Mercurial > repos > mcharles > rapsosnp
view rapsodyn/filtersam_mapped_and_unique.pl @ 0:442a7c88b886 draft
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author | mcharles |
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date | Wed, 10 Sep 2014 09:18:15 -0400 |
parents | |
children | 3f7b0788a1c4 |
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#!/usr/bin/perl use strict; use warnings; open(IN, $ARGV[0]) or die ("Can't open $ARGV[0]\n"); while (my $line=<IN>){ if ($line =~ /^\@/){ #Header conservation print $line; } else { #Optionnal flag verification if (($line =~ /XT\:A\:U/)&&($line =~ /X0\:i\:1/)&&($line =~ /X1\:i\:0\s/)){ my @fields = split (/\s+/,$line); if (($fields[1]==83)||($fields[1]==163)||($fields[1]==147)||($fields[1]==99)){ print $line; } } } } close (IN);