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0
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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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7
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11 COLUMNGAPS=$1
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12 shift
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0
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13 SAMPLENS=$1
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14 shift
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7
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15 SAMPLEGAPS=$1
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16 shift
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0
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17 REFERENCE=$1
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18 shift
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19 INCLUDE=$1
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20 shift
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21 EXCLUDE=$1
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22 shift
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7
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23 STATS=$1
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24 shift
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0
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25 INPUT=$@
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26
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27 CMD="phenix.py vcf2fasta --out $OUTPUT --input $INPUT"
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28
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29 if [ $WITHMIXTURES != "NOTTHERE" ]; then
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30 CMD="$CMD --with-mixtures $WITHMIXTURES"
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31 fi
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32
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33 if [ $COLUMNNS != "NOTTHERE" ]; then
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34 CMD="$CMD --column-Ns $COLUMNNS"
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35 fi
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36
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7
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37 if [ $COLUMNGAPS != "NOTTHERE" ]; then
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38 CMD="$CMD --column-gaps $COLUMNGAPS"
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39 fi
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40
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0
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41 if [ $SAMPLENS != "NOTTHERE" ]; then
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42 CMD="$CMD --sample-Ns $SAMPLENS"
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43 fi
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44
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7
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45 if [ $SAMPLEGAPS != "NOTTHERE" ]; then
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46 CMD="$CMD --sample-gaps $SAMPLEGAPS"
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47 fi
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48
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0
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49 if [ $REFERENCE != "NOTTHERE" ]; then
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50 CMD="$CMD --reference $REFERENCE"
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51 fi
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52
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53 if [ $INCLUDE != "NOTTHERE" ]; then
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7
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54 CMD="$CMD --include $INCLUDE"
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0
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55 fi
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56
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57 if [ $EXCLUDE != "NOTTHERE" ]; then
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7
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58 CMD="$CMD --exclude $EXCLUDE"
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0
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59 fi
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60
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61 echo $CMD
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62 eval $CMD
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