Update by ialbert on Fri Oct 27 15:31:18 EDT 2017 from yolo.local
@@ -31,6 +31,9 @@ bwa mem -t 4 ${INDEX} ${INPUT} | samtools view -b |samtools sort >${OUTPUT}
samtools index ${OUTPUT}
echo "Computing statistics."
+echo "--------------------"
+samtools flagstat ${OUTPUT}
+echo "--------------------"
# Get statistics based on flags.
ALIGNMENTS=$(samtools view -c ${OUTPUT})
