jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified February 17, 2015
jpayne@69: 
jpayne@69: Description:  Concatenates barcodes and quality onto read names.
jpayne@69: 
jpayne@69: Usage:        mergebarcodes.sh in=<file> out=<file> barcode=<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: Optional parameters (and their defaults)
jpayne@69: 
jpayne@69: Input parameters:
jpayne@69: in=<file>       Input reads. 'in=stdin.fq' will pipe from standard in.
jpayne@69: bar=<file>      File containing barcodes.
jpayne@69: int=auto        (interleaved) 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: 
jpayne@69: Output parameters:
jpayne@69: out=<file>      Write muxed sequences here.  'out=stdout.fa' will pipe to standard out.
jpayne@69: overwrite=t     (ow) Set to false to force the program to abort rather than overwrite an existing file.
jpayne@69: ziplevel=2      (zl) Set to 1 (lowest) through 9 (max) to change compression level; lower compression is faster.
jpayne@69: qout=auto       ASCII offset for output quality.  May be 33 (Sanger), 64 (Illumina), or auto (same as input).
jpayne@69: 
jpayne@69: Other parameters:
jpayne@69: pigz=t          Use pigz to compress.  If argument is a number, that will set the number of pigz threads.
jpayne@69: unpigz=t        Use pigz to decompress.
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 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: 
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 [[ $set == 1 ]]; then
jpayne@69: 	return
jpayne@69: 	fi
jpayne@69: 	freeRam 3200m 84
jpayne@69: 	z="-Xmx${RAM}m"
jpayne@69: 	z2="-Xms${RAM}m"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: mergebarcodes() {
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP jgi.MergeBarcodes $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: mergebarcodes "$@"