jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified December 19, 2018
jpayne@69: Description:  Generates a length histogram of input reads.
jpayne@69: 
jpayne@69: Usage:	readlength.sh in=<input file>
jpayne@69: 
jpayne@69: in=<file>    	The 'in=' flag is needed only if the input file is not the first parameter.  'in=stdin.fq' will pipe from standard in.
jpayne@69: in2=<file>   	Use this if 2nd read of pairs are in a different file.
jpayne@69: out=<file>   	Write the histogram to this file.  Default is stdout.
jpayne@69: bin=10       	Set the histogram bin size.
jpayne@69: max=80000    	Set the max read length to track.
jpayne@69: round=f      	Places reads in the closest bin, rather than the highest bin of at least readlength.
jpayne@69: nzo=t        	(nonzeroonly) Do not print empty bins.
jpayne@69: reads=-1     	If nonnegative, stop after this many reads.
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: 
jpayne@69: z="-Xmx400m"
jpayne@69: z2="-Xms400m"
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 "$@"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: stats() {
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP jgi.MakeLengthHistogram $@"
jpayne@69: #	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: stats "$@"