#!/bin/bash

usage(){
echo "
Written by Brian Bushnell
Last modified May 2, 2017

Description:  Remove Smart Bell adapters from PacBio reads.

Usage:        removesmartbell in=<input> out=<output> split=t

Input may be fasta or fastq, compressed or uncompressed (not H5 files).

Parameters:
in=file         Specify the input file, or stdin.
out=file        Specify the output file, or stdout.
adapter=        Specify the adapter sequence (default is normal SmrtBell).
split=t         'split=t' splits reads at adapters;
                'split=f' masks adapters with X symbols.

Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
"
}

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="-Xmx400m"
EA="-ea"
EOOM=""
set=0

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

calcXmx () {
	source "$DIR""/calcmem.sh"
	parseXmx "$@"
}
calcXmx "$@"

removesmartbell() {
	if [[ $SHIFTER_RUNTIME == 1 ]]; then
		#Ignore NERSC_HOST
		shifter=1
	elif [[ $NERSC_HOST == genepool ]]; then
		module unload oracle-jdk
		module load oracle-jdk/1.8_144_64bit
		module load pigz
	elif [[ $NERSC_HOST == denovo ]]; then
		module unload java
		module load java/1.8.0_144
		module load pigz
	elif [[ $NERSC_HOST == cori ]]; then
		module use /global/common/software/m342/nersc-builds/denovo/Modules/jgi
		module use /global/common/software/m342/nersc-builds/denovo/Modules/usg
		module unload java
		module load java/1.8.0_144
		module load pigz
	fi
	local CMD="java $EA $EOOM $z -cp $CP pacbio.RemoveAdapters2 $@"
	echo $CMD >&2
	eval $CMD
}

removesmartbell "$@"
