jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified January 13, 2022
jpayne@69: Description:  Shreds sequences into shorter, potentially overlapping sequences.
jpayne@69: 
jpayne@69: Usage:	shred.sh in=<file> out=<file> length=<number> minlength=<number> overlap=<number>
jpayne@69: 
jpayne@69: in=<file>       Input sequences.
jpayne@69: out=<file>      Destination of output shreds.
jpayne@69: length=500      Desired length of shreds.
jpayne@69: minlength=1     Shortest allowed shred.  The last shred of each input sequence may be shorter than desired length.
jpayne@69: overlap=0       Amount of overlap between successive reads.
jpayne@69: reads=-1        If nonnegative, stop after this many input sequences.
jpayne@69: equal=f         Shred each sequence into subsequences of equal size of at most 'length', instead of a fixed size.
jpayne@69: median=0        If nonzero, randomly shred reads to a length with this median.
jpayne@69: variance=0      If median is nonzero, shred to lengths of median +-variance.
jpayne@69: qfake=30        Quality score, if using fastq output.
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="-Xmx1400m"
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.Shred $@"
jpayne@69: #	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: stats "$@"