#!/bin/bash

usage(){
echo "
Last modified February 13, 2020

Description:  Wrapper for BBMap to allow multiple input and output files for the same reference.

To index:                 bbwrap.sh ref=<reference fasta>
To map:                   bbwrap.sh in=<file,file,...> out=<file,file,...>
To map without an index:  bbwrap.sh ref=<reference fasta> in=<file,file,...> out=<file,file,...> nodisk
To map pairs and singletons and output them into the same file:
bbwrap.sh in1=read1.fq,singleton.fq in2=read2.fq,null out=mapped.sam append

BBWrap will not work with stdin and stdout, or histogram output.

Other Parameters:

in=<file,file>  Input sequences to map.
inlist=<fofn>   Alternately, input and output can be a file of filenames,
                one line per file, using the flag inlist, outlist, outmlist,
                in2list, etc.
mapper=bbmap    Select mapper.  May be BBMap, BBMapPacBio, 
                or BBMapPacBioSkimmer.
append=f        Append to files rather than overwriting them.  
                If append is enabled, and there is exactly one output file,
                all output will be written to that file.

***** All BBMap parameters can be used; see bbmap.sh for more details. *****
"
}

#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/"
JNI="-Djava.library.path=""$DIR""jni/"
JNI=""

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${RAM}m"
}
calcXmx "$@"

bbwrap() {
	local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP align2.BBWrap build=1 overwrite=true fastareadlen=500 $@"
	echo $CMD >&2
	eval $CMD
}

bbwrap "$@"