Mercurial > repos > mcharles > rapsosnp
annotate rapsodyn/filtersam_mapped_and_unique.pl @ 0:442a7c88b886 draft
Uploaded
author | mcharles |
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date | Wed, 10 Sep 2014 09:18:15 -0400 |
parents | |
children | 3f7b0788a1c4 |
rev | line source |
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0 | 1 #!/usr/bin/perl |
2 use strict; | |
3 use warnings; | |
4 | |
5 open(IN, $ARGV[0]) or die ("Can't open $ARGV[0]\n"); | |
6 while (my $line=<IN>){ | |
7 if ($line =~ /^\@/){ | |
8 #Header conservation | |
9 print $line; | |
10 } | |
11 else { | |
12 #Optionnal flag verification | |
13 if (($line =~ /XT\:A\:U/)&&($line =~ /X0\:i\:1/)&&($line =~ /X1\:i\:0\s/)){ | |
14 my @fields = split (/\s+/,$line); | |
15 if (($fields[1]==83)||($fields[1]==163)||($fields[1]==147)||($fields[1]==99)){ | |
16 print $line; | |
17 } | |
18 } | |
19 } | |
20 } | |
21 | |
22 | |
23 close (IN); |