Mercurial > repos > nilesh > somaticsniper
diff somatic_sniper_wrapper.pl @ 1:de08d9401816 default tip
first commit
author | nilesh |
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date | Fri, 12 Jul 2013 15:21:36 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/somatic_sniper_wrapper.pl Fri Jul 12 15:21:36 2013 -0500 @@ -0,0 +1,54 @@ +use strict; +use warnings; +use File::Basename; +use Cwd; +use File::Path qw(make_path remove_tree); +die qq( +Bad numbr of inputs + +) if(!@ARGV); + +my $options =""; +my $normal=""; +my $tumor=""; +my $output=""; + + +foreach my $input (@ARGV) +{ + my @tmp = split "::", $input; + if($tmp[0] eq "NORMAL") + { + $normal = $tmp[1]; + } + elsif($tmp[0] eq "TUMOR") + { + $tumor = $tmp[1]; + } + elsif($tmp[0] eq "OUTPUT") + { + $output = $tmp[1]; + } + elsif($tmp[0] eq "OPTION") + { + $options = "$options ${tmp[1]}"; + } + + else + { + die("Unknown Input: $input\n"); + } +} + + +my $working_dir = cwd(); + +system ("ln -s $normal $working_dir/normal.bam"); +system ("samtools index $working_dir/normal.bam"); + +system ("ln -s $tumor $working_dir/tumor.bam"); +system ("samtools index $working_dir/tumor.bam"); + +system ("bam-somaticsniper $options $working_dir/tumor.bam $working_dir/normal.bam $output"); + +