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14
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1 #!/bin/bash
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2
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3 echo $@
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4
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5 OUTPUT=$1
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6 shift
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7 WITHMIXTURES=$1
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8 shift
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9 COLUMNNS=$1
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10 shift
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11 SAMPLENS=$1
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12 shift
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13 REFERENCE=$1
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14 shift
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15 INCLUDE=$1
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16 shift
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17 EXCLUDE=$1
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18 shift
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19 INPUT=$@
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20
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21 DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
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22 export PATH=$PATH:$DIR
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23
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24 CMD="vcfs2fasta.py --out $OUTPUT --input $INPUT"
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25
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26 if [ $WITHMIXTURES != "NOTTHERE" ]; then
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27 CMD="$CMD --with-mixtures $WITHMIXTURES"
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28 fi
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29
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30 if [ $COLUMNNS != "NOTTHERE" ]; then
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31 CMD="$CMD --column-Ns $COLUMNNS"
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32 fi
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33
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34 if [ $SAMPLENS != "NOTTHERE" ]; then
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35 CMD="$CMD --sample-Ns $SAMPLENS"
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36 fi
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37
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38 if [ $REFERENCE != "NOTTHERE" ]; then
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39 CMD="$CMD --reference $REFERENCE"
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40 fi
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41
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42 if [ $INCLUDE != "NOTTHERE" ]; then
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43 CMD="$CMD --include INCLUDE"
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44 fi
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45
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46 if [ $EXCLUDE != "NOTTHERE" ]; then
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47 CMD="$CMD --exclude EXCLUDE"
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48 fi
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49
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50 echo $CMD
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51 eval $CMD
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