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jpayne@69
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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 11, 2019
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7
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8 Description: Uses paired read insert sizes to estimate the correct
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9 length of scaffold gaps, and resizes incorrectly-sized gaps.
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10
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11 Usage: fixgaps.sh in=mapped.sam ref=scaffolds.fa out=fixed.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; may be fasta or fastq.
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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 Consider any consecutive streak of Ns at least this long to
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22 be a scaffold break. Gaps will not be resized to less than
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23 this.
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24 border=0.4 Ignore the outermost (border*readlen) of an insert (read pair)
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25 when incrementing coverage. A higher value is more accurate
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26 but requires more coverage and/or longer inserts. Range: 0-1.
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27 mindepth=10 Minimum spanning read pairs to correct a gap.
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28
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29 Java Parameters:
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30 -Xmx This will set Java's memory usage, overriding autodetection.
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31 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
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32 specify 200 megs. The max is typically 85% of physical memory.
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33 -eoom This flag will cause the process to exit if an out-of-memory
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34 exception occurs. Requires Java 8u92+.
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35 -da Disable assertions.
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36
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37 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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38 "
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39 }
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40
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41 #This block allows symlinked shellscripts to correctly set classpath.
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42 pushd . > /dev/null
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43 DIR="${BASH_SOURCE[0]}"
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44 while [ -h "$DIR" ]; do
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45 cd "$(dirname "$DIR")"
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46 DIR="$(readlink "$(basename "$DIR")")"
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47 done
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48 cd "$(dirname "$DIR")"
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49 DIR="$(pwd)/"
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50 popd > /dev/null
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51
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52 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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53 CP="$DIR""current/"
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54
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55 z="-Xmx4g"
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56 z2="-Xms4g"
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57 set=0
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58
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59 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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60 usage
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61 exit
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62 fi
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63
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64 calcXmx () {
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65 source "$DIR""/calcmem.sh"
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66 setEnvironment
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67 parseXmx "$@"
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68 if [[ $set == 1 ]]; then
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69 return
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70 fi
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71 freeRam 4000m 84
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72 z="-Xmx${RAM}m"
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73 z2="-Xms${RAM}m"
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74 }
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75 calcXmx "$@"
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76
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77 fixgaps() {
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78 local CMD="java $EA $EOOM $z -cp $CP consensus.FixScaffoldGaps $@"
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79 echo $CMD >&2
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80 eval $CMD
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81 }
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82
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83 fixgaps "$@"
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