jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified February 27, 2017
jpayne@69: 
jpayne@69: Description:  Prints sequence gc content once per interval.
jpayne@69: 
jpayne@69: Usage:  plotgc.sh in=<input file> out=<output file>
jpayne@69: 
jpayne@69: Parameters:
jpayne@69: in=<file>       Input file. in=stdin.fa will pipe from stdin.
jpayne@69: out=<file>      Output file.  out=stdout will pipe to stdout.
jpayne@69: interval=1000   Interval length.
jpayne@69: offset=0        Position offset.  For 1-based indexing use offset=1.
jpayne@69: psb=t           (printshortbins) Print gc content for the last bin of a contig
jpayne@69:                 even when shorter than interval.
jpayne@69: 
jpayne@69: Java Parameters:
jpayne@69: 
jpayne@69: -Xmx            This will set Java's memory usage, overriding automatic
jpayne@69:                 memory detection. -Xmx20g will 
jpayne@69:                 specify 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: JNI="-Djava.library.path=""$DIR""jni/"
jpayne@69: JNI=""
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 [[ $set == 1 ]]; then
jpayne@69: 		return
jpayne@69: 	fi
jpayne@69: 	freeRam 1400m 42
jpayne@69: 	z="-Xmx${RAM}m"
jpayne@69: 	z2="-Xms${RAM}m"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: plotgc() {
jpayne@69: 	local CMD="java $EA $EOOM $z $z2 -cp $CP driver.PlotGC $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: plotgc "$@"