From e6c829aa0ff764b1ee614257c13004756c759c7b Mon Sep 17 00:00:00 2001
From: Goldberg <golddc72@pennmedicine.upenn.edu>
Date: Fri, 17 Mar 2023 14:29:01 -0400
Subject: [PATCH] fix for loop for mapping features

---
 Snippets/20220105_Infinium_mapping.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Snippets/20220105_Infinium_mapping.sh b/Snippets/20220105_Infinium_mapping.sh
index 6951a3c..1ad5239 100644
--- a/Snippets/20220105_Infinium_mapping.sh
+++ b/Snippets/20220105_Infinium_mapping.sh
@@ -266,7 +266,7 @@ function buildFeatureOverlaps {
   [[ -f tsv_manifest/${PLATFORM}.${REFCODE}.manifest.tsv.gz ]] || exit 1;
   zcat tsv_manifest/${PLATFORM}.${REFCODE}.manifest.tsv.gz | awk 'NR>1&&$1!="NA"&&$9~/^c[gh]/' | sortbed >$TMPFDR/${PLATFORM}_${REFCODE}.bed
   
-  for f in $FEATURES; do
+  for f in ${FEATURES[@]}; do
     echo -n Processing feature $f;
     bedtools intersect -b $TMPFDR/${PLATFORM}_${REFCODE}.bed -a ~/references/${REFCODE}/features/$f.bed.gz -sorted -wo | awk 'BEGIN{print "Probe_ID\tKnowledgebase"}{print $14,$4;}' | sort | uniq | gzip -c >features/${PLATFORM}_${REFCODE}/$f.gz
     echo " (captured" $(zcat features/${PLATFORM}_${REFCODE}/$f.gz | wc -l) "rows)"