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#!/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 $CMD
}
bbwrap "$@"
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