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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 March 6, 2015
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7
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8 Description: Splits Nextera LMP libraries into subsets based on linker orientation:
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9 LMP, fragment, unknown, and singleton.
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10 Please read bbmap/docs/guides/SplitNexteraGuide.txt for more information.
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11
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12 Usage: splitnextera.sh in=<file> out=<file> outf=<file> outu=<file> outs=<file>
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13
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14 For pairs in two files, use in1, in2, out1, out2, etc.
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15
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16 *** Note ***
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17 For maximal speed, before running splitnextera, the linkers can be replaced with a constant first.
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18
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19 In other words, you can either do this (which is slightly faster):
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20 bbduk.sh in=reads.fq out=replaced.fq ktmask=J k=19 hdist=1 mink=11 hdist2=0 literal=CTGTCTCTTATACACATCTAGATGTGTATAAGAGACAG
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21 splitnextera.sh in=replaced.fq out=longmate.fq outf=frag.fq outu=unknown.fq outs=singleton.fq
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22
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23 Or this:
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24 splitnextera.sh in=reads.fq out=longmate.fq outf=frag.fq outu=unknown.fq outs=singleton.fq mask=t
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25
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26
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27 I/O parameters:
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28 in=<file> Input reads. Set to 'stdin.fq' to read from stdin.
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29 out=<file> Output for pairs with LMP orientation.
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30 outf=<file> Output for pairs with fragment orientation.
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31 outu=<file> Pairs with unknown orientation.
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32 outs=<file> Singleton output.
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33 ow=f (overwrite) Overwrites files that already exist.
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34 app=f (append) Append to files that already exist.
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35 zl=4 (ziplevel) Set compression level, 1 (low) to 9 (max).
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36 int=f (interleaved) Determines whether INPUT file is considered interleaved.
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37 qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.
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38 qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input).
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39
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40 Processing Parameters:
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41 mask=f Set to true if you did not already convert junctions to some symbol, and it will be done automatically.
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42 junction=J Look for this symbol to designate the junction bases.
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43 innerlmp=f Generate long mate pairs from the inner pair also, when the junction is found in both reads.
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44 rename=t Rename read 2 of output when using single-ended input.
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45 minlength=40 (ml) Do not output reads shorter than this.
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46 merge=f Attempt to merge overlapping reads before looking for junctions.
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47 testmerge=0.0 If nonzero, only merge reads if at least the fraction of input reads are mergable.
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48
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49 Sampling parameters:
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50
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51 reads=-1 Set to a positive number to only process this many INPUT reads (or pairs), then quit.
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52 samplerate=1 Randomly output only this fraction of reads; 1 means sampling is disabled.
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53 sampleseed=-1 Set to a positive number to use that prng seed for sampling (allowing deterministic sampling).
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54
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55 Java Parameters:
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56 -Xmx This will set Java's memory usage, overriding autodetection.
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57 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
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58 The max is typically 85% of physical memory.
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59 -eoom This flag will cause the process to exit if an out-of-memory
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60 exception occurs. Requires Java 8u92+.
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61 -da Disable assertions.
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62
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63 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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64 "
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65 }
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66
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67 #This block allows symlinked shellscripts to correctly set classpath.
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68 pushd . > /dev/null
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69 DIR="${BASH_SOURCE[0]}"
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70 while [ -h "$DIR" ]; do
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71 cd "$(dirname "$DIR")"
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72 DIR="$(readlink "$(basename "$DIR")")"
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73 done
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74 cd "$(dirname "$DIR")"
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75 DIR="$(pwd)/"
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76 popd > /dev/null
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77
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78 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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79 CP="$DIR""current/"
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80
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81 z="-Xmx200m"
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82 set=0
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83
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84 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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85 usage
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86 exit
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87 fi
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88
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89 calcXmx () {
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90 source "$DIR""/calcmem.sh"
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91 setEnvironment
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92 parseXmx "$@"
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93 }
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94 calcXmx "$@"
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95
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96 function splitnextera() {
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97 local CMD="java $EA $EOOM $z -cp $CP jgi.SplitNexteraLMP $@"
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98 echo $CMD >&2
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99 eval $CMD
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100 }
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101
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102 splitnextera "$@"
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