# HG changeset patch
# User iuc
# Date 1597675057 14400
# Node ID 2af5a5ca9c87333426a5bf69ed6891f4cb3c9678
# Parent  9ee3bf9797575a62c0777c4db0766be3c0128fb4
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 0ed02865f048ad7471ea79509c0e23162bc29166"

diff -r 9ee3bf979757 -r 2af5a5ca9c87 discosnp_RAD.xml
--- a/discosnp_RAD.xml	Wed Jan 22 17:26:07 2020 -0500
+++ b/discosnp_RAD.xml	Mon Aug 17 10:37:37 2020 -0400
@@ -25,7 +25,13 @@
         run_discoSnpRad.sh
         @discosnp_inputs@
         -S "\$CONNECTOR_DIR"
+        --max_size_cluster ${max_size_cluster}
         -a ${a}
+        ${high_precision}
+        --max_missing ${max_missing}
+        --min_rank ${min_rank}
+
+        --max_threads \${GALAXY_SLOTS:-1}
 
   ]]></command>
 
@@ -33,20 +39,23 @@
 
       <expand macro="discosnp_inputs" />
 
-      <param argument="-b" type="select" label="Branching strategy">
-          <option value="1">forbid SNPs for wich the two paths are branching</option>
-          <option value="2">No limitation on branching</option>
-      </param>
+      <param argument="--high_precision" type="boolean" checked="false" truevalue="--high_precision" falsevalue="" label="Lower recall / higher precision mode." help="With this parameter no symmetrical crossroads may be traversed during bubble detection (by default up to 5 symmetrical crossroads may be traversed during bubble detection)." />
 
       <param argument="-a" type="integer" label="Maximal size of ambiguity of INDELs" value="20" help="INDELS whose ambiguity is higher than this value are not output"/>
 
+      <param argument="--max_size_cluster" type="integer" label="Discards cluster of variants containing more than this number of variants." value="150"/>
+
+      <param argument="--max_missing" type="float" label="Remove variants with more than this proportion of missing values" value="0.95" help="Default 0.95, removes variants detected in 5% and less populations"/>
+
+      <param argument="--min_rank" type="float" label="Remove variants whose rank is smaller than this threshold" value="0.4"/>
+
       <expand macro="discosnp_options" />
 
   </inputs>
 
   <outputs>
-      <data name="vcf" from_work_dir="*_coherent_sorted_with_clusters.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/>
-      <data name="fasta" from_work_dir="discoRad_*_coherent.fa" format="fasta" label="Fasta with ${tool.name} on $on_string"/>
+      <data name="vcf" from_work_dir="discoRad_*_clustered.vcf" format="vcf" label="VCF with ${tool.name} on $on_string"/>
+      <data name="fasta" from_work_dir="discoRad_*_raw.fa" format="fasta" label="Fasta with ${tool.name} on $on_string"/>
   </outputs>
 
   <tests>
@@ -59,14 +68,22 @@
           <param name="P" value="4"/>
           <param name="k" value="31"/>
           <param name="b" value="2"/>
+          <param name="max_size_cluster" value="50"/>
+          <param name="max_missing" value="0.95"/>
+          <param name="min_rank" value="0.0"/>
           <output name="fasta" file="discosnpRAD/fasta.fa"/>
           <output name="vcf">
               <assert_contents>
-                  <has_n_lines n="8"/>
-                  <has_text text="Ty=SNP;Rk=0;UL=23;UR=39;CL=.;CR=.;Genome=.;Sd=."/>
+                  <has_n_lines n="31"/>
+                  <has_text text="Ty=SNP;Rk=0.0;UL=23;UR=39;CL=23;CR=39;Genome=.;Sd=.;Cluster=0;ClSize=2"/>
                   <has_text text="0/1:84:604,15,604:42,42:0,0"/>
               </assert_contents>
           </output>
+          <assert_command>
+              <has_text text="--max_size_cluster 50"/>
+              <has_text text="--max_missing 0.95"/>
+              <has_text text="--min_rank 0.0"/>
+          </assert_command>
       </test>
   </tests>
 
diff -r 9ee3bf979757 -r 2af5a5ca9c87 macros.xml
--- a/macros.xml	Wed Jan 22 17:26:07 2020 -0500
+++ b/macros.xml	Mon Aug 17 10:37:37 2020 -0400
@@ -1,12 +1,12 @@
 <macros>
+    <token name="@DISCOSNP_VERSION@">2.5.4</token>
+
     <xml name="discosnp_requirements">
         <requirements>
-            <requirement type="package" version="2.3.0">discosnp</requirement>
+            <requirement type="package" version="@DISCOSNP_VERSION@">discosnp</requirement>
         </requirements>
     </xml>
 
-    <token name="@DISCOSNP_VERSION@">2.3.0</token>
-
     <token name="@discosnp_single_reads@"><![CDATA[
         #for $input in $input_type_options.list_reads
             #set $filename = os.path.basename(str($input)) + "." + $input.ext
@@ -64,7 +64,7 @@
             </param>
             <when value="auto" />
             <when value="custom">
-                <param argument="-c" type="text" label="Minimal coverage per read set" value="4" help="e.g. 4 / 4,5,17 / 4,auto,auto"/>
+                <param argument="-c" type="text" label="Minimal coverage per read set" value="3" help="e.g. 3 / 3,5,17 / 3,auto,auto"/>
             </when>
         </conditional>
 
@@ -75,7 +75,6 @@
 
     <token name="@discosnp_inputs@"><![CDATA[
         -r input.lst
-        -b ${b}
         -D ${D}
         -P ${P}
         ${low_complexity}
diff -r 9ee3bf979757 -r 2af5a5ca9c87 test-data/discosnp/multifasta.fa
--- a/test-data/discosnp/multifasta.fa	Wed Jan 22 17:26:07 2020 -0500
+++ b/test-data/discosnp/multifasta.fa	Mon Aug 17 10:37:37 2020 -0400
@@ -1,12 +1,12 @@
->SNP_higher_path_3|P_1:24_A/T|high|nb_pol_1|C1_74|C2_0|Q1_0|Q2_0|G1_0/0:8,227,1484|G2_1/1:1724,263,8|rank_1
-AGGGCCGGGCTACATGTTAACTACAAGGCTATAACCTATTGATGACCCG
->SNP_lower_path_3|P_1:24_A/T|high|nb_pol_1|C1_0|C2_86|Q1_0|Q2_0|G1_0/0:8,227,1484|G2_1/1:1724,263,8|rank_1
-AGGGCCGGGCTACATGTTAACTACTAGGCTATAACCTATTGATGACCCG
->SNP_higher_path_2|P_1:24_C/G|high|nb_pol_1|C1_0|C2_134|Q1_0|Q2_0|G1_1/1:2484,378,10|G2_0/0:10,408,2684|rank_1
-ATTACAGAGCTGCCGGGTGGATGACTCTCTACCGCGCTCTGTGGAAGTG
->SNP_lower_path_2|P_1:24_C/G|high|nb_pol_1|C1_124|C2_0|Q1_0|Q2_0|G1_1/1:2484,378,10|G2_0/0:10,408,2684|rank_1
-ATTACAGAGCTGCCGGGTGGATGAGTCTCTACCGCGCTCTGTGGAAGTG
->SNP_higher_path_1|P_1:24_A/T|high|nb_pol_1|C1_0|C2_114|Q1_0|Q2_0|G1_1/1:2204,335,9|G2_0/0:9,347,2284|rank_1
-CAACAACGCAACAGCTCGAGGTGTACTTCGCAGAGAAACCGCACGTCCA
->SNP_lower_path_1|P_1:24_A/T|high|nb_pol_1|C1_110|C2_0|Q1_0|Q2_0|G1_1/1:2204,335,9|G2_0/0:9,347,2284|rank_1
-CAACAACGCAACAGCTCGAGGTGTTCTTCGCAGAGAAACCGCACGTCCA
+>SNP_higher_path_3|P_1:24_A/T|high|nb_pol_1|left_unitig_length_92|right_unitig_length_55|C1_74|C2_0|Q1_0|Q2_0|G1_0/0:8,227,1484|G2_1/1:1724,263,8|rank_1
+tctctaccgcgctctgtggaagtgcacttgatcgttttgctgtagaaaaaacttaataaacagaatgccgatgaaggcactactgtactaatAGGGCCGGGCTACATGTTAACTACAAGGCTATAACCTATTGATGACCCGgtccatacataacttggtatcgtgcatgtagcgttcaagggctatagcaattccg
+>SNP_lower_path_3|P_1:24_A/T|high|nb_pol_1|left_unitig_length_92|right_unitig_length_55|C1_0|C2_86|Q1_0|Q2_0|G1_0/0:8,227,1484|G2_1/1:1724,263,8|rank_1
+tctctaccgcgctctgtggaagtgcacttgatcgttttgctgtagaaaaaacttaataaacagaatgccgatgaaggcactactgtactaatAGGGCCGGGCTACATGTTAACTACTAGGCTATAACCTATTGATGACCCGgtccatacataacttggtatcgtgcatgtagcgttcaagggctatagcaattccg
+>SNP_higher_path_2|P_1:24_C/G|high|nb_pol_1|left_unitig_length_267|right_unitig_length_92|C1_0|C2_134|Q1_0|Q2_0|G1_1/1:2484,378,10|G2_0/0:10,408,2684|rank_1
+cttcgcagagaaaccgcacgtccagttctaacactctcatatgtgctcgtcgtttatgctttcggcgtgaaaactggtgcgccggtgtctggagaccatccttcttgcgtatgactccaaggacagccatcacggtttgtgggttcactgggactgtcacgcttaaccggacggaactcgagaaggcatacgactggtcgtaagaccgctctgatccgacaccaccataacgcggcactcatgattatcatcacttttttagtccctATTACAGAGCTGCCGGGTGGATGACTCTCTACCGCGCTCTGTGGAAGTGcacttgatcgttttgctgtagaaaaaacttaataaacagaatgccgatgaaggcactactgtactaatagggccgggctacatgttaactac
+>SNP_lower_path_2|P_1:24_C/G|high|nb_pol_1|left_unitig_length_267|right_unitig_length_92|C1_124|C2_0|Q1_0|Q2_0|G1_1/1:2484,378,10|G2_0/0:10,408,2684|rank_1
+cttcgcagagaaaccgcacgtccagttctaacactctcatatgtgctcgtcgtttatgctttcggcgtgaaaactggtgcgccggtgtctggagaccatccttcttgcgtatgactccaaggacagccatcacggtttgtgggttcactgggactgtcacgcttaaccggacggaactcgagaaggcatacgactggtcgtaagaccgctctgatccgacaccaccataacgcggcactcatgattatcatcacttttttagtccctATTACAGAGCTGCCGGGTGGATGAGTCTCTACCGCGCTCTGTGGAAGTGcacttgatcgttttgctgtagaaaaaacttaataaacagaatgccgatgaaggcactactgtactaatagggccgggctacatgttaactac
+>SNP_higher_path_1|P_1:24_A/T|high|nb_pol_1|left_unitig_length_475|right_unitig_length_267|C1_0|C2_114|Q1_0|Q2_0|G1_1/1:2204,335,9|G2_0/0:9,347,2284|rank_1
+cggataccgttgagacatcttataagtagacgcaatgcggaatcttatagaatcgcccgatagcgttgtgttggtggacacggctgattaccctctcacccgcgctattagcttccataccacctgcggccatccattaagatccgctgctcctcacgaaaaaagaattaataagaagtcccgtaacatgcggatttggtagtcgttatagacaactttactggggcgaactaaaacgcttgtggacagaattttggcagtggcaattaatctctaatgatgtgatattagggtctaaaatgtaagaattcggtgagttagattggacaaggggatccgaagatgttttggcgcagttagtcacagggggagcccctgcctacaaaaagcgcttactgttgactgtctagggatacagcgaaagcggcagtcgttgaagcaaaagtgatatgtgcgacactgcatctaggcagcgCAACAACGCAACAGCTCGAGGTGTACTTCGCAGAGAAACCGCACGTCCAgttctaacactctcatatgtgctcgtcgtttatgctttcggcgtgaaaactggtgcgccggtgtctggagaccatccttcttgcgtatgactccaaggacagccatcacggtttgtgggttcactgggactgtcacgcttaaccggacggaactcgagaaggcatacgactggtcgtaagaccgctctgatccgacaccaccataacgcggcactcatgattatcatcacttttttagtccctattacagagctgccgggtggatga
+>SNP_lower_path_1|P_1:24_A/T|high|nb_pol_1|left_unitig_length_475|right_unitig_length_267|C1_110|C2_0|Q1_0|Q2_0|G1_1/1:2204,335,9|G2_0/0:9,347,2284|rank_1
+cggataccgttgagacatcttataagtagacgcaatgcggaatcttatagaatcgcccgatagcgttgtgttggtggacacggctgattaccctctcacccgcgctattagcttccataccacctgcggccatccattaagatccgctgctcctcacgaaaaaagaattaataagaagtcccgtaacatgcggatttggtagtcgttatagacaactttactggggcgaactaaaacgcttgtggacagaattttggcagtggcaattaatctctaatgatgtgatattagggtctaaaatgtaagaattcggtgagttagattggacaaggggatccgaagatgttttggcgcagttagtcacagggggagcccctgcctacaaaaagcgcttactgttgactgtctagggatacagcgaaagcggcagtcgttgaagcaaaagtgatatgtgcgacactgcatctaggcagcgCAACAACGCAACAGCTCGAGGTGTTCTTCGCAGAGAAACCGCACGTCCAgttctaacactctcatatgtgctcgtcgtttatgctttcggcgtgaaaactggtgcgccggtgtctggagaccatccttcttgcgtatgactccaaggacagccatcacggtttgtgggttcactgggactgtcacgcttaaccggacggaactcgagaaggcatacgactggtcgtaagaccgctctgatccgacaccaccataacgcggcactcatgattatcatcacttttttagtccctattacagagctgccgggtggatga
diff -r 9ee3bf979757 -r 2af5a5ca9c87 test-data/discosnp/multifasta_paired.fa
--- a/test-data/discosnp/multifasta_paired.fa	Wed Jan 22 17:26:07 2020 -0500
+++ b/test-data/discosnp/multifasta_paired.fa	Mon Aug 17 10:37:37 2020 -0400
@@ -1,12 +1,12 @@
->SNP_higher_path_3|P_1:30_C/G|high|nb_pol_1|C1_124|Q1_0|G1_0/1:1927,18,1727|rank_0
-CAAGTGCACTTCCACAGAGCGCGGTAGAGACTCATCCACCCGGCAGCTCTGTAATAGGGAC
->SNP_lower_path_3|P_1:30_C/G|high|nb_pol_1|C1_134|Q1_0|G1_0/1:1927,18,1727|rank_0
-CAAGTGCACTTCCACAGAGCGCGGTAGAGAGTCATCCACCCGGCAGCTCTGTAATAGGGAC
->SNP_higher_path_2|P_1:30_A/T|high|nb_pol_1|C1_74|Q1_0|G1_0/1:1260,18,1020|rank_0
-ACTAATAGGGCCGGGCTACATGTTAACTACAAGGCTATAACCTATTGATGACCCGGTCCAT
->SNP_lower_path_2|P_1:30_A/T|high|nb_pol_1|C1_86|Q1_0|G1_0/1:1260,18,1020|rank_0
-ACTAATAGGGCCGGGCTACATGTTAACTACTAGGCTATAACCTATTGATGACCCGGTCCAT
->SNP_higher_path_1|P_1:30_A/T|high|nb_pol_1|C1_114|Q1_0|G1_0/1:1548,17,1628|rank_0
-GCAGCGCAACAACGCAACAGCTCGAGGTGTACTTCGCAGAGAAACCGCACGTCCAGTTCTA
->SNP_lower_path_1|P_1:30_A/T|high|nb_pol_1|C1_110|Q1_0|G1_0/1:1548,17,1628|rank_0
-GCAGCGCAACAACGCAACAGCTCGAGGTGTTCTTCGCAGAGAAACCGCACGTCCAGTTCTA
+>SNP_higher_path_3|P_1:30_C/G|high|nb_pol_1|left_unitig_length_86|right_unitig_length_261|C1_124|Q1_0|G1_0/1:1927,18,1727|rank_0
+gtagttaacatgtagcccggccctattagtacagtagtgccttcatcggcattctgtttattaagttttttctacagcaaaacgatCAAGTGCACTTCCACAGAGCGCGGTAGAGACTCATCCACCCGGCAGCTCTGTAATAGGGACtaaaaaagtgatgataatcatgagtgccgcgttatggtggtgtcggatcagagcggtcttacgaccagtcgtatgccttctcgagttccgtccggttaagcgtgacagtcccagtgaacccacaaaccgtgatggctgtccttggagtcatacgcaagaaggatggtctccagacaccggcgcaccagttttcacgccgaaagcataaacgacgagcacatatgagagtgttagaactggacgtgcggtttctctgcgaag
+>SNP_lower_path_3|P_1:30_C/G|high|nb_pol_1|left_unitig_length_86|right_unitig_length_261|C1_134|Q1_0|G1_0/1:1927,18,1727|rank_0
+gtagttaacatgtagcccggccctattagtacagtagtgccttcatcggcattctgtttattaagttttttctacagcaaaacgatCAAGTGCACTTCCACAGAGCGCGGTAGAGAGTCATCCACCCGGCAGCTCTGTAATAGGGACtaaaaaagtgatgataatcatgagtgccgcgttatggtggtgtcggatcagagcggtcttacgaccagtcgtatgccttctcgagttccgtccggttaagcgtgacagtcccagtgaacccacaaaccgtgatggctgtccttggagtcatacgcaagaaggatggtctccagacaccggcgcaccagttttcacgccgaaagcataaacgacgagcacatatgagagtgttagaactggacgtgcggtttctctgcgaag
+>SNP_higher_path_2|P_1:30_A/T|high|nb_pol_1|left_unitig_length_86|right_unitig_length_52|C1_74|Q1_0|G1_0/1:1260,18,1020|rank_0
+tctctaccgcgctctgtggaagtgcacttgatcgttttgctgtagaaaaaacttaataaacagaatgccgatgaaggcactactgtACTAATAGGGCCGGGCTACATGTTAACTACAAGGCTATAACCTATTGATGACCCGGTCCATacataacttggtatcgtgcatgtagcgttcaagggctatagcaattccgacg
+>SNP_lower_path_2|P_1:30_A/T|high|nb_pol_1|left_unitig_length_86|right_unitig_length_52|C1_86|Q1_0|G1_0/1:1260,18,1020|rank_0
+tctctaccgcgctctgtggaagtgcacttgatcgttttgctgtagaaaaaacttaataaacagaatgccgatgaaggcactactgtACTAATAGGGCCGGGCTACATGTTAACTACTAGGCTATAACCTATTGATGACCCGGTCCATacataacttggtatcgtgcatgtagcgttcaagggctatagcaattccgacg
+>SNP_higher_path_1|P_1:30_A/T|high|nb_pol_1|left_unitig_length_472|right_unitig_length_261|C1_114|Q1_0|G1_0/1:1548,17,1628|rank_0
+ttgcggataccgttgagacatcttataagtagacgcaatgcggaatcttatagaatcgcccgatagcgttgtgttggtggacacggctgattaccctctcacccgcgctattagcttccataccacctgcggccatccattaagatccgctgctcctcacgaaaaaagaattaataagaagtcccgtaacatgcggatttggtagtcgttatagacaactttactggggcgaactaaaacgcttgtggacagaattttggcagtggcaattaatctctaatgatgtgatattagggtctaaaatgtaagaattcggtgagttagattggacaaggggatccgaagatgttttggcgcagttagtcacagggggagcccctgcctacaaaaagcgcttactgttgactgtctagggatacagcgaaagcggcagtcgttgaagcaaaagtgatatgtgcgacactgcatctagGCAGCGCAACAACGCAACAGCTCGAGGTGTACTTCGCAGAGAAACCGCACGTCCAGTTCTAacactctcatatgtgctcgtcgtttatgctttcggcgtgaaaactggtgcgccggtgtctggagaccatccttcttgcgtatgactccaaggacagccatcacggtttgtgggttcactgggactgtcacgcttaaccggacggaactcgagaaggcatacgactggtcgtaagaccgctctgatccgacaccaccataacgcggcactcatgattatcatcacttttttagtccctattacagagctgccgggtggatga
+>SNP_lower_path_1|P_1:30_A/T|high|nb_pol_1|left_unitig_length_472|right_unitig_length_261|C1_110|Q1_0|G1_0/1:1548,17,1628|rank_0
+ttgcggataccgttgagacatcttataagtagacgcaatgcggaatcttatagaatcgcccgatagcgttgtgttggtggacacggctgattaccctctcacccgcgctattagcttccataccacctgcggccatccattaagatccgctgctcctcacgaaaaaagaattaataagaagtcccgtaacatgcggatttggtagtcgttatagacaactttactggggcgaactaaaacgcttgtggacagaattttggcagtggcaattaatctctaatgatgtgatattagggtctaaaatgtaagaattcggtgagttagattggacaaggggatccgaagatgttttggcgcagttagtcacagggggagcccctgcctacaaaaagcgcttactgttgactgtctagggatacagcgaaagcggcagtcgttgaagcaaaagtgatatgtgcgacactgcatctagGCAGCGCAACAACGCAACAGCTCGAGGTGTTCTTCGCAGAGAAACCGCACGTCCAGTTCTAacactctcatatgtgctcgtcgtttatgctttcggcgtgaaaactggtgcgccggtgtctggagaccatccttcttgcgtatgactccaaggacagccatcacggtttgtgggttcactgggactgtcacgcttaaccggacggaactcgagaaggcatacgactggtcgtaagaccgctctgatccgacaccaccataacgcggcactcatgattatcatcacttttttagtccctattacagagctgccgggtggatga
diff -r 9ee3bf979757 -r 2af5a5ca9c87 test-data/discosnp/vcf_file.vcf
--- a/test-data/discosnp/vcf_file.vcf	Wed Jan 22 17:26:07 2020 -0500
+++ b/test-data/discosnp/vcf_file.vcf	Mon Aug 17 10:37:37 2020 -0400
@@ -1,5 +1,5 @@
 ##fileformat=VCFv4.1
-##filedate=2017102
+##filedate=2020814XX
 ##source=VCF_creator
 ##SAMPLE=file://discoRes_k_25_c_auto_D_0_P_1_b_0_coherent.fa
 ##REF=<ID=REF,Number=1,Type=String,Description="Allele of the path Disco aligned with the least mismatches">
@@ -12,13 +12,13 @@
 ##INFO=<ID=CR,Number=1,Type=Integer,Description="length of the contig right">
 ##INFO=<ID=Genome,Number=1,Type=String,Description="Allele of the reference;for indel reference is . ">
 ##INFO=<ID=Sd,Number=1,Type=Integer,Description="Reverse (-1) or Forward (1) Alignement">
-##INFO=<ID=XA,Number=0/1,Type=String,Description="Other mapping positions (chromosome_position). Position is negative in case of Reverse alignment. The position designs the starting position of the alignment, not the position of the variant itself.">
+##INFO=<ID=XA,Number=.,Type=String,Description="Other mapping positions (chromosome_position). Position is negative in case of Reverse alignment. The position designs the starting position of the alignment, not the position of the variant itself.">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Cumulated depth accross samples (sum)">
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled Genotype Likelihoods">
 ##FORMAT=<ID=AD,Number=2,Type=Integer,Description="Depth of each allele by sample">
 ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	G1	G2
-SNP_higher_path_3	24	3	A	T	.	.	Ty=SNP;Rk=1;UL=.;UR=.;CL=.;CR=.;Genome=.;Sd=.	GT:DP:PL:AD:HQ	0/0:74:8,227,1484:74,0:0,0	1/1:86:1724,263,8:0,86:0,0
-SNP_higher_path_2	24	2	C	G	.	.	Ty=SNP;Rk=1;UL=.;UR=.;CL=.;CR=.;Genome=.;Sd=.	GT:DP:PL:AD:HQ	1/1:124:2484,378,10:0,124:0,0	0/0:134:10,408,2684:134,0:0,0
-SNP_higher_path_1	24	1	A	T	.	.	Ty=SNP;Rk=1;UL=.;UR=.;CL=.;CR=.;Genome=.;Sd=.	GT:DP:PL:AD:HQ	1/1:110:2204,335,9:0,110:0,0	0/0:114:9,347,2284:114,0:0,0
+SNP_higher_path_3	116	3	A	T	.	.	Ty=SNP;Rk=1;UL=92;UR=55;CL=.;CR=.;Genome=.;Sd=.	GT:DP:PL:AD:HQ	0/0:74:8,227,1484:74,0:0,0	1/1:86:1724,263,8:0,86:0,0
+SNP_higher_path_2	291	2	C	G	.	.	Ty=SNP;Rk=1;UL=267;UR=92;CL=.;CR=.;Genome=.;Sd=.	GT:DP:PL:AD:HQ	1/1:124:2484,378,10:0,124:0,0	0/0:134:10,408,2684:134,0:0,0
+SNP_higher_path_1	499	1	A	T	.	.	Ty=SNP;Rk=1;UL=475;UR=267;CL=.;CR=.;Genome=.;Sd=.	GT:DP:PL:AD:HQ	1/1:110:2204,335,9:0,110:0,0	0/0:114:9,347,2284:114,0:0,0
diff -r 9ee3bf979757 -r 2af5a5ca9c87 test-data/discosnp/vcf_file_paired.vcf
--- a/test-data/discosnp/vcf_file_paired.vcf	Wed Jan 22 17:26:07 2020 -0500
+++ b/test-data/discosnp/vcf_file_paired.vcf	Mon Aug 17 10:37:37 2020 -0400
@@ -1,5 +1,5 @@
 ##fileformat=VCFv4.1
-##filedate=2017102
+##filedate=2020814XX
 ##source=VCF_creator
 ##SAMPLE=file://discoRes_k_31_c_auto_D_0_P_1_b_0_coherentBWA_MEM.sam
 ##REF=<ID=REF,Number=1,Type=String,Description="Allele of the path Disco aligned with the least mismatches">
@@ -12,13 +12,13 @@
 ##INFO=<ID=CR,Number=1,Type=Integer,Description="length of the contig right">
 ##INFO=<ID=Genome,Number=1,Type=String,Description="Allele of the reference;for indel reference is . ">
 ##INFO=<ID=Sd,Number=1,Type=Integer,Description="Reverse (-1) or Forward (1) Alignement">
-##INFO=<ID=XA,Number=0/1,Type=String,Description="Other mapping positions (chromosome_position). Position is negative in case of Reverse alignment. The position designs the starting position of the alignment, not the position of the variant itself.">
+##INFO=<ID=XA,Number=.,Type=String,Description="Other mapping positions (chromosome_position). Position is negative in case of Reverse alignment. The position designs the starting position of the alignment, not the position of the variant itself.">
 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Cumulated depth accross samples (sum)">
 ##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled Genotype Likelihoods">
 ##FORMAT=<ID=AD,Number=2,Type=Integer,Description="Depth of each allele by sample">
 ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
 #CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	G1
-read661_contig0_position139_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0	62	3	C	G	.	MULTIPLE	Ty=SNP;Rk=0;UL=.;UR=.;CL=.;CR=.;Genome=C;Sd=1	GT:DP:PL:AD:HQ	0/1:258:1927,18,1727:124,134:0,0
-read780_contig0_position26_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1	43	2	A	T	.	MULTIPLE	Ty=SNP;Rk=0;UL=.;UR=.;CL=.;CR=.;Genome=A;Sd=1	GT:DP:PL:AD:HQ	0/1:160:1260,18,1020:74,86:0,0
-read656_contig0_position454_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1	62	1	T	A	.	MULTIPLE	Ty=SNP;Rk=0;UL=.;UR=.;CL=.;CR=.;Genome=T;Sd=1	GT:DP:PL:AD:HQ	0/1:224:1628,17,1548:110,114:0,0
+read661_contig0_position139_M0_I0_D0_NG0______er0__indel0__rgeom0_rev0	62	3	C	G	.	MULTIPLE	Ty=SNP;Rk=0;UL=86;UR=261;CL=.;CR=.;Genome=C;Sd=1;XA=read547_51,read624_39,read871_45,read688_36,read201_34,read45_68,read71_47,read728_35,read302_36,read492_42,read901_69,read237_35,read912_67,read120_38,read779_39,read161_45,read63_55,read872_67,read281_36,read900_43,read891_67,read943_45,read793_31,read300_58,read168_52,read315_58,read650_53,read918_70,read839_58,read215_68,read388_62,read479_63,read543_64,read418_35,read515_39,read661_62,read77_54,read241_35,read427_43,read268_67,read115_36,read915_50,read838_45,read382_44,read811_38,read438_35,read503_52,read472_46,read804_70,read510_30,read500_30,read759_70,read855_70,read171_70,read51_28,read464_70,read36_27,read579_70,read140_70,read720_26,read906_25,read454_24,read187_70,read75_24,read5_24,read729_24,read702_23,read433_23,read118_22,read377_22,read914_70,read691_21,read270_21,read112_70,read459_20,read240_20	GT:DP:PL:AD:HQ	0/1:258:1927,18,1727:124,134:0,0
+read780_contig0_position26_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1	43	2	A	T	.	MULTIPLE	Ty=SNP;Rk=0;UL=86;UR=52;CL=.;CR=.;Genome=A;Sd=1;XA=read653_58,read292_70,read858_59,read808_53,read335_36,read233_53,read596_53,read132_33,read721_66,read378_67,read103_53,read928_33,read998_31,read484_51,read834_38,read387_38,read182_41,read111_60,read272_70,read325_59,read853_44,read480_37,read559_67,read244_32,read642_43,read780_43,read8_32,read170_49,read602_66,read973_58,read475_46,read347_69,read843_49,read612_65,read153_51,read78_30,read85_70,read420_30,read899_70,read805_70,read303_70,read104_27,read970_27,read328_70,read806_70,read202_70,read757_26,read521_26,read962_70,read696_23,read566_70,read321_70,read649_20,read253_20	GT:DP:PL:AD:HQ	0/1:160:1260,18,1020:74,86:0,0
+read656_contig0_position454_M0_I0_D0_NG0______er0__indel0__rgeom0_rev1	62	1	T	A	.	MULTIPLE	Ty=SNP;Rk=0;UL=472;UR=261;CL=.;CR=.;Genome=T;Sd=1;XA=read639_58,read567_37,read836_63,read727_33,read44_68,read625_48,read121_42,read298_56,read840_35,read62_69,read868_60,read38_56,read629_55,read896_35,read213_36,read897_67,read837_50,read994_50,read756_48,read113_59,read32_52,read129_38,read575_68,read957_34,read765_69,read94_41,read218_34,read297_51,read437_50,read256_48,read322_70,read716_52,read101_62,read254_50,read198_36,read12_44,read905_61,read760_67,read185_52,read761_66,read311_51,read357_43,read260_70	GT:DP:PL:AD:HQ	0/1:224:1628,17,1548:110,114:0,0
diff -r 9ee3bf979757 -r 2af5a5ca9c87 test-data/discosnpRAD/fasta.fa
--- a/test-data/discosnpRAD/fasta.fa	Wed Jan 22 17:26:07 2020 -0500
+++ b/test-data/discosnpRAD/fasta.fa	Mon Aug 17 10:37:37 2020 -0400
@@ -1,28 +1,28 @@
->SNP_higher_path_7|P_1:30_C/T,P_2:49_C/G|high|nb_pol_2|left_unitig_length_1|right_unitig_length_16|C1_49|Q1_0|G1_0/1:702,15,702|rank_0
-gATTGGATGCGAGCTTCTTTACCCGATCATACGTCCAGCGAAGGGATTAGCTGTCGTTAGGGCCCTAATTCCTGCCTGGAGcggacaacaaagtagt
->SNP_lower_path_7|P_1:30_C/T,P_2:49_C/G|high|nb_pol_2|left_unitig_length_1|right_unitig_length_16|C1_49|Q1_0|G1_0/1:702,15,702|rank_0
-gATTGGATGCGAGCTTCTTTACCCGATCATATGTCCAGCGAAGGGATTAGGTGTCGTTAGGGCCCTAATTCCTGCCTGGAGcggacaacaaagtagt
->SNP_higher_path_6|P_1:30_C/G|high|nb_pol_1|left_unitig_length_1|right_unitig_length_8|C1_49|Q1_0|G1_0/1:702,15,702|rank_0
-tATGATCGGGTAAAGAAGCTCGCATCCAATCCCTATTGACTAAGTAGGACACTAATTATCGGacgctccc
->SNP_lower_path_6|P_1:30_C/G|high|nb_pol_1|left_unitig_length_1|right_unitig_length_8|C1_49|Q1_0|G1_0/1:702,15,702|rank_0
-tATGATCGGGTAAAGAAGCTCGCATCCAATCGCTATTGACTAAGTAGGACACTAATTATCGGacgctccc
->SNP_higher_path_5|P_1:30_A/C|high|nb_pol_1|left_unitig_length_5|right_unitig_length_51|C1_44|Q1_0|G1_0/1:632,15,632|rank_0
+>SNP_higher_path_7|P_1:30_C/T,P_2:49_C/G|high|nb_pol_2|left_unitig_length_1|right_unitig_length_16|left_contig_length_40|right_contig_length_16|C1_49|Q1_0|G1_0/1:702,15,702|rank_0
+gggagcgtccgataattagtgtcctacttagtcaatagggATTGGATGCGAGCTTCTTTACCCGATCATACGTCCAGCGAAGGGATTAGCTGTCGTTAGGGCCCTAATTCCTGCCTGGAGcggacaacaaagtagt
+>SNP_lower_path_7|P_1:30_C/T,P_2:49_C/G|high|nb_pol_2|left_unitig_length_1|right_unitig_length_16|left_contig_length_40|right_contig_length_16|C1_49|Q1_0|G1_0/1:702,15,702|rank_0
+gggagcgtccgataattagtgtcctacttagtcaatagggATTGGATGCGAGCTTCTTTACCCGATCATATGTCCAGCGAAGGGATTAGGTGTCGTTAGGGCCCTAATTCCTGCCTGGAGcggacaacaaagtagt
+>SNP_higher_path_6|P_1:30_C/G|high|nb_pol_1|left_unitig_length_1|right_unitig_length_8|left_contig_length_67|right_contig_length_8|C1_49|Q1_0|G1_0/1:702,15,702|rank_0
+actactttgttgtccgctccaggcaggaattagggccctaacgacagctaatcccttcgctggacgtATGATCGGGTAAAGAAGCTCGCATCCAATCCCTATTGACTAAGTAGGACACTAATTATCGGacgctccc
+>SNP_lower_path_6|P_1:30_C/G|high|nb_pol_1|left_unitig_length_1|right_unitig_length_8|left_contig_length_67|right_contig_length_8|C1_49|Q1_0|G1_0/1:702,15,702|rank_0
+actactttgttgtccgctccaggcaggaattagggccctaacgacagctaatcccttcgctggacgtATGATCGGGTAAAGAAGCTCGCATCCAATCGCTATTGACTAAGTAGGACACTAATTATCGGacgctccc
+>SNP_higher_path_5|P_1:30_A/C|high|nb_pol_1|left_unitig_length_5|right_unitig_length_51|left_contig_length_5|right_contig_length_51|C1_44|Q1_0|G1_0/1:632,15,632|rank_0
 ctatcGCGGCTGTTCGTATGATGACCTATGCGGAGAGGGGAAACCAGATGGGTGACCCAAAAACGCacgcgacctctgtaatagggctccaggtgggaattaggcgtggtccgtcag
->SNP_lower_path_5|P_1:30_A/C|high|nb_pol_1|left_unitig_length_5|right_unitig_length_51|C1_44|Q1_0|G1_0/1:632,15,632|rank_0
+>SNP_lower_path_5|P_1:30_A/C|high|nb_pol_1|left_unitig_length_5|right_unitig_length_51|left_contig_length_5|right_contig_length_51|C1_44|Q1_0|G1_0/1:632,15,632|rank_0
 ctatcGCGGCTGTTCGTATGATGACCTATGCGGAGCGGGGAAACCAGATGGGTGACCCAAAAACGCacgcgacctctgtaatagggctccaggtgggaattaggcgtggtccgtcag
->SNP_higher_path_4|P_1:30_A/G|high|nb_pol_1|left_unitig_length_51|right_unitig_length_0|C1_44|Q1_0|G1_0/1:632,15,632|rank_0
-ggggaaaccagatgggtgacccaaaaacgcacgcgacctctgtaatagggcTCCAGGTGGGAATTAGGCGTGGTCCGTCAGAAATATAGGAGACGAAAACATAGCTCTTCTT
->SNP_lower_path_4|P_1:30_A/G|high|nb_pol_1|left_unitig_length_51|right_unitig_length_0|C1_44|Q1_0|G1_0/1:632,15,632|rank_0
-ggggaaaccagatgggtgacccaaaaacgcacgcgacctctgtaatagggcTCCAGGTGGGAATTAGGCGTGGTCCGTCAGGAATATAGGAGACGAAAACATAGCTCTTCTT
->SNP_higher_path_3|P_1:30_A/C|high|nb_pol_1|left_unitig_length_23|right_unitig_length_0|C1_42|Q1_0|G1_0/1:604,15,604|rank_0
-ccctttatattggctagacggtcTAGTTTTCAATAACCCCTGAGGAGCGGCACAGTATGATACAGGGAGTGAAGGAGGGA
->SNP_lower_path_3|P_1:30_A/C|high|nb_pol_1|left_unitig_length_23|right_unitig_length_0|C1_42|Q1_0|G1_0/1:604,15,604|rank_0
-ccctttatattggctagacggtcTAGTTTTCAATAACCCCTGAGGAGCGGCACCGTATGATACAGGGAGTGAAGGAGGGA
->SNP_higher_path_2|P_1:30_C/T|high|nb_pol_1|left_unitig_length_8|right_unitig_length_0|C1_49|Q1_0|G1_0/1:702,15,702|rank_0
-ctattgacTAAGTAGGACACTAATTATCGGACGCTCCCCGGGGGAGGTCAAC
->SNP_lower_path_2|P_1:30_C/T|high|nb_pol_1|left_unitig_length_8|right_unitig_length_0|C1_49|Q1_0|G1_0/1:702,15,702|rank_0
-ctattgacTAAGTAGGACACTAATTATCGGACGCTCCCTGGGGGAGGTCAAC
->SNP_higher_path_1|P_1:30_A/T|high|nb_pol_1|left_unitig_length_23|right_unitig_length_39|C1_42|Q1_0|G1_0/1:604,15,604|rank_0
+>SNP_higher_path_4|P_1:30_A/G|high|nb_pol_1|left_unitig_length_51|right_unitig_length_0|left_contig_length_87|right_contig_length_0|C1_44|Q1_0|G1_0/1:632,15,632|rank_0
+ctatcgcggctgttcgtatgatgacctatgcggagcggggaaaccagatgggtgacccaaaaacgcacgcgacctctgtaatagggcTCCAGGTGGGAATTAGGCGTGGTCCGTCAGAAATATAGGAGACGAAAACATAGCTCTTCTT
+>SNP_lower_path_4|P_1:30_A/G|high|nb_pol_1|left_unitig_length_51|right_unitig_length_0|left_contig_length_87|right_contig_length_0|C1_44|Q1_0|G1_0/1:632,15,632|rank_0
+ctatcgcggctgttcgtatgatgacctatgcggagcggggaaaccagatgggtgacccaaaaacgcacgcgacctctgtaatagggcTCCAGGTGGGAATTAGGCGTGGTCCGTCAGGAATATAGGAGACGAAAACATAGCTCTTCTT
+>SNP_higher_path_3|P_1:30_A/C|high|nb_pol_1|left_unitig_length_23|right_unitig_length_0|left_contig_length_93|right_contig_length_0|C1_42|Q1_0|G1_0/1:604,15,604|rank_0
+gtcgttgagtcagctcataagccaacgaccagctcactcgccctggacaggagaggcgatcttacaagttccctttatattggctagacggtcTAGTTTTCAATAACCCCTGAGGAGCGGCACAGTATGATACAGGGAGTGAAGGAGGGA
+>SNP_lower_path_3|P_1:30_A/C|high|nb_pol_1|left_unitig_length_23|right_unitig_length_0|left_contig_length_93|right_contig_length_0|C1_42|Q1_0|G1_0/1:604,15,604|rank_0
+gtcgttgagtcagctcataagccaacgaccagctcactcgccctggacaggagaggcgatcttacaagttccctttatattggctagacggtcTAGTTTTCAATAACCCCTGAGGAGCGGCACCGTATGATACAGGGAGTGAAGGAGGGA
+>SNP_higher_path_2|P_1:30_C/T|high|nb_pol_1|left_unitig_length_8|right_unitig_length_0|left_contig_length_106|right_contig_length_0|C1_49|Q1_0|G1_0/1:702,15,702|rank_0
+actactttgttgtccgctccaggcaggaattagggccctaacgacagctaatcccttcgctggacgtatgatcgggtaaagaagctcgcatccaatcgctattgacTAAGTAGGACACTAATTATCGGACGCTCCCCGGGGGAGGTCAAC
+>SNP_lower_path_2|P_1:30_C/T|high|nb_pol_1|left_unitig_length_8|right_unitig_length_0|left_contig_length_106|right_contig_length_0|C1_49|Q1_0|G1_0/1:702,15,702|rank_0
+actactttgttgtccgctccaggcaggaattagggccctaacgacagctaatcccttcgctggacgtatgatcgggtaaagaagctcgcatccaatcgctattgacTAAGTAGGACACTAATTATCGGACGCTCCCTGGGGGAGGTCAAC
+>SNP_higher_path_1|P_1:30_A/T|high|nb_pol_1|left_unitig_length_23|right_unitig_length_39|left_contig_length_23|right_contig_length_39|C1_42|Q1_0|G1_0/1:604,15,604|rank_0
 gtgccgctcctcaggggttattgAAAACTAGACCGTCTAGCCAATATAAAGGGAACTTGTAAGATCGCCTCTCCTGTCCAGGGCgagtgagctggtcgttggcttatgagctgactcaacgac
->SNP_lower_path_1|P_1:30_A/T|high|nb_pol_1|left_unitig_length_23|right_unitig_length_39|C1_42|Q1_0|G1_0/1:604,15,604|rank_0
+>SNP_lower_path_1|P_1:30_A/T|high|nb_pol_1|left_unitig_length_23|right_unitig_length_39|left_contig_length_23|right_contig_length_39|C1_42|Q1_0|G1_0/1:604,15,604|rank_0
 gtgccgctcctcaggggttattgAAAACTAGACCGTCTAGCCAATATAAAGGGTACTTGTAAGATCGCCTCTCCTGTCCAGGGCgagtgagctggtcgttggcttatgagctgactcaacgac
diff -r 9ee3bf979757 -r 2af5a5ca9c87 test-data/lordec/stat_file.txt
--- a/test-data/lordec/stat_file.txt	Wed Jan 22 17:26:07 2020 -0500
+++ b/test-data/lordec/stat_file.txt	Mon Aug 17 10:37:37 2020 -0400
@@ -3,7 +3,7 @@
 0 1821 -1 1821
 0 11808 -1 11808
 0 6928 -1 6928
-79 6317 61 6134 58 21
+0 6317 -1 6317
 0 6872 -1 6872
 0 6308 -1 6308
 0 1314 -1 1314