# HG changeset patch
# User iuc
# Date 1548531408 18000
# Node ID 82f2b6f20fa2f97c5573a5d1ad6ccac341d0fbfb
# Parent  c9a8ef2aa380f28cd00400f4dced8d7c96e71e0f
planemo upload commit c295a06009ccafd0c1dc8aba5dd87239795d2b61

diff -r c9a8ef2aa380 -r 82f2b6f20fa2 snippy.xml
--- a/snippy.xml	Fri Feb 16 13:40:16 2018 -0500
+++ b/snippy.xml	Sat Jan 26 14:36:48 2019 -0500
@@ -1,4 +1,4 @@
-<tool id="snippy" name="snippy" version="@VERSION@">
+<tool id="snippy" name="snippy" version="@VERSION@+galaxy1">
   <description>
       Snippy finds SNPs between a haploid reference genome and your NGS sequence reads.
   </description>
@@ -40,14 +40,14 @@
                 --pe2 '$fastq_input.fastq_input2'
             #end if
             #if str( $fastq_input.fastq_input_selector ) == "paired_collection"
-                --pe1 '$fastq_input.fastq_input1.forward'
-                --pe2 '$fastq_input.fastq_input1.reverse'
+                --pe1 '$fastq_input.fastq_input.forward'
+                --pe2 '$fastq_input.fastq_input.reverse'
             #end if
             #if str( $fastq_input.fastq_input_selector ) == "single"
-                --se '$fastq_input.fastq_input1'
+                --se '$fastq_input.fastq_input'
             #end if
             #if str( $fastq_input.fastq_input_selector ) == "paired_iv"
-                --peil '$fastq_input.fastq_input1'
+                --peil '$fastq_input.fastq_input'
             #end if
 
         &&
@@ -57,9 +57,13 @@
         &&
 
         #import re
-        #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
-        mkdir -p ${dir_name}/reference && cp out/snps.tab out/snps.aligned.fa ${dir_name}/ && cp out/reference/ref.fa ${dir_name}/reference/ &&
+        #if str( $fastq_input.fastq_input_selector ) == "paired"
+            #set $dir_name = re.sub('[^\w_]', '_', $fastq_input.fastq_input1.element_identifier)
+        #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 ${dir_name}/ &&
         tar -czf out.tgz ${dir_name}
 
 
@@ -81,13 +85,13 @@
                 <param name="fastq_input2" type="data" format="fastqsanger,fasta" label="Select second set of reads" help="Specify dataset with reverse reads"/>
             </when>
             <when value="single">
-                <param name="fastq_input1" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
+                <param name="fastq_input" type="data" format="fastqsanger,fasta" label="Select fastq dataset" help="Specify dataset with single reads"/>
             </when>
             <when value="paired_collection">
-                <param name="fastq_input1" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
+                <param name="fastq_input" format="fastqsanger,fasta" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
             </when>
             <when value="paired_iv">
-                <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
+                <param name="fastq_input" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with interleaved reads"/>
             </when>
         </conditional>
 
@@ -204,6 +208,20 @@
             <output name="snpgff" ftype="gff3" file="min_frac/snps.gff" />
         </test>
 
+        <test> <!-- test 6 - fasta ref default paired_collection -->
+	    <param name="ref" value="wildtype.fna" ftype="fasta" />
+            <param name="fastq_input_selector" value="paired_collection" />
+            <param name="fastq_input">
+                <collection type="paired">
+                    <element name="forward" ftype="fastqsanger" value="mutant_R1.fastq" />
+                    <element name="reverse" ftype="fastqsanger" value="mutant_R2.fastq" />
+                </collection>
+            </param>
+            <param name="outputs" value="outgff,outsum" />
+            <output name="snpsum" ftype="tabular" file="fna_ref/snps.txt" lines_diff="6" />
+            <output name="snpgff" ftype="gff3" file="fna_ref/snps.gff" />
+        </test>
+
     </tests>
 
 
diff -r c9a8ef2aa380 -r 82f2b6f20fa2 test-data/fna_ref/snps.gff
--- a/test-data/fna_ref/snps.gff	Fri Feb 16 13:40:16 2018 -0500
+++ b/test-data/fna_ref/snps.gff	Sat Jan 26 14:36:48 2019 -0500
@@ -1,16 +1,17 @@
 ##gff-version 3
 Wildtype	snippy:3.2-dev	variation	24388	24388	.	.	0	note=snp A=>G G:22 A:0
 Wildtype	snippy:3.2-dev	variation	29479	29479	.	.	0	note=snp T=>G G:21 T:0
-Wildtype	snippy:3.2-dev	variation	47299	47299	.	.	0	note=snp T=>A A:24 T:0
+Wildtype	snippy:3.2-dev	variation	47299	47299	.	.	0	note=snp T=>A A:25 T:0
 Wildtype	snippy:3.2-dev	variation	102969	102969	.	.	0	note=snp G=>C C:16 G:0
-Wildtype	snippy:3.2-dev	variation	103048	103048	.	.	0	note=snp T=>A A:20 T:0
-Wildtype	snippy:3.2-dev	variation	103379	103379	.	.	0	note=del GAA=>GA GA:11 GAA:0
-Wildtype	snippy:3.2-dev	variation	106602	106602	.	.	0	note=snp T=>G G:21 T:0
-Wildtype	snippy:3.2-dev	variation	109833	109833	.	.	0	note=snp T=>A A:16 T:0
-Wildtype	snippy:3.2-dev	variation	114540	114540	.	.	0	note=del ATT=>AT AT:25 ATT:0
-Wildtype	snippy:3.2-dev	variation	129881	129881	.	.	0	note=mnp GT=>AA AA:18 GT:0
+Wildtype	snippy:3.2-dev	variation	103048	103048	.	.	0	note=snp T=>A A:21 T:0
+Wildtype	snippy:3.2-dev	variation	103379	103379	.	.	0	note=del GAAAATAG=>GAAATAG GAAATAG:11 GAAAATAG:0
+Wildtype	snippy:3.2-dev	variation	106602	106602	.	.	0	note=snp T=>G G:22 T:0
+Wildtype	snippy:3.2-dev	variation	106722	106722	.	.	0	note=ins GTTTTTAAC=>GTTTTTTAAC GTTTTTTAAC:11 GTTTTTAAC:0
+Wildtype	snippy:3.2-dev	variation	109833	109833	.	.	0	note=snp T=>A A:17 T:0
+Wildtype	snippy:3.2-dev	variation	114540	114540	.	.	0	note=del ATTGTGA=>ATGTGA ATGTGA:26 ATTGTGA:0
+Wildtype	snippy:3.2-dev	variation	129881	129881	.	.	0	note=mnp GT=>AA AA:19 GT:0
 Wildtype	snippy:3.2-dev	variation	138877	138877	.	.	0	note=snp G=>C C:14 G:0
 Wildtype	snippy:3.2-dev	variation	138920	138920	.	.	0	note=snp A=>G G:10 A:0
+Wildtype	snippy:3.2-dev	variation	138954	138954	.	.	0	note=snp A=>G G:10 A:0
 Wildtype	snippy:3.2-dev	variation	160547	160547	.	.	0	note=del GTC=>GC GC:18 GTC:0
-Wildtype	snippy:3.2-dev	variation	160552	160552	.	.	0	note=del CTA=>CA CA:20 CTA:0
-Wildtype	snippy:3.2-dev	variation	190866	190866	.	.	0	note=del GTT=>GT GT:18 GTT:0
+Wildtype	snippy:3.2-dev	variation	190866	190866	.	.	0	note=del GTTTTCTTTAA=>GTTTCTTTAA GTTTCTTTAA:17 GTTTTCTTTAA:0
diff -r c9a8ef2aa380 -r 82f2b6f20fa2 test-data/fna_ref/snps.txt
--- a/test-data/fna_ref/snps.txt	Fri Feb 16 13:40:16 2018 -0500
+++ b/test-data/fna_ref/snps.txt	Sat Jan 26 14:36:48 2019 -0500
@@ -1,9 +1,10 @@
-DateTime	2017-07-12T04:51:24
-ReadFiles	/home/ubuntu/snippy/test-data/mutant_R1.fastq /home/ubuntu/snippy/test-data/mutant_R2.fastq
-Reference	/home/ubuntu/snippy/test-data/wildtype.fna
+DateTime	2019-01-24T13:08:34
+ReadFiles	/home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R2.fastq
+Reference	/home/dfornika/Code/tools-iuc/tools/snippy/test-data/wildtype.fna
 ReferenceSize	200694
 Software	snippy 3.2-dev
-Variant-DEL	5
+Variant-DEL	4
+Variant-INS	1
 Variant-MNP	1
-Variant-SNP	9
-VariantTotal	15
+Variant-SNP	10
+VariantTotal	16
diff -r c9a8ef2aa380 -r 82f2b6f20fa2 test-data/gbk_ref/snps.gff
--- a/test-data/gbk_ref/snps.gff	Fri Feb 16 13:40:16 2018 -0500
+++ b/test-data/gbk_ref/snps.gff	Sat Jan 26 14:36:48 2019 -0500
@@ -1,16 +1,17 @@
 ##gff-version 3
 Wildtype	snippy:3.2-dev	variation	24388	24388	.	.	0	note=snp A=>G G:22 A:0 CDS + 1/702 1/233 initiator_codon_variant c.1A>G p.Met1? WILD_00022 walR Transcriptional regulatory protein WalR
 Wildtype	snippy:3.2-dev	variation	29479	29479	.	.	0	note=snp T=>G G:21 T:0 CDS + 39/792 13/263 synonymous_variant c.39T>G p.Gly13Gly WILD_00026 yycJ Putative metallo-hydrolase YycJ
-Wildtype	snippy:3.2-dev	variation	47299	47299	.	.	0	note=snp T=>A A:24 T:0 CDS + 54/1758 18/585 stop_gained c.54T>A p.Cys18* WILD_00043 mecR1 Methicillin resistance mecR1 protein
+Wildtype	snippy:3.2-dev	variation	47299	47299	.	.	0	note=snp T=>A A:25 T:0 CDS + 54/1758 18/585 stop_gained c.54T>A p.Cys18* WILD_00043 mecR1 Methicillin resistance mecR1 protein
 Wildtype	snippy:3.2-dev	variation	102969	102969	.	.	0	note=snp G=>C C:16 G:0 CDS - 87/1281 29/426 synonymous_variant c.87C>G p.Gly29Gly WILD_00093 spa Immunoglobulin G-binding protein A
-Wildtype	snippy:3.2-dev	variation	103048	103048	.	.	0	note=snp T=>A A:20 T:0 CDS - 8/1281 3/426 missense_variant c.8A>T p.Lys3Met WILD_00093 spa Immunoglobulin G-binding protein A
-Wildtype	snippy:3.2-dev	variation	103379	103379	.	.	0	note=del GAA=>GA GA:11 GAA:0
-Wildtype	snippy:3.2-dev	variation	106602	106602	.	.	0	note=snp T=>G G:21 T:0 CDS - 993/993 331/330 stop_lost&splice_region_variant c.993A>C p.Ter331Tyrext*? WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY
-Wildtype	snippy:3.2-dev	variation	109833	109833	.	.	0	note=snp T=>A A:16 T:0 CDS + 1/1755 1/584 initiator_codon_variant c.1T>A p.Leu1? WILD_00100 iucC_1 Aerobactin synthase
-Wildtype	snippy:3.2-dev	variation	114540	114540	.	.	0	note=del ATT=>AT AT:25 ATT:0 CDS + 1717/1737 573/578 frameshift_variant c.1717delT p.Cys573fs WILD_00102 iucA N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase
-Wildtype	snippy:3.2-dev	variation	129881	129881	.	.	0	note=mnp GT=>AA AA:18 GT:0 CDS + 55/708 19/235 missense_variant c.55_56delGTinsAA p.Val19Asn WILD_00117 deoD Purine nucleoside phosphorylase DeoD-type
+Wildtype	snippy:3.2-dev	variation	103048	103048	.	.	0	note=snp T=>A A:21 T:0 CDS - 8/1281 3/426 missense_variant c.8A>T p.Lys3Met WILD_00093 spa Immunoglobulin G-binding protein A
+Wildtype	snippy:3.2-dev	variation	103379	103379	.	.	0	note=del GAAAATAG=>GAAATAG GAAATAG:11 GAAAATAG:0
+Wildtype	snippy:3.2-dev	variation	106602	106602	.	.	0	note=snp T=>G G:22 T:0 CDS - 993/993 331/330 stop_lost&splice_region_variant c.993A>C p.Ter331Tyrext*? WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY
+Wildtype	snippy:3.2-dev	variation	106722	106722	.	.	0	note=ins GTTTTTAAC=>GTTTTTTAAC GTTTTTTAAC:11 GTTTTTAAC:0 CDS - 867/993 289/330 frameshift_variant c.867_868insA p.Asn291fs WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY
+Wildtype	snippy:3.2-dev	variation	109833	109833	.	.	0	note=snp T=>A A:17 T:0 CDS + 1/1755 1/584 initiator_codon_variant c.1T>A p.Leu1? WILD_00100 iucC_1 Aerobactin synthase
+Wildtype	snippy:3.2-dev	variation	114540	114540	.	.	0	note=del ATTGTGA=>ATGTGA ATGTGA:26 ATTGTGA:0 CDS + 1717/1737 573/578 frameshift_variant c.1717delT p.Cys573fs WILD_00102 iucA N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase
+Wildtype	snippy:3.2-dev	variation	129881	129881	.	.	0	note=mnp GT=>AA AA:19 GT:0 CDS + 55/708 19/235 missense_variant c.55_56delGTinsAA p.Val19Asn WILD_00117 deoD Purine nucleoside phosphorylase DeoD-type
 Wildtype	snippy:3.2-dev	variation	138877	138877	.	.	0	note=snp G=>C C:14 G:0 CDS + 1119/1545 373/514 missense_variant c.1119G>C p.Trp373Cys WILD_00125  hypothetical protein
 Wildtype	snippy:3.2-dev	variation	138920	138920	.	.	0	note=snp A=>G G:10 A:0 CDS + 1162/1545 388/514 missense_variant c.1162A>G p.Lys388Glu WILD_00125  hypothetical protein
+Wildtype	snippy:3.2-dev	variation	138954	138954	.	.	0	note=snp A=>G G:10 A:0 CDS + 1196/1545 399/514 missense_variant c.1196A>G p.Asp399Gly WILD_00125  hypothetical protein
 Wildtype	snippy:3.2-dev	variation	160547	160547	.	.	0	note=del GTC=>GC GC:18 GTC:0
-Wildtype	snippy:3.2-dev	variation	160552	160552	.	.	0	note=del CTA=>CA CA:20 CTA:0
-Wildtype	snippy:3.2-dev	variation	190866	190866	.	.	0	note=del GTT=>GT GT:18 GTT:0 CDS - 28/1356 10/451 frameshift_variant c.28delA p.Asn10fs WILD_00166 brnQ Branched-chain amino acid transport system 2 carrier protein
+Wildtype	snippy:3.2-dev	variation	190866	190866	.	.	0	note=del GTTTTCTTTAA=>GTTTCTTTAA GTTTCTTTAA:17 GTTTTCTTTAA:0 CDS - 26/1356 9/451 frameshift_variant c.26delA p.Asn10fs WILD_00166 brnQ Branched-chain amino acid transport system 2 carrier protein
diff -r c9a8ef2aa380 -r 82f2b6f20fa2 test-data/gbk_ref/snps.txt
--- a/test-data/gbk_ref/snps.txt	Fri Feb 16 13:40:16 2018 -0500
+++ b/test-data/gbk_ref/snps.txt	Sat Jan 26 14:36:48 2019 -0500
@@ -1,9 +1,10 @@
-DateTime	2017-07-12T04:52:49
-ReadFiles	/home/ubuntu/snippy/test-data/mutant_R1.fastq /home/ubuntu/snippy/test-data/mutant_R2.fastq
-Reference	/home/ubuntu/snippy/test-data/wildtype.gbk
+DateTime	2019-01-24T13:29:29
+ReadFiles	/home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R2.fastq
+Reference	/home/dfornika/Code/tools-iuc/tools/snippy/test-data/wildtype.gbk
 ReferenceSize	200727
 Software	snippy 3.2-dev
-Variant-DEL	5
+Variant-DEL	4
+Variant-INS	1
 Variant-MNP	1
-Variant-SNP	9
-VariantTotal	15
+Variant-SNP	10
+VariantTotal	16
diff -r c9a8ef2aa380 -r 82f2b6f20fa2 test-data/map_qual/snps.gff
--- a/test-data/map_qual/snps.gff	Fri Feb 16 13:40:16 2018 -0500
+++ b/test-data/map_qual/snps.gff	Sat Jan 26 14:36:48 2019 -0500
@@ -1,16 +1,17 @@
 ##gff-version 3
 Wildtype	snippy:3.2-dev	variation	24388	24388	.	.	0	note=snp A=>G G:22 A:0 CDS + 1/702 1/233 initiator_codon_variant c.1A>G p.Met1? WILD_00022 walR Transcriptional regulatory protein WalR
 Wildtype	snippy:3.2-dev	variation	29479	29479	.	.	0	note=snp T=>G G:21 T:0 CDS + 39/792 13/263 synonymous_variant c.39T>G p.Gly13Gly WILD_00026 yycJ Putative metallo-hydrolase YycJ
-Wildtype	snippy:3.2-dev	variation	47299	47299	.	.	0	note=snp T=>A A:24 T:0 CDS + 54/1758 18/585 stop_gained c.54T>A p.Cys18* WILD_00043 mecR1 Methicillin resistance mecR1 protein
+Wildtype	snippy:3.2-dev	variation	47299	47299	.	.	0	note=snp T=>A A:25 T:0 CDS + 54/1758 18/585 stop_gained c.54T>A p.Cys18* WILD_00043 mecR1 Methicillin resistance mecR1 protein
 Wildtype	snippy:3.2-dev	variation	102969	102969	.	.	0	note=snp G=>C C:16 G:0 CDS - 87/1281 29/426 synonymous_variant c.87C>G p.Gly29Gly WILD_00093 spa Immunoglobulin G-binding protein A
-Wildtype	snippy:3.2-dev	variation	103048	103048	.	.	0	note=snp T=>A A:20 T:0 CDS - 8/1281 3/426 missense_variant c.8A>T p.Lys3Met WILD_00093 spa Immunoglobulin G-binding protein A
-Wildtype	snippy:3.2-dev	variation	103379	103379	.	.	0	note=del GAA=>GA GA:11 GAA:0
-Wildtype	snippy:3.2-dev	variation	106602	106602	.	.	0	note=snp T=>G G:21 T:0 CDS - 993/993 331/330 stop_lost&splice_region_variant c.993A>C p.Ter331Tyrext*? WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY
-Wildtype	snippy:3.2-dev	variation	109833	109833	.	.	0	note=snp T=>A A:16 T:0 CDS + 1/1755 1/584 initiator_codon_variant c.1T>A p.Leu1? WILD_00100 iucC_1 Aerobactin synthase
-Wildtype	snippy:3.2-dev	variation	114540	114540	.	.	0	note=del ATT=>AT AT:25 ATT:0 CDS + 1717/1737 573/578 frameshift_variant c.1717delT p.Cys573fs WILD_00102 iucA N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase
-Wildtype	snippy:3.2-dev	variation	129881	129881	.	.	0	note=mnp GT=>AA AA:18 GT:0 CDS + 55/708 19/235 missense_variant c.55_56delGTinsAA p.Val19Asn WILD_00117 deoD Purine nucleoside phosphorylase DeoD-type
+Wildtype	snippy:3.2-dev	variation	103048	103048	.	.	0	note=snp T=>A A:21 T:0 CDS - 8/1281 3/426 missense_variant c.8A>T p.Lys3Met WILD_00093 spa Immunoglobulin G-binding protein A
+Wildtype	snippy:3.2-dev	variation	103379	103379	.	.	0	note=del GAAAATAG=>GAAATAG GAAATAG:11 GAAAATAG:0
+Wildtype	snippy:3.2-dev	variation	106602	106602	.	.	0	note=snp T=>G G:22 T:0 CDS - 993/993 331/330 stop_lost&splice_region_variant c.993A>C p.Ter331Tyrext*? WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY
+Wildtype	snippy:3.2-dev	variation	106722	106722	.	.	0	note=ins GTTTTTAAC=>GTTTTTTAAC GTTTTTTAAC:11 GTTTTTAAC:0 CDS - 867/993 289/330 frameshift_variant c.867_868insA p.Asn291fs WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY
+Wildtype	snippy:3.2-dev	variation	109833	109833	.	.	0	note=snp T=>A A:17 T:0 CDS + 1/1755 1/584 initiator_codon_variant c.1T>A p.Leu1? WILD_00100 iucC_1 Aerobactin synthase
+Wildtype	snippy:3.2-dev	variation	114540	114540	.	.	0	note=del ATTGTGA=>ATGTGA ATGTGA:26 ATTGTGA:0 CDS + 1717/1737 573/578 frameshift_variant c.1717delT p.Cys573fs WILD_00102 iucA N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase
+Wildtype	snippy:3.2-dev	variation	129881	129881	.	.	0	note=mnp GT=>AA AA:19 GT:0 CDS + 55/708 19/235 missense_variant c.55_56delGTinsAA p.Val19Asn WILD_00117 deoD Purine nucleoside phosphorylase DeoD-type
 Wildtype	snippy:3.2-dev	variation	138877	138877	.	.	0	note=snp G=>C C:14 G:0 CDS + 1119/1545 373/514 missense_variant c.1119G>C p.Trp373Cys WILD_00125  hypothetical protein
 Wildtype	snippy:3.2-dev	variation	138920	138920	.	.	0	note=snp A=>G G:10 A:0 CDS + 1162/1545 388/514 missense_variant c.1162A>G p.Lys388Glu WILD_00125  hypothetical protein
+Wildtype	snippy:3.2-dev	variation	138954	138954	.	.	0	note=snp A=>G G:10 A:0 CDS + 1196/1545 399/514 missense_variant c.1196A>G p.Asp399Gly WILD_00125  hypothetical protein
 Wildtype	snippy:3.2-dev	variation	160547	160547	.	.	0	note=del GTC=>GC GC:18 GTC:0
-Wildtype	snippy:3.2-dev	variation	160552	160552	.	.	0	note=del CTA=>CA CA:20 CTA:0
-Wildtype	snippy:3.2-dev	variation	190866	190866	.	.	0	note=del GTT=>GT GT:18 GTT:0 CDS - 28/1356 10/451 frameshift_variant c.28delA p.Asn10fs WILD_00166 brnQ Branched-chain amino acid transport system 2 carrier protein
+Wildtype	snippy:3.2-dev	variation	190866	190866	.	.	0	note=del GTTTTCTTTAA=>GTTTCTTTAA GTTTCTTTAA:17 GTTTTCTTTAA:0 CDS - 26/1356 9/451 frameshift_variant c.26delA p.Asn10fs WILD_00166 brnQ Branched-chain amino acid transport system 2 carrier protein
diff -r c9a8ef2aa380 -r 82f2b6f20fa2 test-data/map_qual/snps.txt
--- a/test-data/map_qual/snps.txt	Fri Feb 16 13:40:16 2018 -0500
+++ b/test-data/map_qual/snps.txt	Sat Jan 26 14:36:48 2019 -0500
@@ -1,9 +1,10 @@
-DateTime	2017-07-13T05:37:56
-ReadFiles	/home/ubuntu/snippy/test-data/mutant_R1.fastq /home/ubuntu/snippy/test-data/mutant_R2.fastq
-Reference	/home/ubuntu/snippy/test-data/wildtype.gbk
+DateTime	2019-01-24T14:57:31
+ReadFiles	/home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R2.fastq
+Reference	/home/dfornika/Code/tools-iuc/tools/snippy/test-data/wildtype.gbk
 ReferenceSize	200727
 Software	snippy 3.2-dev
-Variant-DEL	5
+Variant-DEL	4
+Variant-INS	1
 Variant-MNP	1
-Variant-SNP	9
-VariantTotal	15
+Variant-SNP	10
+VariantTotal	16
diff -r c9a8ef2aa380 -r 82f2b6f20fa2 test-data/min_cov/snps.gff
--- a/test-data/min_cov/snps.gff	Fri Feb 16 13:40:16 2018 -0500
+++ b/test-data/min_cov/snps.gff	Sat Jan 26 14:36:48 2019 -0500
@@ -1,13 +1,12 @@
 ##gff-version 3
 Wildtype	snippy:3.2-dev	variation	24388	24388	.	.	0	note=snp A=>G G:22 A:0 CDS + 1/702 1/233 initiator_codon_variant c.1A>G p.Met1? WILD_00022 walR Transcriptional regulatory protein WalR
 Wildtype	snippy:3.2-dev	variation	29479	29479	.	.	0	note=snp T=>G G:21 T:0 CDS + 39/792 13/263 synonymous_variant c.39T>G p.Gly13Gly WILD_00026 yycJ Putative metallo-hydrolase YycJ
-Wildtype	snippy:3.2-dev	variation	47299	47299	.	.	0	note=snp T=>A A:24 T:0 CDS + 54/1758 18/585 stop_gained c.54T>A p.Cys18* WILD_00043 mecR1 Methicillin resistance mecR1 protein
+Wildtype	snippy:3.2-dev	variation	47299	47299	.	.	0	note=snp T=>A A:25 T:0 CDS + 54/1758 18/585 stop_gained c.54T>A p.Cys18* WILD_00043 mecR1 Methicillin resistance mecR1 protein
 Wildtype	snippy:3.2-dev	variation	102969	102969	.	.	0	note=snp G=>C C:16 G:0 CDS - 87/1281 29/426 synonymous_variant c.87C>G p.Gly29Gly WILD_00093 spa Immunoglobulin G-binding protein A
-Wildtype	snippy:3.2-dev	variation	103048	103048	.	.	0	note=snp T=>A A:20 T:0 CDS - 8/1281 3/426 missense_variant c.8A>T p.Lys3Met WILD_00093 spa Immunoglobulin G-binding protein A
-Wildtype	snippy:3.2-dev	variation	106602	106602	.	.	0	note=snp T=>G G:21 T:0 CDS - 993/993 331/330 stop_lost&splice_region_variant c.993A>C p.Ter331Tyrext*? WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY
-Wildtype	snippy:3.2-dev	variation	109833	109833	.	.	0	note=snp T=>A A:16 T:0 CDS + 1/1755 1/584 initiator_codon_variant c.1T>A p.Leu1? WILD_00100 iucC_1 Aerobactin synthase
-Wildtype	snippy:3.2-dev	variation	114540	114540	.	.	0	note=del ATT=>AT AT:25 ATT:0 CDS + 1717/1737 573/578 frameshift_variant c.1717delT p.Cys573fs WILD_00102 iucA N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase
-Wildtype	snippy:3.2-dev	variation	129881	129881	.	.	0	note=mnp GT=>AA AA:18 GT:0 CDS + 55/708 19/235 missense_variant c.55_56delGTinsAA p.Val19Asn WILD_00117 deoD Purine nucleoside phosphorylase DeoD-type
+Wildtype	snippy:3.2-dev	variation	103048	103048	.	.	0	note=snp T=>A A:21 T:0 CDS - 8/1281 3/426 missense_variant c.8A>T p.Lys3Met WILD_00093 spa Immunoglobulin G-binding protein A
+Wildtype	snippy:3.2-dev	variation	106602	106602	.	.	0	note=snp T=>G G:22 T:0 CDS - 993/993 331/330 stop_lost&splice_region_variant c.993A>C p.Ter331Tyrext*? WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY
+Wildtype	snippy:3.2-dev	variation	109833	109833	.	.	0	note=snp T=>A A:17 T:0 CDS + 1/1755 1/584 initiator_codon_variant c.1T>A p.Leu1? WILD_00100 iucC_1 Aerobactin synthase
+Wildtype	snippy:3.2-dev	variation	114540	114540	.	.	0	note=del ATTGTGA=>ATGTGA ATGTGA:26 ATTGTGA:0 CDS + 1717/1737 573/578 frameshift_variant c.1717delT p.Cys573fs WILD_00102 iucA N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase
+Wildtype	snippy:3.2-dev	variation	129881	129881	.	.	0	note=mnp GT=>AA AA:19 GT:0 CDS + 55/708 19/235 missense_variant c.55_56delGTinsAA p.Val19Asn WILD_00117 deoD Purine nucleoside phosphorylase DeoD-type
 Wildtype	snippy:3.2-dev	variation	160547	160547	.	.	0	note=del GTC=>GC GC:18 GTC:0
-Wildtype	snippy:3.2-dev	variation	160552	160552	.	.	0	note=del CTA=>CA CA:20 CTA:0
-Wildtype	snippy:3.2-dev	variation	190866	190866	.	.	0	note=del GTT=>GT GT:18 GTT:0 CDS - 28/1356 10/451 frameshift_variant c.28delA p.Asn10fs WILD_00166 brnQ Branched-chain amino acid transport system 2 carrier protein
+Wildtype	snippy:3.2-dev	variation	190866	190866	.	.	0	note=del GTTTTCTTTAA=>GTTTCTTTAA GTTTCTTTAA:17 GTTTTCTTTAA:0 CDS - 26/1356 9/451 frameshift_variant c.26delA p.Asn10fs WILD_00166 brnQ Branched-chain amino acid transport system 2 carrier protein
diff -r c9a8ef2aa380 -r 82f2b6f20fa2 test-data/min_cov/snps.txt
--- a/test-data/min_cov/snps.txt	Fri Feb 16 13:40:16 2018 -0500
+++ b/test-data/min_cov/snps.txt	Sat Jan 26 14:36:48 2019 -0500
@@ -1,9 +1,9 @@
-DateTime	2017-07-12T04:54:55
-ReadFiles	/home/ubuntu/snippy/test-data/mutant_R1.fastq /home/ubuntu/snippy/test-data/mutant_R2.fastq
-Reference	/home/ubuntu/snippy/test-data/wildtype.gbk
+DateTime	2019-01-24T15:21:35
+ReadFiles	/home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R2.fastq
+Reference	/home/dfornika/Code/tools-iuc/tools/snippy/test-data/wildtype.gbk
 ReferenceSize	200727
 Software	snippy 3.2-dev
-Variant-DEL	4
+Variant-DEL	3
 Variant-MNP	1
 Variant-SNP	7
-VariantTotal	12
+VariantTotal	11
diff -r c9a8ef2aa380 -r 82f2b6f20fa2 test-data/min_frac/snps.gff
--- a/test-data/min_frac/snps.gff	Fri Feb 16 13:40:16 2018 -0500
+++ b/test-data/min_frac/snps.gff	Sat Jan 26 14:36:48 2019 -0500
@@ -1,17 +1,18 @@
 ##gff-version 3
 Wildtype	snippy:3.2-dev	variation	24388	24388	.	.	0	note=snp A=>G G:22 A:0 CDS + 1/702 1/233 initiator_codon_variant c.1A>G p.Met1? WILD_00022 walR Transcriptional regulatory protein WalR
 Wildtype	snippy:3.2-dev	variation	29479	29479	.	.	0	note=snp T=>G G:21 T:0 CDS + 39/792 13/263 synonymous_variant c.39T>G p.Gly13Gly WILD_00026 yycJ Putative metallo-hydrolase YycJ
-Wildtype	snippy:3.2-dev	variation	47299	47299	.	.	0	note=snp T=>A A:24 T:0 CDS + 54/1758 18/585 stop_gained c.54T>A p.Cys18* WILD_00043 mecR1 Methicillin resistance mecR1 protein
+Wildtype	snippy:3.2-dev	variation	47299	47299	.	.	0	note=snp T=>A A:25 T:0 CDS + 54/1758 18/585 stop_gained c.54T>A p.Cys18* WILD_00043 mecR1 Methicillin resistance mecR1 protein
 Wildtype	snippy:3.2-dev	variation	102969	102969	.	.	0	note=snp G=>C C:16 G:0 CDS - 87/1281 29/426 synonymous_variant c.87C>G p.Gly29Gly WILD_00093 spa Immunoglobulin G-binding protein A
-Wildtype	snippy:3.2-dev	variation	103048	103048	.	.	0	note=snp T=>A A:20 T:0 CDS - 8/1281 3/426 missense_variant c.8A>T p.Lys3Met WILD_00093 spa Immunoglobulin G-binding protein A
-Wildtype	snippy:3.2-dev	variation	103379	103379	.	.	0	note=del GAA=>GA GA:11 GAA:0
-Wildtype	snippy:3.2-dev	variation	106602	106602	.	.	0	note=snp T=>G G:21 T:0 CDS - 993/993 331/330 stop_lost&splice_region_variant c.993A>C p.Ter331Tyrext*? WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY
-Wildtype	snippy:3.2-dev	variation	106722	106722	.	.	0	note=ins GTTTTTA=>GTTTTTTA GTTTTTTA:11 GTTTTTA:0 CDS - 867/993 289/330 frameshift_variant c.867_868insA p.Asn291fs WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY
-Wildtype	snippy:3.2-dev	variation	109833	109833	.	.	0	note=snp T=>A A:16 T:0 CDS + 1/1755 1/584 initiator_codon_variant c.1T>A p.Leu1? WILD_00100 iucC_1 Aerobactin synthase
-Wildtype	snippy:3.2-dev	variation	114540	114540	.	.	0	note=del ATT=>AT AT:25 ATT:0 CDS + 1717/1737 573/578 frameshift_variant c.1717delT p.Cys573fs WILD_00102 iucA N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase
-Wildtype	snippy:3.2-dev	variation	129881	129881	.	.	0	note=mnp GT=>AA AA:18 GT:0 CDS + 55/708 19/235 missense_variant c.55_56delGTinsAA p.Val19Asn WILD_00117 deoD Purine nucleoside phosphorylase DeoD-type
+Wildtype	snippy:3.2-dev	variation	103048	103048	.	.	0	note=snp T=>A A:21 T:0 CDS - 8/1281 3/426 missense_variant c.8A>T p.Lys3Met WILD_00093 spa Immunoglobulin G-binding protein A
+Wildtype	snippy:3.2-dev	variation	103379	103379	.	.	0	note=del GAAAATAG=>GAAATAG GAAATAG:11 GAAAATAG:0
+Wildtype	snippy:3.2-dev	variation	106602	106602	.	.	0	note=snp T=>G G:22 T:0 CDS - 993/993 331/330 stop_lost&splice_region_variant c.993A>C p.Ter331Tyrext*? WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY
+Wildtype	snippy:3.2-dev	variation	106722	106722	.	.	0	note=ins GTTTTTAAC=>GTTTTTTAAC GTTTTTTAAC:11 GTTTTTAAC:0 CDS - 867/993 289/330 frameshift_variant c.867_868insA p.Asn291fs WILD_00097 yfiY putative siderophore-binding lipoprotein YfiY
+Wildtype	snippy:3.2-dev	variation	109833	109833	.	.	0	note=snp T=>A A:17 T:0 CDS + 1/1755 1/584 initiator_codon_variant c.1T>A p.Leu1? WILD_00100 iucC_1 Aerobactin synthase
+Wildtype	snippy:3.2-dev	variation	114540	114540	.	.	0	note=del ATTGTGA=>ATGTGA ATGTGA:26 ATTGTGA:0 CDS + 1717/1737 573/578 frameshift_variant c.1717delT p.Cys573fs WILD_00102 iucA N(2)-citryl-N(6)-acetyl-N(6)-hydroxylysine synthase
+Wildtype	snippy:3.2-dev	variation	129881	129881	.	.	0	note=mnp GT=>AA AA:19 GT:0 CDS + 55/708 19/235 missense_variant c.55_56delGTinsAA p.Val19Asn WILD_00117 deoD Purine nucleoside phosphorylase DeoD-type
 Wildtype	snippy:3.2-dev	variation	138877	138877	.	.	0	note=snp G=>C C:14 G:0 CDS + 1119/1545 373/514 missense_variant c.1119G>C p.Trp373Cys WILD_00125  hypothetical protein
 Wildtype	snippy:3.2-dev	variation	138920	138920	.	.	0	note=snp A=>G G:10 A:0 CDS + 1162/1545 388/514 missense_variant c.1162A>G p.Lys388Glu WILD_00125  hypothetical protein
+Wildtype	snippy:3.2-dev	variation	138954	138954	.	.	0	note=snp A=>G G:10 A:0 CDS + 1196/1545 399/514 missense_variant c.1196A>G p.Asp399Gly WILD_00125  hypothetical protein
 Wildtype	snippy:3.2-dev	variation	160547	160547	.	.	0	note=del GTC=>GC GC:18 GTC:0
-Wildtype	snippy:3.2-dev	variation	160552	160552	.	.	0	note=del CTA=>CA CA:20 CTA:0
-Wildtype	snippy:3.2-dev	variation	190866	190866	.	.	0	note=del GTT=>GT GT:18 GTT:0 CDS - 28/1356 10/451 frameshift_variant c.28delA p.Asn10fs WILD_00166 brnQ Branched-chain amino acid transport system 2 carrier protein
+Wildtype	snippy:3.2-dev	variation	160552	160552	.	.	0	note=del CTATTA=>CATTA CATTA:18 CTATTA:0
+Wildtype	snippy:3.2-dev	variation	190866	190866	.	.	0	note=del GTTTTCTTTAA=>GTTTCTTTAA GTTTCTTTAA:17 GTTTTCTTTAA:0 CDS - 26/1356 9/451 frameshift_variant c.26delA p.Asn10fs WILD_00166 brnQ Branched-chain amino acid transport system 2 carrier protein
diff -r c9a8ef2aa380 -r 82f2b6f20fa2 test-data/min_frac/snps.txt
--- a/test-data/min_frac/snps.txt	Fri Feb 16 13:40:16 2018 -0500
+++ b/test-data/min_frac/snps.txt	Sat Jan 26 14:36:48 2019 -0500
@@ -1,10 +1,10 @@
-DateTime	2017-07-12T04:56:36
-ReadFiles	/home/ubuntu/snippy/test-data/mutant_R1.fastq /home/ubuntu/snippy/test-data/mutant_R2.fastq
-Reference	/home/ubuntu/snippy/test-data/wildtype.gbk
+DateTime	2019-01-24T15:35:47
+ReadFiles	/home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R1.fastq /home/dfornika/Code/tools-iuc/tools/snippy/test-data/mutant_R2.fastq
+Reference	/home/dfornika/Code/tools-iuc/tools/snippy/test-data/wildtype.gbk
 ReferenceSize	200727
 Software	snippy 3.2-dev
 Variant-DEL	5
 Variant-INS	1
 Variant-MNP	1
-Variant-SNP	9
-VariantTotal	16
+Variant-SNP	10
+VariantTotal	17