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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 3, 2019
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7
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8 Description: Shrinks or expands homopolymers.
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9
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10 Usage: adjusthomopolymers.sh in=<input file> out=<output file> rate=<float>
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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 Standard parameters:
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15 in=<file> Primary input, or read 1 input.
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16 in2=<file> Read 2 input if reads are in two files.
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17 out=<file> Primary output, or read 1 output.
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18 out2=<file> Read 2 output if reads are in two files.
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19 overwrite=f (ow) Set to false to force the program to abort rather than
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20 overwrite an existing file.
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21 ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression
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22 level; lower compression is faster.
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23
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24 Processing parameters:
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25 rate=0.0 0.1 will expand by 10%; -0.1 will shrink by 10%.
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26
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27 Java Parameters:
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28 -Xmx This will set Java's memory usage, overriding autodetection.
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29 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
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30 specify 200 megs. The max is typically 85% of physical memory.
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31 -eoom This flag will cause the process to exit if an out-of-memory
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32 exception occurs. Requires Java 8u92+.
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33 -da Disable assertions.
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34
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35 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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36 "
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37 }
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38
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39 #This block allows symlinked shellscripts to correctly set classpath.
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40 pushd . > /dev/null
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41 DIR="${BASH_SOURCE[0]}"
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42 while [ -h "$DIR" ]; do
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43 cd "$(dirname "$DIR")"
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44 DIR="$(readlink "$(basename "$DIR")")"
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45 done
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46 cd "$(dirname "$DIR")"
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47 DIR="$(pwd)/"
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48 popd > /dev/null
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49
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50 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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51 CP="$DIR""current/"
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52
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53 z="-Xmx1g"
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54 z2="-Xms1g"
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55 set=0
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56
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57 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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58 usage
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59 exit
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60 fi
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61
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62 calcXmx () {
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63 source "$DIR""/calcmem.sh"
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64 setEnvironment
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65 parseXmx "$@"
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66 if [[ $set == 1 ]]; then
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67 return
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68 fi
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69 freeRam 1000m 30
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70 z="-Xmx${RAM}m"
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71 z2="-Xms${RAM}m"
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72 }
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73 calcXmx "$@"
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74
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75 adjusthomopolymers() {
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76 local CMD="java $EA $EOOM $z -cp $CP jgi.AdjustHomopolymers $@"
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77 echo $CMD >&2
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78 eval $CMD
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79 }
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80
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81 adjusthomopolymers "$@"
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