jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified November 25, 2014
jpayne@69: 
jpayne@69: Description:  Generates an identity matrix via all-to-all alignment.
jpayne@69: 
jpayne@69: *** WARNING: This program may produce incorrect results in some cirumstances.
jpayne@69: *** It is not advisable to use until fixed.
jpayne@69: 
jpayne@69: Usage:	idmatrix.sh in=<file> out=<file>
jpayne@69: 
jpayne@69: Parameters:
jpayne@69: in=<file>       File containing reads. in=stdin.fa will pipe from stdin.
jpayne@69: out=<file>      Matrix output. out=stdout will pipe to stdout.
jpayne@69: threads=auto    (t) Set number of threads to use; default is number of 
jpayne@69:                 logical processors.
jpayne@69: percent=f       Output identity as percent rather than a fraction.
jpayne@69: edits=          Allow at most this much edit distance.  Default is the
jpayne@69:                 length of the longest input sequence. Lower is faster.
jpayne@69: width=          Alignment bandwidth, lower is faster.  Default: 2*edits+1.
jpayne@69: usejni=f        (jni) Do alignments faster, in C code.  Requires 
jpayne@69:                 compiling the C code; details are in /jni/README.txt.
jpayne@69: 
jpayne@69: Java Parameters:
jpayne@69: -Xmx            This will set Java's memory usage, overriding automatic
jpayne@69:                 memory detection. -Xmx20g will specify 
jpayne@69:                 20 gigs of RAM, and -Xmx200m will specify 200 megs.  
jpayne@69:                 The max is typically 85% of physical memory.
jpayne@69: -eoom           This flag will cause the process to exit if an out-of-memory
jpayne@69:                 exception occurs.  Requires Java 8u92+.
jpayne@69: -da             Disable assertions.
jpayne@69: 
jpayne@69: Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
jpayne@69: "
jpayne@69: }
jpayne@69: 
jpayne@69: #This block allows symlinked shellscripts to correctly set classpath.
jpayne@69: pushd . > /dev/null
jpayne@69: DIR="${BASH_SOURCE[0]}"
jpayne@69: while [ -h "$DIR" ]; do
jpayne@69:   cd "$(dirname "$DIR")"
jpayne@69:   DIR="$(readlink "$(basename "$DIR")")"
jpayne@69: done
jpayne@69: cd "$(dirname "$DIR")"
jpayne@69: DIR="$(pwd)/"
jpayne@69: popd > /dev/null
jpayne@69: 
jpayne@69: #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
jpayne@69: CP="$DIR""current/"
jpayne@69: JNI="-Djava.library.path=""$DIR""jni/"
jpayne@69: JNI=""
jpayne@69: 
jpayne@69: z="-Xmx2g"
jpayne@69: z2="-Xms2g"
jpayne@69: set=0
jpayne@69: 
jpayne@69: if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
jpayne@69: 	usage
jpayne@69: 	exit
jpayne@69: fi
jpayne@69: 
jpayne@69: calcXmx () {
jpayne@69: 	source "$DIR""/calcmem.sh"
jpayne@69: 	setEnvironment
jpayne@69: 	parseXmx "$@"
jpayne@69: 	if [[ $set == 1 ]]; then
jpayne@69: 		return
jpayne@69: 	fi
jpayne@69: 	freeRam 3200m 84
jpayne@69: 	z="-Xmx${RAM}m"
jpayne@69: 	z2="-Xms${RAM}m"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: idmatrix() {
jpayne@69: 	local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP jgi.IdentityMatrix $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: idmatrix "$@"