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jpayne@69
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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 February 17, 2015
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7
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8 Description: Generates synthetic cross-contaminated files from clean files.
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9 Intended for use with synthetic reads generated by SynthMDA or RandomReads.
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10
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11 Usage: crosscontaminate.sh in=<file,file,...> out=<file,file,...>
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12
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13 Input parameters:
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14 in=<file,file,...> Clean input reads.
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15 innamefile=<file> A file containing the names of input files,
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16 one name per line.
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17 interleaved=auto (int) t/f overrides interleaved autodetection.
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18 qin=auto Input quality offset: 33 (Sanger), 64, or auto.
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19 reads=-1 If positive, quit after processing X reads or pairs.
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20
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21 Processing Parameters:
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22 minsinks=1 Min contamination destinations from one source.
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23 maxsinks=8 Max contamination destinations from one source.
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24 minprob=0.000005 Min allowed contamination rate (geometric distribution).
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25 maxprob=0.025 Max allowed contamination rate.
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26
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27 Output parameters:
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28 out=<file,file,...> Contaminated output reads.
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29 outnamefile=<file> A file containing the names of output files,
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30 one name per line.
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31 overwrite=t (ow) Grant permission to overwrite files.
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32 #showspeed=t (ss) 'f' suppresses display of processing speed.
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33 ziplevel=2 (zl) Compression level; 1 (min) through 9 (max).
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34 threads=auto (t) Set number of threads to use; default is number of
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35 logical processors.
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36 qout=auto Output quality offset: 33 (Sanger), 64, or auto.
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37 shuffle=f Shuffle contents of output files.
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38 shufflethreads=3 Use this many threads for shuffling (uses more memory).
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39
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40 Java Parameters:
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41 -Xmx This will set Java's memory usage, overriding autodetection.
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42 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
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43 The max is typically 85% of physical memory.
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44 -eoom This flag will cause the process to exit if an
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45 out-of-memory exception occurs. Requires Java 8u92+.
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46 -da Disable assertions.
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47
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48 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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49 "
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50 }
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51
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52 #This block allows symlinked shellscripts to correctly set classpath.
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53 pushd . > /dev/null
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54 DIR="${BASH_SOURCE[0]}"
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55 while [ -h "$DIR" ]; do
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56 cd "$(dirname "$DIR")"
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57 DIR="$(readlink "$(basename "$DIR")")"
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58 done
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59 cd "$(dirname "$DIR")"
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60 DIR="$(pwd)/"
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61 popd > /dev/null
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62
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63 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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64 CP="$DIR""current/"
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65
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66 z="-Xmx4g"
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67 z2="-Xms4g"
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68 set=0
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69
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70 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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71 usage
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72 exit
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73 fi
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74
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75 calcXmx () {
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76 source "$DIR""/calcmem.sh"
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77 setEnvironment
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78 parseXmx "$@"
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79 if [[ $set == 1 ]]; then
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80 return
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81 fi
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82 freeRam 4000m 42
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83 z="-Xmx${RAM}m"
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84 }
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85 calcXmx "$@"
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86
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87 crosscontaminate() {
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88 local CMD="java $EA $EOOM $z -cp $CP jgi.CrossContaminate $@"
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89 echo $CMD >&2
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90 eval $CMD
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91 }
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92
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93 crosscontaminate "$@"
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