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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: Generates fake read pairs from ends of contigs or single reads.
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9
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10 Usage: bbfakereads.sh in=<file> out=<outfile> out2=<outfile2>
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11
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12 Out2 is optional; if there is only one output file, it will be written interleaved.
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13
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14 Standard parameters:
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15 ow=f (overwrite) Overwrites files that already exist.
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16 zl=4 (ziplevel) Set compression level, 1 (low) to 9 (max).
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17 fastawrap=100 Length of lines in fasta output.
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18 tuc=f (touppercase) Change lowercase letters in reads to uppercase.
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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 qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input).
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21 qfin=<.qual file> Read qualities from this qual file, for the reads coming from 'in=<fasta file>'
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22 qfout=<.qual file> Write qualities from this qual file, for the reads going to 'out=<fasta file>'
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23 qfout2=<.qual file> Write qualities from this qual file, for the reads coming from 'out2=<fasta file>'
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24 verifyinterleaved=f (vint) When true, checks a file to see if the names look paired. Prints an error message if not.
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25 tossbrokenreads=f (tbr) Discard reads that have different numbers of bases and qualities. By default this will be detected and cause a crash.
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26
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27 Faking parameters:
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28 length=250 Generate reads of this length.
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29 minlength=1 Don't generate reads shorter than this.
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30 overlap=0 If you set overlap, then reads will by variable length, overlapping by 'overlap' in the middle.
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31 identifier=null (id) Output read names are prefixed with this.
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32 addspace=t Set to false to omit the space before /1 and /2 of paired reads.
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33
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34 Java Parameters:
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35 -Xmx This will set Java's memory usage, overriding autodetection.
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36 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
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37 The max is typically 85% of physical memory.
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38 -eoom This flag will cause the process to exit if an
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39 out-of-memory exception occurs. Requires Java 8u92+.
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40 -da Disable assertions.
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41
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42 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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43 "
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44 }
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45
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46 #This block allows symlinked shellscripts to correctly set classpath.
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47 pushd . > /dev/null
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48 DIR="${BASH_SOURCE[0]}"
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49 while [ -h "$DIR" ]; do
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50 cd "$(dirname "$DIR")"
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51 DIR="$(readlink "$(basename "$DIR")")"
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52 done
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53 cd "$(dirname "$DIR")"
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54 DIR="$(pwd)/"
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55 popd > /dev/null
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56
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57 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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58 CP="$DIR""current/"
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59
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60 z="-Xmx600m"
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61 set=0
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62
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63 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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64 usage
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65 exit
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66 fi
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67
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68
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69 calcXmx () {
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70 source "$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 function fakereads() {
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77 local CMD="java $EA $EOOM $z -cp $CP jgi.FakeReads $@"
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78 echo $CMD >&2
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79 eval $CMD
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80 }
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81
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82 fakereads "$@"
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