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2
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1 #/bin/bash
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2
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3 #grab output files
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4 merged_reads=$1
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5 shift
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6 not_combined_1=$1
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7 shift
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8 not_combined_2=$1
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9 shift
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10 inter_not_combined=$1
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11 shift
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12 reads_and_pairs=$1
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13 shift
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14 log_file=$1
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15 shift
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16
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17 flash $@ > $log_file
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18 sleep 5 #sleep because phil says so
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19
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20 if [ -f out.notCombined_2.fastq ];
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21 then
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22 mv out.notCombined_2.fastq $not_combined_2
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23 fi
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24 if [ -f out.notCombined_1.fastq ];
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25 then
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26 mv out.notCombined_1.fastq $not_combined_1
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27 fi
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28 if [ -f out.notCombined.fastq ];
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29 then
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30 mv out.notCombined.fastq $inter_not_combined
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31 fi
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32 if [ -f out.readsAndPairs.tab ];
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33 then
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34 mv out.readsAndPairs.tab $reads_and_pairs
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35 fi
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36 if [ -f out.extendedFrags.fastq ];
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37 then
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38 mv out.extendedFrags.fastq $merged_reads
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39 fi
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40
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41 exit 0
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