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#!/bin/bash
usage(){
echo "
bbmerge-auto.sh is a wrapper for BBMerge that attempts to use all available
memory, instead of a fixed amount. This is for use with the Tadpole options
of error-correction (ecct) and extension, which require more memory.
For merging by overlap only, please use bbmerge.sh. If you set memory
manually with the -Xmx flag, bbmerge.sh and bbmerge-auto.sh are equivalent.
For information about usage and parameters, please run bbmerge.sh.
"
}
#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="-Xmx14g"
z2="-Xms14g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 15000m 84
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
function merge() {
local CMD="java $EA $EOOM $z $z2 $JNI -cp $CP jgi.BBMerge $@"
echo $CMD >&2
eval $CMD
}
merge "$@"
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