# HG changeset patch
# User gandres
# Date 1460544897 14400
# Node ID b726ff436103fd803813ba225186ca72e9f52602
# Parent  18fdec90ed8c2bc251bc2049923a8f86cd095752
planemo upload

diff -r 18fdec90ed8c -r b726ff436103 VCFToolFilter/GetChromOfVCF.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/VCFToolFilter/GetChromOfVCF.pl	Wed Apr 13 06:54:57 2016 -0400
@@ -0,0 +1,25 @@
+#!/usr/bin/perl
+
+use strict;
+
+my $vcf = $ARGV[0];
+
+my %chrs;
+my $ok = 0;
+open(my $V,$vcf);
+while(<$V>)
+{
+	if ($ok)
+	{
+		my ($chr,$pos) = split(/\t/,$_);
+		$chrs{$chr}++;
+	}
+	if (/#CHROM/){$ok = 1;}
+}
+close($V);
+
+foreach my $chr(sort keys(%chrs))
+{
+	my $nb = $chrs{$chr};
+	print "$chr	$nb\n";
+}
diff -r 18fdec90ed8c -r b726ff436103 VCFToolFilter/find_indiv.py
--- a/VCFToolFilter/find_indiv.py	Wed Apr 13 04:28:32 2016 -0400
+++ b/VCFToolFilter/find_indiv.py	Wed Apr 13 06:54:57 2016 -0400
@@ -18,7 +18,7 @@
 			opt=re.search('^##contig=<ID=(\w+),length=',line).group(1)
 			options.append((opt,opt, True))
 	else :
-        	chrs=os.popen("grep -v '#' %s | cut -f1 | sort -u "%dataset.file_name).read()[:-1].split('\n')
+        	chrs=os.popen("perl GetChromOfVCF.pl %s | cut -f1 "%dataset.file_name).read()[:-1].split('\n')
         	for opt in chrs:
                 	options.append((opt,opt, True))
         return options