Mercurial > repos > dktanwar > removesnps

annotate 01_RemoveSNPs/RemoveSNPs @ 0:21aaaa2d3004 draft

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author dktanwar
date Mon, 16 Oct 2017 13:24:04 -0400
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/bin/bash
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2
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3 #if [ "$1" == "-h" ]; then
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4 if [[ -z $1 || -z $2 || $1 == "-h" ]]; then
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5 echo "This program will remove mismatches from sam file."
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6 echo "Usage: `basename $0` test.sam 3"
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7 exit 0
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8 fi
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9
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10 cmd="echo perl -ne 'print if((/XM:i:[0-$2][^0-9]/) || (/^@/));' $1"
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11 eval `$cmd`