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comparison gbsx_demultiplexer.sh @ 2:b0d5949b88dd draft

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Uploaded gbsx_demultiplexer.sh
author koen
date Wed, 13 Jan 2016 10:45:58 -0500
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1:29fc2bb7bc18 2:b0d5949b88dd
1 #!/usr/bin/env bash
2
3 #export PATH=$PATH:$(dirname $0)
4 #BASEDIR=$(dirname $0)
5
6
7 read1=$1
8 read2=$2
9 infofile=$3
10 barcodeMismatch=$4
11 enzymeMismatch=$5
12 rad_gbs_select=$6
13 demultiplex_stats=$7
14
15 extra=""
16 if [ "$read2" != "0" ];
17 then
18 extra="-f2 $read2";
19 fi
20 mkdir gbsx_demultiplex;
21
22 java -jar $GBSX_PATH/GBSX.jar --Demultiplexer -o gbsx_demultiplex -f1 $read1 $extra -i $infofile -mb $barcodeMismatch -me $enzymeMismatch -rad $rad_gbs_select
23
24 cat gbsx_demultiplex/gbsDemultiplex.stats > $demultiplex_stats
25 rm gbsx_demultiplex/*.log
26 rm gbsx_demultiplex/*.stats
27 rm gbsx_demultiplex/undetermined*
28