# HG changeset patch
# User gandres
# Date 1460536112 14400
# Node ID 18fdec90ed8c2bc251bc2049923a8f86cd095752
# Parent  2c6f8de56bc5ac860741399c91fc6c4057ad60c0
planemo upload

diff -r 2c6f8de56bc5 -r 18fdec90ed8c VCFToolFilter/find_indiv.py
--- a/VCFToolFilter/find_indiv.py	Tue Apr 12 11:24:28 2016 -0400
+++ b/VCFToolFilter/find_indiv.py	Wed Apr 13 04:28:32 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("grep -v '#' %s | cut -f1 | sort -u "%dataset.file_name).read()[:-1].split('\n')
+        	for opt in chrs:
+                	options.append((opt,opt, True))
         return options
 
diff -r 2c6f8de56bc5 -r 18fdec90ed8c VCFToolsStats/vcfToolsStats.xml
--- a/VCFToolsStats/vcfToolsStats.xml	Tue Apr 12 11:24:28 2016 -0400
+++ b/VCFToolsStats/vcfToolsStats.xml	Wed Apr 13 04:28:32 2016 -0400
@@ -67,8 +67,8 @@
 ---------------------------------------------------
 
 
-================
-VCF tools filter
+===============
+VCF tools Stats
 ================
 
 -----------