diff --git a/test/testAll.sh b/test/testAll.sh index cd6b979..1f70699 100755 --- a/test/testAll.sh +++ b/test/testAll.sh @@ -32,8 +32,11 @@ if [[ $? -ne 0 ]]; then echo "Problem running command: ${CMD}" RVAL=$((4+RVAL)) fi -samtools view ./data/f570b1db7c.dedup.filtered.rname.bam|sort|md5sum + +CHK="$(samtools view ./data/f570b1db7c.dedup.filtered.rname.bam|sort|md5sum|cut -f1 -d \" \")" +echo ${CHK} exit 0; + mkdir -p output echo "Running getdamage global"