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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified October 16, 2015
Description: Counts the number of reads with each barcode.
Usage: countbarcodes.sh in=<file> counts=<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
Input parameters:
in=<file> Input reads, whose names end in a colon then barcode.
counts=<file> Output of counts.
interleaved=auto (int) 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.
unpigz=t Use pigz to decompress.
expected= Comma-delimited list of expected bar codes.
valid= Comma-delimited list of valid bar codes.
countundefined=t Count barcodes that contain non-ACGT symbols.
printheader=t Print a header.
maxrows=-1 Optionally limit the number of rows printed.
Output parameters:
out=<file> Write bar codes and counts here. 'out=stdout' will pipe to standard out.
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 "$@"
}
calcXmx "$@"
countbarcodes() {
local CMD="java $EA $EOOM $z -cp $CP barcode.CountBarcodes $@"
echo $CMD >&2
eval $CMD
}
countbarcodes "$@"
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