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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified February 17, 2015
Description: Filters barcodes by quality, and generates quality histograms.
Usage: filterbarcodes.sh in=<file> out=<file> maq=<integer>
Input parameters:
in=<file> Reads that have already been muxed with barcode qualities using mergebarcodes.sh.
int=auto (interleaved) If true, forces fastq input to be paired and interleaved.
qin=auto ASCII offset for input quality. May be 33 (Sanger), 64 (Illumina), or auto.
Output parameters:
out=<file> Write filtered reads here. 'out=stdout.fq' will pipe to standard out.
cor=<file> Correlation between read and index qualities.
bqhist=<file> Barcode quality histogram by position.
baqhist=<file> Barcode average quality histogram.
bmqhist=<file> Barcode min quality histogram.
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.
fastawrap=80 Length of lines in fasta output.
qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input).
maq=0 Filter reads with barcode average quality less than this.
mmq=0 Filter reads with barcode minimum quality less than this.
Other parameters:
pigz=t Use pigz to compress. If argument is a number, that will set the number of pigz threads.
unpigz=t Use pigz to decompress.
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 "$@"
}
calcXmx "$@"
filterbarcodes() {
local CMD="java $EA $EOOM $z -cp $CP jgi.CorrelateBarcodes $@"
echo $CMD >&2
eval $CMD
}
filterbarcodes "$@"
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