Mercurial > repos > mcharles > rapsosnp

comparison rapsodyn/MergeSamFiles.pl @ 7:3f7b0788a1c4 draft

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author mcharles
date Tue, 07 Oct 2014 10:34:34 -0400
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6:1776b8ddd87e 7:3f7b0788a1c4
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