# HG changeset patch
# User Cathy Riemer <cathy+hg@bx.psu.edu>
# Date 1426781194 14400
# Node ID edf12470a1a667b52f08995da16bb24e643d5ece
# Parent  35c20b109be584ccd88a6f25462a4641a06ed4b5
Bugfix from Belinda, in vcf2pgSnp.pl

diff -r 35c20b109be5 -r edf12470a1a6 vcf2pgSnp.pl
--- a/vcf2pgSnp.pl	Tue May 28 17:54:02 2013 -0400
+++ b/vcf2pgSnp.pl	Thu Mar 19 12:06:34 2015 -0400
@@ -13,7 +13,7 @@
    $stCol = shift @ARGV;
    $in = shift @ARGV;
    if ($stCol eq 'all') { $stCol = 10; }
-   else { $endCol = $stCol; }
+   else {  $endCol = $stCol - 1; }  #want 0 based column number
    $stCol--; #go from 1 based to zero based column number
    if ($stCol < 9) { 
       print "ERROR genotype fields don't start until column 10\n";
@@ -21,7 +21,7 @@
    }
 }elsif (@ARGV && scalar @ARGV == 1) {
    $in = shift @ARGV;
-}elsif (@ARGV) {
+}else {
    print "usage: vcf2pgSnp.pl [indColNum default=all] file.vcf > file.pgSnp\n";
    exit;
 }
diff -r 35c20b109be5 -r edf12470a1a6 vcf2pgSnp.xml
--- a/vcf2pgSnp.xml	Tue May 28 17:54:02 2013 -0400
+++ b/vcf2pgSnp.xml	Thu Mar 19 12:06:34 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="vcf2pgSnp" name="VCF to pgSnp" version="1.0.0" hidden="false">
+<tool id="vcf2pgSnp" name="VCF to pgSnp" version="1.1.0" hidden="false">
   <description>: Convert from VCF to pgSnp format</description>
   <command interpreter="perl">
     #if $inType.how == "all" #vcf2pgSnp.pl all $input1 > $out_file1