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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified July 16, 2018
Description: Compresses sequence data into a fasta file containing each kmer
exactly once. Allows arbitrary kmer set operations via multiple passes.
Usage: kcompress.sh in=<reads> out=<contigs> min=<1> max=<2147483647>
Input parameters:
in=<file> Primary input file for reads to use as kmer data.
in2=<file> Second input file for paired data.
reads=-1 Only process this number of reads, then quit (-1 means all).
Output parameters:
out=<file> Write contigs (in contig mode).
showstats=t Print assembly statistics after writing contigs.
fuse=0 Fuse output sequences into chunks at least this long,
padded with 1 N between sequences.
Prefiltering parameters:
prefilter=0 If set to a positive integer, use a countmin sketch
to ignore kmers with depth of that value or lower.
prehashes=2 Number of hashes for prefilter.
prefiltersize=0.2 (pff) Fraction of memory to use for prefilter.
minprobprefilter=t (mpp) Use minprob for the prefilter.
prepasses=1 Use this many prefiltering passes; higher be more thorough
if the filter is very full. Set to 'auto' to iteratively
prefilter until the remaining kmers will fit in memory.
Hashing parameters:
k=31 Kmer length (1 to 31).
prealloc=t Pre-allocate memory rather than dynamically growing;
faster and more memory-efficient. A float fraction (0-1)
may be specified; default is 1.
minprob=0.5 Ignore kmers with overall probability of correctness below this.
minprobmain=t (mpm) Use minprob for the primary kmer counts.
threads=X Spawn X threads (default is number of logical processors).
Assembly parameters:
mincount=1 (min) Only retain kmers that occur at least this many times.
maxcount=BIG (max) Only retain kmers that occur at most this many times.
requiresamecount (rsc) Only build contigs from kmers with exactly the same count.
rcomp=t Store forward and reverse kmers together. Setting this to
false will only use forward kmers.
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.
"
}
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="-Xmx14g"
z2="-Xms14g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 15000m 84
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
kcompress() {
local CMD="java $EA $EOOM $z $z2 -cp $CP assemble.KmerCompressor $@"
echo $CMD >&2
eval $CMD
}
kcompress "$@"
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