reference snippy:4.3.6 variation 4 4 . . 0 note=snp A=>T T:10 A:0
diff -r 0e733df972b5 -r 0bf16c8aca73 test-data/fna_ref_b/snps.txt
--- a/test-data/fna_ref_b/snps.txt Tue Mar 12 17:37:29 2019 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-DateTime 1970-01-01T00:00:00
-ReadFiles b_1.fastq b_2.fastq
-Reference reference.fasta
-ReferenceSize 700
-Software snippy 4.3.6
-Variant-SNP 1
-VariantTotal 1