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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 Last modified February 13, 2020
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6
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7 Description: Wrapper for BBMap to allow multiple input and output files for the same reference.
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8
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9 To index: bbwrap.sh ref=<reference fasta>
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10 To map: bbwrap.sh in=<file,file,...> out=<file,file,...>
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11 To map without an index: bbwrap.sh ref=<reference fasta> in=<file,file,...> out=<file,file,...> nodisk
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12 To map pairs and singletons and output them into the same file:
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13 bbwrap.sh in1=read1.fq,singleton.fq in2=read2.fq,null out=mapped.sam append
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14
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15 BBWrap will not work with stdin and stdout, or histogram output.
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16
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17 Other Parameters:
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18
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19 in=<file,file> Input sequences to map.
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20 inlist=<fofn> Alternately, input and output can be a file of filenames,
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21 one line per file, using the flag inlist, outlist, outmlist,
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22 in2list, etc.
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23 mapper=bbmap Select mapper. May be BBMap, BBMapPacBio,
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24 or BBMapPacBioSkimmer.
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25 append=f Append to files rather than overwriting them.
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26 If append is enabled, and there is exactly one output file,
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27 all output will be written to that file.
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28
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29 ***** All BBMap parameters can be used; see bbmap.sh for more details. *****
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30 "
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31 }
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32
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33 #This block allows symlinked shellscripts to correctly set classpath.
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34 pushd . > /dev/null
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35 DIR="${BASH_SOURCE[0]}"
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36 while [ -h "$DIR" ]; do
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37 cd "$(dirname "$DIR")"
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38 DIR="$(readlink "$(basename "$DIR")")"
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39 done
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40 cd "$(dirname "$DIR")"
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41 DIR="$(pwd)/"
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42 popd > /dev/null
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43
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44 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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45 CP="$DIR""current/"
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46 JNI="-Djava.library.path=""$DIR""jni/"
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47 JNI=""
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48
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49 z="-Xmx1g"
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50 z2="-Xms1g"
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51 set=0
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52
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53 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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54 usage
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55 exit
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56 fi
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57
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58 calcXmx () {
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59 source "$DIR""/calcmem.sh"
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60 setEnvironment
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61 parseXmx "$@"
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62 if [[ $set == 1 ]]; then
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63 return
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64 fi
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65 freeRam 3200m 84
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66 z="-Xmx${RAM}m"
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67 z2="-Xms${RAM}m"
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68 }
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69 calcXmx "$@"
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70
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71 bbwrap() {
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72 local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP align2.BBWrap build=1 overwrite=true fastareadlen=500 $@"
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73 echo $CMD >&2
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74 eval $CMD
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75 }
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76
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77 bbwrap "$@"
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