cutprimers.sh

#!/bin/bash

usage(){
echo "
Written by Brian Bushnell
Last modified May 15, 2018

Description:  Cuts out sequences between primers identified in sam files.
Intended for use with sam files generated by msa.sh; one sam file for the
forward primer, and one for the reverse primer.

Usage:	cutprimers.sh in=<file> out=<file> sam1=<file> sam2=<file>

Parameters:

in=<file>       File containing reads. in=stdin.fa will pipe from stdin.
out=<file>      Output sequences. out=stdout will pipe to stdout.
sam1=<file>     Sam file containing mapped locations of primer sequence 1.
sam2=<file>     Sam file containing mapped locations of primer sequence 2.
fake=t          Output 1bp 'N' reads in cases where there is no primer.
include=f       Include the flanking primer sequences in output.

Java Parameters:

-Xmx            This will set Java's memory usage, overriding automatic
                memory detection. -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.
For documentation and the latest version, visit: https://bbmap.org
"
}

if [ -z "$1" ] || [ "$1" = "-h" ] || [ "$1" = "--help" ]; then
	usage
	exit
fi

resolveSymlinks(){
	SCRIPT="$(cd "$(dirname "$0")" && pwd)/$(basename "$0")"
	while [ -h "$SCRIPT" ]; do
		DIR="$(dirname "$SCRIPT")"
		SCRIPT="$(readlink "$SCRIPT")"
		[ "${SCRIPT#/}" = "$SCRIPT" ] && SCRIPT="$DIR/$SCRIPT"
	done
	DIR="$(cd "$(dirname "$SCRIPT")" && pwd)"
	if [ -f "$DIR/bbtools.jar" ]; then
		CP="$DIR/bbtools.jar"
	else
		CP="$DIR/current/"
	fi
}

setEnv(){
	. "$DIR/javasetup.sh"
	. "$DIR/memdetect.sh"

	parseJavaArgs "--xmx=1g" "--xms=1g" "--percent=42" "--mode=auto" "$@"
	setEnvironment
}

launch() {
	CMD="java $EA $EOOM $SIMD $XMX $XMS -cp $CP jgi.CutPrimers $@"
	echo "$CMD" >&2
	eval $CMD
}

resolveSymlinks
setEnv "$@"
launch "$@"