Mercurial > repos > simon-gladman > trimmomatic_032

comparison trimmomatic_wrapper.pl @ 8:18bd222a110e draft

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Uploaded
author simon-gladman
date Thu, 10 Jul 2014 13:25:10 -0400
parents 7d626189cc4c
children f6cf40363396
comparison
equal deleted inserted replaced
7:76d1aebc44bf 8:18bd222a110e
43 my $numthreads = $stuff{"threads"}; 43 my $numthreads = $stuff{"threads"};
44 44
45 45
46 my $cmd = "java -cp $jar org.usadellab.trimmomatic.Trimmomatic"; 46 my $cmd = "java -cp $jar org.usadellab.trimmomatic.Trimmomatic";
47 47
48 if($stuff{"paired"} eq "True"){ 48 if($stuff{"paired"} eq "single"){
49 $cmd .= "PE"; 49 $cmd .= "SE";
50 } 50 }
51 else { 51 else {
52 $cmd .= "SE"; 52 $cmd .= "PE";
53 } 53 }
54 54
55 $cmd .= " -threads $numthreads"; 55 $cmd .= " -threads $numthreads";
56 56
57 $cmd .= " -phred33" if($stuff{"phred"} eq "phred33"); 57 $cmd .= " -phred33" if($stuff{"phred"} eq "phred33");