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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 October 22, 2015
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7
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8 Description: Generates synthetic reads following an MDA-amplified single cell's coverage distribution.
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9
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10 Usage: synthmda.sh in=<reference> out=<reads out file>
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11
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12 Input may be fasta or fastq, compressed or uncompressed.
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13
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14 Parameters:
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15 reads=12000000 Generate this many reads.
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16 paired=t Generate paired reads.
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17 length=150 Reads should be this long.
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18 minlen=4000 Min length of MDA contig.
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19 maxlen=150000 Max length of MDA contig.
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20 cycles=9 Number of MDA cycles; higher is more spiky.
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21 initialratio=1.3 Fraction of genome initially replicated;
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22 lower is more spiky.
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23 ratio=1.7 Fraction of genome replicated per cycle.
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24 refout=null Write MDA'd genome to this file.
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25 perfect=0 This fraction of reads will be error-free.
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26 amp=200 'amp' flag sent to RandomReads (higher is more spiky).
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27 build=7 Index MDA'd genome in this location.
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28 prefix=null Generated reads will start with this prefix.
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29 overwrite=t (ow) Set to false to force the program to abort rather
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30 than overwrite an existing file.
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31
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32 Java Parameters:
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33 -Xmx This will set Java's memory usage, overriding autodetection.
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34 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
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35 The max is typically 85% of physical memory.
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36 -eoom This flag will cause the process to exit if an
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37 out-of-memory exception occurs. Requires Java 8u92+.
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38 -da Disable assertions.
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39
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40 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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41 "
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42 }
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43
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44 #This block allows symlinked shellscripts to correctly set classpath.
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45 pushd . > /dev/null
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46 DIR="${BASH_SOURCE[0]}"
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47 while [ -h "$DIR" ]; do
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48 cd "$(dirname "$DIR")"
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49 DIR="$(readlink "$(basename "$DIR")")"
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50 done
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51 cd "$(dirname "$DIR")"
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52 DIR="$(pwd)/"
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53 popd > /dev/null
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54
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55 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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56 CP="$DIR""current/"
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57
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58 z="-Xmx4g"
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59 z2="-Xms4g"
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60 set=0
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61
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62 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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63 usage
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64 exit
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65 fi
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66
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67 calcXmx () {
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68 source "$DIR""/calcmem.sh"
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69 setEnvironment
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70 parseXmx "$@"
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71 if [[ $set == 1 ]]; then
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72 return
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73 fi
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74 freeRam 4000m 80
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75 z="-Xmx${RAM}m"
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76 z2="-Xms${RAM}m"
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77 }
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78 calcXmx "$@"
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79
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80 synthmda() {
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81 local CMD="java $EA $EOOM $z -cp $CP jgi.SynthMDA $@"
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82 echo $CMD >&2
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83 eval $CMD
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84 }
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85
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86 synthmda "$@"
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