Workaround for HTSJDK removing additional ALT headers (#553)

* Workaround for HTSJDK removing additional ALT headers * Only reinsert headers if there are any
molgenis · Jan 18, 2024 · 41f060b · 41f060b
1 parent 463c019
commit 41f060b
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diff --git a/modules/vcf/templates/classify.sh b/modules/vcf/templates/classify.sh
@@ -26,8 +26,28 @@ index () {
   ${CMD_BCFTOOLS} index --stats "!{vcfOut}" > "!{vcfOutStats}"
 }
 
+
+#Workaround for https://github.com/samtools/htsjdk/issues/500https://github.com/samtools/htsjdk/issues/500
+store_alt(){
+  #store ALT headers
+  zcat "!{vcf}" | sed --quiet --expression='/^##ALT/p' > header.tmp
+}
+
+insert_alt(){
+  if [ -s header.tmp ]; then
+    #remove remaining ALT header (since htsjdk stores in a map, a single ALT remains)
+    zcat "!{vcfOut}" | sed '/^##ALT/d' > "!{vcfOut}".tmp
+    #re-insert the ALT headers
+    f1=$(<header.tmp)
+    awk -vf1="$f1" '/^#CHROM/{print f1;print;next}1' "!{vcfOut}".tmp | ${CMD_BGZIP} -c > "!{vcfOut}"
+    #rm header.tmp
+  fi
+}
+
 main () {
+  store_alt
   classify
+  insert_alt
   index
 }
 

diff --git a/modules/vcf/templates/classify_samples.sh b/modules/vcf/templates/classify_samples.sh
@@ -29,8 +29,28 @@ index () {
   ${CMD_BCFTOOLS} index --stats "!{vcfOut}" > "!{vcfOutStats}"
 }
 
+
+#Workaround for https://github.com/samtools/htsjdk/issues/500https://github.com/samtools/htsjdk/issues/500
+store_alt(){
+  #store ALT headers
+  zcat "!{vcf}" | sed --quiet --expression='/^##ALT/p' > header.tmp
+}
+
+insert_alt(){
+  if [ -s header.tmp ]; then
+    #remove remaining ALT header (since htsjdk stores in a map, a single ALT remains)
+    zcat "!{vcfOut}" | sed '/^##ALT/d' > "!{vcfOut}".tmp
+    #re-insert the ALT headers
+    f1=$(<header.tmp)
+    awk -vf1="$f1" '/^#CHROM/{print f1;print;next}1' "!{vcfOut}".tmp | ${CMD_BGZIP} -c > "!{vcfOut}"
+    #rm header.tmp
+  fi
+}
+
 main() {
+  store_alt
   classify_samples
+  insert_alt
   index
 }
 

diff --git a/modules/vcf/templates/inheritance.sh b/modules/vcf/templates/inheritance.sh
@@ -28,9 +28,28 @@ index () {
   ${CMD_BCFTOOLS} index --stats "!{vcfOut}" > "!{vcfOutStats}"
 }
 
+#Workaround for https://github.com/samtools/htsjdk/issues/500https://github.com/samtools/htsjdk/issues/500
+store_alt(){
+  #store ALT headers
+  zcat "!{vcf}" | sed --quiet --expression='/^##ALT/p' > header.tmp
+}
+
+insert_alt(){
+  if [ -s header.tmp ]; then
+    #remove remaining ALT header (since htsjdk stores in a map, a single ALT remains)
+    zcat "!{vcfOut}" | sed '/^##ALT/d' > "!{vcfOut}".tmp
+    #re-insert the ALT headers
+    f1=$(<header.tmp)
+    awk -vf1="$f1" '/^#CHROM/{print f1;print;next}1' "!{vcfOut}".tmp | ${CMD_BGZIP} -c > "!{vcfOut}"
+    #rm header.tmp
+  fi
+}
+
 main() {
   create_ped
+  store_alt
   inheritance
+  insert_alt
   index
 }