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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified July 31, 2018
Description: Subsamples reads to reach a target unique kmer limit.
Differences between versions:
kmerlimit.sh uses 1 pass and outputs all reads until a limit is hit,
meaning the input reads should be in random order with respect to sequence.
kmerlimit2.sh uses 2 passes and randomly subsamples from the file, so
it works with reads in any order.
Usage: kmerlimit2.sh in=<input file> out=<output file> limit=<number>
Standard parameters:
in=<file> Primary input, or read 1 input.
in2=<file> Read 2 input if reads are in two files.
out=<file> Primary output, or read 1 output.
out2=<file> Read 2 output if reads are in two files.
overwrite=t (ow) Set to false to force the program to abort rather than
overwrite an existing file.
ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression
level; lower compression is faster.
Processing parameters:
k=31 Kmer length, 1-32.
limit= The number of unique kmers to produce.
mincount=1 Ignore kmers seen fewer than this many times.
minqual=0 Ignore bases with quality below this.
minprob=0.2 Ignore kmers with correctness probability below this.
trials=25 Simulation trials.
seed=-1 Set to a positive number for deterministic output.
maxlen=50m Max length of a temp array used in simulation.
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="-Xmx1000m"
z2="-Xms1000m"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
}
calcXmx "$@"
kmerlimit2() {
local CMD="java $EA $EOOM $z -cp $CP sketch.KmerLimit2 $@"
echo $CMD >&2
eval $CMD
}
kmerlimit2 "$@"
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