jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified February 5, 2020
jpayne@69: 
jpayne@69: Description:  Aligns a query sequence to reference sequences.
jpayne@69: Outputs the best matching position per reference sequence.
jpayne@69: If there are multiple queries, only the best-matching query will be used.
jpayne@69: MSA in this context stands for MultiStateAligner, not Multiple Sequence Alignment.
jpayne@69: 
jpayne@69: Usage:
jpayne@69: msa.sh in=<file> out=<file> literal=<literal,literal,...>
jpayne@69: or
jpayne@69: msa.sh in=<file> out=<file> ref=<lfile>
jpayne@69: 
jpayne@69: Parameters:
jpayne@69: in=<file>       File containing reads.
jpayne@69: out=<file>      Sam output file.
jpayne@69: literal=        A sequence of bases to match, or a comma-delimited list.
jpayne@69: ref=<file>      A fasta file of bases to match.  Please set either ref
jpayne@69:                 or literal, not both.
jpayne@69: rcomp=t         Also look for reverse-complements of the sequences.
jpayne@69: addr=f          Add r_ prefix to reverse-complemented alignments.
jpayne@69: replicate=f     Make copies of sequences with undefined bases for every
jpayne@69:                 possible combination.  For example, ATN would expand to
jpayne@69:                 ATA, ATC, ATG, and ATT.
jpayne@69: cutoff=0        Ignore alignments with identity below this (range 0-1).
jpayne@69: swap=f          Swap the reference and query; e.g., report read alignments
jpayne@69:                 to the reference instead of reference alignments to the reads.
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: 
jpayne@69: z="-Xmx1g"
jpayne@69: z2="-Xms1g"
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 [[ $set == 1 ]]; then
jpayne@69: 		return
jpayne@69: 	fi
jpayne@69: 	freeRam 2000m 84
jpayne@69: 	z="-Xmx${RAM}m"
jpayne@69: 	z2="-Xms${RAM}m"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: msa() {
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP jgi.FindPrimers $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: msa "$@"