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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 July 31, 2018
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7
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8 Description: Stops producing reads when the unique kmer limit is reached.
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9 This is approximate. If the input has been Clumpified, the order should be
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10 randomized first with shuffle2.sh or sortbyname.sh with the flowcell flag.
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11
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12 Differences between versions:
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13 kmerlimit.sh uses 1 pass and outputs all reads until a limit is hit,
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14 meaning the input reads should be in random order with respect to sequence.
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15 kmerlimit2.sh uses 2 passes and randomly subsamples from the file, so
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16 it works with reads in any order.
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17
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18 Usage: kmerlimit.sh in=<input file> out=<output file> limit=<number>
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19
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20 Standard parameters:
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21 in=<file> Primary input, or read 1 input.
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22 in2=<file> Read 2 input if reads are in two files.
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23 out=<file> Primary output, or read 1 output.
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24 out2=<file> Read 2 output if reads are in two files.
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25 overwrite=t (ow) Set to false to force the program to abort rather than
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26 overwrite an existing file.
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27 ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression
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28 level; lower compression is faster.
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29
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30 Processing parameters:
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31 k=31 Kmer length, 1-32.
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32 limit= The number of unique kmers to produce.
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33 mincount=1 Ignore kmers seen fewer than this many times.
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34 minqual=0 Ignore bases with quality below this.
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35 minprob=0.2 Ignore kmers with correctness probability below this.
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36
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37 Java Parameters:
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38 -Xmx This will set Java's memory usage, overriding autodetection.
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39 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
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40 specify 200 megs. The max is typically 85% of physical memory.
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41 -eoom This flag will cause the process to exit if an out-of-memory
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42 exception occurs. Requires Java 8u92+.
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43 -da Disable assertions.
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44
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45 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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46 "
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47 }
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48
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49 #This block allows symlinked shellscripts to correctly set classpath.
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50 pushd . > /dev/null
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51 DIR="${BASH_SOURCE[0]}"
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52 while [ -h "$DIR" ]; do
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53 cd "$(dirname "$DIR")"
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54 DIR="$(readlink "$(basename "$DIR")")"
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55 done
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56 cd "$(dirname "$DIR")"
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57 DIR="$(pwd)/"
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58 popd > /dev/null
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59
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60 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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61 CP="$DIR""current/"
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62
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63 z="-Xmx1000m"
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64 z2="-Xms1000m"
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65 set=0
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66
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67 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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68 usage
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69 exit
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70 fi
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71
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72 calcXmx () {
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73 source "$DIR""/calcmem.sh"
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74 setEnvironment
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75 parseXmx "$@"
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76 }
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77 calcXmx "$@"
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78
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79 kmerlimit() {
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80 local CMD="java $EA $EOOM $z -cp $CP sketch.KmerLimit $@"
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81 echo $CMD >&2
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82 eval $CMD
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83 }
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84
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85 kmerlimit "$@"
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