jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified October 16, 2015
jpayne@69: 
jpayne@69: Description: Counts the number of reads with each barcode.
jpayne@69: 
jpayne@69: Usage:   countbarcodes.sh in=<file> counts=<file>
jpayne@69: 
jpayne@69: Input may be stdin or a fasta or fastq file, raw or gzipped.
jpayne@69: If you pipe via stdin/stdout, please include the file type; e.g. for gzipped fasta input, set in=stdin.fa.gz
jpayne@69: 
jpayne@69: Input parameters:
jpayne@69: in=<file>           Input reads, whose names end in a colon then barcode.
jpayne@69: counts=<file>       Output of counts.
jpayne@69: interleaved=auto    (int) If true, forces fastq input to be paired and interleaved.
jpayne@69: qin=auto            ASCII offset for input quality.  May be 33 (Sanger), 64 (Illumina), or auto.
jpayne@69: unpigz=t            Use pigz to decompress.
jpayne@69: expected=           Comma-delimited list of expected bar codes.
jpayne@69: valid=              Comma-delimited list of valid bar codes.
jpayne@69: countundefined=t    Count barcodes that contain non-ACGT symbols.
jpayne@69: printheader=t       Print a header.
jpayne@69: maxrows=-1          Optionally limit the number of rows printed.
jpayne@69: 
jpayne@69: Output parameters:
jpayne@69: out=<file>          Write bar codes and counts here.  'out=stdout' will pipe to standard out.
jpayne@69: 
jpayne@69: Java Parameters:
jpayne@69: -Xmx                This will set Java's memory usage, overriding autodetection.
jpayne@69:                     -Xmx20g will 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
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="-Xmx200m"
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: countbarcodes() {
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP jgi.CountBarcodes $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: countbarcodes "$@"