Mercurial > repos > geert-vandeweyer > coverage_report

comparison CoverageReport.pl @ 27:576bfc1586f9 draft default tip

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bugfix
author geert-vandeweyer
date Wed, 29 Nov 2017 08:39:31 -0500
parents 859999cb135b
children
comparison
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26:859999cb135b 27:576bfc1586f9
36 while (-d $wd) { 36 while (-d $wd) {
37 $wd = "/tmp/Coverage.".int(rand(1000)); 37 $wd = "/tmp/Coverage.".int(rand(1000));
38 38
39 } 39 }
40 system("mkdir $wd"); 40 system("mkdir $wd");
41 $wd = "/tmp/Coverage.993";
42 print "wd : $wd\n";
43 ## variables 41 ## variables
44 our %commandsrun = (); 42 our %commandsrun = ();
45 43
46 if (!exists($opts{'b'}) || !-e $opts{'b'}) { 44 if (!exists($opts{'b'}) || !-e $opts{'b'}) {
47 die('Bam File not found'); 45 die('Bam File not found');
911 system("cp -Rf $wd/Targets.Position.Coverage $wd/Results/"); 909 system("cp -Rf $wd/Targets.Position.Coverage $wd/Results/");
912 } 910 }
913 911
914 system("cd $wd && tar czf '$tarfile' Results/"); 912 system("cd $wd && tar czf '$tarfile' Results/");
915 ## clean up (galaxy stores outside wd) 913 ## clean up (galaxy stores outside wd)
916 #system("rm -Rf $wd"); 914 system("rm -Rf $wd");
917 ############### 915 ###############
918 ## FUNCTIONS ## 916 ## FUNCTIONS ##
919 ############### 917 ###############
920 sub arraystats{ 918 sub arraystats{
921 my @array = @_; 919 my @array = @_;