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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified March 25, 2025
Description: Makes vectors for QuickBin network training.
Usage: makequickbinvector.sh in=contigs.fa out=vector.txt cov=cov.txt lines=1m
Parameters:
in=<file> Assembly input; only required parameter.
cov=<file> Cov file generated by Quickbin from sam files.
out=<file> Output file.
lines=1m Lines to output.
rate=0.5 Fraction of vectors with positive results.
mincontig=200 Do not load contigs shorter than this.
minlen=0 Do not print comparisons where either contig is shorter
than this.
maxlen=2B Do not print comparisons where both contigs are longer
than this.
maxgcdif=1.0 Max allowed GC difference for output.
maxkmerdif=1.0 Max allowed TNF cosine difference for output.
maxdepthratio=1000.0 Max allowed depth ratio for output.
Java Parameters:
-Xmx This will set Java's memory usage, overriding autodetection.
-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="-Xmx4g"
z2="-Xms4g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 4000m 42
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
vector() {
local CMD="java $EA $EOOM $z -cp $CP bin.AllToAllVectorMaker $@"
echo $CMD >&2
eval $CMD
}
vector "$@"
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