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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified March 6, 2015
Description: Splits Nextera LMP libraries into subsets based on linker orientation:
LMP, fragment, unknown, and singleton.
Please read bbmap/docs/guides/SplitNexteraGuide.txt for more information.
Usage: splitnextera.sh in=<file> out=<file> outf=<file> outu=<file> outs=<file>
For pairs in two files, use in1, in2, out1, out2, etc.
*** Note ***
For maximal speed, before running splitnextera, the linkers can be replaced with a constant first.
In other words, you can either do this (which is slightly faster):
bbduk.sh in=reads.fq out=replaced.fq ktmask=J k=19 hdist=1 mink=11 hdist2=0 literal=CTGTCTCTTATACACATCTAGATGTGTATAAGAGACAG
splitnextera.sh in=replaced.fq out=longmate.fq outf=frag.fq outu=unknown.fq outs=singleton.fq
Or this:
splitnextera.sh in=reads.fq out=longmate.fq outf=frag.fq outu=unknown.fq outs=singleton.fq mask=t
I/O parameters:
in=<file> Input reads. Set to 'stdin.fq' to read from stdin.
out=<file> Output for pairs with LMP orientation.
outf=<file> Output for pairs with fragment orientation.
outu=<file> Pairs with unknown orientation.
outs=<file> Singleton output.
ow=f (overwrite) Overwrites files that already exist.
app=f (append) Append to files that already exist.
zl=4 (ziplevel) Set compression level, 1 (low) to 9 (max).
int=f (interleaved) Determines whether INPUT file is considered interleaved.
qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.
qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input).
Processing Parameters:
mask=f Set to true if you did not already convert junctions to some symbol, and it will be done automatically.
junction=J Look for this symbol to designate the junction bases.
innerlmp=f Generate long mate pairs from the inner pair also, when the junction is found in both reads.
rename=t Rename read 2 of output when using single-ended input.
minlength=40 (ml) Do not output reads shorter than this.
merge=f Attempt to merge overlapping reads before looking for junctions.
testmerge=0.0 If nonzero, only merge reads if at least the fraction of input reads are mergable.
Sampling parameters:
reads=-1 Set to a positive number to only process this many INPUT reads (or pairs), then quit.
samplerate=1 Randomly output only this fraction of reads; 1 means sampling is disabled.
sampleseed=-1 Set to a positive number to use that prng seed for sampling (allowing deterministic sampling).
Java Parameters:
-Xmx This will set Java's memory usage, overriding autodetection.
-Xmx20g will specify 20 gigs of RAM, and -Xmx200m will specify 200 megs.
The max is typically 85% of physical memory.
-eoom This flag will cause the process to exit if an out-of-memory
exception occurs. Requires Java 8u92+.
-da Disable assertions.
Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
"
}
#This block allows symlinked shellscripts to correctly set classpath.
pushd . > /dev/null
DIR="${BASH_SOURCE[0]}"
while [ -h "$DIR" ]; do
cd "$(dirname "$DIR")"
DIR="$(readlink "$(basename "$DIR")")"
done
cd "$(dirname "$DIR")"
DIR="$(pwd)/"
popd > /dev/null
#DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
CP="$DIR""current/"
z="-Xmx200m"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
}
calcXmx "$@"
function splitnextera() {
local CMD="java $EA $EOOM $z -cp $CP jgi.SplitNexteraLMP $@"
echo $CMD >&2
eval $CMD
}
splitnextera "$@"
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