diff scripts/get_average_contig_coverage.sh @ 0:05c27700e5ca

initial commit

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/get_average_contig_coverage.sh	Thu Sep 04 18:24:19 2014 -0400
@@ -0,0 +1,38 @@
+#!/bin/bash
+#get_average_contig_coverage $perc $contig $bam
+#returns "1" -> #low coverage, "0" -> #in tolerance
+perc=$1; contig=$2; bam=$3; reference=$4;
+
+pro_coverage=`samtools mpileup -f $reference -r $contig $bam | cut -f 4 | awk '{s+=$1}END{print s}' 2>/dev/null`;
+
+if [ -z "$pro_coverage" ]; then
+	coverage=0;
+else
+	coverage=$pro_coverage;
+fi 
+
+pro_positions=`samtools mpileup -f $reference -r $contig $bam | wc -l 2>/dev/null`
+
+if [ -z "$pro_positions" ]; then
+	positions=0;
+else
+	positions=$pro_positions;
+fi 
+
+if [[ $positions -eq $zero ]]; then
+  echo "1";
+  exit;
+fi
+
+
+average_coverage=`echo "scale=3; $coverage/$positions" | bc`;
+
+		if (( $(echo "$average_coverage < $perc"|bc -l) )); then
+			echo "1"; #low coverage
+		else
+			echo "0"; #in tolerance
+		fi
+
+
+
+