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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 November 25, 2014
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7
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8 Description: Generates an identity matrix via all-to-all alignment.
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9
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10 *** WARNING: This program may produce incorrect results in some cirumstances.
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11 *** It is not advisable to use until fixed.
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12
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13 Usage: idmatrix.sh in=<file> out=<file>
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14
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15 Parameters:
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16 in=<file> File containing reads. in=stdin.fa will pipe from stdin.
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17 out=<file> Matrix output. out=stdout will pipe to stdout.
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18 threads=auto (t) Set number of threads to use; default is number of
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19 logical processors.
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20 percent=f Output identity as percent rather than a fraction.
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21 edits= Allow at most this much edit distance. Default is the
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22 length of the longest input sequence. Lower is faster.
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23 width= Alignment bandwidth, lower is faster. Default: 2*edits+1.
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24 usejni=f (jni) Do alignments faster, in C code. Requires
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25 compiling the C code; details are in /jni/README.txt.
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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 automatic
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29 memory detection. -Xmx20g will specify
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30 20 gigs of RAM, and -Xmx200m will specify 200 megs.
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31 The max is typically 85% of physical memory.
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32 -eoom This flag will cause the process to exit if an out-of-memory
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33 exception occurs. Requires Java 8u92+.
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34 -da Disable assertions.
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35
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36 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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37 "
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38 }
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39
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40 #This block allows symlinked shellscripts to correctly set classpath.
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41 pushd . > /dev/null
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42 DIR="${BASH_SOURCE[0]}"
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43 while [ -h "$DIR" ]; do
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44 cd "$(dirname "$DIR")"
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45 DIR="$(readlink "$(basename "$DIR")")"
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46 done
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47 cd "$(dirname "$DIR")"
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48 DIR="$(pwd)/"
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49 popd > /dev/null
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50
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51 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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52 CP="$DIR""current/"
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53 JNI="-Djava.library.path=""$DIR""jni/"
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54 JNI=""
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55
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56 z="-Xmx2g"
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57 z2="-Xms2g"
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58 set=0
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59
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60 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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61 usage
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62 exit
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63 fi
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64
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65 calcXmx () {
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66 source "$DIR""/calcmem.sh"
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67 setEnvironment
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68 parseXmx "$@"
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69 if [[ $set == 1 ]]; then
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70 return
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71 fi
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72 freeRam 3200m 84
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73 z="-Xmx${RAM}m"
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74 z2="-Xms${RAM}m"
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75 }
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76 calcXmx "$@"
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77
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78 idmatrix() {
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79 local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP jgi.IdentityMatrix $@"
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80 echo $CMD >&2
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81 eval $CMD
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82 }
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83
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84 idmatrix "$@"
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