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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified August 11, 2021
Description: Reorders reads randomly, keeping pairs together.
Unlike Shuffle, Shuffle2 can write temp files to handle large datasets.
Usage: shuffle2.sh in=<file> out=<file>
Standard parameters:
in=<file> The 'in=' flag is needed if the input file is not the first parameter. 'in=stdin' will pipe from standard in.
in2=<file> Use this if 2nd read of pairs are in a different file.
out=<file> The 'out=' flag is needed if the output file is not the second parameter. 'out=stdout' will pipe to standard out.
out2=<file> Use this to write 2nd read of pairs to a different file.
overwrite=t (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.
int=auto (interleaved) Set to t or f to override interleaving autodetection.
Processing parameters:
shuffle Randomly reorders reads (default).
seed=-1 Set to a positive number for deterministic shuffling.
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="-Xmx2g"
z2="-Xms2g"
set=0
if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
usage
exit
fi
calcXmx () {
source "$DIR""/calcmem.sh"
setEnvironment
parseXmx "$@"
if [[ $set == 1 ]]; then
return
fi
freeRam 2000m 84
z="-Xmx${RAM}m"
z2="-Xms${RAM}m"
}
calcXmx "$@"
shuffle() {
local CMD="java $EA $EOOM $z -cp $CP sort.Shuffle2 $@"
echo $CMD >&2
eval $CMD
}
shuffle "$@"
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