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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified February 17, 2015
Description: Concatenates barcodes and quality onto read names.
Usage: mergebarcodes.sh in=<file> out=<file> barcode=<file>
Input may be stdin or a fasta or fastq file, raw or gzipped.
If you pipe via stdin/stdout, please include the file type; e.g. for gzipped fasta input, set in=stdin.fa.gz
Optional parameters (and their defaults)
Input parameters:
in=<file> Input reads. 'in=stdin.fq' will pipe from standard in.
bar=<file> File containing barcodes.
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 muxed sequences here. 'out=stdout.fa' will pipe to standard out.
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.
qout=auto ASCII offset for output quality. May be 33 (Sanger), 64 (Illumina), or auto (same as input).
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="-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${RAM}m"
}
calcXmx "$@"
mergebarcodes() {
local CMD="java $EA $EOOM $z -cp $CP jgi.MergeBarcodes $@"
echo $CMD >&2
eval $CMD
}
mergebarcodes "$@"
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