Support .bai by normalizing index name (#8)

stjude · Apr 26, 2021 · f0ecb0a · f0ecb0a
1 parent 2bfca08
commit f0ecb0a
Showing 1 changed file with 6 additions and 0 deletions.
diff --git a/src/main/docker/RNApeg.sh b/src/main/docker/RNApeg.sh
@@ -31,6 +31,12 @@ while [ ! -z "$1" ]; do
     shift
 done
 
+bam_dir=$(dirname ${BAMFILE})
+bam_name=$(basename ${BAMFILE} ".bam")
+if [[ -f "${bam_dir}/${bam_name}.bai" ]]
+then
+  ln -s ${bam_dir}/${bam_name}.bai ${BAMFILE}.bai
+fi
 
 #######################
 ### Validate inputs ###