Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/processhi-c.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
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| children |
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| 67:0e9998148a16 | 69:33d812a61356 |
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| 1 #!/bin/bash | |
| 2 | |
| 3 usage(){ | |
| 4 echo " | |
| 5 Written by Brian Bushnell | |
| 6 Last modified March 28, 2018 | |
| 7 | |
| 8 Description: Finds and trims junctions in mapped Hi-C reads. | |
| 9 For the purpose of reporting junction motifs, this requires paired-end reads, | |
| 10 because only improper pairs will be considered as possibly containing | |
| 11 junctions. However, all reads that map with soft-clipping will be trimmed | |
| 12 on the 3' (right) end, regardless of pairing status. | |
| 13 | |
| 14 Usage: processhi-c.sh in=<mapped reads> out=<trimmed reads> | |
| 15 | |
| 16 Parameters: | |
| 17 in=<file> A sam/bam file containing mapped reads. | |
| 18 out=<file> Output file of trimmed reads. | |
| 19 overwrite=f (ow) Set to false to force the program to abort rather than | |
| 20 overwrite an existing file. | |
| 21 printkmers=t Generate files with kmer counts at junction sites. | |
| 22 junctions=junctions_k%.txt File pattern for junction output. | |
| 23 | |
| 24 Java Parameters: | |
| 25 -Xmx This will set Java's memory usage, overriding autodetection. | |
| 26 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will | |
| 27 specify 200 megs. The max is typically 85% of physical memory. | |
| 28 -eoom This flag will cause the process to exit if an out-of-memory | |
| 29 exception occurs. Requires Java 8u92+. | |
| 30 -da Disable assertions. | |
| 31 | |
| 32 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. | |
| 33 " | |
| 34 } | |
| 35 | |
| 36 #This block allows symlinked shellscripts to correctly set classpath. | |
| 37 pushd . > /dev/null | |
| 38 DIR="${BASH_SOURCE[0]}" | |
| 39 while [ -h "$DIR" ]; do | |
| 40 cd "$(dirname "$DIR")" | |
| 41 DIR="$(readlink "$(basename "$DIR")")" | |
| 42 done | |
| 43 cd "$(dirname "$DIR")" | |
| 44 DIR="$(pwd)/" | |
| 45 popd > /dev/null | |
| 46 | |
| 47 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 48 CP="$DIR""current/" | |
| 49 | |
| 50 z="-Xmx200m" | |
| 51 set=0 | |
| 52 | |
| 53 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 54 usage | |
| 55 exit | |
| 56 fi | |
| 57 | |
| 58 calcXmx () { | |
| 59 source "$DIR""/calcmem.sh" | |
| 60 setEnvironment | |
| 61 parseXmx "$@" | |
| 62 } | |
| 63 calcXmx "$@" | |
| 64 | |
| 65 process() { | |
| 66 local CMD="java $EA $EOOM $z -cp $CP jgi.FindHiCJunctions $@" | |
| 67 echo $CMD >&2 | |
| 68 eval $CMD | |
| 69 } | |
| 70 | |
| 71 process "$@" |