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view gbsx_demultiplexer.sh @ 11:9d81b6b1c493 draft

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author koen
date Wed, 13 Jan 2016 11:14:33 -0500
parents b0d5949b88dd
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#!/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*