jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified March 21, 2018
jpayne@69: 
jpayne@69: Description:  Converts sam/bam to fastq rapidly with multiple threads.
jpayne@69: bam files require samtools or sambamba in the path.
jpayne@69: 
jpayne@69: Usage:  streamsam.sh in=<file> out=<file>
jpayne@69: 
jpayne@69: Filtering parameters:
jpayne@69: minpos=         Ignore alignments not overlapping this range.
jpayne@69: maxpos=         Ignore alignments not overlapping this range.
jpayne@69: minmapq=        Ignore alignments with mapq below this.
jpayne@69: maxmapq=        Ignore alignments with mapq above this.
jpayne@69: contigs=        Comma-delimited list of contig names to include. These 
jpayne@69:                 should have no spaces, or underscores instead of spaces.
jpayne@69: mapped=t        Include mapped reads.
jpayne@69: unmapped=t      Include unmapped reads.
jpayne@69: secondary=f     Include secondary alignments.
jpayne@69: supplimentary=t Include supplimentary alignments.
jpayne@69: lengthzero=f    Include alignments without bases.
jpayne@69: invert=f        Invert sam filters.
jpayne@69: ordered=t       Keep reads in input order.  False is faster.
jpayne@69: ref=<file>      Optional reference file.
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: 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: streamsam() {
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP stream.SamStreamerWrapper $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: streamsam "$@"