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