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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 September 13, 2019
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7
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8 Description: Uses mapped paired reads to generate scaffolds from contigs.
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9 Designed for use with ordinary paired-end Illumina libraries.
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10
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11 Usage: lilypad.sh in=mapped.sam ref=contigs.fa out=scaffolds.fa
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12
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13 Standard parameters:
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14 in=<file> Reads mapped to the reference; should be sam or bam.
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15 ref=<file> Reference; may be fasta or fastq.
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16 out=<file> Modified reference; should be fasta.
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17 overwrite=f (ow) Set to false to force the program to abort rather than
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18 overwrite an existing file.
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19
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20 Processing parameters:
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21 gap=10 Pad gaps with a minimum of this many Ns.
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22 mindepth=4 Minimum spanning read pairs to join contigs.
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23 maxinsert=3000 Maximum allowed insert size for proper pairs.
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24 mincontig=200 Ignore contigs under this length if there is a
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25 longer alternative.
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26 minwr=0.8 (minWeightRatio) Minimum fraction of outgoing edges
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27 pointing to the same contig. Lower values will increase
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28 continuity at a risk of misassemblies.
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29 minsr=0.8 (minStrandRatio) Minimum fraction of outgoing edges
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30 indicating the same orientation. Lower values will increase
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31 continuity at a possible risk of inversions.
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32 passes=8 More passes may increase continuity.
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33 samestrandpairs=f Read pairs map to the same strand. Currently untested.
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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
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38 specify 200 megs. The max is typically 85% of physical memory.
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39 -eoom This flag will cause the process to exit if an out-of-memory
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40 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="-Xmx4g"
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62 z2="-Xms4g"
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63 set=0
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64
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65 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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66 usage
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67 exit
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68 fi
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69
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70 calcXmx () {
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71 source "$DIR""/calcmem.sh"
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72 setEnvironment
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73 parseXmx "$@"
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74 if [[ $set == 1 ]]; then
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75 return
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76 fi
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77 freeRam 4000m 84
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78 z="-Xmx${RAM}m"
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79 z2="-Xms${RAM}m"
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80 }
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81 calcXmx "$@"
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82
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83 lilypad() {
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84 local CMD="java $EA $EOOM $z -cp $CP consensus.Lilypad $@"
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85 echo $CMD >&2
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86 eval $CMD
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87 }
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88
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89 lilypad "$@"
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