Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/dedupe2.sh @ 69:33d812a61356

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 17:55:14 -0400
parents
children
comparison
equal deleted inserted replaced
67:0e9998148a16 69:33d812a61356
1 #!/bin/bash
2
3 usage(){
4 echo "
5 Written by Brian Bushnell and Jonathan Rood
6 Last modified September 15, 2015
7
8 Dedupe2 is identical to Dedupe except it supports hashing unlimited kmer
9 prefixes and suffixes per sequence. Dedupe supports at most 2 of each,
10 but uses slightly more memory. You can manually set the number of kmers to
11 hash per read with the numaffixmaps (nam) flag. Dedupe will automatically
12 call Dedupe2 if necessary (if nam=3 or higher) so this script is no longer
13 necessary.
14
15 For documentation, please consult dedupe.sh; syntax is identical.
16 "
17 }
18
19 #This block allows symlinked shellscripts to correctly set classpath.
20 pushd . > /dev/null
21 DIR="${BASH_SOURCE[0]}"
22 while [ -h "$DIR" ]; do
23 cd "$(dirname "$DIR")"
24 DIR="$(readlink "$(basename "$DIR")")"
25 done
26 cd "$(dirname "$DIR")"
27 DIR="$(pwd)/"
28 popd > /dev/null
29
30 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
31 CP="$DIR""current/"
32 JNI="-Djava.library.path=""$DIR""jni/"
33 JNI=""
34
35 z="-Xmx1g"
36 z2="-Xms1g"
37 set=0
38
39 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
40 usage
41 exit
42 fi
43
44 calcXmx () {
45 source "$DIR""/calcmem.sh"
46 setEnvironment
47 parseXmx "$@"
48 if [[ $set == 1 ]]; then
49 return
50 fi
51 freeRam 3200m 84
52 z="-Xmx${RAM}m"
53 z2="-Xms${RAM}m"
54 }
55 calcXmx "$@"
56
57 dedupe() {
58 local CMD="java $JNI $EA $EOOM $z $z2 -cp $CP jgi.Dedupe2 $@"
59 echo $CMD >&2
60 eval $CMD
61 }
62
63 dedupe "$@"