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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified August 1, 2016
Description: Generates a kmer uniqueness histogram, binned by file position.
There are 3 columns for single reads, 6 columns for paired:
count number of reads or pairs processed
r1_first percent unique 1st kmer of read 1
r1_rand percent unique random kmer of read 1
r2_first percent unique 1st kmer of read 2
r2_rand percent unique random kmer of read 2
pair percent unique concatenated kmer from read 1 and 2
Please read bbmap/docs/guides/CalcUniquenessGuide.txt for more information.
Usage: bbcountunique.sh in=<input> out=<output>
Input parameters:
in2=null Second input file for paired reads
interleaved=auto Set true/false to override autodetection of the input file as paired interleaved.
samplerate=1 Set to below 1 to sample a fraction of input reads.
reads=-1 Only process this number of reads, then quit (-1 means all)
Output parameters:
out=<file> File for output stats
Processing parameters:
k=25 Kmer length (range 1-31).
interval=25000 Print one line to the histogram per this many reads.
cumulative=f Show cumulative numbers rather than per-interval numbers.
percent=t Show percentages of unique reads.
count=f Show raw counts of unique reads.
printlastbin=f (plb) Print a line for the final undersized bin.
minprob=0 Ignore kmers with a probability of correctness below this (based on q-scores).
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="-Xmx1g"
z2="-Xms1g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 3200m 84
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
bbcountunique() {
local CMD="java $EA $EOOM $z $z2 -cp $CP jgi.CalcUniqueness $@"
echo $CMD >&2
eval $CMD
}
bbcountunique "$@"
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