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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 December 19, 2019
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7
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8 Description: Merges multiple sketches into a single sketch.
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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: mergesketch.sh in=a.sketch,b.sketch out=c.sketch
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13 With wildcards: mergesketch.sh *.sketch out=c.sketch
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14
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15 Standard parameters:
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16 in=<file> Input sketches or fasta files; may be a comma-delimited
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17 list. in= is optional so wildcards may be used.
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18 out=<file> Output sketch.
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19 amino=f Use amino acid mode.
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20
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21 Sketch-making parameters:
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22 mode=single Possible modes, for fasta input:
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23 single: Generate one sketch per file.
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24 sequence: Generate one sketch per sequence.
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25 autosize=t Produce an output sketch of whatever size the union
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26 happens to be.
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27 size= Restrict output sketch to this upper bound of size.
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28 k=32,24 Kmer length, 1-32.
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29 keyfraction=0.2 Only consider this upper fraction of keyspace.
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30 minkeycount=1 Ignore kmers that occur fewer times than this. Values
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31 over 1 can be used with raw reads to avoid error kmers.
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32 depth=f Retain kmer counts if available.
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33
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34 Metadata parameters: (if blank the values of the first sketch will be used)
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35 taxid=-1 Set the NCBI taxid.
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36 imgid=-1 Set the IMG id.
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37 spid=-1 Set the JGI sequencing project id.
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38 name= Set the name (taxname).
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39 name0= Set name0 (normally the first sequence header).
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40 fname= Set fname (normally the file name).
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41 meta_= Set an arbitrary metadata field.
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42 For example, meta_Month=March.
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43
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44 Java Parameters:
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45 -Xmx This will set Java's memory usage, overriding autodetection.
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46 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
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47 The max is typically 85% of physical memory.
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48 -eoom This flag will cause the process to exit if an out-of-memory
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49 exception occurs. Requires Java 8u92+.
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50 -da Disable assertions.
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51
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52 For more detailed information, please read /bbmap/docs/guides/BBSketchGuide.txt.
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53 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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54 "
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55 }
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56
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57 #This block allows symlinked shellscripts to correctly set classpath.
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58 pushd . > /dev/null
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59 DIR="${BASH_SOURCE[0]}"
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60 while [ -h "$DIR" ]; do
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61 cd "$(dirname "$DIR")"
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62 DIR="$(readlink "$(basename "$DIR")")"
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63 done
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64 cd "$(dirname "$DIR")"
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65 DIR="$(pwd)/"
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66 popd > /dev/null
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67
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68 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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69 CP="$DIR""current/"
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70
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71 z="-Xmx4g"
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72 z2="-Xms4g"
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73 set=0
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74
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75 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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76 usage
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77 exit
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78 fi
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79
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80 calcXmx () {
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81 source "$DIR""/calcmem.sh"
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82 setEnvironment
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83 parseXmx "$@"
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84 if [[ $set == 1 ]]; then
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85 return
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86 fi
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87 freeRam 3200m 84
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88 z="-Xmx${RAM}m"
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89 z2="-Xms${RAM}m"
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90 }
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91 calcXmx "$@"
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92
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93 sendsketch() {
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94 local CMD="java $EA $EOOM $z -cp $CP sketch.MergeSketch $@"
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95 # echo $CMD >&2
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96 eval $CMD
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97 }
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98
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99 sendsketch "$@"
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