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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: Separates paired reads into files of 'good' pairs and 'good' singletons by removing 'bad' reads that are shorter than a min length.
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9 Designed to handle situations where reads become too short to be useful after trimming. This program also optionally performs quality trimming.
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10
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11 Usage: bbsplitpairs.sh in=<input file> out=<pair output file> outs=<singleton output file> minlen=<minimum read length, an integer>
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12
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13 Input may be fasta or fastq, compressed or uncompressed.
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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 in=<file> The 'in=' flag is needed if the input file is not the first parameter. 'in=stdin' will pipe from standard in.
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18 in2=<file> Use this if 2nd read of pairs are in a different file.
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19 out=<file> The 'out=' flag is needed if the output file is not the second parameter. 'out=stdout' will pipe to standard out.
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20 out2=<file> Use this to write 2nd read of pairs to a different file.
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21 outsingle=<file> (outs) Write singleton reads here.
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22
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23 overwrite=t (ow) Set to false to force the program to abort rather than overwrite an existing file.
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24 showspeed=t (ss) Set to 'f' to suppress display of processing speed.
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25 interleaved=auto (int) If true, forces fastq input to be paired and interleaved.
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26 qtrim=f Trim read ends to remove bases with quality below trimq.
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27 Values: rl (trim both ends), f (neither end), r (right end only), l (left end only).
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28 trimq=6 Trim quality threshold.
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29 minlen=20 (ml) Reads shorter than this after trimming will be discarded.
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30 ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression level; lower compression is faster.
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31 fixinterleaving=f (fint) Fixes corrupted interleaved files by examining pair names. Only use on files with broken interleaving.
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32 repair=f (rp) Fixes arbitrarily corrupted paired reads by examining read names. High memory.
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33 ain=f (allowidenticalnames) When detecting pair names, allows identical names, instead of requiring /1 and /2 or 1: and 2:
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34
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35 Java Parameters:
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36 -Xmx This will set Java's memory usage, overriding autodetection.
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37 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
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38 The max is typically 85% of physical memory.
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39 -eoom This flag will cause the process to exit if an
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40 out-of-memory exception occurs. Requires Java 8u92+.
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41 -da Disable assertions.
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42
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43 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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44 "
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45 }
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46
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47 #This block allows symlinked shellscripts to correctly set classpath.
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48 pushd . > /dev/null
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49 DIR="${BASH_SOURCE[0]}"
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50 while [ -h "$DIR" ]; do
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51 cd "$(dirname "$DIR")"
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52 DIR="$(readlink "$(basename "$DIR")")"
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53 done
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54 cd "$(dirname "$DIR")"
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55 DIR="$(pwd)/"
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56 popd > /dev/null
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57
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58 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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59 CP="$DIR""current/"
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60
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61 z="-Xmx200m"
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62 set=0
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63
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64 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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65 usage
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66 exit
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67 fi
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68
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69 calcXmx () {
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70 source "$DIR""/calcmem.sh"
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71 setEnvironment
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72 parseXmx "$@"
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73 }
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74 calcXmx "$@"
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75
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76 splitpairs() {
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77 local CMD="java $EA $EOOM $z -cp $CP jgi.SplitPairsAndSingles $@"
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78 echo $CMD >&2
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79 eval $CMD
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80 }
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81
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82 splitpairs "$@"
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