Mercurial > repos > mcharles > rapsosnp
diff 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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rapsodyn/MergeSamFiles.pl Tue Oct 07 10:34:34 2014 -0400 @@ -0,0 +1,32 @@ +#!/usr/bin/perl +#V1.0.0 +use strict; +use warnings; + +my $header_done = 0; +my @files = split(/,/,$ARGV[0]); +for (my $i=0;$i<=$#files;$i++){ + open(IN, $files[$i]) or die ("Can't open ",$files[$i],"\n"); + while (my $line = <IN>){ + if ($line =~ /^\@PG\s/){ + if ($header_done == 0){ + $header_done = 1; + print $line; + } + else { + } + } + elsif ($line =~ /^\@SQ\s/){ + if ($header_done == 0){ + print $line; + } + else { + } + } + else{ + print $line; + } + } + close (IN); +} +