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comparison libexec/filterSomaticVariants.pl @ 9:0e8e6011082b

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Strelka Workflow 0.0.2
author mini
date Fri, 26 Sep 2014 15:51:35 +0200
parents 87568e5a7d4f
children
comparison
equal deleted inserted replaced
8:2cee4ed50058 9:0e8e6011082b
32 use Getopt::Long; 32 use Getopt::Long;
33 use Pod::Usage; 33 use Pod::Usage;
34 34
35 my $baseDir; 35 my $baseDir;
36 my $libDir; 36 my $libDir;
37 #my $vcftDir;
38 BEGIN { 37 BEGIN {
39 my $thisDir=(File::Spec->splitpath($0))[1]; 38 my $thisDir=(File::Spec->splitpath($0))[1];
40 $baseDir=File::Spec->catdir($thisDir,File::Spec->updir()); 39 $baseDir=File::Spec->catdir($thisDir,File::Spec->updir());
41 $libDir=File::Spec->catdir($baseDir,'lib'); 40 $libDir=File::Spec->catdir($baseDir,'lib');
42 #my $optDir=File::Spec->catdir($baseDir,'opt');
43 #$vcftDir=File::Spec->catdir($optDir,'vcftools','lib','perl5','site_perl');
44 } 41 }
45 use lib $libDir; 42 use lib $libDir;
46 use Utils; 43 use Utils;
47 #use lib $vcftDir; 44 use Vcf;
48 #use Vcf; 45 print "all imported in filter";
49 46
50 47
51 my $scriptName=(File::Spec->splitpath($0))[2]; 48 my $scriptName=(File::Spec->splitpath($0))[2];
52 my $argCount=scalar(@ARGV); 49 my $argCount=scalar(@ARGV);
53 my $cmdline = join(' ',$0,@ARGV); 50 my $cmdline = join(' ',$0,@ARGV);