Mercurial > repos > biomonika > linkyx
view scripts/test.sh @ 2:0d8315be76b7
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author | biomonika |
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date | Tue, 17 Feb 2015 21:59:51 -0500 |
parents | 05c27700e5ca |
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#!/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; )