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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 ***DEPRECATED***
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9
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10 Description: Randomly adds adapters to a file, or grades a trimmed file.
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11 The input is a set of reads, paired or unpaired.
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12 The output is those same reads with adapter sequence replacing some of the bases in some reads.
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13 For paired reads, adapters are located in the same position in read1 and read2.
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14 This is designed for benchmarking adapter-trimming software, and evaluating methodology.
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15 randomreads.sh is better for paired reads, though, as it actually adds adapters at the correct location,
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16 so that overlap may be used for adapter detection.
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17
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18 Usage: addadapters.sh in=<file> in2=<file2> out=<outfile> out2=<outfile2> adapters=<file>
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19
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20 in2 and out2 are for paired reads and are optional.
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21 If input is paired and there is only one output file, it will be written interleaved.
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22
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23 Parameters:
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24 ow=f (overwrite) Overwrites files that already exist.
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25 int=f (interleaved) Determines whether INPUT file is considered interleaved.
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26 qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.
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27 qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input).
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28 add Add adapters to input files. Default mode.
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29 grade Evaluate trimmed input files.
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30 adapters=<file> Fasta file of adapter sequences.
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31 literal=<sequence> Comma-delimited list of adapter sequences.
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32 left Adapters are on the left (3') end of the read.
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33 right Adapters are on the right (5') end of the read. Default mode.
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34 adderrors=t Add errors to adapters based on the quality scores.
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35 addpaired=t Add adapters to the same location for read 1 and read 2.
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36 arc=f Add reverse-complemented adapters as well as forward.
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37 rate=0.5 Add adapters to this fraction of reads.
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38
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39 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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40 "
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41 }
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42
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43 #This block allows symlinked shellscripts to correctly set classpath.
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44 pushd . > /dev/null
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45 DIR="${BASH_SOURCE[0]}"
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46 while [ -h "$DIR" ]; do
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47 cd "$(dirname "$DIR")"
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48 DIR="$(readlink "$(basename "$DIR")")"
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49 done
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50 cd "$(dirname "$DIR")"
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51 DIR="$(pwd)/"
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52 popd > /dev/null
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53
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54 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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55 CP="$DIR""current/"
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56
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57 z="-Xmx200m"
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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 function addadapters() {
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73 local CMD="java $EA $EOOM $z -cp $CP jgi.AddAdapters $@"
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74 echo $CMD >&2
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75 eval $CMD
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76 }
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77
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78 addadapters "$@"
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