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jpayne@69
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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 December 19, 2018
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7
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8 Description: Calls peaks from a 2-column (x, y) tab-delimited histogram.
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9
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10 Usage: callpeaks.sh in=<histogram file> out=<output file>
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11
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12 Peak-calling parameters:
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13 in=<file> 'in=stdin.fq' will pipe from standard in.
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14 out=<file> Write the peaks to this file. Default is stdout.
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15 minHeight=2 (h) Ignore peaks shorter than this.
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16 minVolume=5 (v) Ignore peaks with less area than this.
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17 minWidth=3 (w) Ignore peaks narrower than this.
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18 minPeak=2 (minp) Ignore peaks with an X-value below this.
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19 Useful when low-count kmers are filtered).
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20 maxPeak=BIG (maxp) Ignore peaks with an X-value above this.
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21 maxPeakCount=10 (maxpc) Print up to this many peaks (prioritizing height).
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22 countColumn=1 (col) For multi-column input, this column, zero-based,
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23 contains the counts.
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24 ploidy=-1 Specify ploidy; otherwise it will be autodetected.
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25 logscale=f Transform to log-scale prior to peak-calling. Useful
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26 for kmer-frequency histograms.
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27
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28 Smoothing parameters:
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29 smoothradius=0 Integer radius of triangle filter. Set above zero to
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30 smooth data prior to peak-calling. Higher values are
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31 smoother.
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32 smoothprogressive=f Set to true to widen the filter as the x-coordinate
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33 increases. Useful for kmer-frequency histograms.
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34 maxradius=10 Maximum radius of progressive smoothing function.
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35 progressivemult=2 Increment radius each time depth increases by this factor.
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36
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37 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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38 "
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39 }
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40
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41 #This block allows symlinked shellscripts to correctly set classpath.
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42 pushd . > /dev/null
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43 DIR="${BASH_SOURCE[0]}"
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44 while [ -h "$DIR" ]; do
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45 cd "$(dirname "$DIR")"
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46 DIR="$(readlink "$(basename "$DIR")")"
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47 done
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48 cd "$(dirname "$DIR")"
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49 DIR="$(pwd)/"
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50 popd > /dev/null
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51
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52 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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53 CP="$DIR""current/"
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54
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55 z="-Xmx200m"
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56 set=0
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57
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58 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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59 usage
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60 exit
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61 fi
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62
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63 calcXmx () {
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64 source "$DIR""/calcmem.sh"
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65 setEnvironment
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66 parseXmx "$@"
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67 }
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68 calcXmx "$@"
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69
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70 stats() {
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71 local CMD="java $EA $EOOM -Xmx120m -cp $CP jgi.CallPeaks $@"
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72 # echo $CMD >&2
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73 eval $CMD
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74 }
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75
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76 stats "$@"
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