From 7e515c7ab85417c5a0db2394a5c254d9f1911d95 Mon Sep 17 00:00:00 2001
From: tcezard <tcezard@ebi.ac.uk>
Date: Mon, 15 Apr 2024 09:23:01 +0100
Subject: [PATCH] Apply annotation to all split RS

---
 .../gather_clustering_counts/bash/count_rs_for_all_files.sh     | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/eva-accession-release-automation/gather_clustering_counts/bash/count_rs_for_all_files.sh b/eva-accession-release-automation/gather_clustering_counts/bash/count_rs_for_all_files.sh
index 9ed94b2f8..75c7407b9 100755
--- a/eva-accession-release-automation/gather_clustering_counts/bash/count_rs_for_all_files.sh
+++ b/eva-accession-release-automation/gather_clustering_counts/bash/count_rs_for_all_files.sh
@@ -20,7 +20,7 @@ do
     if [[ ${INPUT} == *.vcf.gz ]]
     then
         # There are sometime multiple rs (separated by ;) in one line that needs to be split across multiple lines
-        zcat  "${INPUT}" | grep -v '^#' | awk -v annotation="${ASSEMBLY}-${SC_NAME}-${TYPE}" '{gsub(";","\n",$3); print $3" "annotation}' > ${OUTPUT}
+        zcat  "${INPUT}" | grep -v '^#' | awk '{gsub(";","\n",$3); print $3}' | awk -v annotation="${ASSEMBLY}-${SC_NAME}-${TYPE}" '{print $0" "annotation}' > ${OUTPUT}
     elif [[ ${INPUT} == *_unmapped_ids.txt.gz ]]
     then
         SC_NAME=$(basename $(dirname ${INPUT}));