# HG changeset patch
# User gandres
# Date 1460544579 14400
# Node ID 2b7eb79f0ba03fe6c0c3c7c2b133f0d777610ade
# Parent  ce984119f66930b2a376a20ac84e9c752ec5df57
planemo upload

diff -r ce984119f669 -r 2b7eb79f0ba0 VCFToolFilter/GetChromOfVCF.pl
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/VCFToolFilter/GetChromOfVCF.pl	Wed Apr 13 06:49:39 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 ce984119f669 -r 2b7eb79f0ba0 VCFToolFilter/find_indiv.py
--- a/VCFToolFilter/find_indiv.py	Wed Apr 13 03:32:59 2016 -0400
+++ b/VCFToolFilter/find_indiv.py	Wed Apr 13 06:49:39 2016 -0400
@@ -12,8 +12,14 @@
 
 def get_field_chrs_options(dataset):
         options = []
-        chrs=os.popen("grep -v '#' %s | cut -f1 | sort -u "%dataset.file_name).read()[:-1].split('\n')
-        for opt in chrs:
-                options.append((opt,opt, True))
+	chrs=os.popen("grep '##contig' %s"%dataset.file_name).read()[:-1].split('\n')
+	if len(chr)>0:
+		for line in chrs:
+			opt=re.search('^##contig=<ID=(\w+),length=',line).group(1)
+			options.append((opt,opt, True))
+	else :
+        	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