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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified November 5, 2024
Description: Generates histograms from a tile dump.
Also works on other 2D numeric matrices with a header.
Output files are automatically named from the header columns.
Usage: plothist.sh in=<input file> bins=<number>
Parameters:
in=<file> Input dump file.
bins=1000 Bins per histogram.
overwrite=t (ow) Set to false to force the program to abort rather than
overwrite an existing file.
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="-Xmx300m"
z2="-Xms300m"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
}
calcXmx "$@"
plothist() {
local CMD="java $EA $EOOM $z $z2 -cp $CP hiseq.PlotHist $@"
echo $CMD >&2
eval $CMD
}
plothist "$@"
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