From 396f5bbd63e29f995dad0c58631ce7d4ef22bd0c Mon Sep 17 00:00:00 2001 From: AndreaGuarracino Date: Thu, 22 Aug 2024 09:06:36 +0200 Subject: [PATCH 1/3] PanSN requres a number for the haplotype_id --- partition-before-pggb | 2 +- pggb | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/partition-before-pggb b/partition-before-pggb index 53c3c5f..481ddf1 100755 --- 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 index 672824c..243e8f6 100755 --- 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 From bbcc2b41da9ae4c5224f88a0f3ba7b929d325e0f Mon Sep 17 00:00:00 2001 From: AndreaGuarracino Date: Thu, 22 Aug 2024 09:09:52 +0200 Subject: [PATCH 2/3] typo --- pggb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pggb b/pggb index 243e8f6..ba49afe 100755 --- 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 From f6908ebd87c877611bc58c4e0aeb9f138843a0dc Mon Sep 17 00:00:00 2001 From: AndreaGuarracino Date: Thu, 22 Aug 2024 09:10:35 +0200 Subject: [PATCH 3/3] formatting --- partition-before-pggb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/partition-before-pggb b/partition-before-pggb index 481ddf1..4bad653 100755 --- 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 [[ ! $line =~ ^([^#]+#)[0-9]+#[^#]+$ ]] && [[ "$pansn_not_respected" == "false" ]]; then + if [[ ! $line =~ ^([^#]+#)[0-9]+#[^#]+$ ]] && [[ "$pansn_not_respected" == "false" ]]; then pansn_not_respected=$line break fi