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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 Jan 7, 2020
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7
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8 Description: Shrinks sketches to a smaller fixed length.
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9
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10 Please read bbmap/docs/guides/BBSketchGuide.txt for more information.
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11
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12 Usage: subsketch.sh in=file.sketch out=sub.sketch size=1000 autosize=f
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13 Bulk usage: subsketch.sh in=big#.sketch out=small#.sketch sizemult=0.5
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14
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15 Standard parameters:
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16 in=<file> Input sketch file containing one or more sketches.
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17 out=<file> Output sketch file.
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18 size=10000 Size of sketches to generate, if autosize=f.
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19 autosize=t Autosize sketches based on genome size.
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20 sizemult=1 Adjust default sketch autosize by this factor.
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21 blacklist= Apply a blacklist to the sketch before resizing.
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22 files=31 If the output filename contains a # symbol,
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23 spread the output across this many files, replacing
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24 the # with a number.
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25
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26 Java Parameters:
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27 -Xmx This will set Java's memory usage, overriding autodetection.
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28 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
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29 The max is typically 85% of physical memory.
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30 -eoom This flag will cause the process to exit if an out-of-memory
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31 exception occurs. Requires Java 8u92+.
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32 -da Disable assertions.
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33
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34 For more detailed information, please read /bbmap/docs/guides/BBSketchGuide.txt.
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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="-Xmx4g"
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54 z2="-Xms4g"
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55 set=0
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56
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57 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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58 usage
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59 exit
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60 fi
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61
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62 calcXmx () {
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63 source "$DIR""/calcmem.sh"
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64 setEnvironment
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65 parseXmx "$@"
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66 if [[ $set == 1 ]]; then
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67 return
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68 fi
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69 freeRam 3200m 84
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70 z="-Xmx${RAM}m"
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71 z2="-Xms${RAM}m"
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72 }
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73 calcXmx "$@"
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74
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75 sendsketch() {
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76 local CMD="java $EA $EOOM $z -cp $CP sketch.SubSketch $@"
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77 # echo $CMD >&2
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78 eval $CMD
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79 }
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80
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81 sendsketch "$@"
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