# HG changeset patch
# User ulfschaefer
# Date 1462360584 14400
# Node ID a6079f6217f53d9c5153731ec0177266f18eb7aa
# Parent  5a01186499dc56f84eac36594c35ca128b792f88
Uploaded

diff -r 5a01186499dc -r a6079f6217f5 filter_vcf.sh
--- a/filter_vcf.sh	Fri Apr 29 09:57:48 2016 -0400
+++ b/filter_vcf.sh	Wed May 04 07:16:24 2016 -0400
@@ -6,11 +6,17 @@
 shift
 VCF=$1
 shift
+ONLYGOOD=$1
+shift
 FILTERS=$@
 
 FILTERS=$(echo -n $FILTERS | sed 's/ /,/g')
 
 CMD="phenix.py filter_vcf --vcf $VCF --filters $FILTERS --output $OUTPUT"
 
+if [ $ONLYGOOD != "NOTTHERE" ]; then
+    CMD="$CMD --only-good"
+fi
+
 echo "CMD: "$CMD
 eval $CMD