# HG changeset patch
# User koen
# Date 1452700295 18000
# Node ID ac7b4d03ab2f1838ca1b12aa83fadb64459aa8e7
# Parent  8fc38a4f9db64366aa03fbd12f54ede1b375eae6
Uploaded

diff -r 8fc38a4f9db6 -r ac7b4d03ab2f gbsx_demultiplexer.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gbsx_demultiplexer.sh	Wed Jan 13 10:51:35 2016 -0500
@@ -0,0 +1,28 @@
+#!/usr/bin/env bash
+
+#export PATH=$PATH:$(dirname $0)
+#BASEDIR=$(dirname $0)
+
+
+read1=$1
+read2=$2
+infofile=$3
+barcodeMismatch=$4
+enzymeMismatch=$5
+rad_gbs_select=$6
+demultiplex_stats=$7
+
+extra=""
+if [ "$read2" != "0" ];
+then
+    extra="-f2 $read2";
+fi
+mkdir gbsx_demultiplex;
+
+java -jar $GBSX_PATH/GBSX.jar --Demultiplexer -o gbsx_demultiplex -f1 $read1 $extra -i $infofile -mb $barcodeMismatch -me $enzymeMismatch -rad $rad_gbs_select
+
+cat gbsx_demultiplex/gbsDemultiplex.stats > $demultiplex_stats
+rm gbsx_demultiplex/*.log
+rm gbsx_demultiplex/*.stats
+rm gbsx_demultiplex/undetermined*
+