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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 June 22, 2016
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7
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8 Description: Multiplexes reads from multiple files after renaming them based on their initial file.
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9 Opposite of demuxbyname.
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10
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11 Usage: muxbyname.sh in=<file,file,file...> out=<output file>
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12 Input files may also be given without an in= prefix, so that you can use wildcards:
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13 muxbyname.sh *.fastq out=muxed.fastq
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14
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15
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16 Standard parameters:
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17 in=<file,file> A list of input files.
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18 in2=<file,file> Read 2 input if reads are in paired files.
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19 out=<file> Primary output, or read 1 output.
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20 out2=<file> Read 2 output if reads are in paired files.
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21 overwrite=f (ow) Set to false to force the program to abort rather than
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22 overwrite an existing file.
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23 showspeed=t (ss) Set to 'f' to suppress display of processing speed.
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24 ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression
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25 level; lower compression is faster.
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26
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27 Processing parameters:
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28 None yet!
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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
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33 specify 200 megs. The max is typically 85% of physical memory.
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34 -eoom This flag will cause the process to exit if an out-of-memory
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35 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="-Xmx400m"
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57 z2="-Xms400m"
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58 set=0
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59
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60 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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61 usage
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62 exit
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63 fi
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64
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65 calcXmx () {
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66 source "$DIR""/calcmem.sh"
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67 setEnvironment
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68 parseXmx "$@"
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69 }
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70 calcXmx "$@"
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71
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72 muxbyname() {
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73 local CMD="java $EA $EOOM $z -cp $CP driver.RenameAndMux $@"
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74 echo $CMD >&2
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75 eval $CMD
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76 }
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77
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78 muxbyname "$@"
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