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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: Concatenates barcodes and quality onto read names.
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9
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10 Usage: mergebarcodes.sh in=<file> out=<file> barcode=<file>
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11
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12 Input may be stdin or a fasta or fastq file, raw or gzipped.
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13 If you pipe via stdin/stdout, please include the file type; e.g. for gzipped fasta input, set in=stdin.fa.gz
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14
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15 Optional parameters (and their defaults)
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16
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17 Input parameters:
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18 in=<file> Input reads. 'in=stdin.fq' will pipe from standard in.
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19 bar=<file> File containing barcodes.
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20 int=auto (interleaved) If true, forces fastq input to be paired and interleaved.
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21 qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.
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22
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23 Output parameters:
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24 out=<file> Write muxed sequences here. 'out=stdout.fa' will pipe to standard out.
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25 overwrite=t (ow) Set to false to force the program to abort rather than overwrite an existing file.
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26 ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression level; lower compression is faster.
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27 qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input).
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28
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29 Other parameters:
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30 pigz=t Use pigz to compress. If argument is a number, that will set the number of pigz threads.
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31 unpigz=t Use pigz to decompress.
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32
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33 Java Parameters:
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34 -Xmx This will set Java's memory usage, overriding autodetection.
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35 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
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36 The max is typically 85% of physical memory.
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37 -eoom This flag will cause the process to exit if an out-of-memory
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38 exception occurs. Requires Java 8u92+.
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39 -da Disable assertions.
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40
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41 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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42 "
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43 }
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44
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45 #This block allows symlinked shellscripts to correctly set classpath.
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46 pushd . > /dev/null
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47 DIR="${BASH_SOURCE[0]}"
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48 while [ -h "$DIR" ]; do
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49 cd "$(dirname "$DIR")"
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50 DIR="$(readlink "$(basename "$DIR")")"
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51 done
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52 cd "$(dirname "$DIR")"
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53 DIR="$(pwd)/"
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54 popd > /dev/null
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55
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56 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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57 CP="$DIR""current/"
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58
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59 z="-Xmx1g"
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60 z2="-Xms1g"
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61 set=0
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62
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63 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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64 usage
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65 exit
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66 fi
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67
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68 calcXmx () {
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69 source "$DIR""/calcmem.sh"
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70 setEnvironment
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71 parseXmx "$@"
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72 if [[ $set == 1 ]]; then
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73 return
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74 fi
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75 freeRam 3200m 84
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76 z="-Xmx${RAM}m"
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77 z2="-Xms${RAM}m"
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78 }
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79 calcXmx "$@"
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80
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81 mergebarcodes() {
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82 local CMD="java $EA $EOOM $z -cp $CP jgi.MergeBarcodes $@"
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83 echo $CMD >&2
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84 eval $CMD
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85 }
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86
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87 mergebarcodes "$@"
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