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1 #!/bin/bash
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2
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3
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4 while getopts "p:w:o:h:" optionName; do
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5 case "$optionName" in
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6
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7 p) PEAKS_FILE="$OPTARG";;
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8 w) WIG_FILE="$OPTARG";;
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9 o) SUB_PEAKS_FILE="$OPTARG";;
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10 h) GALAXY_HOME="$OPTARG";;
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11
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12 esac
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13 done
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14
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15 ROOT_NAME=`basename $PEAKS_FILE .dat`
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16 SUB_PEAKS_FILENAME=${ROOT_NAME}.subpeaks.dat
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17 TMP_DIR=`mktemp -d`
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18
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19 trackNumber=$(grep -c "track" $WIG_FILE)
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20 if [[ trackNumber > 1 ]]; then
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21 cp $WIG_FILE $WIG_FILE.tmp
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22 sed -i "/track/d" $WIG_FILE.tmp
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23 line=$(head -n 1 $WIG_FILE)
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24 sed -i "1s/^/$line\n/" $WIG_FILE.tmp
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25 /usr/bin/peaksplitter/PeakSplitter_v1/PeakSplitter -p $PEAKS_FILE -w $WIG_FILE.tmp -o $TMP_DIR -f
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26 rm -f $WIG_FILE.tmp
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27 else
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28 /usr/bin/peaksplitter/PeakSplitter_v1/PeakSplitter -p $PEAKS_FILE -w $WIG_FILE -o $TMP_DIR -f
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29 fi
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30
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31 mv $TMP_DIR/$SUB_PEAKS_FILENAME $SUB_PEAKS_FILE
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