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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified October 3, 2017
Description: Creates polymer sequences.
Can be used in conjunction with mutate.sh to generate low-complexity sequence.
Usage: makepolymers.sh out=<output file> k=<repeat length> minlen=<sequence length>
I/O parameters:
out=<file> Output genome.
overwrite=f (ow) Set to false to force the program to abort rather than
overwrite an existing file.
Processing parameters:
k=1 Length of repeating polymeric units.
To generate a sweep of multiple values of k,
specify both mink and maxk.
minlen=31 Ensure sequences are at least this long.
Specifically, minlen=X will ensure sequences are long enough
that all possible kmers of length X are present.
Java Parameters:
-Xmx This will set Java's memory usage, overriding autodetection.
-Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
specify 200 megs. The max is typically 85% of physical memory.
-eoom This flag will cause the process to exit if an out-of-memory
exception occurs. Requires Java 8u92+.
-da Disable assertions.
Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
"
}
#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/"
z="-Xmx4g"
z2="-Xms4g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 4000m 84
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
makepolymers() {
local CMD="java $EA $EOOM $z $z2 -cp $CP jgi.MakePolymers $@"
echo $CMD >&2
eval $CMD
}
makepolymers "$@"
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