PanSN requres a number for the haplotype_id

pangenome · Aug 22, 2024 · 396f5bb · 396f5bb
1 parent c09b848
commit 396f5bb
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git a/partition-before-pggb b/partition-before-pggb
@@ -308,7 +308,7 @@ fi
 # Check Pangenome Sequence Naming (PanSN)
 pansn_not_respected=false
 while IFS= read -r line; do
-  if [[ ! $line =~ ^([^#]+#)+[^#]+$ ]] && [[ "$pansn_not_respected" == "false" ]]; then
+    if [[ ! $line =~ ^([^#]+#)[0-9]+#[^#]+$ ]] && [[ "$pansn_not_respected" == "false" ]]; then
     pansn_not_respected=$line
     break
   fi

diff --git a/pggb b/pggb
@@ -278,7 +278,7 @@ check_tool_availability "gfaffix" "gfaffix"
 if [ "$vcf_spec" != "false" ]; then
 check_tool_availability "vg" "vg"
 check_tool_availability "vcfbub" "vcfbub"
-check_tool_availability "vcfwave" "vcfwave"
+#check_tool_availability "vcfwave" "vcfwave"
 check_tool_availability "bcftools" "bcftools"
 fi
 if [[ $multiqc == true ]]; then
@@ -308,7 +308,7 @@ fi
 # Check Pangenome Sequence Naming (PanSN)
 pansn_not_respected=false
 while IFS= read -r line; do
-  if [[ ! $line =~ ^([^#]+#)+[^#]+$ ]] && [[ "$pansn_not_respected" == "false" ]]; then
+  if [[ ! $line =~ ^([^#]+#)[0-9]+#[^#]+$ ]] && [[ "$pansn_not_respected" == "false" ]]; then
     pansn_not_respected=$line
     break
   fi