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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 CMD="phenix.py vcfs2fasta --out $OUTPUT --input $INPUT"
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22
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23 if [ $WITHMIXTURES != "NOTTHERE" ]; then
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24 CMD="$CMD --with-mixtures $WITHMIXTURES"
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25 fi
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26
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27 if [ $COLUMNNS != "NOTTHERE" ]; then
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28 CMD="$CMD --column-Ns $COLUMNNS"
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29 fi
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30
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31 if [ $SAMPLENS != "NOTTHERE" ]; then
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32 CMD="$CMD --sample-Ns $SAMPLENS"
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33 fi
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34
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35 if [ $REFERENCE != "NOTTHERE" ]; then
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36 CMD="$CMD --reference $REFERENCE"
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37 fi
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38
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39 if [ $INCLUDE != "NOTTHERE" ]; then
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40 CMD="$CMD --include INCLUDE"
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41 fi
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42
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43 if [ $EXCLUDE != "NOTTHERE" ]; then
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44 CMD="$CMD --exclude EXCLUDE"
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45 fi
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46
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47 echo $CMD
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48 eval $CMD
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