Mercurial > repos > ulfschaefer > phephenix

changeset 15:a6079f6217f5 draft

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Uploaded
author ulfschaefer
date Wed, 04 May 2016 07:16:24 -0400
parents 5a01186499dc
children 4e64e338cc06
files filter_vcf.sh
diffstat 1 files changed, 6 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- 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