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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified October 4, 2019
Description: Discards all but the best copy of a ribosomal gene per TaxID.
Gene sequences should be named like this: >tid|123|whatever
Sequences are selected based on the number of fully defined bases.
Usage: keepbest.sh in=<input file> out=<output file> rate=<float>
Input may be fasta or fastq, compressed or uncompressed.
Standard parameters:
in=<file> Input sequences.
out=<file> Output sequences.
overwrite=f (ow) Set to false to force the program to abort rather than
overwrite an existing file.
ziplevel=2 (zl) Set to 1 (lowest) through 9 (max) to change compression
level; lower compression is faster.
Processing parameters:
maxlen=1600 Prefer sequences shorter than this.
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="-Xmx8g"
z2="-Xms8g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 8g 84
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
keepbest() {
local CMD="java $EA $EOOM $z -cp $CP jgi.KeepBestCopy $@"
echo $CMD >&2
eval $CMD
}
keepbest "$@"
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