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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified March 24, 2020
Description: Estimates cardinality of unique kmers in sequence data.
See also kmercountmulti.sh.
Usage: loglog.sh in=<file> k=<31>
Parameters:
in=<file> (in1) Input file, or comma-delimited list of files.
in2=<file> ptional second file for paired reads.
k=31 Use this kmer length for counting.
buckets=2048 Use this many buckets for counting; higher decreases
variance, for large datasets. Must be a power of 2.
seed=-1 Use this seed for hash functions. A negative number forces
a random seed.
minprob=0 Set to a value between 0 and 1 to exclude kmers with a lower
probability of being correct.
Shortcuts:
The # symbol will be substituted for 1 and 2.
For example:
loglog.sh in=read#.fq
...is equivalent to:
loglog.sh in1=read1.fq in2=read2.fq
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.
Supported input formats are fastq, fasta, scarf, sam, and bam.
Supported compression formats are gzip and bz2.
To read from stdin, set 'in=stdin'. The format should be specified with an extension, like 'in=stdin.fq.gz'
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 loglog() {
local CMD="java $EA $EOOM $z -cp $CP cardinality.LogLogWrapper $@"
echo $CMD >&2
eval $CMD
}
loglog "$@"
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