jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified March 6, 2015
jpayne@69: 
jpayne@69: Description:  Splits Nextera LMP libraries into subsets based on linker orientation:
jpayne@69: LMP, fragment, unknown, and singleton.
jpayne@69: Please read bbmap/docs/guides/SplitNexteraGuide.txt for more information.
jpayne@69: 
jpayne@69: Usage:  splitnextera.sh in=<file> out=<file> outf=<file> outu=<file> outs=<file>
jpayne@69: 
jpayne@69: For pairs in two files, use in1, in2, out1, out2, etc.
jpayne@69: 
jpayne@69: *** Note ***
jpayne@69: For maximal speed, before running splitnextera, the linkers can be replaced with a constant first.
jpayne@69: 
jpayne@69: In other words, you can either do this (which is slightly faster):
jpayne@69: bbduk.sh in=reads.fq out=replaced.fq ktmask=J k=19 hdist=1 mink=11 hdist2=0 literal=CTGTCTCTTATACACATCTAGATGTGTATAAGAGACAG
jpayne@69: splitnextera.sh in=replaced.fq out=longmate.fq outf=frag.fq outu=unknown.fq outs=singleton.fq
jpayne@69: 
jpayne@69: Or this:
jpayne@69: splitnextera.sh in=reads.fq out=longmate.fq outf=frag.fq outu=unknown.fq outs=singleton.fq mask=t
jpayne@69: 
jpayne@69: 
jpayne@69: I/O parameters:
jpayne@69: in=<file>       Input reads.  Set to 'stdin.fq' to read from stdin.
jpayne@69: out=<file>      Output for pairs with LMP orientation.
jpayne@69: outf=<file>     Output for pairs with fragment orientation.
jpayne@69: outu=<file>     Pairs with unknown orientation.
jpayne@69: outs=<file>     Singleton output.
jpayne@69: ow=f            (overwrite) Overwrites files that already exist.
jpayne@69: app=f           (append) Append to files that already exist.
jpayne@69: zl=4            (ziplevel) Set compression level, 1 (low) to 9 (max).
jpayne@69: int=f           (interleaved) Determines whether INPUT file is considered interleaved.
jpayne@69: qin=auto        ASCII offset for input quality.  May be 33 (Sanger), 64 (Illumina), or auto.
jpayne@69: qout=auto       ASCII offset for output quality.  May be 33 (Sanger), 64 (Illumina), or auto (same as input).
jpayne@69: 
jpayne@69: Processing Parameters:
jpayne@69: mask=f          Set to true if you did not already convert junctions to some symbol, and it will be done automatically.
jpayne@69: junction=J      Look for this symbol to designate the junction bases.
jpayne@69: innerlmp=f      Generate long mate pairs from the inner pair also, when the junction is found in both reads.
jpayne@69: rename=t        Rename read 2 of output when using single-ended input.
jpayne@69: minlength=40    (ml) Do not output reads shorter than this.
jpayne@69: merge=f         Attempt to merge overlapping reads before looking for junctions.
jpayne@69: testmerge=0.0   If nonzero, only merge reads if at least the fraction of input reads are mergable.
jpayne@69: 
jpayne@69: Sampling parameters:
jpayne@69: 
jpayne@69: reads=-1        Set to a positive number to only process this many INPUT reads (or pairs), then quit.
jpayne@69: samplerate=1    Randomly output only this fraction of reads; 1 means sampling is disabled.
jpayne@69: sampleseed=-1   Set to a positive number to use that prng seed for sampling (allowing deterministic sampling).
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="-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: function splitnextera() {
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP jgi.SplitNexteraLMP $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: splitnextera "$@"