Mercurial > repos > mcharles > rapsosnp
comparison rapsodyn/MergeSamFiles.pl @ 7:3f7b0788a1c4 draft
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author | mcharles |
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date | Tue, 07 Oct 2014 10:34:34 -0400 |
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6:1776b8ddd87e | 7:3f7b0788a1c4 |
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1 #!/usr/bin/perl | |
2 #V1.0.0 | |
3 use strict; | |
4 use warnings; | |
5 | |
6 my $header_done = 0; | |
7 my @files = split(/,/,$ARGV[0]); | |
8 for (my $i=0;$i<=$#files;$i++){ | |
9 open(IN, $files[$i]) or die ("Can't open ",$files[$i],"\n"); | |
10 while (my $line = <IN>){ | |
11 if ($line =~ /^\@PG\s/){ | |
12 if ($header_done == 0){ | |
13 $header_done = 1; | |
14 print $line; | |
15 } | |
16 else { | |
17 } | |
18 } | |
19 elsif ($line =~ /^\@SQ\s/){ | |
20 if ($header_done == 0){ | |
21 print $line; | |
22 } | |
23 else { | |
24 } | |
25 } | |
26 else{ | |
27 print $line; | |
28 } | |
29 } | |
30 close (IN); | |
31 } | |
32 |