Mercurial > repos > biomonika > linkyx
comparison scripts/test.sh @ 0:05c27700e5ca
initial commit
author | biomonika <biomonika@psu.edu> |
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date | Thu, 04 Sep 2014 18:24:19 -0400 |
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-1:000000000000 | 0:05c27700e5ca |
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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 |