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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified November 25, 2014
Description: Generates an identity matrix via all-to-all alignment.
*** WARNING: This program may produce incorrect results in some cirumstances.
*** It is not advisable to use until fixed.
Usage: idmatrix.sh in=<file> out=<file>
Parameters:
in=<file> File containing reads. in=stdin.fa will pipe from stdin.
out=<file> Matrix output. out=stdout will pipe to stdout.
threads=auto (t) Set number of threads to use; default is number of
logical processors.
percent=f Output identity as percent rather than a fraction.
edits= Allow at most this much edit distance. Default is the
length of the longest input sequence. Lower is faster.
width= Alignment bandwidth, lower is faster. Default: 2*edits+1.
usejni=f (jni) Do alignments faster, in C code. Requires
compiling the C code; details are in /jni/README.txt.
Java Parameters:
-Xmx This will set Java's memory usage, overriding automatic
memory detection. -Xmx20g will specify
20 gigs of RAM, and -Xmx200m will specify 200 megs.
The max is typically 85% of physical memory.
-eoom This flag will cause the process to exit if an out-of-memory
exception occurs. Requires Java 8u92+.
-da Disable assertions.
Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
"
}
#This block allows symlinked shellscripts to correctly set classpath.
pushd . > /dev/null
DIR="${BASH_SOURCE[0]}"
while [ -h "$DIR" ]; do
cd "$(dirname "$DIR")"
DIR="$(readlink "$(basename "$DIR")")"
done
cd "$(dirname "$DIR")"
DIR="$(pwd)/"
popd > /dev/null
#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
CP="$DIR""current/"
JNI="-Djava.library.path=""$DIR""jni/"
JNI=""
z="-Xmx2g"
z2="-Xms2g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 3200m 84
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
idmatrix() {
local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP jgi.IdentityMatrix $@"
echo $CMD >&2
eval $CMD
}
idmatrix "$@"
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