--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/MACARON-GenMed-LabEx/MACARON_validate.sh	Wed Sep 12 08:45:03 2018 -0400
@@ -0,0 +1,49 @@
+#!/bin/bash
+
+#sub1.chr22_21349676-21349677.sample02.bam
+
+bam=$1;
+name=$(echo $bam | cut -d'.' -f1)
+region=$(echo $bam | cut -d'.' -f2)
+sample=$(echo $bam | cut -d'.' -f3)
+
+chr=$(echo $region | cut -d'_' -f1)
+pos=$(echo $region | cut -d'_' -f2)
+
+beg=$(echo $pos | cut -d'-' -f1)
+end=$(echo $pos | cut -d'-' -f2)
+
+#beg=$(($beg+50))
+#end=$((end-50))
+
+#echo "name $name"
+#echo "region $region"
+#echo "sample $sample"
+
+echo "$name $chr:$beg-$end $sample"
+echo  "$name $chr:$beg-$end $sample" >> MACARON_validate.txt
+
+samtools view $bam | awk -v start=$beg -v stop=$end '
+{
+  pos=$4;
+  if(pos < start){
+    cstart=1+start-pos;
+    cstop=1+stop-pos;
+    print cstart"."cstop"."$10;
+  }
+}' > tmp
+
+while read line;
+do
+  cb=$(echo $line | cut -d'.' -f1);
+  ce=$(echo $line | cut -d'.' -f2);
+  seq=$(echo $line | cut -d'.' -f3);
+  echo $seq | cut -c$cb-$ce;
+done <tmp | sort | uniq -c | sort -n >> MACARON_validate.txt
+rm tmp
+
+
+
+
+exit 0
+