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comparison vcf2pgSnp.pl @ 3:edf12470a1a6 default tip

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Bugfix from Belinda, in vcf2pgSnp.pl
author Cathy Riemer <cathy+hg@bx.psu.edu>
date Thu, 19 Mar 2015 12:06:34 -0400
parents 35c20b109be5
children
comparison
equal deleted inserted replaced
2:35c20b109be5 3:edf12470a1a6
11 my $endCol; 11 my $endCol;
12 if (@ARGV && scalar @ARGV == 2) { 12 if (@ARGV && scalar @ARGV == 2) {
13 $stCol = shift @ARGV; 13 $stCol = shift @ARGV;
14 $in = shift @ARGV; 14 $in = shift @ARGV;
15 if ($stCol eq 'all') { $stCol = 10; } 15 if ($stCol eq 'all') { $stCol = 10; }
16 else { $endCol = $stCol; } 16 else { $endCol = $stCol - 1; } #want 0 based column number
17 $stCol--; #go from 1 based to zero based column number 17 $stCol--; #go from 1 based to zero based column number
18 if ($stCol < 9) { 18 if ($stCol < 9) {
19 print "ERROR genotype fields don't start until column 10\n"; 19 print "ERROR genotype fields don't start until column 10\n";
20 exit; 20 exit;
21 } 21 }
22 }elsif (@ARGV && scalar @ARGV == 1) { 22 }elsif (@ARGV && scalar @ARGV == 1) {
23 $in = shift @ARGV; 23 $in = shift @ARGV;
24 }elsif (@ARGV) { 24 }else {
25 print "usage: vcf2pgSnp.pl [indColNum default=all] file.vcf > file.pgSnp\n"; 25 print "usage: vcf2pgSnp.pl [indColNum default=all] file.vcf > file.pgSnp\n";
26 exit; 26 exit;
27 } 27 }
28 28
29 open(FH, $in) or die "Couldn't open $in, $!\n"; 29 open(FH, $in) or die "Couldn't open $in, $!\n";