# HG changeset patch
# User koen
# Date 1452699958 18000
# Node ID b0d5949b88dd4d716cb4408aa5591c93e00ac779
# Parent  29fc2bb7bc1804acd01d9321bd7c310bbdb2448f
Uploaded gbsx_demultiplexer.sh

diff -r 29fc2bb7bc18 -r b0d5949b88dd gbsx_demultiplexer.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gbsx_demultiplexer.sh	Wed Jan 13 10:45:58 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*
+