Mercurial > repos > geert-vandeweyer > dc_genotyper

comparison DC_Genotyper.pl @ 12:8cc26598eeac draft

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author geert-vandeweyer
date Sat, 27 Sep 2014 05:49:23 -0400
parents 845a87ad254a
children 7e4a9ee69f0b
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11:845a87ad254a 12:8cc26598eeac
23 #################### 23 ####################
24 ## get paramaters ## 24 ## get paramaters ##
25 #################### 25 ####################
26 # t: target file 26 # t: target file
27 # b: bam file 27 # b: bam file
28 # R: 2bit version of reference fasta. 28 # R: reference genome files for twobit and IGV.
29 # p: number of threads. 29 # p: number of threads.
30 # s: dbsnp file 30 # s: dbsnp file
31 # m: minimal coverage (defaults 400x) 31 # m: minimal coverage (defaults 400x)
32 # P: ploidy 32 # P: ploidy
33 # a: outfile for allele distributions 33 # a: outfile for allele distributions
38 my $twobit :shared; 38 my $twobit :shared;
39 my $igvgenome :shared; 39 my $igvgenome :shared;
40 if (!defined($opts{'R'})) { 40 if (!defined($opts{'R'})) {
41 die("Reference Genomes not specified\n"); 41 die("Reference Genomes not specified\n");
42 } 42 }
43 my @refgenomes = split(",",$opts{'r'}); 43 my @refgenomes = split(",",$opts{'R'});
44 if (!-e $refgenomes[0]) { 44 if (!-e $refgenomes[0]) {
45 die("'$refgenomes[0]' is not a valid file path."); 45 die("'$refgenomes[0]' is not a valid file path.");
46 } 46 }
47 else { 47 else {
48 $twobit = $refgenomes[0]; 48 $twobit = $refgenomes[0];