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1 #!/bin/bash
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2
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3 usage(){
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4 echo "
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5 Written by Brian Bushnell
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6 Last modified October 25, 2016
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7
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8 Description: Generates the conservative consensus of multiple
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9 error-correction tools. Corrections will be accepted only
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10 if all tools agree. This tool is designed for substitutions only,
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11 not indel corrections.
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12
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13 Usage: consect.sh in=<file,file,file,...> out=<file>
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14
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15 Standard parameters:
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16 in= A comma-delimited list of files; minimum of 3.
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17 All files must have reads in the same order.
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18 The first file must contain the uncorrected reads.
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19 All additional files must contain corrected reads.
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20 out=<file> Output of consensus reads.
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21 overwrite=f (ow) Set to false to force the program to abort rather than
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22 overwrite an existing file.
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23
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24 Processing parameters:
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25 None yet!
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26
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27 Java Parameters:
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28 -Xmx This will set Java's memory usage, overriding autodetection.
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29 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
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30 The max is typically 85% of physical memory.
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31 -eoom This flag will cause the process to exit if an out-of-memory
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32 exception occurs. Requires Java 8u92+.
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33 -da Disable assertions.
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34
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35 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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36 "
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37 }
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38
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39 #This block allows symlinked shellscripts to correctly set classpath.
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40 pushd . > /dev/null
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41 DIR="${BASH_SOURCE[0]}"
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42 while [ -h "$DIR" ]; do
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43 cd "$(dirname "$DIR")"
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44 DIR="$(readlink "$(basename "$DIR")")"
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45 done
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46 cd "$(dirname "$DIR")"
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47 DIR="$(pwd)/"
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48 popd > /dev/null
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49
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50 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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51 CP="$DIR""current/"
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52
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53 z="-Xmx2g"
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54 set=0
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55
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56 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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57 usage
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58 exit
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59 fi
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60
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61 calcXmx () {
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62 source "$DIR""/calcmem.sh"
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63 setEnvironment
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64 parseXmx "$@"
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65 }
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66 calcXmx "$@"
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67
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68 consect() {
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69 local CMD="java $EA $EOOM $z -cp $CP jgi.Consect $@"
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70 echo $CMD >&2
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71 eval $CMD
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72 }
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73
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74 consect "$@"
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