comparison scripts/test.sh @ 0:05c27700e5ca

initial commit
author biomonika <biomonika@psu.edu>
date Thu, 04 Sep 2014 18:24:19 -0400
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1 #!/bin/bash
2 #example usage: ./test.sh comp100628_c0_seq1 5 A/contig_pos_ref_alt_father mother.bam
3
4 contig_to_check=$1
5 percentage=$2
6 forbidden=$3
7 bam=$4
8 dir=$5;
9
10 hits=0;
11
12 grep $contig_to_check $forbidden | (while read line; do
13
14 #tresholds described in table 1C
15 result=`bash ${LINKYX_PATH}/scripts/contains_these_variants.sh $percentage $bam ${line}`
16
17 echo "result: " $result >>kontrola;
18 hits=$(($hits + $result))
19 echo "hits: " $hits >>kontrola;
20 done;
21
22 echo $hits;
23 )
24