diff scripts/test.sh @ 0:05c27700e5ca

initial commit

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/test.sh	Thu Sep 04 18:24:19 2014 -0400
@@ -0,0 +1,24 @@
+#!/bin/bash
+#example usage: ./test.sh comp100628_c0_seq1 5 A/contig_pos_ref_alt_father mother.bam
+
+contig_to_check=$1
+percentage=$2
+forbidden=$3
+bam=$4
+dir=$5;
+
+hits=0;
+
+grep $contig_to_check $forbidden | (while read line; do 
+
+	#tresholds described in table 1C
+		result=`bash ${LINKYX_PATH}/scripts/contains_these_variants.sh $percentage $bam ${line}`
+	
+	echo "result: " $result  >>kontrola;
+	hits=$(($hits + $result))
+	echo "hits: " $hits  >>kontrola;
+done;
+
+echo $hits;
+)
+