Mercurial > repos > rliterman > csp2
comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/idmatrix.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 November 25, 2014 | |
| 7 | |
| 8 Description: Generates an identity matrix via all-to-all alignment. | |
| 9 | |
| 10 *** WARNING: This program may produce incorrect results in some cirumstances. | |
| 11 *** It is not advisable to use until fixed. | |
| 12 | |
| 13 Usage: idmatrix.sh in=<file> out=<file> | |
| 14 | |
| 15 Parameters: | |
| 16 in=<file> File containing reads. in=stdin.fa will pipe from stdin. | |
| 17 out=<file> Matrix output. out=stdout will pipe to stdout. | |
| 18 threads=auto (t) Set number of threads to use; default is number of | |
| 19 logical processors. | |
| 20 percent=f Output identity as percent rather than a fraction. | |
| 21 edits= Allow at most this much edit distance. Default is the | |
| 22 length of the longest input sequence. Lower is faster. | |
| 23 width= Alignment bandwidth, lower is faster. Default: 2*edits+1. | |
| 24 usejni=f (jni) Do alignments faster, in C code. Requires | |
| 25 compiling the C code; details are in /jni/README.txt. | |
| 26 | |
| 27 Java Parameters: | |
| 28 -Xmx This will set Java's memory usage, overriding automatic | |
| 29 memory detection. -Xmx20g will specify | |
| 30 20 gigs of RAM, and -Xmx200m will specify 200 megs. | |
| 31 The max is typically 85% of physical memory. | |
| 32 -eoom This flag will cause the process to exit if an out-of-memory | |
| 33 exception occurs. Requires Java 8u92+. | |
| 34 -da Disable assertions. | |
| 35 | |
| 36 Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems. | |
| 37 " | |
| 38 } | |
| 39 | |
| 40 #This block allows symlinked shellscripts to correctly set classpath. | |
| 41 pushd . > /dev/null | |
| 42 DIR="${BASH_SOURCE[0]}" | |
| 43 while [ -h "$DIR" ]; do | |
| 44 cd "$(dirname "$DIR")" | |
| 45 DIR="$(readlink "$(basename "$DIR")")" | |
| 46 done | |
| 47 cd "$(dirname "$DIR")" | |
| 48 DIR="$(pwd)/" | |
| 49 popd > /dev/null | |
| 50 | |
| 51 #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/" | |
| 52 CP="$DIR""current/" | |
| 53 JNI="-Djava.library.path=""$DIR""jni/" | |
| 54 JNI="" | |
| 55 | |
| 56 z="-Xmx2g" | |
| 57 z2="-Xms2g" | |
| 58 set=0 | |
| 59 | |
| 60 if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then | |
| 61 usage | |
| 62 exit | |
| 63 fi | |
| 64 | |
| 65 calcXmx () { | |
| 66 source "$DIR""/calcmem.sh" | |
| 67 setEnvironment | |
| 68 parseXmx "$@" | |
| 69 if [[ $set == 1 ]]; then | |
| 70 return | |
| 71 fi | |
| 72 freeRam 3200m 84 | |
| 73 z="-Xmx${RAM}m" | |
| 74 z2="-Xms${RAM}m" | |
| 75 } | |
| 76 calcXmx "$@" | |
| 77 | |
| 78 idmatrix() { | |
| 79 local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP jgi.IdentityMatrix $@" | |
| 80 echo $CMD >&2 | |
| 81 eval $CMD | |
| 82 } | |
| 83 | |
| 84 idmatrix "$@" |