jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified August 9, 2018
jpayne@69: 
jpayne@69: Description:  Generates statistics about flowcell positions.
jpayne@69: 
jpayne@69: Usage:	plotflowcell.sh in=<input> out=<output>
jpayne@69: 
jpayne@69: Input parameters:
jpayne@69: in=<file>           Primary input file.
jpayne@69: in2=<file>          Second input file for paired reads in two files.
jpayne@69: indump=<file>       Specify an already-made dump file to use instead of
jpayne@69:                     analyzing the input reads.
jpayne@69: reads=-1            Process this number of reads, then quit (-1 means all).
jpayne@69: interleaved=auto    Set true/false to override autodetection of the
jpayne@69:                     input file as paired interleaved.
jpayne@69: 
jpayne@69: Output parameters:
jpayne@69: out=<file>          Output file for filtered reads.
jpayne@69: dump=<file>         Write a summary of quality information by coordinates.
jpayne@69: 
jpayne@69: Tile parameters:
jpayne@69: xsize=500           Initial width of micro-tiles.
jpayne@69: ysize=500           Initial height of micro-tiles.
jpayne@69: size=               Allows setting xsize and ysize tot he same value.
jpayne@69: target=800          Iteratively increase the size of micro-tiles until they
jpayne@69:                     contain an average of at least this number of reads.
jpayne@69: 
jpayne@69: Other parameters:
jpayne@69: trimq=-1            If set to a positive number, trim reads to that quality
jpayne@69:                     level instead of filtering them.
jpayne@69: qtrim=r             If trimq is positive, to quality trimming on this end
jpayne@69:                     of the reads.  Values are r, l, and rl for right,
jpayne@69:                     left, and both ends.
jpayne@69: 
jpayne@69: Java Parameters:
jpayne@69: -Xmx                This will set Java's memory usage, overriding autodetection.
jpayne@69:                     -Xmx20g will specify 20 GB of RAM; -Xmx200m will specify 
jpayne@69:                     200 MB.  The max is typically 85% of physical memory.
jpayne@69: -eoom               This flag will cause the process to exit if an
jpayne@69:                     out-of-memory 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: 
jpayne@69: z="-Xmx8g"
jpayne@69: z2="-Xms8g"
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 [[ $set == 1 ]]; then
jpayne@69: 	return
jpayne@69: 	fi
jpayne@69: 	freeRam 3200m 84
jpayne@69: 	z="-Xmx${RAM}m"
jpayne@69: 	z2="-Xms${RAM}m"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: plotflowcell() {
jpayne@69: 	local CMD="java $EA $EOOM $z $z2 -cp $CP hiseq.PlotFlowCell $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: plotflowcell "$@"