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