Mercurial > repos > geert-vandeweyer > dc_genotyper

comparison DC_Genotyper.pl @ 3:61b6d523acd9 draft

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syntax error in perl script
author geert-vandeweyer
date Thu, 25 Sep 2014 05:36:54 -0400
parents e8a32d824f39
children
comparison
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2:fa8566bd4a51 3:61b6d523acd9
108 $snpfile = "$wd/dbSNP.vcf.bgz"; 108 $snpfile = "$wd/dbSNP.vcf.bgz";
109 } 109 }
110 elsif (!-e "$snpfile.tbi") { 110 elsif (!-e "$snpfile.tbi") {
111 print "tabix index file is missing for '$snpfile'. creating now.\n"; 111 print "tabix index file is missing for '$snpfile'. creating now.\n";
112 ## check if I can write it out for future use 112 ## check if I can write it out for future use
113 $snpfile =~ m/(.*)/([^\/]+)$/; 113 $snpfile =~ m/(.*)([^\/]+)$/;
114 my $d = $1; 114 my $d = $1;
115 if (-w $d) { 115 if (-w $d) {
116 open OUT, ">$d/lock"; 116 open OUT, ">$d/lock";
117 flock(OUT,2); 117 flock(OUT,2);
118 system("cd $d && tabix -p vcf $snpfile"); 118 system("cd $d && tabix -p vcf $snpfile");