Mercurial > repos > rliterman > csp2
annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/dedupe2.sh @ 69:33d812a61356
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
| author | jpayne |
|---|---|
| date | Tue, 18 Mar 2025 17:55:14 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| jpayne@69 | 1 #!/bin/bash |
| jpayne@69 | 2 |
| jpayne@69 | 3 usage(){ |
| jpayne@69 | 4 echo " |
| jpayne@69 | 5 Written by Brian Bushnell and Jonathan Rood |
| jpayne@69 | 6 Last modified September 15, 2015 |
| jpayne@69 | 7 |
| jpayne@69 | 8 Dedupe2 is identical to Dedupe except it supports hashing unlimited kmer |
| jpayne@69 | 9 prefixes and suffixes per sequence. Dedupe supports at most 2 of each, |
| jpayne@69 | 10 but uses slightly more memory. You can manually set the number of kmers to |
| jpayne@69 | 11 hash per read with the numaffixmaps (nam) flag. Dedupe will automatically |
| jpayne@69 | 12 call Dedupe2 if necessary (if nam=3 or higher) so this script is no longer |
| jpayne@69 | 13 necessary. |
| jpayne@69 | 14 |
| jpayne@69 | 15 For documentation, please consult dedupe.sh; syntax is identical. |
| jpayne@69 | 16 " |
| jpayne@69 | 17 } |
| jpayne@69 | 18 |
| jpayne@69 | 19 #This block allows symlinked shellscripts to correctly set classpath. |
| jpayne@69 | 20 pushd . > /dev/null |
| jpayne@69 | 21 DIR="${BASH_SOURCE[0]}" |
| jpayne@69 | 22 while [ -h "$DIR" ]; do |
| jpayne@69 | 23 cd "$(dirname "$DIR")" |
| jpayne@69 | 24 DIR="$(readlink "$(basename "$DIR")")" |
| jpayne@69 | 25 done |
| jpayne@69 | 26 cd "$(dirname "$DIR")" |
| jpayne@69 | 27 DIR="$(pwd)/" |
| jpayne@69 | 28 popd > /dev/null |
| jpayne@69 | 29 |
| jpayne@69 | 30 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" |
| jpayne@69 | 31 CP="$DIR""current/" |
| jpayne@69 | 32 JNI="-Djava.library.path=""$DIR""jni/" |
| jpayne@69 | 33 JNI="" |
| jpayne@69 | 34 |
| jpayne@69 | 35 z="-Xmx1g" |
| jpayne@69 | 36 z2="-Xms1g" |
| jpayne@69 | 37 set=0 |
| jpayne@69 | 38 |
| jpayne@69 | 39 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then |
| jpayne@69 | 40 usage |
| jpayne@69 | 41 exit |
| jpayne@69 | 42 fi |
| jpayne@69 | 43 |
| jpayne@69 | 44 calcXmx () { |
| jpayne@69 | 45 source "$DIR""/calcmem.sh" |
| jpayne@69 | 46 setEnvironment |
| jpayne@69 | 47 parseXmx "$@" |
| jpayne@69 | 48 if [[ $set == 1 ]]; then |
| jpayne@69 | 49 return |
| jpayne@69 | 50 fi |
| jpayne@69 | 51 freeRam 3200m 84 |
| jpayne@69 | 52 z="-Xmx${RAM}m" |
| jpayne@69 | 53 z2="-Xms${RAM}m" |
| jpayne@69 | 54 } |
| jpayne@69 | 55 calcXmx "$@" |
| jpayne@69 | 56 |
| jpayne@69 | 57 dedupe() { |
| jpayne@69 | 58 local CMD="java $JNI $EA $EOOM $z $z2 -cp $CP jgi.Dedupe2 $@" |
| jpayne@69 | 59 echo $CMD >&2 |
| jpayne@69 | 60 eval $CMD |
| jpayne@69 | 61 } |
| jpayne@69 | 62 |
| jpayne@69 | 63 dedupe "$@" |