Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/commonkmers.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| 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 February 20, 2015 | |
| 7 | |
| 8 Description: Prints the most common kmers in each sequence. | |
| 9 This is intended for short kmers only! | |
| 10 | |
| 11 Usage: commonkmers.sh in=<file> out=<file> | |
| 12 | |
| 13 Parameters: | |
| 14 k=2 Kmer length, 0-12. | |
| 15 display=3 Print this many kmers per sequence. | |
| 16 count=f Print the kmer counts as well. | |
| 17 | |
| 18 ow=f (overwrite) Overwrites files that already exist. | |
| 19 app=f (append) Append to files that already exist. | |
| 20 zl=4 (ziplevel) Set compression level, 1 (low) to 9 (max). | |
| 21 qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto. | |
| 22 | |
| 23 Java Parameters: | |
| 24 -Xmx This will set Java's memory usage, overriding autodetection. | |
| 25 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs. | |
| 26 The max is typically 85% of physical memory. | |
| 27 -eoom This flag will cause the process to exit if an out-of-memory | |
| 28 exception occurs. Requires Java 8u92+. | |
| 29 -da Disable assertions. | |
| 30 | |
| 31 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. | |
| 32 " | |
| 33 } | |
| 34 | |
| 35 #This block allows symlinked shellscripts to correctly set classpath. | |
| 36 pushd . > /dev/null | |
| 37 DIR="${BASH_SOURCE[0]}" | |
| 38 while [ -h "$DIR" ]; do | |
| 39 cd "$(dirname "$DIR")" | |
| 40 DIR="$(readlink "$(basename "$DIR")")" | |
| 41 done | |
| 42 cd "$(dirname "$DIR")" | |
| 43 DIR="$(pwd)/" | |
| 44 popd > /dev/null | |
| 45 | |
| 46 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 47 CP="$DIR""current/" | |
| 48 | |
| 49 z="-Xmx800m" | |
| 50 set=0 | |
| 51 | |
| 52 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 53 usage | |
| 54 exit | |
| 55 fi | |
| 56 | |
| 57 calcXmx () { | |
| 58 source "$DIR""/calcmem.sh" | |
| 59 setEnvironment | |
| 60 parseXmx "$@" | |
| 61 } | |
| 62 calcXmx "$@" | |
| 63 | |
| 64 function commonkmers() { | |
| 65 local CMD="java $EA $EOOM $z -cp $CP jgi.SmallKmerFrequency $@" | |
| 66 echo $CMD >&2 | |
| 67 eval $CMD | |
| 68 } | |
| 69 | |
| 70 commonkmers "$@" |