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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 October 16, 2015
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7
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8 Description: Counts the number of reads with each barcode.
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9
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10 Usage: countbarcodes.sh in=<file> counts=<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 Input parameters:
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16 in=<file> Input reads, whose names end in a colon then barcode.
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17 counts=<file> Output of counts.
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18 interleaved=auto (int) If true, forces fastq input to be paired and interleaved.
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19 qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.
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20 unpigz=t Use pigz to decompress.
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21 expected= Comma-delimited list of expected bar codes.
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22 valid= Comma-delimited list of valid bar codes.
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23 countundefined=t Count barcodes that contain non-ACGT symbols.
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24 printheader=t Print a header.
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25 maxrows=-1 Optionally limit the number of rows printed.
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26
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27 Output parameters:
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28 out=<file> Write bar codes and counts here. 'out=stdout' will pipe to standard out.
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29
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30 Java Parameters:
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31 -Xmx This will set Java's memory usage, overriding autodetection.
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32 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
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33 The max is typically 85% of physical memory.
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34 -eoom This flag will cause the process to exit if an
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35 out-of-memory exception occurs. Requires Java 8u92+.
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36 -da Disable assertions.
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37
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38 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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39 "
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40 }
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41
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42 #This block allows symlinked shellscripts to correctly set classpath.
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43 pushd . > /dev/null
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44 DIR="${BASH_SOURCE[0]}"
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45 while [ -h "$DIR" ]; do
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46 cd "$(dirname "$DIR")"
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47 DIR="$(readlink "$(basename "$DIR")")"
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48 done
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49 cd "$(dirname "$DIR")"
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50 DIR="$(pwd)/"
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51 popd > /dev/null
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52
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53 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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54 CP="$DIR""current/"
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55
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56 z="-Xmx200m"
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57 set=0
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58
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59 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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60 usage
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61 exit
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62 fi
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63
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64 calcXmx () {
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65 source "$DIR""/calcmem.sh"
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66 setEnvironment
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67 parseXmx "$@"
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68 }
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69 calcXmx "$@"
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70
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71 countbarcodes() {
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72 local CMD="java $EA $EOOM $z -cp $CP jgi.CountBarcodes $@"
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73 echo $CMD >&2
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74 eval $CMD
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75 }
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76
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77 countbarcodes "$@"
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