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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 March 28, 2018
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7
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8 Description: Finds and trims junctions in mapped Hi-C reads.
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9 For the purpose of reporting junction motifs, this requires paired-end reads,
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10 because only improper pairs will be considered as possibly containing
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11 junctions. However, all reads that map with soft-clipping will be trimmed
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12 on the 3' (right) end, regardless of pairing status.
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13
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14 Usage: processhi-c.sh in=<mapped reads> out=<trimmed reads>
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15
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16 Parameters:
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17 in=<file> A sam/bam file containing mapped reads.
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18 out=<file> Output file of trimmed reads.
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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 printkmers=t Generate files with kmer counts at junction sites.
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22 junctions=junctions_k%.txt File pattern for junction output.
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23
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24 Java Parameters:
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25 -Xmx This will set Java's memory usage, overriding autodetection.
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26 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
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27 specify 200 megs. The max is typically 85% of physical memory.
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28 -eoom This flag will cause the process to exit if an out-of-memory
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29 exception occurs. Requires Java 8u92+.
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30 -da Disable assertions.
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31
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32 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
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33 "
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34 }
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35
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36 #This block allows symlinked shellscripts to correctly set classpath.
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37 pushd . > /dev/null
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38 DIR="${BASH_SOURCE[0]}"
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39 while [ -h "$DIR" ]; do
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40 cd "$(dirname "$DIR")"
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41 DIR="$(readlink "$(basename "$DIR")")"
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42 done
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43 cd "$(dirname "$DIR")"
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44 DIR="$(pwd)/"
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45 popd > /dev/null
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46
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47 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
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48 CP="$DIR""current/"
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49
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50 z="-Xmx200m"
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51 set=0
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52
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53 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
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54 usage
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55 exit
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56 fi
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57
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58 calcXmx () {
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59 source "$DIR""/calcmem.sh"
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60 setEnvironment
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61 parseXmx "$@"
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62 }
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63 calcXmx "$@"
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64
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65 process() {
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66 local CMD="java $EA $EOOM $z -cp $CP jgi.FindHiCJunctions $@"
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67 echo $CMD >&2
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68 eval $CMD
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69 }
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70
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71 process "$@"
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