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