Merge pull request #405 from pangenome/strict_pansn_check

PanSN requires a number as haplotype_id
pangenome · Aug 22, 2024 · 9c2a8b8 · 9c2a8b8
2 parents c09b848 + f6908eb
commit 9c2a8b8
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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
@@ -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