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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified August 11, 2023
Description: Fuses sequences together, padding gaps with Ns.
Usage: fuse.sh in=<input file> out=<output file> pad=<number of Ns>
Parameters:
in=<file> The 'in=' flag is needed if the input file is not the
first parameter. 'in=stdin' will pipe from standard in.
out=<file> The 'out=' flag is needed if the output file is not the
second parameter. 'out=stdout' will pipe to standard out.
pad=300 Pad this many N between sequences.
maxlen=2g If positive, don't make fused sequences longer than this.
quality=30 Fake quality scores, if generating fastq from fasta.
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.
fusepairs=f Default mode fuses all sequences into one long sequence.
Setting fusepairs=t will instead fuse each pair together.
name= Set name of output sequence. Default is the name of
the first input sequence.
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${RAM}m"
}
calcXmx "$@"
fuse() {
local CMD="java $EA $EOOM $z -cp $CP jgi.FuseSequence $@"
echo $CMD >&2
eval $CMD
}
fuse "$@"
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