jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell.
jpayne@69: Last modified March 5, 2018
jpayne@69: 
jpayne@69: Description:  Removes reads with barcodes containing non-ACGT bases.
jpayne@69: Read headers must be in standard Illumina format.
jpayne@69: 
jpayne@69: Usage:  removebadbarcodes.sh in=<file> out=<file>
jpayne@69: 
jpayne@69: Parameters:
jpayne@69: in=<file>       Input reads; required parameter.
jpayne@69: out=<file>      Destination for good reads; optional.
jpayne@69: ziplevel=2      (zl) Compression level for gzip output.
jpayne@69: pigz=f          Spawn a pigz (parallel gzip) process for faster 
jpayne@69:                 compression than Java.  Requires pigz to be installed.
jpayne@69: 
jpayne@69: Java Parameters:
jpayne@69: -Xmx            This will set Java's memory usage, overriding autodetection.
jpayne@69:                 -Xmx20g will specify 20 gigs of RAM, and -Xmx800m will specify 800 megs.
jpayne@69:                     The max is typically 85% of physical memory.
jpayne@69: -eoom           This flag will cause the process to exit if an out-of-memory
jpayne@69:                 exception occurs.  Requires Java 8u92+.
jpayne@69: -da             Disable assertions.
jpayne@69: 
jpayne@69: Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
jpayne@69: "
jpayne@69: }
jpayne@69: 
jpayne@69: #This block allows symlinked shellscripts to correctly set classpath.
jpayne@69: pushd . > /dev/null
jpayne@69: DIR="${BASH_SOURCE[0]}"
jpayne@69: while [ -h "$DIR" ]; do
jpayne@69:   cd "$(dirname "$DIR")"
jpayne@69:   DIR="$(readlink "$(basename "$DIR")")"
jpayne@69: done
jpayne@69: cd "$(dirname "$DIR")"
jpayne@69: DIR="$(pwd)/"
jpayne@69: popd > /dev/null
jpayne@69: 
jpayne@69: #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
jpayne@69: CP="$DIR""current/"
jpayne@69: JNI="-Djava.library.path=""$DIR""jni/"
jpayne@69: JNI=""
jpayne@69: 
jpayne@69: z="-Xmx200m"
jpayne@69: z2="-Xms200m"
jpayne@69: set=0
jpayne@69: 
jpayne@69: if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
jpayne@69: 	usage
jpayne@69: 	exit
jpayne@69: fi
jpayne@69: 
jpayne@69: calcXmx () {
jpayne@69: 	source "$DIR""/calcmem.sh"
jpayne@69: 	setEnvironment
jpayne@69: 	parseXmx "$@"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: 
jpayne@69: removebadbarcodes() {
jpayne@69: 	local CMD="java $EA $EOOM $z $z2 -cp $CP jgi.RemoveBadBarcodes $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: removebadbarcodes "$@"