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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 February 5, 2020
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7
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8 Description: Aligns a query sequence to reference sequences.
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9 Outputs the best matching position per reference sequence.
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10 If there are multiple queries, only the best-matching query will be used.
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11 MSA in this context stands for MultiStateAligner, not Multiple Sequence Alignment.
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12
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13 Usage:
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14 msa.sh in=<file> out=<file> literal=<literal,literal,...>
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15 or
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16 msa.sh in=<file> out=<file> ref=<lfile>
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17
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18 Parameters:
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19 in=<file> File containing reads.
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20 out=<file> Sam output file.
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21 literal= A sequence of bases to match, or a comma-delimited list.
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22 ref=<file> A fasta file of bases to match. Please set either ref
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23 or literal, not both.
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24 rcomp=t Also look for reverse-complements of the sequences.
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25 addr=f Add r_ prefix to reverse-complemented alignments.
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26 replicate=f Make copies of sequences with undefined bases for every
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27 possible combination. For example, ATN would expand to
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28 ATA, ATC, ATG, and ATT.
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29 cutoff=0 Ignore alignments with identity below this (range 0-1).
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30 swap=f Swap the reference and query; e.g., report read alignments
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31 to the reference instead of reference alignments to the reads.
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32
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33 Java Parameters:
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34 -Xmx This will set Java's memory usage, overriding automatic
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35 memory detection. -Xmx20g will specify
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36 20 gigs of RAM, and -Xmx200m will specify 200 megs.
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37 The max is typically 85% of physical memory.
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38 -eoom This flag will cause the process to exit if an out-of-memory
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39 exception occurs. Requires Java 8u92+.
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40 -da Disable assertions.
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41
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42 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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43 "
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44 }
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45
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46 #This block allows symlinked shellscripts to correctly set classpath.
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47 pushd . > /dev/null
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48 DIR="${BASH_SOURCE[0]}"
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49 while [ -h "$DIR" ]; do
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50 cd "$(dirname "$DIR")"
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51 DIR="$(readlink "$(basename "$DIR")")"
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52 done
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53 cd "$(dirname "$DIR")"
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54 DIR="$(pwd)/"
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55 popd > /dev/null
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56
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57 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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58 CP="$DIR""current/"
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59
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60 z="-Xmx1g"
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61 z2="-Xms1g"
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62 set=0
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63
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64 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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65 usage
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66 exit
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67 fi
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68
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69 calcXmx () {
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70 source "$DIR""/calcmem.sh"
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71 setEnvironment
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72 parseXmx "$@"
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73 if [[ $set == 1 ]]; then
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74 return
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75 fi
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76 freeRam 2000m 84
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77 z="-Xmx${RAM}m"
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78 z2="-Xms${RAM}m"
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79 }
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80 calcXmx "$@"
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81
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82 msa() {
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83 local CMD="java $EA $EOOM $z -cp $CP jgi.FindPrimers $@"
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84 echo $CMD >&2
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85 eval $CMD
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86 }
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87
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88 msa "$@"
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