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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 January 26, 2021
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7
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8 Description: Mutates a reference by applying a set of variants.
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9 When 2 variants overlap, the one with the higher allele count is used.
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10
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11 Usage: applyvariants.sh in=<input file> vcf=<vcf file> out=<output file>
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12
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13 Standard parameters:
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14 in=<file> Reference fasta.
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15 vcf=<file> Variants.
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16 basecov=<file> Optional per-base coverage from BBMap or Pileup.
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17 out=<file> Output fasta.
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18 overwrite=f (ow) Set to false to force the program to abort rather than
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19 overwrite an existing file.
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20 ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression
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21 level; lower compression is faster.
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22
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23 Processing parameters:
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24 mincov=0 If positive and depth is below this, change ref to N.
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25 Requires a coverage file.
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26 maxindel=-1 If positive, ignore indels longer than this.
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27 noframeshifts=f Ignore indels that are not a multiple of 3 in length.
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28
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29 Renaming:
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30 name= Optionally rename sequences to this.
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31 addnumbers=f Add _1 and so forth to ensure sequence names are unique.
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32 prefix=t Use the name as a prefix to the old name, instead of replacing
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33 the old name.
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34 delimiter=_ Symbol to place between parts of the new name.
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35 For space or tab, use the literal word.
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36
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37 Java Parameters:
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38 -Xmx This will set Java's memory usage, overriding autodetection.
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39 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
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40 specify 200 megs. The max is typically 85% of physical memory.
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41 -eoom This flag will cause the process to exit if an out-of-memory
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42 exception occurs. Requires Java 8u92+.
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43 -da Disable assertions.
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44
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45 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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46 "
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47 }
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48
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49 #This block allows symlinked shellscripts to correctly set classpath.
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50 pushd . > /dev/null
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51 DIR="${BASH_SOURCE[0]}"
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52 while [ -h "$DIR" ]; do
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53 cd "$(dirname "$DIR")"
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54 DIR="$(readlink "$(basename "$DIR")")"
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55 done
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56 cd "$(dirname "$DIR")"
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57 DIR="$(pwd)/"
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58 popd > /dev/null
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59
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60 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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61 CP="$DIR""current/"
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62
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63 z="-Xmx4g"
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64 z2="-Xms4g"
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65 set=0
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66
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67 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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68 usage
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69 exit
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70 fi
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71
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72 calcXmx () {
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73 source "$DIR""/calcmem.sh"
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74 setEnvironment
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75 parseXmx "$@"
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76 if [[ $set == 1 ]]; then
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77 return
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78 fi
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79 freeRam 4000m 84
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80 z="-Xmx${RAM}m"
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81 z2="-Xms${RAM}m"
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82 }
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83 calcXmx "$@"
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84
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85 applyvariants() {
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86 local CMD="java $EA $EOOM $z -cp $CP var2.ApplyVariants $@"
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87 echo $CMD >&2
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88 eval $CMD
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89 }
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90
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91 applyvariants "$@"
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