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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified February 27, 2017
Description: Prints sequence gc content once per interval.
Usage: plotgc.sh in=<input file> out=<output file>
Parameters:
in=<file> Input file. in=stdin.fa will pipe from stdin.
out=<file> Output file. out=stdout will pipe to stdout.
interval=1000 Interval length.
offset=0 Position offset. For 1-based indexing use offset=1.
psb=t (printshortbins) Print gc content for the last bin of a contig
even when shorter than interval.
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/"
JNI="-Djava.library.path=""$DIR""jni/"
JNI=""
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 [[ $set == 1 ]]; then
return
fi
freeRam 1400m 42
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
plotgc() {
local CMD="java $EA $EOOM $z $z2 -cp $CP driver.PlotGC $@"
echo $CMD >&2
eval $CMD
}
plotgc "$@"
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