changeset 21:0e733df972b5 draft

planemo upload commit d65fe6718a4e9a9fa6dba28e6702335222c3e221-dirty
author dfornika
date Tue, 12 Mar 2019 17:37:29 -0400
parents 3bbfe41787af
children 0bf16c8aca73
files snippy.xml test-data/a/ref.fa test-data/a/ref.fa.fai test-data/a/reference/genomes/ref.fa test-data/a/reference/ref.fa test-data/a/reference/ref.fa.amb test-data/a/reference/ref.fa.ann test-data/a/reference/ref.fa.bwt test-data/a/reference/ref.fa.fai test-data/a/reference/ref.fa.pac test-data/a/reference/ref.fa.sa test-data/a/reference/ref.gff test-data/a/reference/ref.txt test-data/a/reference/ref/genes.gff.gz test-data/a/snps.aligned.fa test-data/a/snps.bam test-data/a/snps.bam.bai test-data/a/snps.bed test-data/a/snps.consensus.fa test-data/a/snps.consensus.subs.fa test-data/a/snps.csv test-data/a/snps.filt.vcf test-data/a/snps.gff test-data/a/snps.html test-data/a/snps.log test-data/a/snps.raw.vcf test-data/a/snps.subs.vcf test-data/a/snps.tab test-data/a/snps.txt test-data/a/snps.vcf test-data/a/snps.vcf.gz test-data/a/snps.vcf.gz.csi test-data/b/ref.fa test-data/b/ref.fa.fai test-data/b/reference/genomes/ref.fa test-data/b/reference/ref.fa test-data/b/reference/ref.fa.amb test-data/b/reference/ref.fa.ann test-data/b/reference/ref.fa.bwt test-data/b/reference/ref.fa.fai test-data/b/reference/ref.fa.pac test-data/b/reference/ref.fa.sa test-data/b/reference/ref.gff test-data/b/reference/ref.txt test-data/b/reference/ref/genes.gff.gz test-data/b/snps.aligned.fa test-data/b/snps.bam test-data/b/snps.bam.bai test-data/b/snps.bed test-data/b/snps.consensus.fa test-data/b/snps.consensus.subs.fa test-data/b/snps.csv test-data/b/snps.filt.vcf test-data/b/snps.gff test-data/b/snps.html test-data/b/snps.log test-data/b/snps.raw.vcf test-data/b/snps.subs.vcf test-data/b/snps.tab test-data/b/snps.txt test-data/b/snps.vcf test-data/b/snps.vcf.gz test-data/b/snps.vcf.gz.csi test-data/b_gbk/ref.fa test-data/b_gbk/ref.fa.fai test-data/b_gbk/reference/genomes/ref.fa test-data/b_gbk/reference/ref.fa test-data/b_gbk/reference/ref.fa.amb test-data/b_gbk/reference/ref.fa.ann test-data/b_gbk/reference/ref.fa.bwt test-data/b_gbk/reference/ref.fa.fai test-data/b_gbk/reference/ref.fa.pac test-data/b_gbk/reference/ref.fa.sa test-data/b_gbk/reference/ref.gff test-data/b_gbk/reference/ref.txt test-data/b_gbk/reference/ref/genes.gff.gz test-data/b_gbk/reference/ref/snpEffectPredictor.bin test-data/b_gbk/reference/snpeff.config test-data/b_gbk/snps.bam test-data/b_gbk/snps.bam.bai test-data/b_gbk/snps.filt.vcf test-data/b_gbk/snps.log test-data/b_gbk/snps.raw.vcf test-data/b_gbk/snps.vcf test-data/b_out_dev/ref.fa test-data/b_out_dev/ref.fa.fai test-data/b_out_dev/reference/genomes/ref.fa test-data/b_out_dev/reference/ref.fa test-data/b_out_dev/reference/ref.fa.amb test-data/b_out_dev/reference/ref.fa.ann test-data/b_out_dev/reference/ref.fa.bwt test-data/b_out_dev/reference/ref.fa.fai test-data/b_out_dev/reference/ref.fa.pac test-data/b_out_dev/reference/ref.fa.sa test-data/b_out_dev/reference/ref.gff test-data/b_out_dev/reference/ref.txt test-data/b_out_dev/reference/ref/genes.gff.gz test-data/b_out_dev/snps.aligned.fa test-data/b_out_dev/snps.bam test-data/b_out_dev/snps.bam.bai test-data/b_out_dev/snps.bed test-data/b_out_dev/snps.consensus.fa test-data/b_out_dev/snps.consensus.subs.fa test-data/b_out_dev/snps.csv test-data/b_out_dev/snps.filt.vcf test-data/b_out_dev/snps.gff test-data/b_out_dev/snps.html test-data/b_out_dev/snps.log test-data/b_out_dev/snps.raw.vcf test-data/b_out_dev/snps.subs.vcf test-data/b_out_dev/snps.tab test-data/b_out_dev/snps.txt test-data/b_out_dev/snps.vcf test-data/b_out_dev/snps.vcf.gz test-data/b_out_dev/snps.vcf.gz.csi test-data/c/ref.fa test-data/c/ref.fa.fai test-data/c/reference/genomes/ref.fa test-data/c/reference/ref.fa test-data/c/reference/ref.fa.amb test-data/c/reference/ref.fa.ann test-data/c/reference/ref.fa.bwt test-data/c/reference/ref.fa.fai test-data/c/reference/ref.fa.pac test-data/c/reference/ref.fa.sa test-data/c/reference/ref.gff test-data/c/reference/ref.txt test-data/c/reference/ref/genes.gff.gz test-data/c/snps.aligned.fa test-data/c/snps.bam test-data/c/snps.bam.bai test-data/c/snps.bed test-data/c/snps.consensus.fa test-data/c/snps.consensus.subs.fa test-data/c/snps.csv test-data/c/snps.filt.vcf test-data/c/snps.gff test-data/c/snps.html test-data/c/snps.log test-data/c/snps.raw.vcf test-data/c/snps.subs.vcf test-data/c/snps.tab test-data/c/snps.txt test-data/c/snps.vcf test-data/c/snps.vcf.gz test-data/c/snps.vcf.gz.csi test-data/c_gbk/ref.fa test-data/c_gbk/ref.fa.fai test-data/c_gbk/reference/genomes/ref.fa test-data/c_gbk/reference/ref.fa test-data/c_gbk/reference/ref.fa.amb test-data/c_gbk/reference/ref.fa.ann test-data/c_gbk/reference/ref.fa.bwt test-data/c_gbk/reference/ref.fa.fai test-data/c_gbk/reference/ref.fa.pac test-data/c_gbk/reference/ref.fa.sa test-data/c_gbk/reference/ref.gff test-data/c_gbk/reference/ref.txt test-data/c_gbk/reference/ref/genes.gff.gz test-data/c_gbk/reference/ref/snpEffectPredictor.bin test-data/c_gbk/reference/snpeff.config test-data/c_gbk/snps.bam test-data/c_gbk/snps.bam.bai test-data/c_gbk/snps.filt.vcf test-data/c_gbk/snps.log test-data/c_gbk/snps.raw.vcf test-data/c_gbk/snps.vcf test-data/fna_ref_b_testing/ref.fa test-data/fna_ref_b_testing/ref.fa.fai test-data/fna_ref_b_testing/reference/genomes/ref.fa test-data/fna_ref_b_testing/reference/ref.fa test-data/fna_ref_b_testing/reference/ref.fa.amb test-data/fna_ref_b_testing/reference/ref.fa.ann test-data/fna_ref_b_testing/reference/ref.fa.bwt test-data/fna_ref_b_testing/reference/ref.fa.fai test-data/fna_ref_b_testing/reference/ref.fa.pac test-data/fna_ref_b_testing/reference/ref.fa.sa test-data/fna_ref_b_testing/reference/ref.gff test-data/fna_ref_b_testing/reference/ref.txt test-data/fna_ref_b_testing/reference/ref/genes.gff.gz test-data/fna_ref_b_testing/snps.aligned.fa test-data/fna_ref_b_testing/snps.bam test-data/fna_ref_b_testing/snps.bam.bai test-data/fna_ref_b_testing/snps.bed test-data/fna_ref_b_testing/snps.consensus.fa test-data/fna_ref_b_testing/snps.consensus.subs.fa test-data/fna_ref_b_testing/snps.csv test-data/fna_ref_b_testing/snps.filt.vcf test-data/fna_ref_b_testing/snps.gff test-data/fna_ref_b_testing/snps.html test-data/fna_ref_b_testing/snps.log test-data/fna_ref_b_testing/snps.raw.vcf test-data/fna_ref_b_testing/snps.subs.vcf test-data/fna_ref_b_testing/snps.tab test-data/fna_ref_b_testing/snps.txt test-data/fna_ref_b_testing/snps.vcf test-data/fna_ref_b_testing/snps.vcf.gz test-data/fna_ref_b_testing/snps.vcf.gz.csi test-data/gbk_ref_b/snps.vcf test-data/prokka-out/PROKKA_02062019.err test-data/prokka-out/PROKKA_02062019.faa test-data/prokka-out/PROKKA_02062019.ffn test-data/prokka-out/PROKKA_02062019.fna test-data/prokka-out/PROKKA_02062019.fsa test-data/prokka-out/PROKKA_02062019.gbk test-data/prokka-out/PROKKA_02062019.gff test-data/prokka-out/PROKKA_02062019.log test-data/prokka-out/PROKKA_02062019.sqn test-data/prokka-out/PROKKA_02062019.tbl test-data/prokka-out/PROKKA_02062019.tsv test-data/prokka-out/PROKKA_02062019.txt test-data/ref.fna test-data/reference.fasta.fai test-data/reference.gbk test-data/snippy-core-out/core.aln test-data/snippy-core-out/core.full.aln test-data/snippy-core-out/core.ref.fa test-data/snippy-core-out/core.tab test-data/snippy-core-out/core.txt test-data/snippy-core-out/core.vcf
diffstat 211 files changed, 547 insertions(+), 3833 deletions(-) [+]
line wrap: on
line diff
--- a/snippy.xml	Fri Mar 08 20:46:56 2019 -0500
+++ b/snippy.xml	Tue Mar 12 17:37:29 2019 -0400
@@ -30,7 +30,7 @@
             --minfrac $adv.minfrac
             --minqual $adv.minqual
             #if $adv.rgid
-                --rgid '$advanced.rgid'
+                --rgid '$adv.rgid'
             #end if
             #if $adv.bwaopt
                 --bwaopt '$advanced.bwaopt'
@@ -56,12 +56,17 @@
         #import re
         #if str( $fastq_input.fastq_input_selector ) == "paired"
             #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)
         #end if
 
         mkdir -p ${dir_name} && cp -r out/reference out/snps.tab out/snps.aligned.fa out/snps.vcf ${dir_name}/ &&
         tar -czf out.tgz ${dir_name}
+        #if "outcon" in str($outputs) and $adv.rename_cons
+          && sed -i 's/>.*/>${dir_name}/' out/snps.consensus.fa
+        #end if
 
 
     ]]></command>
@@ -99,6 +104,7 @@
 	    <param name="minqual" type="float" value="100.0" label="Minumum QUALITY in VCF column 6" help="Minumum QUALITY in VCF column 6" />
             <param name="rgid" type="text" value="" label="Bam header @RG ID" help="Use this @RG ID: in the BAM header" />
             <param name="bwaopt" type="text" value="" label="Extra BWA MEM options" help="Extra BWA MEM options, eg. -x pacbio" />
+	    <param name="rename_cons" type="boolean" truevalue="rename_cons" falsevalue="" help="When producing an output of the reference genome with variants instantiated, edit the header so that it is named after the input VCF" />
         </section>
 
         <param name="outputs" type="select" multiple="true" display="checkboxes" label="Output selection">
--- a/test-data/a/ref.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /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
--- a/test-data/a/ref.fa.fai	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference	700	11	60	61
--- a/test-data/a/reference/genomes/ref.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /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
--- a/test-data/a/reference/ref.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /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
--- a/test-data/a/reference/ref.fa.amb	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-700 1 0
--- a/test-data/a/reference/ref.fa.ann	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-700 1 11
-0 reference (null)
-0 700 0
Binary file test-data/a/reference/ref.fa.bwt has changed
--- a/test-data/a/reference/ref.fa.fai	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference	700	11	60	61
Binary file test-data/a/reference/ref.fa.pac has changed
Binary file test-data/a/reference/ref.fa.sa has changed
--- a/test-data/a/reference/ref.txt	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference:0-700
Binary file test-data/a/reference/ref/genes.gff.gz has changed
--- a/test-data/a/snps.aligned.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
->reference
-TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACT---------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-----------------------------------------
Binary file test-data/a/snps.bam has changed
Binary file test-data/a/snps.bam.bai has changed
--- a/test-data/a/snps.consensus.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /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
--- a/test-data/a/snps.consensus.subs.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /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
--- a/test-data/a/snps.csv	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-CHROM,POS,TYPE,REF,ALT,EVIDENCE,FTYPE,STRAND,NT_POS,AA_POS,EFFECT,LOCUS_TAG,GENE,PRODUCT
--- a/test-data/a/snps.filt.vcf	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-##fileformat=VCFv4.2
-##FILTER=<ID=PASS,Description="All filters passed">
-##fileDate=20190206
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=<ID=reference,length=700>
-##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=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
-##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
-##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
-##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
-##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
-##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
-##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
-##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
-##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
-##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
-##bcftools_viewVersion=1.9+htslib-1.9
-##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb  6 11:34:57 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=Wed Feb  6 11:34:57 2019
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	a
--- a/test-data/a/snps.gff	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-##gff-version 3
--- a/test-data/a/snps.html	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
-<TABLE ID='snps' BORDER=1>
-<TR>
-<TH>CHROM
-<TH>POS
-<TH>TYPE
-<TH>REF
-<TH>ALT
-<TH>EVIDENCE
-<TH>FTYPE
-<TH>STRAND
-<TH>NT_POS
-<TH>AA_POS
-<TH>EFFECT
-<TH>LOCUS_TAG
-<TH>GENE
-<TH>PRODUCT
-</TABLE>
--- a/test-data/a/snps.log	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,348 +0,0 @@
-### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
-
-### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --outdir a --ref reference.fasta --R1 a_1.fastq --R2 a_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: 0.068 sec; CPU: 0.004 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:a\tSM:a' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/a_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/a_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.13194. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.13194. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.13194. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### 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 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05  -f reference/ref.fa snps.bam > snps.raw.vcf
-
-
-### bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' 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 0 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 --mincov 2 --force --outdir a --ref reference.fasta --R1 a_1.fastq --R2 a_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: 0.071 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:a\tSM:a' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/a_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/a_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.14292. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.14292. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.14292. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### 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>=100 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' 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 0 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 --mincov 2 --minqual 20 --force --outdir a --ref reference.fasta --R1 a_1.fastq --R2 a_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: 0.071 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:a\tSM:a' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/a_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/a_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.15235. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.15235. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.15235. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### 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>=20 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' 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 0 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 --mincov 2 --minqual 60 --force --outdir a --ref reference.fasta --R1 a_1.fastq --R2 a_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: 0.071 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:a\tSM:a' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/a_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/a_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.16998. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.16998. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.16998. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### 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 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' 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 0 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
-
--- a/test-data/a/snps.raw.vcf	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,61 +0,0 @@
-##fileformat=VCFv4.2
-##fileDate=20190206
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=<ID=reference,length=700>
-##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=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
-##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
-##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
-##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
-##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
-##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
-##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
-##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
-##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
-##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
-##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
-##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
-##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
-##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
-##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
-##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
-##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
-##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
-##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
-##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio.  Ratio between depth in samples with each called alternate allele and those without.">
-##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
-##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
-##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
-##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
-##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
-##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
-##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
-##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
-##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
-##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
-##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
-##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
-##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record.">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
-##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele">
-##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
-##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
-##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
-##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
-##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	a
--- a/test-data/a/snps.subs.vcf	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-##fileformat=VCFv4.2
-##snippy="snippy-vcf_extract_subs snps.filt.vcf"
-##fileformat=VCFv4.2
-##FILTER=<ID=PASS,Description="All filters passed">
-##fileDate=20190206
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=<ID=reference,length=700>
-##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=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
-##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
-##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
-##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
-##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
-##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
-##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
-##bcftools_viewVersion=1.9+htslib-1.9
-##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb  6 11:34:57 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=Wed Feb  6 11:34:57 2019
-##INFO=<ID=OLDVAR,Number=R,Type=String,Description="Original REF,ALT before decomposition">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	a
--- a/test-data/a/snps.tab	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-CHROM	POS	TYPE	REF	ALT	EVIDENCE	FTYPE	STRAND	NT_POS	AA_POS	EFFECT	LOCUS_TAG	GENE	PRODUCT
--- a/test-data/a/snps.txt	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,6 +0,0 @@
-DateTime	2019-02-06T11:34:56
-ReadFiles	/home/dfornika/Code/tools-iuc/tools/snippy/test-data/a_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/a_2.fastq
-Reference	/home/dfornika/Code/tools-iuc/tools/snippy/test-data/reference.fasta
-ReferenceSize	700
-Software	snippy 4.3.6
-VariantTotal	0
--- a/test-data/a/snps.vcf	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,27 +0,0 @@
-##fileformat=VCFv4.2
-##FILTER=<ID=PASS,Description="All filters passed">
-##fileDate=20190206
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=<ID=reference,length=700>
-##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=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
-##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
-##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
-##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
-##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
-##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
-##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
-##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
-##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
-##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
-##bcftools_viewVersion=1.9+htslib-1.9
-##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb  6 11:34:57 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=Wed Feb  6 11:34:57 2019
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	a
Binary file test-data/a/snps.vcf.gz has changed
Binary file test-data/a/snps.vcf.gz.csi has changed
--- a/test-data/b/ref.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /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
--- a/test-data/b/ref.fa.fai	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference	700	11	60	61
--- a/test-data/b/reference/genomes/ref.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /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
--- a/test-data/b/reference/ref.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /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
--- a/test-data/b/reference/ref.fa.amb	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-700 1 0
--- a/test-data/b/reference/ref.fa.ann	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-700 1 11
-0 reference (null)
-0 700 0
Binary file test-data/b/reference/ref.fa.bwt has changed
--- a/test-data/b/reference/ref.fa.fai	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference	700	11	60	61
Binary file test-data/b/reference/ref.fa.pac has changed
Binary file test-data/b/reference/ref.fa.sa has changed
--- a/test-data/b/reference/ref.txt	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference:0-700
Binary file test-data/b/reference/ref/genes.gff.gz has changed
--- a/test-data/b/snps.aligned.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
->reference
-TCCTCAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACT---------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-----------------------------------------
Binary file test-data/b/snps.bam has changed
Binary file test-data/b/snps.bam.bai has changed
--- a/test-data/b/snps.bed	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference	3	4
--- a/test-data/b/snps.consensus.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /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
--- a/test-data/b/snps.consensus.subs.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /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
--- a/test-data/b/snps.csv	Fri Mar 08 20:46:56 2019 -0500
+++ /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:2 A:0
--- a/test-data/b/snps.filt.vcf	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-##fileformat=VCFv4.2
-##FILTER=<ID=PASS,Description="All filters passed">
-##fileDate=20190206
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=<ID=reference,length=700>
-##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=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
-##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
-##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
-##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
-##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
-##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
-##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
-##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
-##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
-##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
-##bcftools_viewVersion=1.9+htslib-1.9
-##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb  6 12:11:01 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=Wed Feb  6 12:11:01 2019
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	b
-reference	4	.	A	T	63.8794	.	AB=0;AO=2;DP=2;QA=80;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:2:0:0:2:80:-7.59179,-0.60206,0
--- a/test-data/b/snps.gff	Fri Mar 08 20:46:56 2019 -0500
+++ /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:2 A:0
--- a/test-data/b/snps.html	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-<TABLE ID='snps' BORDER=1>
-<TR>
-<TH>CHROM
-<TH>POS
-<TH>TYPE
-<TH>REF
-<TH>ALT
-<TH>EVIDENCE
-<TH>FTYPE
-<TH>STRAND
-<TH>NT_POS
-<TH>AA_POS
-<TH>EFFECT
-<TH>LOCUS_TAG
-<TH>GENE
-<TH>PRODUCT
-<TR>
-<TD>reference
-<TD>4
-<TD>snp
-<TD>A
-<TD>T
-<TD>T:2 A:0
-</TABLE>
--- a/test-data/b/snps.log	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,435 +0,0 @@
-### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
-
-### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --outdir b --ref reference.fasta --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: 0.070 sec; CPU: 0.004 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.13430. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.13430. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.13430. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### 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 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05  -f reference/ref.fa snps.bam > snps.raw.vcf
-
-
-### bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' 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 0 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 --mincov 2 --force --outdir b --ref reference.fasta --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: 0.070 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.14512. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.14512. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.14512. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### 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>=100 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' 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 0 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 --mincov 2 --minqual 20 --force --outdir b --ref reference.fasta --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: 0.071 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.15458. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.15458. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.15458. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### 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>=20 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' 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 --mincov 2 --minqual 60 --force --outdir b --ref reference.fasta --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: 0.070 sec; CPU: 0.004 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.17221. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.17221. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.17221. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### 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 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' 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 --mincov 2 --minqual 60 --force --outdir b --ref reference.fasta --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: 0.071 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.23600. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.23600. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.23600. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### 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 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' 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
-
--- a/test-data/b/snps.raw.vcf	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,62 +0,0 @@
-##fileformat=VCFv4.2
-##fileDate=20190206
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=<ID=reference,length=700>
-##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=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
-##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
-##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
-##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
-##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
-##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
-##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
-##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
-##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
-##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
-##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
-##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
-##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
-##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
-##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
-##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
-##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
-##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
-##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
-##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio.  Ratio between depth in samples with each called alternate allele and those without.">
-##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
-##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
-##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
-##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
-##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
-##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
-##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
-##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
-##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
-##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
-##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
-##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
-##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record.">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
-##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele">
-##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
-##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
-##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
-##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
-##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	b
-reference	4	.	A	T	63.8794	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=7.37776;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=0;RO=0;RPL=0;RPP=7.35324;RPPR=0;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	1/1:2:0,2:0:0:2:80:-7.59179,-0.60206,0
--- a/test-data/b/snps.subs.vcf	Fri Mar 08 20:46:56 2019 -0500
+++ /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=<ID=PASS,Description="All filters passed">
-##fileDate=20190206
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=<ID=reference,length=700>
-##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=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
-##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
-##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
-##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
-##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
-##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
-##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
-##bcftools_viewVersion=1.9+htslib-1.9
-##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb  6 12:11:01 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=Wed Feb  6 12:11:01 2019
-##INFO=<ID=OLDVAR,Number=R,Type=String,Description="Original REF,ALT before decomposition">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	b
-reference	4	.	A	T	63.8794	.	TYPE=snp;DP=2;RO=0;AO=2	GT:DP:RO:AO:QR:QA	1/1:2:0:2:0:80
--- a/test-data/b/snps.tab	Fri Mar 08 20:46:56 2019 -0500
+++ /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:2 A:0								
--- a/test-data/b/snps.txt	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-DateTime	2019-02-06T12:11:00
-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/reference.fasta
-ReferenceSize	700
-Software	snippy 4.3.6
-Variant-SNP	1
-VariantTotal	1
--- a/test-data/b/snps.vcf	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-##fileformat=VCFv4.2
-##FILTER=<ID=PASS,Description="All filters passed">
-##fileDate=20190206
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=<ID=reference,length=700>
-##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=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
-##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
-##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
-##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
-##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
-##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
-##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
-##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
-##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
-##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
-##bcftools_viewVersion=1.9+htslib-1.9
-##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb  6 12:11:01 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=Wed Feb  6 12:11:01 2019
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	b
-reference	4	.	A	T	63.8794	.	AB=0;AO=2;DP=2;QA=80;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:2:0:0:2:80:-7.59179,-0.60206,0
Binary file test-data/b/snps.vcf.gz has changed
Binary file test-data/b/snps.vcf.gz.csi has changed
--- a/test-data/b_gbk/ref.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
->reference Listeria monocytogenes strain strain.
-TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA
-GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT
-CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT
-GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT
-ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC
-AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC
-AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA
-AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT
-TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA
-ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG
-TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT
-TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA
--- a/test-data/b_gbk/ref.fa.fai	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference	700	49	60	61
--- a/test-data/b_gbk/reference/genomes/ref.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
->reference Listeria monocytogenes strain strain.
-TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA
-GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT
-CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT
-GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT
-ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC
-AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC
-AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA
-AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT
-TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA
-ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG
-TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT
-TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA
--- a/test-data/b_gbk/reference/ref.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
->reference Listeria monocytogenes strain strain.
-TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA
-GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT
-CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT
-GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT
-ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC
-AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC
-AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA
-AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT
-TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA
-ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG
-TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT
-TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA
--- a/test-data/b_gbk/reference/ref.fa.amb	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-700 1 0
--- a/test-data/b_gbk/reference/ref.fa.ann	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-700 1 11
-0 reference Listeria monocytogenes strain strain.
-0 700 0
Binary file test-data/b_gbk/reference/ref.fa.bwt has changed
--- a/test-data/b_gbk/reference/ref.fa.fai	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference	700	49	60	61
Binary file test-data/b_gbk/reference/ref.fa.pac has changed
Binary file test-data/b_gbk/reference/ref.fa.sa has changed
--- a/test-data/b_gbk/reference/ref.gff	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-##gff-version 3
-reference	snippy	CDS	188	658	.	+	0	ID=KPFNHDNB_00001;codon_start=1;inference=ab initio prediction:Prodigal:2.6;locus_tag=KPFNHDNB_00001;product=hypothetical protein;transl_table=11;translation=MIFQRLLKTRDTEFYRVIQNRNIDDVFGYLLIHDKREPAEIDDFKVFAKSNINKEAFSVNIKKNHIYTMFFHFTDLEEEQEIPKFTKVIRFIEGLLSFQPETSHYVDNYLIKEKLIFEYPAEFEKIGEFAKYLVKLSGRKITIPDTTREKYIYLTQ
--- a/test-data/b_gbk/reference/ref.txt	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference:0-700
Binary file test-data/b_gbk/reference/ref/genes.gff.gz has changed
Binary file test-data/b_gbk/reference/ref/snpEffectPredictor.bin has changed
--- a/test-data/b_gbk/reference/snpeff.config	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-codon.Standard								: TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Vertebrate_Mitochondrial				: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/*, AGG/*, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Yeast_Mitochondrial					: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/T, CTC/T, CTA/T, CTG/T, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Mold_Mitochondrial					: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Protozoan_Mitochondrial				: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Coelenterate							: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Mitochondrial							: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Mycoplasma							: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Spiroplasma							: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Invertebrate_Mitochondrial			: TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Ciliate_Nuclear						: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Q, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Dasycladacean_Nuclear					: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Q, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Hexamita_Nuclear						: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Q, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Echinoderm_Mitochondrial				: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Flatworm_Mitochondrial				: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Euplotid_Nuclear						: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/C, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Bacterial_and_Plant_Plastid			: TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Alternative_Yeast_Nuclear				: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/S+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Ascidian_Mitochondrial				: TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/G, AGG/G, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Alternative_Flatworm_Mitochondrial	: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Y, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Blepharisma_Macronuclear				: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Chlorophycean_Mitochondrial			: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/L, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Trematode_Mitochondrial				: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Scenedesmus_obliquus_Mitochondrial	: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/*, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/L, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Thraustochytrium_Mitochondrial		: TTT/F, TTC/F, TTA/*, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-ref.genome : Snippy Reference
-	ref.chromosome : reference
-	ref.reference.codonTable : Bacterial_and_Plant_Plastid
Binary file test-data/b_gbk/snps.bam has changed
Binary file test-data/b_gbk/snps.bam.bai has changed
--- a/test-data/b_gbk/snps.filt.vcf	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-##fileformat=VCFv4.2
-##FILTER=<ID=PASS,Description="All filters passed">
-##fileDate=20190206
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=<ID=reference,length=700>
-##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=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
-##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
-##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
-##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
-##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
-##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
-##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
-##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
-##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
-##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
-##bcftools_viewVersion=1.9+htslib-1.9
-##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb  6 12:11:38 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=Wed Feb  6 12:11:38 2019
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	b_gbk
-reference	4	.	A	T	63.8794	.	AB=0;AO=2;DP=2;QA=80;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:2:0:0:2:80:-7.59179,-0.60206,0
--- a/test-data/b_gbk/snps.log	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,168 +0,0 @@
-### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
-
-### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --minqual 60 --force --outdir b_gbk --ref reference.gbk --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: 0.070 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
-
-
-### snpEff build -c reference/snpeff.config -dataDir . -gff3 ref
-
-
-### bwa mem  -Y -M -R '@RG\tID:b_gbk\tSM:b_gbk' -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.22845. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.22845. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.22845. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### 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 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' 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
-
-
-### snpEff ann -noLog -noStats -no-downstream -no-upstream -no-utr -t -c reference/snpeff.config -dataDir . ref snps.filt.vcf > snps.vcf
-
-### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
-
-### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --minqual 60 --force --outdir b_gbk --ref reference.gbk --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: 0.070 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
-
-
-### snpEff build -c reference/snpeff.config -dataDir . -gff3 ref
-
-
-### bwa mem  -Y -M -R '@RG\tID:b_gbk\tSM:b_gbk' -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.23270. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.23270. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.23270. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### 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 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' 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
-
-
-### snpEff ann -noLog -noStats -no-downstream -no-upstream -no-utr -t -c reference/snpeff.config -dataDir . ref snps.filt.vcf > snps.vcf
-
-### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
-
-### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --minqual 60 --force --outdir b_gbk --ref reference.gbk --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: 0.070 sec; CPU: 0.004 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
-
-
-### snpEff build -c reference/snpeff.config -dataDir . -gff3 ref
-
-
-### bwa mem  -Y -M -R '@RG\tID:b_gbk\tSM:b_gbk' -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.23837. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.23837. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.23837. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### 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 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' 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
-
-
-### snpEff ann -noLog -noStats -no-downstream -no-upstream -no-utr -t -c reference/snpeff.config -dataDir . ref snps.filt.vcf > snps.vcf
-
--- a/test-data/b_gbk/snps.raw.vcf	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,62 +0,0 @@
-##fileformat=VCFv4.2
-##fileDate=20190206
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=<ID=reference,length=700>
-##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=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
-##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
-##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
-##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
-##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
-##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
-##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
-##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
-##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
-##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
-##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
-##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
-##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
-##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
-##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
-##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
-##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
-##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
-##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
-##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio.  Ratio between depth in samples with each called alternate allele and those without.">
-##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
-##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
-##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
-##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
-##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
-##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
-##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
-##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
-##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
-##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
-##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
-##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
-##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record.">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
-##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele">
-##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
-##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
-##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
-##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
-##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	b_gbk
-reference	4	.	A	T	63.8794	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=7.37776;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=0;RO=0;RPL=0;RPP=7.35324;RPPR=0;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	1/1:2:0,2:0:0:2:80:-7.59179,-0.60206,0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/ref.fa	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,13 @@
+>reference
+TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA
+GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT
+CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT
+GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT
+ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC
+AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC
+AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA
+AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT
+TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA
+ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG
+TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT
+TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/ref.fa.fai	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,1 @@
+reference	700	11	60	61
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/reference/genomes/ref.fa	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,13 @@
+>reference
+TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA
+GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT
+CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT
+GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT
+ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC
+AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC
+AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA
+AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT
+TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA
+ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG
+TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT
+TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/reference/ref.fa	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,13 @@
+>reference
+TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA
+GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT
+CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT
+GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT
+ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC
+AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC
+AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA
+AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT
+TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA
+ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG
+TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT
+TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/reference/ref.fa.amb	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,1 @@
+700 1 0
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/reference/ref.fa.ann	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,3 @@
+700 1 11
+0 reference (null)
+0 700 0
Binary file test-data/b_out_dev/reference/ref.fa.bwt has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/reference/ref.fa.fai	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,1 @@
+reference	700	11	60	61
Binary file test-data/b_out_dev/reference/ref.fa.pac has changed
Binary file test-data/b_out_dev/reference/ref.fa.sa has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/reference/ref.txt	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,1 @@
+reference:0-700
Binary file test-data/b_out_dev/reference/ref/genes.gff.gz has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/snps.aligned.fa	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,13 @@
+>reference
+TCCTCAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACT---------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+------------------------------------------------------------
+----------------------------------------
Binary file test-data/b_out_dev/snps.bam has changed
Binary file test-data/b_out_dev/snps.bam.bai has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/snps.bed	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,1 @@
+reference	3	4
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/snps.consensus.fa	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,13 @@
+>reference
+TCCTCAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA
+GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT
+CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT
+GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT
+ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC
+AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC
+AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA
+AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT
+TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA
+ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG
+TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT
+TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/snps.consensus.subs.fa	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,13 @@
+>reference
+TCCTCAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA
+GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT
+CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT
+GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT
+ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC
+AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC
+AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA
+AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT
+TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA
+ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG
+TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT
+TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/snps.csv	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,2 @@
+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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/snps.filt.vcf	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,28 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20190312
+##source=freeBayes v1.2.0-dirty
+##reference=reference/ref.fa
+##contig=<ID=reference,length=700>
+##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=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
+##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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/snps.gff	Tue Mar 12 17:37:29 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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/snps.html	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,24 @@
+<TABLE ID='snps' BORDER=1>
+<TR>
+<TH>CHROM
+<TH>POS
+<TH>TYPE
+<TH>REF
+<TH>ALT
+<TH>EVIDENCE
+<TH>FTYPE
+<TH>STRAND
+<TH>NT_POS
+<TH>AA_POS
+<TH>EFFECT
+<TH>LOCUS_TAG
+<TH>GENE
+<TH>PRODUCT
+<TR>
+<TD>reference
+<TD>4
+<TD>snp
+<TD>A
+<TD>T
+<TD>T:10 A:0
+</TABLE>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/snps.log	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,261 @@
+### 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
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/snps.raw.vcf	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,62 @@
+##fileformat=VCFv4.2
+##fileDate=20190312
+##source=freeBayes v1.2.0-dirty
+##reference=reference/ref.fa
+##contig=<ID=reference,length=700>
+##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=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
+##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
+##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
+##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
+##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
+##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
+##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
+##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
+##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
+##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
+##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
+##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
+##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
+##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
+##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
+##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
+##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio.  Ratio between depth in samples with each called alternate allele and those without.">
+##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
+##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
+##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
+##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
+##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
+##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
+##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
+##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
+##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
+##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
+##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
+##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
+##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
+#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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/snps.subs.vcf	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,27 @@
+##fileformat=VCFv4.2
+##snippy="snippy-vcf_extract_subs snps.filt.vcf"
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20190312
+##source=freeBayes v1.2.0-dirty
+##reference=reference/ref.fa
+##contig=<ID=reference,length=700>
+##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=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
+##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=<ID=OLDVAR,Number=R,Type=String,Description="Original REF,ALT before decomposition">
+#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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/snps.tab	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,2 @@
+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								
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/snps.txt	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,7 @@
+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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/b_out_dev/snps.vcf	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,28 @@
+##fileformat=VCFv4.2
+##FILTER=<ID=PASS,Description="All filters passed">
+##fileDate=20190312
+##source=freeBayes v1.2.0-dirty
+##reference=reference/ref.fa
+##contig=<ID=reference,length=700>
+##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=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
+##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
+##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
+##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
+##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
+##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
+##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
+##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
+##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
+##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
+##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
Binary file test-data/b_out_dev/snps.vcf.gz has changed
Binary file test-data/b_out_dev/snps.vcf.gz.csi has changed
--- a/test-data/c/ref.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /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
--- a/test-data/c/ref.fa.fai	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference	700	11	60	61
--- a/test-data/c/reference/genomes/ref.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /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
--- a/test-data/c/reference/ref.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /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
--- a/test-data/c/reference/ref.fa.amb	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-700 1 0
--- a/test-data/c/reference/ref.fa.ann	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-700 1 11
-0 reference (null)
-0 700 0
Binary file test-data/c/reference/ref.fa.bwt has changed
--- a/test-data/c/reference/ref.fa.fai	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference	700	11	60	61
Binary file test-data/c/reference/ref.fa.pac has changed
Binary file test-data/c/reference/ref.fa.sa has changed
--- a/test-data/c/reference/ref.txt	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference:0-700
Binary file test-data/c/reference/ref/genes.gff.gz has changed
--- a/test-data/c/snps.aligned.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
->reference
-TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTACACT---------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-----------------------------------------
Binary file test-data/c/snps.bam has changed
Binary file test-data/c/snps.bam.bai has changed
--- a/test-data/c/snps.bed	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference	47	48
--- a/test-data/c/snps.consensus.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
->reference
-TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTACACTAATTGAAAA
-GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT
-CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT
-GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT
-ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC
-AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC
-AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA
-AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT
-TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA
-ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG
-TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT
-TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA
--- a/test-data/c/snps.consensus.subs.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
->reference
-TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTACACTAATTGAAAA
-GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT
-CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT
-GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT
-ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC
-AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC
-AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA
-AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT
-TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA
-ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG
-TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT
-TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA
--- a/test-data/c/snps.csv	Fri Mar 08 20:46:56 2019 -0500
+++ /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,48,snp,A,C,C:2 A:0
--- a/test-data/c/snps.filt.vcf	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-##fileformat=VCFv4.2
-##FILTER=<ID=PASS,Description="All filters passed">
-##fileDate=20190206
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=<ID=reference,length=700>
-##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=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
-##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
-##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
-##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
-##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
-##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
-##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
-##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
-##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
-##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
-##bcftools_viewVersion=1.9+htslib-1.9
-##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb  6 12:42:19 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=Wed Feb  6 12:42:19 2019
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	c
-reference	48	.	A	C	63.8794	.	AB=0;AO=2;DP=2;QA=80;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:2:0:0:2:80:-7.59179,-0.60206,0
--- a/test-data/c/snps.gff	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-##gff-version 3
-reference	snippy:4.3.6	variation	48	48	.	.	0	note=snp A=>C C:2 A:0
--- a/test-data/c/snps.html	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-<TABLE ID='snps' BORDER=1>
-<TR>
-<TH>CHROM
-<TH>POS
-<TH>TYPE
-<TH>REF
-<TH>ALT
-<TH>EVIDENCE
-<TH>FTYPE
-<TH>STRAND
-<TH>NT_POS
-<TH>AA_POS
-<TH>EFFECT
-<TH>LOCUS_TAG
-<TH>GENE
-<TH>PRODUCT
-<TR>
-<TD>reference
-<TD>48
-<TD>snp
-<TD>A
-<TD>C
-<TD>C:2 A:0
-</TABLE>
--- a/test-data/c/snps.log	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,783 +0,0 @@
-### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
-
-### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --outdir c --ref reference.fasta --R1 c_1.fastq --R2 c_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: 0.070 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:c\tSM:c' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.13651. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.13651. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.13651. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### 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 10 --min-repeat-entropy 1.5 --strict-vcf -q 13 -m 60 --min-coverage 10 -F 0.05  -f reference/ref.fa snps.bam > snps.raw.vcf
-
-
-### bcftools view --include 'FMT/GT="1/1" && QUAL>=100 && FMT/DP>=10 && (FMT/AO)/(FMT/DP)>=0' 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 0 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 --mincov 2 --force --outdir c --ref reference.fasta --R1 c_1.fastq --R2 c_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: 0.070 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:c\tSM:c' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.14000. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.14000. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.14000. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### 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>=100 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' 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 0 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 --mincov 2 --force --outdir c --ref reference.fasta --R1 c_1.fastq --R2 c_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: 0.070 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:c\tSM:c' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.14733. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.14733. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.14733. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### 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>=100 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' 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 0 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 --mincov 2 --minqual 20 --force --outdir c --ref reference.fasta --R1 c_1.fastq --R2 c_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: 0.070 sec; CPU: 0.004 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:c\tSM:c' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.15004. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.15004. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.15004. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### 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>=20 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' 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 --mincov 2 --minqual 60 --force --outdir c --ref reference.fasta --R1 c_1.fastq --R2 c_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: 0.071 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:c\tSM:c' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.17443. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.17443. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.17443. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### 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 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' 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 --mincov 2 --force --outdir c --ref reference.fasta --R1 c_1.fastq --R2 c_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: 0.070 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:c\tSM:c' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.25837. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.25837. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.25837. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### 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>=100 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' 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 0 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 --mincov 2 --minqual 80 --force --outdir c --ref reference.fasta --R1 c_1.fastq --R2 c_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: 0.070 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:c\tSM:c' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.26070. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.26070. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.26070. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### 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>=80 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' 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 0 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 --mincov 2 --minqual 65 --force --outdir c --ref reference.fasta --R1 c_1.fastq --R2 c_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: 0.071 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:c\tSM:c' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.26290. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.26290. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.26290. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### 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>=65 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' 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 0 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 --mincov 2 --minqual 60 --force --outdir c --ref reference.fasta --R1 c_1.fastq --R2 c_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: 0.070 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:c\tSM:c' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.26511. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.26511. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.26511. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### 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 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' 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
-
--- a/test-data/c/snps.raw.vcf	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,62 +0,0 @@
-##fileformat=VCFv4.2
-##fileDate=20190206
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=<ID=reference,length=700>
-##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=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
-##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
-##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
-##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
-##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
-##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
-##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
-##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
-##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
-##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
-##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
-##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
-##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
-##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
-##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
-##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
-##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
-##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
-##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
-##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio.  Ratio between depth in samples with each called alternate allele and those without.">
-##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
-##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
-##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
-##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
-##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
-##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
-##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
-##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
-##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
-##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
-##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
-##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
-##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record.">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
-##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele">
-##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
-##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
-##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
-##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
-##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	c
-reference	48	.	A	C	63.8794	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=7.37776;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=0;RO=0;RPL=2;RPP=7.35324;RPPR=0;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	1/1:2:0,2:0:0:2:80:-7.59179,-0.60206,0
--- a/test-data/c/snps.subs.vcf	Fri Mar 08 20:46:56 2019 -0500
+++ /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=<ID=PASS,Description="All filters passed">
-##fileDate=20190206
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=<ID=reference,length=700>
-##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=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
-##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
-##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
-##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
-##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
-##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
-##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
-##bcftools_viewVersion=1.9+htslib-1.9
-##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb  6 12:42:19 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=Wed Feb  6 12:42:19 2019
-##INFO=<ID=OLDVAR,Number=R,Type=String,Description="Original REF,ALT before decomposition">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	c
-reference	48	.	A	C	63.8794	.	TYPE=snp;DP=2;RO=0;AO=2	GT:DP:RO:AO:QR:QA	1/1:2:0:2:0:80
--- a/test-data/c/snps.tab	Fri Mar 08 20:46:56 2019 -0500
+++ /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	48	snp	A	C	C:2 A:0								
--- a/test-data/c/snps.txt	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-DateTime	2019-02-06T12:42:18
-ReadFiles	/home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_2.fastq
-Reference	/home/dfornika/Code/tools-iuc/tools/snippy/test-data/reference.fasta
-ReferenceSize	700
-Software	snippy 4.3.6
-Variant-SNP	1
-VariantTotal	1
--- a/test-data/c/snps.vcf	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-##fileformat=VCFv4.2
-##FILTER=<ID=PASS,Description="All filters passed">
-##fileDate=20190206
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=<ID=reference,length=700>
-##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=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
-##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
-##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
-##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
-##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
-##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
-##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
-##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
-##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
-##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
-##bcftools_viewVersion=1.9+htslib-1.9
-##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb  6 12:42:19 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=Wed Feb  6 12:42:19 2019
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	c
-reference	48	.	A	C	63.8794	.	AB=0;AO=2;DP=2;QA=80;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:2:0:0:2:80:-7.59179,-0.60206,0
Binary file test-data/c/snps.vcf.gz has changed
Binary file test-data/c/snps.vcf.gz.csi has changed
--- a/test-data/c_gbk/ref.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /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
--- a/test-data/c_gbk/ref.fa.fai	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference	700	49	60	61
--- a/test-data/c_gbk/reference/genomes/ref.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
->reference Listeria monocytogenes strain strain.
-TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA
-GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT
-CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT
-GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT
-ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC
-AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC
-AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA
-AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT
-TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA
-ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG
-TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT
-TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA
--- a/test-data/c_gbk/reference/ref.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /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
--- a/test-data/c_gbk/reference/ref.fa.amb	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-700 1 0
--- a/test-data/c_gbk/reference/ref.fa.ann	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-700 1 11
-0 reference Listeria monocytogenes strain strain.
-0 700 0
Binary file test-data/c_gbk/reference/ref.fa.bwt has changed
--- a/test-data/c_gbk/reference/ref.fa.fai	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference	700	49	60	61
Binary file test-data/c_gbk/reference/ref.fa.pac has changed
Binary file test-data/c_gbk/reference/ref.fa.sa has changed
--- a/test-data/c_gbk/reference/ref.gff	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-##gff-version 3
-reference	snippy	CDS	188	658	.	+	0	ID=KPFNHDNB_00001;codon_start=1;inference=ab initio prediction:Prodigal:2.6;locus_tag=KPFNHDNB_00001;product=hypothetical protein;transl_table=11;translation=MIFQRLLKTRDTEFYRVIQNRNIDDVFGYLLIHDKREPAEIDDFKVFAKSNINKEAFSVNIKKNHIYTMFFHFTDLEEEQEIPKFTKVIRFIEGLLSFQPETSHYVDNYLIKEKLIFEYPAEFEKIGEFAKYLVKLSGRKITIPDTTREKYIYLTQ
--- a/test-data/c_gbk/reference/ref.txt	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference:0-700
Binary file test-data/c_gbk/reference/ref/genes.gff.gz has changed
Binary file test-data/c_gbk/reference/ref/snpEffectPredictor.bin has changed
--- a/test-data/c_gbk/reference/snpeff.config	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-codon.Standard								: TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Vertebrate_Mitochondrial				: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/*, AGG/*, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Yeast_Mitochondrial					: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/T, CTC/T, CTA/T, CTG/T, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Mold_Mitochondrial					: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Protozoan_Mitochondrial				: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Coelenterate							: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Mitochondrial							: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Mycoplasma							: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Spiroplasma							: TTT/F, TTC/F, TTA/L+, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Invertebrate_Mitochondrial			: TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Ciliate_Nuclear						: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Q, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Dasycladacean_Nuclear					: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Q, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Hexamita_Nuclear						: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Q, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Echinoderm_Mitochondrial				: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Flatworm_Mitochondrial				: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Euplotid_Nuclear						: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/C, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Bacterial_and_Plant_Plastid			: TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I+, ATA/I+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Alternative_Yeast_Nuclear				: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/S+, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Ascidian_Mitochondrial				: TTT/F, TTC/F, TTA/L, TTG/L+, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M+, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/G, AGG/G, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Alternative_Flatworm_Mitochondrial	: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/Y, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Blepharisma_Macronuclear				: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/Q, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Chlorophycean_Mitochondrial			: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/L, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Trematode_Mitochondrial				: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/W, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/M, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/N, AAG/K, AGT/S, AGC/S, AGA/S, AGG/S, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Scenedesmus_obliquus_Mitochondrial	: TTT/F, TTC/F, TTA/L, TTG/L, TCT/S, TCC/S, TCA/*, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/L, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-codon.Thraustochytrium_Mitochondrial		: TTT/F, TTC/F, TTA/*, TTG/L, TCT/S, TCC/S, TCA/S, TCG/S, TAT/Y, TAC/Y, TAA/*, TAG/*, TGT/C, TGC/C, TGA/*, TGG/W, CTT/L, CTC/L, CTA/L, CTG/L, CCT/P, CCC/P, CCA/P, CCG/P, CAT/H, CAC/H, CAA/Q, CAG/Q, CGT/R, CGC/R, CGA/R, CGG/R, ATT/I+, ATC/I, ATA/I, ATG/M+, ACT/T, ACC/T, ACA/T, ACG/T, AAT/N, AAC/N, AAA/K, AAG/K, AGT/S, AGC/S, AGA/R, AGG/R, GTT/V, GTC/V, GTA/V, GTG/V+, GCT/A, GCC/A, GCA/A, GCG/A, GAT/D, GAC/D, GAA/E, GAG/E, GGT/G, GGC/G, GGA/G, GGG/G
-ref.genome : Snippy Reference
-	ref.chromosome : reference
-	ref.reference.codonTable : Bacterial_and_Plant_Plastid
Binary file test-data/c_gbk/snps.bam has changed
Binary file test-data/c_gbk/snps.bam.bai has changed
--- a/test-data/c_gbk/snps.filt.vcf	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-##fileformat=VCFv4.2
-##FILTER=<ID=PASS,Description="All filters passed">
-##fileDate=20190206
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=<ID=reference,length=700>
-##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=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
-##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
-##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
-##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
-##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
-##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
-##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
-##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
-##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
-##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
-##bcftools_viewVersion=1.9+htslib-1.9
-##bcftools_viewCommand=view --include 'FMT/GT="1/1" && QUAL>=60 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' snps.raw.vcf; Date=Wed Feb  6 12:30:20 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=Wed Feb  6 12:30:20 2019
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	c_gbk
-reference	48	.	A	C	63.8794	.	AB=0;AO=2;DP=2;QA=80;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:2:0:0:2:80:-7.59179,-0.60206,0
--- a/test-data/c_gbk/snps.log	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,56 +0,0 @@
-### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
-
-### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --mincov 2 --minqual 60 --force --outdir c_gbk --ref reference.gbk --R1 c_1.fastq --R2 c_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: 0.071 sec; CPU: 0.004 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
-
-
-### snpEff build -c reference/snpeff.config -dataDir . -gff3 ref
-
-
-### bwa mem  -Y -M -R '@RG\tID:c_gbk\tSM:c_gbk' -t 8 reference/ref.fa /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/c_2.fastq | samclip --max 10 --ref reference/ref.fa.fai | samtools sort -n -l 0 -T /tmp/snippy.24822. --threads 8 -m 1000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.24822. --threads 8 -m 1000M | samtools markdup -T /tmp/snippy.24822. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### 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 && FMT/DP>=2 && (FMT/AO)/(FMT/DP)>=0' 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
-
-
-### snpEff ann -noLog -noStats -no-downstream -no-upstream -no-utr -t -c reference/snpeff.config -dataDir . ref snps.filt.vcf > snps.vcf
-
--- a/test-data/c_gbk/snps.raw.vcf	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,62 +0,0 @@
-##fileformat=VCFv4.2
-##fileDate=20190206
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=<ID=reference,length=700>
-##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=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
-##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
-##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
-##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
-##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
-##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
-##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
-##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
-##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
-##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
-##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
-##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
-##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
-##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
-##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
-##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
-##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
-##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
-##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
-##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio.  Ratio between depth in samples with each called alternate allele and those without.">
-##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
-##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
-##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
-##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
-##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
-##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
-##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
-##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
-##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
-##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
-##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
-##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
-##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record.">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
-##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele">
-##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
-##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
-##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
-##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
-##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	c_gbk
-reference	48	.	A	C	63.8794	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=7.37776;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=0;RO=0;RPL=2;RPP=7.35324;RPPR=0;RPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	1/1:2:0,2:0:0:2:80:-7.59179,-0.60206,0
--- a/test-data/fna_ref_b_testing/ref.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /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
--- a/test-data/fna_ref_b_testing/ref.fa.fai	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference	700	11	60	61
--- a/test-data/fna_ref_b_testing/reference/genomes/ref.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /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
--- a/test-data/fna_ref_b_testing/reference/ref.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /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
--- a/test-data/fna_ref_b_testing/reference/ref.fa.amb	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-700 1 0
--- a/test-data/fna_ref_b_testing/reference/ref.fa.ann	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-700 1 11
-0 reference (null)
-0 700 0
Binary file test-data/fna_ref_b_testing/reference/ref.fa.bwt has changed
--- a/test-data/fna_ref_b_testing/reference/ref.fa.fai	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference	700	11	60	61
Binary file test-data/fna_ref_b_testing/reference/ref.fa.pac has changed
Binary file test-data/fna_ref_b_testing/reference/ref.fa.sa has changed
--- a/test-data/fna_ref_b_testing/reference/ref.txt	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference:0-700
Binary file test-data/fna_ref_b_testing/reference/ref/genes.gff.gz has changed
--- a/test-data/fna_ref_b_testing/snps.aligned.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
->reference
-TCCTCAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACT---------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-----------------------------------------
Binary file test-data/fna_ref_b_testing/snps.bam has changed
Binary file test-data/fna_ref_b_testing/snps.bam.bai has changed
--- a/test-data/fna_ref_b_testing/snps.bed	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference	3	4
--- a/test-data/fna_ref_b_testing/snps.consensus.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /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
--- a/test-data/fna_ref_b_testing/snps.consensus.subs.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /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
--- a/test-data/fna_ref_b_testing/snps.csv	Fri Mar 08 20:46:56 2019 -0500
+++ /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:2 A:0
--- a/test-data/fna_ref_b_testing/snps.filt.vcf	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-##fileformat=VCFv4.2
-##FILTER=<ID=PASS,Description="All filters passed">
-##fileDate=20190211
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=<ID=reference,length=700>
-##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=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
-##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
-##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
-##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
-##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
-##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
-##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
-##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
-##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
-##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
-##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=Mon Feb 11 11:46:35 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=Mon Feb 11 11:46:35 2019
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	fna_ref_b_testing
-reference	4	.	A	T	63.8794	.	AB=0;AO=2;DP=2;QA=80;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:2:0:0:2:80:-7.59179,-0.60206,0
--- a/test-data/fna_ref_b_testing/snps.gff	Fri Mar 08 20:46:56 2019 -0500
+++ /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:2 A:0
--- a/test-data/fna_ref_b_testing/snps.html	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-<TABLE ID='snps' BORDER=1>
-<TR>
-<TH>CHROM
-<TH>POS
-<TH>TYPE
-<TH>REF
-<TH>ALT
-<TH>EVIDENCE
-<TH>FTYPE
-<TH>STRAND
-<TH>NT_POS
-<TH>AA_POS
-<TH>EFFECT
-<TH>LOCUS_TAG
-<TH>GENE
-<TH>PRODUCT
-<TR>
-<TD>reference
-<TD>4
-<TD>snp
-<TD>A
-<TD>T
-<TD>T:2 A:0
-</TABLE>
--- a/test-data/fna_ref_b_testing/snps.log	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,87 +0,0 @@
-### cd /home/dfornika/Code/tools-iuc/tools/snippy/test-data
-
-### /home/dfornika/miniconda3/envs/snippy-4.3.6/bin/snippy --outdir fna_ref_b_testing --cpus 1 --ref reference.fasta --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:fna_ref_b_testing\tSM:fna_ref_b_testing' -t 1 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.8702. --threads 1 -m 8000M | samtools fixmate -m - - | samtools sort -l 0 -T /tmp/snippy.8702. --threads 1 -m 8000M | samtools markdup -T /tmp/snippy.8702. -r -s - - > snps.bam
-
-READ 10 WRITTEN 2 
-EXCLUDED 0 EXAMINED 10
-PAIRED 10 SINGLE 0
-DULPICATE PAIR 8 DUPLICATE SINGLE 0
-DUPLICATE TOTAL 8
-
-### samtools index snps.bam
-
-
-### fasta_generate_regions.py reference/ref.fa.fai 1000 > reference/ref.txt
-
-
-### freebayes-parallel reference/ref.txt 1 -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
-
--- a/test-data/fna_ref_b_testing/snps.raw.vcf	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,62 +0,0 @@
-##fileformat=VCFv4.2
-##fileDate=20190211
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=<ID=reference,length=700>
-##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=<ID=NS,Number=1,Type=Integer,Description="Number of samples with data">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
-##INFO=<ID=DPB,Number=1,Type=Float,Description="Total read depth per bp at the locus; bases in reads overlapping / bases in haplotype">
-##INFO=<ID=AC,Number=A,Type=Integer,Description="Total number of alternate alleles in called genotypes">
-##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
-##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated allele frequency in the range (0,1]">
-##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
-##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
-##INFO=<ID=PRO,Number=1,Type=Float,Description="Reference allele observation count, with partial observations recorded fractionally">
-##INFO=<ID=PAO,Number=A,Type=Float,Description="Alternate allele observations, with partial observations recorded fractionally">
-##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
-##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
-##INFO=<ID=PQR,Number=1,Type=Float,Description="Reference allele quality sum in phred for partial observations">
-##INFO=<ID=PQA,Number=A,Type=Float,Description="Alternate allele quality sum in phred for partial observations">
-##INFO=<ID=SRF,Number=1,Type=Integer,Description="Number of reference observations on the forward strand">
-##INFO=<ID=SRR,Number=1,Type=Integer,Description="Number of reference observations on the reverse strand">
-##INFO=<ID=SAF,Number=A,Type=Integer,Description="Number of alternate observations on the forward strand">
-##INFO=<ID=SAR,Number=A,Type=Integer,Description="Number of alternate observations on the reverse strand">
-##INFO=<ID=SRP,Number=1,Type=Float,Description="Strand balance probability for the reference allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SRF and SRR given E(SRF/SRR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=SAP,Number=A,Type=Float,Description="Strand balance probability for the alternate allele: Phred-scaled upper-bounds estimate of the probability of observing the deviation between SAF and SAR given E(SAF/SAR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
-##INFO=<ID=ABP,Number=A,Type=Float,Description="Allele balance probability at heterozygous sites: Phred-scaled upper-bounds estimate of the probability of observing the deviation between ABR and ABA given E(ABR/ABA) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=RUN,Number=A,Type=Integer,Description="Run length: the number of consecutive repeats of the alternate allele in the reference genome">
-##INFO=<ID=RPP,Number=A,Type=Float,Description="Read Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=RPPR,Number=1,Type=Float,Description="Read Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between RPL and RPR given E(RPL/RPR) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=RPL,Number=A,Type=Float,Description="Reads Placed Left: number of reads supporting the alternate balanced to the left (5') of the alternate allele">
-##INFO=<ID=RPR,Number=A,Type=Float,Description="Reads Placed Right: number of reads supporting the alternate balanced to the right (3') of the alternate allele">
-##INFO=<ID=EPP,Number=A,Type=Float,Description="End Placement Probability: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=EPPR,Number=1,Type=Float,Description="End Placement Probability for reference observations: Phred-scaled upper-bounds estimate of the probability of observing the deviation between EL and ER given E(EL/ER) ~ 0.5, derived using Hoeffding's inequality">
-##INFO=<ID=DPRA,Number=A,Type=Float,Description="Alternate allele depth ratio.  Ratio between depth in samples with each called alternate allele and those without.">
-##INFO=<ID=ODDS,Number=1,Type=Float,Description="The log odds ratio of the best genotype combination to the second-best.">
-##INFO=<ID=GTI,Number=1,Type=Integer,Description="Number of genotyping iterations required to reach convergence or bailout.">
-##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
-##INFO=<ID=CIGAR,Number=A,Type=String,Description="The extended CIGAR representation of each alternate allele, with the exception that '=' is replaced by 'M' to ease VCF parsing.  Note that INDEL alleles do not have the first matched base (which is provided by default, per the spec) referred to by the CIGAR.">
-##INFO=<ID=NUMALT,Number=1,Type=Integer,Description="Number of unique non-reference alleles in called genotypes at this position.">
-##INFO=<ID=MEANALT,Number=A,Type=Float,Description="Mean number of unique non-reference allele observations per sample with the corresponding alternate alleles.">
-##INFO=<ID=LEN,Number=A,Type=Integer,Description="allele length">
-##INFO=<ID=MQM,Number=A,Type=Float,Description="Mean mapping quality of observed alternate alleles">
-##INFO=<ID=MQMR,Number=1,Type=Float,Description="Mean mapping quality of observed reference alleles">
-##INFO=<ID=PAIRED,Number=A,Type=Float,Description="Proportion of observed alternate alleles which are supported by properly paired read fragments">
-##INFO=<ID=PAIREDR,Number=1,Type=Float,Description="Proportion of observed reference alleles which are supported by properly paired read fragments">
-##INFO=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
-##INFO=<ID=END,Number=1,Type=Integer,Description="Last position (inclusive) in gVCF output record.">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality, the Phred-scaled marginal (or unconditional) probability of the called genotype">
-##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Number of observation for each allele">
-##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
-##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
-##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
-##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
-##FORMAT=<ID=MIN_DP,Number=1,Type=Integer,Description="Minimum depth in gVCF output block.">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	fna_ref_b_testing
-reference	4	.	A	T	63.8794	.	AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=7.37776;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=80;QR=0;RO=0;RPL=0;RPP=7.35324;RPPR=0;RPR=2;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp	GT:DP:AD:RO:QR:AO:QA:GL	1/1:2:0,2:0:0:2:80:-7.59179,-0.60206,0
--- a/test-data/fna_ref_b_testing/snps.subs.vcf	Fri Mar 08 20:46:56 2019 -0500
+++ /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=<ID=PASS,Description="All filters passed">
-##fileDate=20190211
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=<ID=reference,length=700>
-##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=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
-##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
-##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
-##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
-##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
-##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
-##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
-##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=Mon Feb 11 11:46:35 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=Mon Feb 11 11:46:35 2019
-##INFO=<ID=OLDVAR,Number=R,Type=String,Description="Original REF,ALT before decomposition">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	fna_ref_b_testing
-reference	4	.	A	T	63.8794	.	TYPE=snp;DP=2;RO=0;AO=2	GT:DP:RO:AO:QR:QA	1/1:2:0:2:0:80
--- a/test-data/fna_ref_b_testing/snps.tab	Fri Mar 08 20:46:56 2019 -0500
+++ /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:2 A:0								
--- a/test-data/fna_ref_b_testing/snps.txt	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-DateTime	2019-02-11T11:46:34
-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/reference.fasta
-ReferenceSize	700
-Software	snippy 4.3.6
-Variant-SNP	1
-VariantTotal	1
--- a/test-data/fna_ref_b_testing/snps.vcf	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,28 +0,0 @@
-##fileformat=VCFv4.2
-##FILTER=<ID=PASS,Description="All filters passed">
-##fileDate=20190211
-##source=freeBayes v1.2.0-dirty
-##reference=reference/ref.fa
-##contig=<ID=reference,length=700>
-##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=<ID=DP,Number=1,Type=Integer,Description="Total read depth at the locus">
-##INFO=<ID=RO,Number=1,Type=Integer,Description="Count of full observations of the reference haplotype.">
-##INFO=<ID=AO,Number=A,Type=Integer,Description="Count of full observations of this alternate haplotype.">
-##INFO=<ID=QR,Number=1,Type=Integer,Description="Reference allele quality sum in phred">
-##INFO=<ID=QA,Number=A,Type=Integer,Description="Alternate allele quality sum in phred">
-##INFO=<ID=AB,Number=A,Type=Float,Description="Allele balance at heterozygous sites: a number between 0 and 1 representing the ratio of reads showing the reference allele to all reads, considering only reads from individuals called as heterozygous">
-##INFO=<ID=TYPE,Number=A,Type=String,Description="The type of allele, either snp, mnp, ins, del, or complex.">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count">
-##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of the reference observations">
-##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observation count">
-##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of the alternate observations">
-##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=Mon Feb 11 11:46:35 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=Mon Feb 11 11:46:35 2019
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	fna_ref_b_testing
-reference	4	.	A	T	63.8794	.	AB=0;AO=2;DP=2;QA=80;QR=0;RO=0;TYPE=snp	GT:DP:RO:QR:AO:QA:GL	1/1:2:0:0:2:80:-7.59179,-0.60206,0
Binary file test-data/fna_ref_b_testing/snps.vcf.gz has changed
Binary file test-data/fna_ref_b_testing/snps.vcf.gz.csi has changed
--- a/test-data/prokka-out/PROKKA_02062019.err	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,65 +0,0 @@
-Discrepancy Report Results
-
-Summary
-DISC_PROTEIN_NAMES:All proteins have same name "hypothetical protein"
-FATAL: MISSING_PROTEIN_ID:1 proteins have invalid IDs.
-DISC_SOURCE_QUALS_ASNDISC:strain (all present, all unique)
-DISC_SOURCE_QUALS_ASNDISC:taxname (all present, all unique)
-DISC_FEATURE_COUNT:CDS: 1 present
-DISC_COUNT_NUCLEOTIDES:1 nucleotide Bioseqs are present
-FEATURE_LOCATION_CONFLICT:1 features have inconsistent gene locations.
-DISC_QUALITY_SCORES:Quality scores are missing on all sequences.
-ONCALLER_COMMENT_PRESENT:1 comment descriptors were found (all same)
-MISSING_GENOMEASSEMBLY_COMMENTS:1 bioseqs are missing GenomeAssembly structured comments
-MOLTYPE_NOT_MRNA:1 molecule types are not set as mRNA.
-TECHNIQUE_NOT_TSA:1 technique are not set as TSA
-MISSING_STRUCTURED_COMMENT:1 sequences do not include structured comments.
-MISSING_PROJECT:2 sequences do not include project.
-DISC_INCONSISTENT_MOLINFO_TECH:Molinfo Technique Report (some missing, all same)
-
-
-Detailed Report
-
-DiscRep_ALL:DISC_PROTEIN_NAMES::All proteins have same name "hypothetical protein"
-
-FATAL: DiscRep_ALL:MISSING_PROTEIN_ID::1 proteins have invalid IDs.
-prokka-out/PROKKA_02062019:reference_1 (length 156)
-
-DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::strain (all present, all unique)
-DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::1 sources have unique values for strain
-DiscRep_ALL:DISC_SOURCE_QUALS_ASNDISC::taxname (all present, all unique)
-DiscRep_SUB:DISC_SOURCE_QUALS_ASNDISC::1 sources have unique values for taxname
-DiscRep_ALL:DISC_FEATURE_COUNT::CDS: 1 present
-DiscRep_ALL:DISC_COUNT_NUCLEOTIDES::1 nucleotide Bioseqs are present
-prokka-out/PROKKA_02062019:reference (length 700)
-
-DiscRep_ALL:FEATURE_LOCATION_CONFLICT::1 features have inconsistent gene locations.
-DiscRep_SUB:FEATURE_LOCATION_CONFLICT::Coding region xref gene does not exist
-prokka-out/PROKKA_02062019:CDS	hypothetical protein	reference:188-658	KPFNHDNB_00001
-
-DiscRep_ALL:DISC_QUALITY_SCORES::Quality scores are missing on all sequences.
-
-DiscRep_ALL:ONCALLER_COMMENT_PRESENT::1 comment descriptors were found (all same)
-prokka-out/PROKKA_02062019:reference:Annotated using prokka 1.13.3 from https://github.com/tseemann/prokka
-
-DiscRep_ALL:MISSING_GENOMEASSEMBLY_COMMENTS::1 bioseqs are missing GenomeAssembly structured comments
-prokka-out/PROKKA_02062019:reference (length 700)
-
-DiscRep_ALL:MOLTYPE_NOT_MRNA::1 molecule types are not set as mRNA.
-prokka-out/PROKKA_02062019:reference (length 700)
-
-DiscRep_ALL:TECHNIQUE_NOT_TSA::1 technique are not set as TSA
-prokka-out/PROKKA_02062019:reference (length 700)
-
-DiscRep_ALL:MISSING_STRUCTURED_COMMENT::1 sequences do not include structured comments.
-prokka-out/PROKKA_02062019:reference (length 700)
-
-DiscRep_ALL:MISSING_PROJECT::2 sequences do not include project.
-prokka-out/PROKKA_02062019:reference (length 700)
-prokka-out/PROKKA_02062019:reference_1 (length 156)
-
-DiscRep_ALL:DISC_INCONSISTENT_MOLINFO_TECH::Molinfo Technique Report (some missing, all same)
-DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::technique (all missing)
-DiscRep_SUB:DISC_INCONSISTENT_MOLINFO_TECH::1 Molinfos are missing field technique
-prokka-out/PROKKA_02062019:reference (length 700)
-
--- a/test-data/prokka-out/PROKKA_02062019.faa	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
->KPFNHDNB_00001 hypothetical protein
-MIFQRLLKTRDTEFYRVIQNRNIDDVFGYLLIHDKREPAEIDDFKVFAKSNINKEAFSVN
-IKKNHIYTMFFHFTDLEEEQEIPKFTKVIRFIEGLLSFQPETSHYVDNYLIKEKLIFEYP
-AEFEKIGEFAKYLVKLSGRKITIPDTTREKYIYLTQ
--- a/test-data/prokka-out/PROKKA_02062019.ffn	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,9 +0,0 @@
->KPFNHDNB_00001 hypothetical protein
-ATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTATACAAAAC
-AGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACCAGCAGAA
-ATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTCAGTGAAT
-ATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGAAGAACAG
-GAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTTTCAGCCA
-GAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGAATATCCT
-GCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGGTCGTAAA
-ATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAA
--- a/test-data/prokka-out/PROKKA_02062019.fna	Fri Mar 08 20:46:56 2019 -0500
+++ /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
--- a/test-data/prokka-out/PROKKA_02062019.fsa	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,13 +0,0 @@
->reference [gcode=11] [organism=Listeria monocytogenes] [strain=strain]
-TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA
-GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT
-CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT
-GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT
-ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC
-AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC
-AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA
-AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT
-TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA
-ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG
-TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT
-TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA
--- a/test-data/prokka-out/PROKKA_02062019.gbk	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-LOCUS       reference                700 bp    DNA     linear       06-FEB-2019
-DEFINITION  Listeria monocytogenes strain strain.
-ACCESSION   
-VERSION
-KEYWORDS    .
-SOURCE      Listeria monocytogenes
-  ORGANISM  Listeria monocytogenes
-            Unclassified.
-COMMENT     Annotated using prokka 1.13.3 from
-            https://github.com/tseemann/prokka.
-FEATURES             Location/Qualifiers
-     source          1..700
-                     /organism="Listeria monocytogenes"
-                     /mol_type="genomic DNA"
-                     /strain="strain"
-     CDS             188..658
-                     /locus_tag="KPFNHDNB_00001"
-                     /inference="ab initio prediction:Prodigal:2.6"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="hypothetical protein"
-                     /translation="MIFQRLLKTRDTEFYRVIQNRNIDDVFGYLLIHDKREPAEIDDF
-                     KVFAKSNINKEAFSVNIKKNHIYTMFFHFTDLEEEQEIPKFTKVIRFIEGLLSFQPET
-                     SHYVDNYLIKEKLIFEYPAEFEKIGEFAKYLVKLSGRKITIPDTTREKYIYLTQ"
-ORIGIN      
-        1 tccacaagcc attgtgtgta attaaccact aattgtgtat aagtttaaac taattgaaaa
-       61 ggttatccac aataaaaagg cgttattcag gagttatcca cactttctag gaaaggattt
-      121 cattgcgcca atgtgttaaa ctatttaccg aatacgaaaa aaagacaaat aaatgaggtt
-      181 gtgaaaaatg atatttcaac ggcttttgaa aactagagat acagagtttt atcgagttat
-      241 acaaaacagg aatattgacg acgtatttgg atacttatta attcacgata aacgggaacc
-      301 agcagaaatt gacgatttta aggtatttgc aaaaagtaat ataaataaag aagctttttc
-      361 agtgaatatc aaaaaaaatc atatttacac gatgtttttc cactttactg atttagagga
-      421 agaacaggaa attccaaaat ttactaaagt tattcgtttt atagaaggac ttttatcttt
-      481 tcagccagaa acaagccatt acgttgataa ctatttaata aaggaaaaac taatttttga
-      541 atatcctgct gaatttgaga aaatcgggga gtttgctaaa tatttagtaa agctttcggg
-      601 tcgtaaaatt actattccag acacaacgag agaaaaatat atctatttaa cgcaataatt
-      661 ttcgaaaaat ggtttttctc tctataaaaa tatgatatga
-//
--- a/test-data/prokka-out/PROKKA_02062019.gff	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,17 +0,0 @@
-##gff-version 3
-##sequence-region reference 1 700
-reference	Prodigal:2.6	CDS	188	658	.	+	0	ID=KPFNHDNB_00001;inference=ab initio prediction:Prodigal:2.6;locus_tag=KPFNHDNB_00001;product=hypothetical protein
-##FASTA
->reference
-TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA
-GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT
-CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT
-GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT
-ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC
-AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC
-AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA
-AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT
-TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA
-ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG
-TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT
-TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA
--- a/test-data/prokka-out/PROKKA_02062019.log	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,126 +0,0 @@
-[11:29:26] This is prokka 1.13.3
-[11:29:26] Written by Torsten Seemann <torsten.seemann@gmail.com>
-[11:29:26] Homepage is https://github.com/tseemann/prokka
-[11:29:26] Local time is Wed Feb  6 11:29:26 2019
-[11:29:26] You are dfornika
-[11:29:26] Operating system is linux
-[11:29:26] You have BioPerl 1.007002
-[11:29:26] System has 8 cores.
-[11:29:26] Will use maximum of 8 cores.
-[11:29:26] Annotating as >>> Bacteria <<<
-[11:29:26] Generating locus_tag from 'reference.fasta' contents.
-[11:29:26] Setting --locustag KPFNHDNB from MD5 49f71d7b5d5a34956f52c337db5c3269
-[11:29:26] Re-using existing --outdir prokka-out
-[11:29:26] Using filename prefix: PROKKA_02062019.XXX
-[11:29:26] Setting HMMER_NCPU=1
-[11:29:26] Writing log to: prokka-out/PROKKA_02062019.log
-[11:29:26] Command: /home/dfornika/miniconda3/envs/prokka-1.13/bin/prokka reference.fasta --genus Listeria --species monocytogenes --outdir prokka-out --force
-[11:29:26] Appending to PATH: /home/dfornika/miniconda3/envs/prokka-1.13/bin
-[11:29:26] Looking for 'aragorn' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/aragorn
-[11:29:26] Determined aragorn version is 1.2
-[11:29:26] Looking for 'barrnap' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/barrnap
-[11:29:26] Determined barrnap version is 0.9
-[11:29:26] Looking for 'blastp' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/blastp
-[11:29:26] Determined blastp version is 2.7
-[11:29:26] Looking for 'cmpress' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/cmpress
-[11:29:26] Determined cmpress version is 1.1
-[11:29:26] Looking for 'cmscan' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/cmscan
-[11:29:26] Determined cmscan version is 1.1
-[11:29:26] Looking for 'egrep' - found /usr/bin/egrep
-[11:29:26] Looking for 'find' - found /usr/bin/find
-[11:29:26] Looking for 'grep' - found /usr/bin/grep
-[11:29:26] Looking for 'hmmpress' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/hmmpress
-[11:29:26] Determined hmmpress version is 3.2
-[11:29:26] Looking for 'hmmscan' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/hmmscan
-[11:29:26] Determined hmmscan version is 3.2
-[11:29:26] Looking for 'java' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/java
-[11:29:26] Looking for 'less' - found /usr/bin/less
-[11:29:26] Looking for 'makeblastdb' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/makeblastdb
-[11:29:26] Determined makeblastdb version is 2.7
-[11:29:26] Looking for 'minced' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/minced
-[11:29:26] Determined minced version is 3.2
-[11:29:26] Looking for 'parallel' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/parallel
-[11:29:26] Determined parallel version is 20181022
-[11:29:26] Looking for 'prodigal' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/prodigal
-[11:29:26] Determined prodigal version is 2.6
-[11:29:26] Looking for 'prokka-genbank_to_fasta_db' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/prokka-genbank_to_fasta_db
-[11:29:26] Looking for 'sed' - found /usr/bin/sed
-[11:29:26] Looking for 'tbl2asn' - found /home/dfornika/miniconda3/envs/prokka-1.13/bin/tbl2asn
-[11:29:26] Determined tbl2asn version is 25.6
-[11:29:26] Using genetic code table 11.
-[11:29:26] Loading and checking input file: reference.fasta
-[11:29:26] Wrote 1 contigs totalling 700 bp.
-[11:29:26] Predicting tRNAs and tmRNAs
-[11:29:26] Running: aragorn -l -gc11  -w prokka\-out\/PROKKA_02062019\.fna
-[11:29:26] Found 0 tRNAs
-[11:29:26] Predicting Ribosomal RNAs
-[11:29:26] Running Barrnap with 8 threads
-[11:29:26] Found 0 rRNAs
-[11:29:26] Skipping ncRNA search, enable with --rfam if desired.
-[11:29:26] Total of 0 tRNA + rRNA features
-[11:29:26] Searching for CRISPR repeats
-[11:29:26] Found 0 CRISPRs
-[11:29:26] Predicting coding sequences
-[11:29:26] Contigs total 700 bp, so using meta mode
-[11:29:26] Running: prodigal -i prokka\-out\/PROKKA_02062019\.fna -c -m -g 11 -p meta -f sco -q
-[11:29:26] Found 1 CDS
-[11:29:26] Connecting features back to sequences
-[11:29:26] Not using genus-specific database. Try --usegenus to enable it.
-[11:29:26] Annotating CDS, please be patient.
-[11:29:26] Will use 8 CPUs for similarity searching.
-[11:29:26] There are still 1 unannotated CDS left (started with 1)
-[11:29:26] Will use blast to search against /home/dfornika/miniconda3/envs/prokka-1.13/db/kingdom/Bacteria/IS with 8 CPUs
-[11:29:26] Running: cat prokka\-out\/IS\.faa | parallel --gnu --plain -j 8 --block 10 --recstart '>' --pipe blastp -query - -db /home/dfornika/miniconda3/envs/prokka-1.13/db/kingdom/Bacteria/IS -evalue 1e-30 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > prokka\-out\/IS\.blast 2> /dev/null
-[11:29:27] Deleting unwanted file: prokka-out/IS.faa
-[11:29:27] Deleting unwanted file: prokka-out/IS.blast
-[11:29:27] There are still 1 unannotated CDS left (started with 1)
-[11:29:27] Will use blast to search against /home/dfornika/miniconda3/envs/prokka-1.13/db/kingdom/Bacteria/AMR with 8 CPUs
-[11:29:27] Running: cat prokka\-out\/AMR\.faa | parallel --gnu --plain -j 8 --block 10 --recstart '>' --pipe blastp -query - -db /home/dfornika/miniconda3/envs/prokka-1.13/db/kingdom/Bacteria/AMR -evalue 9.99999999999999e-301 -qcov_hsp_perc 90 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > prokka\-out\/AMR\.blast 2> /dev/null
-[11:29:27] Deleting unwanted file: prokka-out/AMR.faa
-[11:29:27] Deleting unwanted file: prokka-out/AMR.blast
-[11:29:27] There are still 1 unannotated CDS left (started with 1)
-[11:29:27] Will use blast to search against /home/dfornika/miniconda3/envs/prokka-1.13/db/kingdom/Bacteria/sprot with 8 CPUs
-[11:29:27] Running: cat prokka\-out\/sprot\.faa | parallel --gnu --plain -j 8 --block 10 --recstart '>' --pipe blastp -query - -db /home/dfornika/miniconda3/envs/prokka-1.13/db/kingdom/Bacteria/sprot -evalue 1e-09 -qcov_hsp_perc 80 -num_threads 1 -num_descriptions 1 -num_alignments 1 -seg no > prokka\-out\/sprot\.blast 2> /dev/null
-[11:29:27] Deleting unwanted file: prokka-out/sprot.faa
-[11:29:27] Deleting unwanted file: prokka-out/sprot.blast
-[11:29:27] There are still 1 unannotated CDS left (started with 1)
-[11:29:27] Will use hmmer3 to search against /home/dfornika/miniconda3/envs/prokka-1.13/db/hmm/HAMAP.hmm with 8 CPUs
-[11:29:27] Running: cat prokka\-out\/HAMAP\.hmm\.faa | parallel --gnu --plain -j 8 --block 10 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-09 --cpu 1 /home/dfornika/miniconda3/envs/prokka-1.13/db/hmm/HAMAP.hmm /dev/stdin > prokka\-out\/HAMAP\.hmm\.hmmer3 2> /dev/null
-[11:29:28] Deleting unwanted file: prokka-out/HAMAP.hmm.faa
-[11:29:28] Deleting unwanted file: prokka-out/HAMAP.hmm.hmmer3
-[11:29:28] Labelling remaining 1 proteins as 'hypothetical protein'
-[11:29:28] Found 0 unique /gene codes.
-[11:29:28] Fixed 0 colliding /gene names.
-[11:29:28] Adding /locus_tag identifiers
-[11:29:28] Assigned 1 locus_tags to CDS and RNA features.
-[11:29:28] Writing outputs to prokka-out/
-[11:29:28] Generating annotation statistics file
-[11:29:28] Generating Genbank and Sequin files
-[11:29:28] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.13.3 from https://github.com/tseemann/prokka' -Z prokka\-out\/PROKKA_02062019\.err -i prokka\-out\/PROKKA_02062019\.fsa 2> /dev/null
-[11:29:28] Deleting unwanted file: prokka-out/errorsummary.val
-[11:29:28] Deleting unwanted file: prokka-out/PROKKA_02062019.dr
-[11:29:28] Deleting unwanted file: prokka-out/PROKKA_02062019.fixedproducts
-[11:29:28] Deleting unwanted file: prokka-out/PROKKA_02062019.ecn
-[11:29:28] Deleting unwanted file: prokka-out/PROKKA_02062019.val
-[11:29:28] Repairing broken .GBK output that tbl2asn produces...
-[11:29:28] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < prokka\-out\/PROKKA_02062019\.gbf > prokka\-out\/PROKKA_02062019\.gbk
-[11:29:28] Deleting unwanted file: prokka-out/PROKKA_02062019.gbf
-[11:29:28] Output files:
-[11:29:28] prokka-out/PROKKA_02062019.faa
-[11:29:28] prokka-out/PROKKA_02062019.log
-[11:29:28] prokka-out/PROKKA_02062019.tbl
-[11:29:28] prokka-out/PROKKA_02062019.ffn
-[11:29:28] prokka-out/PROKKA_02062019.err
-[11:29:28] prokka-out/PROKKA_02062019.txt
-[11:29:28] prokka-out/PROKKA_02062019.gff
-[11:29:28] prokka-out/PROKKA_02062019.tsv
-[11:29:28] prokka-out/PROKKA_02062019.sqn
-[11:29:28] prokka-out/PROKKA_02062019.fna
-[11:29:28] prokka-out/PROKKA_02062019.fsa
-[11:29:28] prokka-out/PROKKA_02062019.gbk
-[11:29:28] Annotation finished successfully.
-[11:29:28] Walltime used: 0.03 minutes
-[11:29:28] If you use this result please cite the Prokka paper:
-[11:29:28] Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics. 30(14):2068-9.
-[11:29:28] Type 'prokka --citation' for more details.
-[11:29:28] Thank you, come again.
--- a/test-data/prokka-out/PROKKA_02062019.sqn	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,145 +0,0 @@
-Seq-entry ::= set {
-  class genbank ,
-  seq-set {
-    set {
-      class nuc-prot ,
-      descr {
-        source {
-          org {
-            taxname "Listeria monocytogenes" ,
-            orgname {
-              mod {
-                {
-                  subtype strain ,
-                  subname "strain" } } ,
-              gcode 11 } } } ,
-        comment "Annotated using prokka 1.13.3 from
- https://github.com/tseemann/prokka" ,
-        user {
-          type
-            str "NcbiCleanup" ,
-          data {
-            {
-              label
-                str "method" ,
-              data
-                str "SeriousSeqEntryCleanup" } ,
-            {
-              label
-                str "version" ,
-              data
-                int 8 } ,
-            {
-              label
-                str "month" ,
-              data
-                int 2 } ,
-            {
-              label
-                str "day" ,
-              data
-                int 6 } ,
-            {
-              label
-                str "year" ,
-              data
-                int 2019 } } } ,
-        create-date
-          std {
-            year 2019 ,
-            month 2 ,
-            day 6 } } ,
-      seq-set {
-        seq {
-          id {
-            local
-              str "reference" } ,
-          descr {
-            molinfo {
-              biomol genomic } } ,
-          inst {
-            repr raw ,
-            mol dna ,
-            length 700 ,
-            seq-data
-              iupacna "TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATT
-GAAAAGGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTTCATTGCGCCAATG
-TGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTTGTGAAAAATGATATTTCAACGGCTTTTGAAA
-ACTAGAGATACAGAGTTTTATCGAGTTATACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGAT
-AAACGGGAACCAGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTCAGTGAAT
-ATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGAAGAACAGGAAATTCCAAAATTTACT
-AAAGTTATTCGTTTTATAGAAGGACTTTTATCTTTTCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAG
-GAAAAACTAATTTTTGAATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGGT
-CGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATTTTCGAAAAATGGTTTTTCT
-CTCTATAAAAATATGATATGA" } } ,
-        seq {
-          id {
-            local
-              str "reference_1" } ,
-          descr {
-            title "hypothetical protein KPFNHDNB_00001 [Listeria
- monocytogenes]" ,
-            molinfo {
-              biomol peptide ,
-              tech concept-trans } } ,
-          inst {
-            repr raw ,
-            mol aa ,
-            length 156 ,
-            seq-data
-              ncbieaa "MIFQRLLKTRDTEFYRVIQNRNIDDVFGYLLIHDKREPAEIDDFKVFAKSNINKE
-AFSVNIKKNHIYTMFFHFTDLEEEQEIPKFTKVIRFIEGLLSFQPETSHYVDNYLIKEKLIFEYPAEFEKIGEFAKYL
-VKLSGRKITIPDTTREKYIYLTQ" } ,
-          annot {
-            {
-              data
-                ftable {
-                  {
-                    id
-                      local
-                        id 2 ,
-                    data
-                      prot {
-                        name {
-                          "hypothetical protein" } } ,
-                    location
-                      int {
-                        from 0 ,
-                        to 155 ,
-                        id
-                          local
-                            str "reference_1" } } } } } } } ,
-      annot {
-        {
-          data
-            ftable {
-              {
-                id
-                  local
-                    id 1 ,
-                data
-                  cdregion {
-                    frame one ,
-                    code {
-                      id 11 } } ,
-                product
-                  whole
-                    local
-                      str "reference_1" ,
-                location
-                  int {
-                    from 187 ,
-                    to 657 ,
-                    strand plus ,
-                    id
-                      local
-                        str "reference" } ,
-                qual {
-                  {
-                    qual "inference" ,
-                    val "ab initio prediction:Prodigal:2.6" } } ,
-                xref {
-                  {
-                    data
-                      gene {
-                        locus-tag "KPFNHDNB_00001" } } } } } } } } } }
--- a/test-data/prokka-out/PROKKA_02062019.tbl	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,5 +0,0 @@
->Feature reference
-188	658	CDS
-			inference	ab initio prediction:Prodigal:2.6
-			locus_tag	KPFNHDNB_00001
-			product	hypothetical protein
--- a/test-data/prokka-out/PROKKA_02062019.tsv	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,2 +0,0 @@
-locus_tag	ftype	length_bp	gene	EC_number	COG	product
-KPFNHDNB_00001	CDS	471				hypothetical protein
--- a/test-data/prokka-out/PROKKA_02062019.txt	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-organism: Listeria monocytogenes strain 
-contigs: 1
-bases: 700
-CDS: 1
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/ref.fna	Tue Mar 12 17:37:29 2019 -0400
@@ -0,0 +1,11 @@
+>reference
+TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAAGGTTATCCAC
+AATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTTCATTGCGCCAATGTGTTAAA
+CTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTTGTGAAAAATGATATTTCAACGGCTTTTGAA
+AACTAGAGATACAGAGTTTTATCGAGTTATACAAAACAGGAATATTGACGACGTATTTGGATACTTATTA
+ATTCACGATAAACGGGAACCAGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAG
+AAGCTTTTTCAGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA
+AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTTTCAGCCAGAA
+ACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGAATATCCTGCTGAATTTGAGA
+AAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGGTCGTAAAATTACTATTCCAGACACAACGAG
+AGAAAAATATATCTATTTAACGCAATAATTTTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA
--- a/test-data/reference.fasta.fai	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-reference	700	11	70	71
--- a/test-data/reference.gbk	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,38 +0,0 @@
-LOCUS       reference                700 bp    DNA     linear       06-FEB-2019
-DEFINITION  Listeria monocytogenes strain strain.
-ACCESSION   
-VERSION
-KEYWORDS    .
-SOURCE      Listeria monocytogenes
-  ORGANISM  Listeria monocytogenes
-            Unclassified.
-COMMENT     Annotated using prokka 1.13.3 from
-            https://github.com/tseemann/prokka.
-FEATURES             Location/Qualifiers
-     source          1..700
-                     /organism="Listeria monocytogenes"
-                     /mol_type="genomic DNA"
-                     /strain="strain"
-     CDS             188..658
-                     /locus_tag="KPFNHDNB_00001"
-                     /inference="ab initio prediction:Prodigal:2.6"
-                     /codon_start=1
-                     /transl_table=11
-                     /product="hypothetical protein"
-                     /translation="MIFQRLLKTRDTEFYRVIQNRNIDDVFGYLLIHDKREPAEIDDF
-                     KVFAKSNINKEAFSVNIKKNHIYTMFFHFTDLEEEQEIPKFTKVIRFIEGLLSFQPET
-                     SHYVDNYLIKEKLIFEYPAEFEKIGEFAKYLVKLSGRKITIPDTTREKYIYLTQ"
-ORIGIN      
-        1 tccacaagcc attgtgtgta attaaccact aattgtgtat aagtttaaac taattgaaaa
-       61 ggttatccac aataaaaagg cgttattcag gagttatcca cactttctag gaaaggattt
-      121 cattgcgcca atgtgttaaa ctatttaccg aatacgaaaa aaagacaaat aaatgaggtt
-      181 gtgaaaaatg atatttcaac ggcttttgaa aactagagat acagagtttt atcgagttat
-      241 acaaaacagg aatattgacg acgtatttgg atacttatta attcacgata aacgggaacc
-      301 agcagaaatt gacgatttta aggtatttgc aaaaagtaat ataaataaag aagctttttc
-      361 agtgaatatc aaaaaaaatc atatttacac gatgtttttc cactttactg atttagagga
-      421 agaacaggaa attccaaaat ttactaaagt tattcgtttt atagaaggac ttttatcttt
-      481 tcagccagaa acaagccatt acgttgataa ctatttaata aaggaaaaac taatttttga
-      541 atatcctgct gaatttgaga aaatcgggga gtttgctaaa tatttagtaa agctttcggg
-      601 tcgtaaaatt actattccag acacaacgag agaaaaatat atctatttaa cgcaataatt
-      661 ttcgaaaaat ggtttttctc tctataaaaa tatgatatga
-//
--- a/test-data/snippy-core-out/core.aln	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
->Reference
-AA
->a
-AA
->b
-TA
->c
-AC
--- a/test-data/snippy-core-out/core.full.aln	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,52 +0,0 @@
->Reference
-TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAA
-GGTTATCCACAATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTT
-CATTGCGCCAATGTGTTAAACTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTT
-GTGAAAAATGATATTTCAACGGCTTTTGAAAACTAGAGATACAGAGTTTTATCGAGTTAT
-ACAAAACAGGAATATTGACGACGTATTTGGATACTTATTAATTCACGATAAACGGGAACC
-AGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAGAAGCTTTTTC
-AGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA
-AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTT
-TCAGCCAGAAACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGA
-ATATCCTGCTGAATTTGAGAAAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGG
-TCGTAAAATTACTATTCCAGACACAACGAGAGAAAAATATATCTATTTAACGCAATAATT
-TTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA
->a
-TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACT---------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-----------------------------------------
->b
-TCCtCAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACT---------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-----------------------------------------
->c
-TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAcACT---------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-------------------------------------------------------------
-----------------------------------------
--- a/test-data/snippy-core-out/core.ref.fa	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,11 +0,0 @@
->reference
-TCCACAAGCCATTGTGTGTAATTAACCACTAATTGTGTATAAGTTTAAACTAATTGAAAAGGTTATCCAC
-AATAAAAAGGCGTTATTCAGGAGTTATCCACACTTTCTAGGAAAGGATTTCATTGCGCCAATGTGTTAAA
-CTATTTACCGAATACGAAAAAAAGACAAATAAATGAGGTTGTGAAAAATGATATTTCAACGGCTTTTGAA
-AACTAGAGATACAGAGTTTTATCGAGTTATACAAAACAGGAATATTGACGACGTATTTGGATACTTATTA
-ATTCACGATAAACGGGAACCAGCAGAAATTGACGATTTTAAGGTATTTGCAAAAAGTAATATAAATAAAG
-AAGCTTTTTCAGTGAATATCAAAAAAAATCATATTTACACGATGTTTTTCCACTTTACTGATTTAGAGGA
-AGAACAGGAAATTCCAAAATTTACTAAAGTTATTCGTTTTATAGAAGGACTTTTATCTTTTCAGCCAGAA
-ACAAGCCATTACGTTGATAACTATTTAATAAAGGAAAAACTAATTTTTGAATATCCTGCTGAATTTGAGA
-AAATCGGGGAGTTTGCTAAATATTTAGTAAAGCTTTCGGGTCGTAAAATTACTATTCCAGACACAACGAG
-AGAAAAATATATCTATTTAACGCAATAATTTTCGAAAAATGGTTTTTCTCTCTATAAAAATATGATATGA
--- a/test-data/snippy-core-out/core.tab	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-CHR	POS	REF	a	b	c
-reference	4	A	A	T	A
-reference	48	A	A	A	C
--- a/test-data/snippy-core-out/core.txt	Fri Mar 08 20:46:56 2019 -0500
+++ /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
--- a/test-data/snippy-core-out/core.vcf	Fri Mar 08 20:46:56 2019 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,8 +0,0 @@
-##fileformat=VCFv4.2
-##commandLine="snippy-core --ref reference.fasta a b c"
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##INFO=<ID=TYPE,Number=A,Type=String,Description="Allele type: snp ins del">
-##contig=<ID=reference,len=700>
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	a	b	c
-reference	4	.	A	T	.	PASS	TYPE=snp	GT	0	1	0
-reference	48	.	A	C	.	PASS	TYPE=snp	GT	0	0	1