jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Last modified February 13, 2020
jpayne@69: 
jpayne@69: Description:  Wrapper for BBMap to allow multiple input and output files for the same reference.
jpayne@69: 
jpayne@69: To index:                 bbwrap.sh ref=<reference fasta>
jpayne@69: To map:                   bbwrap.sh in=<file,file,...> out=<file,file,...>
jpayne@69: To map without an index:  bbwrap.sh ref=<reference fasta> in=<file,file,...> out=<file,file,...> nodisk
jpayne@69: To map pairs and singletons and output them into the same file:
jpayne@69: bbwrap.sh in1=read1.fq,singleton.fq in2=read2.fq,null out=mapped.sam append
jpayne@69: 
jpayne@69: BBWrap will not work with stdin and stdout, or histogram output.
jpayne@69: 
jpayne@69: Other Parameters:
jpayne@69: 
jpayne@69: in=<file,file>  Input sequences to map.
jpayne@69: inlist=<fofn>   Alternately, input and output can be a file of filenames,
jpayne@69:                 one line per file, using the flag inlist, outlist, outmlist,
jpayne@69:                 in2list, etc.
jpayne@69: mapper=bbmap    Select mapper.  May be BBMap, BBMapPacBio, 
jpayne@69:                 or BBMapPacBioSkimmer.
jpayne@69: append=f        Append to files rather than overwriting them.  
jpayne@69:                 If append is enabled, and there is exactly one output file,
jpayne@69:                 all output will be written to that file.
jpayne@69: 
jpayne@69: ***** All BBMap parameters can be used; see bbmap.sh for more details. *****
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="-Xmx1g"
jpayne@69: z2="-Xms1g"
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: 	if [[ $set == 1 ]]; then
jpayne@69: 		return
jpayne@69: 	fi
jpayne@69: 	freeRam 3200m 84
jpayne@69: 	z="-Xmx${RAM}m"
jpayne@69: 	z2="-Xms${RAM}m"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: bbwrap() {
jpayne@69: 	local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP align2.BBWrap build=1 overwrite=true fastareadlen=500 $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: bbwrap "$@"