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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 August 1, 2016
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7
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8 Description: Generates a kmer uniqueness histogram, binned by file position.
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9 There are 3 columns for single reads, 6 columns for paired:
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10 count number of reads or pairs processed
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11 r1_first percent unique 1st kmer of read 1
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12 r1_rand percent unique random kmer of read 1
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13 r2_first percent unique 1st kmer of read 2
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14 r2_rand percent unique random kmer of read 2
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15 pair percent unique concatenated kmer from read 1 and 2
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16
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17 Please read bbmap/docs/guides/CalcUniquenessGuide.txt for more information.
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18
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19 Usage: bbcountunique.sh in=<input> out=<output>
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20
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21 Input parameters:
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22 in2=null Second input file for paired reads
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23 interleaved=auto Set true/false to override autodetection of the input file as paired interleaved.
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24 samplerate=1 Set to below 1 to sample a fraction of input reads.
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25 reads=-1 Only process this number of reads, then quit (-1 means all)
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26
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27 Output parameters:
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28 out=<file> File for output stats
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29
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30 Processing parameters:
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31 k=25 Kmer length (range 1-31).
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32 interval=25000 Print one line to the histogram per this many reads.
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33 cumulative=f Show cumulative numbers rather than per-interval numbers.
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34 percent=t Show percentages of unique reads.
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35 count=f Show raw counts of unique reads.
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36 printlastbin=f (plb) Print a line for the final undersized bin.
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37 minprob=0 Ignore kmers with a probability of correctness below this (based on q-scores).
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38
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39 Java Parameters:
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40 -Xmx This will set Java's memory usage, overriding autodetection.
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41 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
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42 The max is typically 85% of physical memory.
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43 -eoom This flag will cause the process to exit if an
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44 out-of-memory exception occurs. Requires Java 8u92+.
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45 -da Disable assertions.
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46
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47 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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48 "
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49 }
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50
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51 #This block allows symlinked shellscripts to correctly set classpath.
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52 pushd . > /dev/null
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53 DIR="${BASH_SOURCE[0]}"
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54 while [ -h "$DIR" ]; do
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55 cd "$(dirname "$DIR")"
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56 DIR="$(readlink "$(basename "$DIR")")"
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57 done
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58 cd "$(dirname "$DIR")"
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59 DIR="$(pwd)/"
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60 popd > /dev/null
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61
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62 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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63 CP="$DIR""current/"
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64
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65 z="-Xmx1g"
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66 z2="-Xms1g"
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67 set=0
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68
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69 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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70 usage
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71 exit
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72 fi
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73
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74 calcXmx () {
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75 source "$DIR""/calcmem.sh"
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76 setEnvironment
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77 parseXmx "$@"
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78 if [[ $set == 1 ]]; then
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79 return
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80 fi
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81 freeRam 3200m 84
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82 z="-Xmx${RAM}m"
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83 z2="-Xms${RAM}m"
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84 }
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85 calcXmx "$@"
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86
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87 bbcountunique() {
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88 local CMD="java $EA $EOOM $z $z2 -cp $CP jgi.CalcUniqueness $@"
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89 echo $CMD >&2
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90 eval $CMD
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91 }
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92
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93 bbcountunique "$@"
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