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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 20, 2015
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7
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8 Description: Prints the most common kmers in each sequence.
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9 This is intended for short kmers only!
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10
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11 Usage: commonkmers.sh in=<file> out=<file>
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12
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13 Parameters:
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14 k=2 Kmer length, 0-12.
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15 display=3 Print this many kmers per sequence.
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16 count=f Print the kmer counts as well.
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17
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18 ow=f (overwrite) Overwrites files that already exist.
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19 app=f (append) Append to files that already exist.
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20 zl=4 (ziplevel) Set compression level, 1 (low) to 9 (max).
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21 qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.
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22
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23 Java Parameters:
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24 -Xmx This will set Java's memory usage, overriding autodetection.
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25 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
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26 The max is typically 85% of physical memory.
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27 -eoom This flag will cause the process to exit if an out-of-memory
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28 exception occurs. Requires Java 8u92+.
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29 -da Disable assertions.
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30
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31 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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32 "
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33 }
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34
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35 #This block allows symlinked shellscripts to correctly set classpath.
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36 pushd . > /dev/null
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37 DIR="${BASH_SOURCE[0]}"
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38 while [ -h "$DIR" ]; do
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39 cd "$(dirname "$DIR")"
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40 DIR="$(readlink "$(basename "$DIR")")"
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41 done
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42 cd "$(dirname "$DIR")"
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43 DIR="$(pwd)/"
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44 popd > /dev/null
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45
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46 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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47 CP="$DIR""current/"
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48
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49 z="-Xmx800m"
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50 set=0
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51
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52 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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53 usage
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54 exit
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55 fi
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56
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57 calcXmx () {
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58 source "$DIR""/calcmem.sh"
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59 setEnvironment
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60 parseXmx "$@"
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61 }
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62 calcXmx "$@"
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63
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64 function commonkmers() {
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65 local CMD="java $EA $EOOM $z -cp $CP jgi.SmallKmerFrequency $@"
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66 echo $CMD >&2
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67 eval $CMD
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68 }
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69
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70 commonkmers "$@"
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