Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/khist.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 Description: Generates a histogram of kmer counts for the input reads or assemblies. | |
| 6 | |
| 7 Usage: khist.sh in=<input> hist=<histogram output> | |
| 8 | |
| 9 Please see bbnorm.sh for more information. | |
| 10 All the flags are the same, only the parameters (near the bottom of this file) differ. | |
| 11 " | |
| 12 } | |
| 13 | |
| 14 #This block allows symlinked shellscripts to correctly set classpath. | |
| 15 pushd . > /dev/null | |
| 16 DIR="${BASH_SOURCE[0]}" | |
| 17 while [ -h "$DIR" ]; do | |
| 18 cd "$(dirname "$DIR")" | |
| 19 DIR="$(readlink "$(basename "$DIR")")" | |
| 20 done | |
| 21 cd "$(dirname "$DIR")" | |
| 22 DIR="$(pwd)/" | |
| 23 popd > /dev/null | |
| 24 | |
| 25 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 26 CP="$DIR""current/" | |
| 27 | |
| 28 z="-Xmx31g" | |
| 29 z2="-Xms31g" | |
| 30 set=0 | |
| 31 | |
| 32 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 33 usage | |
| 34 exit | |
| 35 fi | |
| 36 | |
| 37 calcXmx () { | |
| 38 source "$DIR""/calcmem.sh" | |
| 39 setEnvironment | |
| 40 parseXmx "$@" | |
| 41 if [[ $set == 1 ]]; then | |
| 42 return | |
| 43 fi | |
| 44 freeRam 31000m 84 | |
| 45 z="-Xmx${RAM}m" | |
| 46 z2="-Xms${RAM}m" | |
| 47 } | |
| 48 calcXmx "$@" | |
| 49 | |
| 50 khist() { | |
| 51 local CMD="java $EA $EOOM $z $z2 -cp $CP jgi.KmerNormalize bits=32 ecc=f passes=1 keepall dr=f prefilter hist=stdout minprob=0 minqual=0 mindepth=0 minkmers=1 hashes=3 $@" | |
| 52 echo $CMD >&2 | |
| 53 eval $CMD | |
| 54 } | |
| 55 | |
| 56 khist "$@" |