# HG changeset patch
# User ulfschaefer
# Date 1466073602 14400
# Node ID 29a682a7dd16b685802a1631f2993baa02c892ac
# Parent  74f595df6e51133f5495d0746e8ec124f0c2c163
Uploaded

diff -r 74f595df6e51 -r 29a682a7dd16 vcfs2fasta.sh
--- a/vcfs2fasta.sh	Thu Jun 16 06:39:51 2016 -0400
+++ b/vcfs2fasta.sh	Thu Jun 16 06:40:02 2016 -0400
@@ -8,14 +8,20 @@
 shift
 COLUMNNS=$1
 shift
+COLUMNGAPS=$1
+shift
 SAMPLENS=$1
 shift
+SAMPLEGAPS=$1
+shift
 REFERENCE=$1
 shift
 INCLUDE=$1
 shift
 EXCLUDE=$1
 shift
+STATS=$1
+shift
 INPUT=$@
 
 CMD="phenix.py vcf2fasta --out $OUTPUT --input $INPUT"
@@ -28,20 +34,28 @@
     CMD="$CMD --column-Ns $COLUMNNS"
 fi
 
+if [ $COLUMNGAPS != "NOTTHERE" ]; then
+    CMD="$CMD --column-gaps $COLUMNGAPS"
+fi
+
 if [ $SAMPLENS != "NOTTHERE" ]; then
     CMD="$CMD --sample-Ns $SAMPLENS"
 fi
 
+if [ $SAMPLEGAPS != "NOTTHERE" ]; then
+    CMD="$CMD --sample-gaps $SAMPLEGAPS"
+fi
+
 if [ $REFERENCE != "NOTTHERE" ]; then
     CMD="$CMD --reference $REFERENCE"
 fi
 
 if [ $INCLUDE != "NOTTHERE" ]; then
-    CMD="$CMD --include INCLUDE"
+    CMD="$CMD --include $INCLUDE"
 fi
 
 if [ $EXCLUDE != "NOTTHERE" ]; then
-    CMD="$CMD --exclude EXCLUDE"
+    CMD="$CMD --exclude $EXCLUDE"
 fi
 
 echo $CMD