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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified April 24, 2019
Description: Reformats a fungal assembly for release.
Also creates contig and agp files.
Usage: fungalrelease.sh in=<input file> out=<output file>
I/O parameters:
in=<file> Input scaffolds.
out=<file> Output scaffolds.
outc=<file> Output contigs.
qfin=<file> Optional quality scores input.
qfout=<file> Optional quality scores output.
qfoutc=<file> Optional contig quality scores output.
agp=<file> Output AGP file.
legend=<file> Output name legend file.
overwrite=f (ow) Set to false to force the program to abort rather than
overwrite an existing file.
Processing parameters:
fastawrap=60 Wrap length for fasta lines.
tuc=t Convert sequence to upper case.
baniupac=t Crash on encountering a non-ACGTN base call.
mingap=10 Expand all gaps (Ns) to be at least this long.
mingapin=1 Only expand gaps that are at least this long.
sortcscaffolds=t Sort scaffolds descending by length.
sortcontigs=f Sort contigs descending by length.
renamescaffolds=t Rename scaffolds to 'scaffold_#'.
scafnum=1 Number of first scaffold.
renamecontigs=f Rename contigs to 'contig_#' instead of 'scafname_c#'.
contignum=1 Number of first contig; only used if renamecontigs=t.
minscaf=1 Only retain scaffolds at least this long.
mincontig=1 Only retain contigs at least this long.
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.
"
}
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 [[ $set == 1 ]]; then
return
fi
}
calcXmx "$@"
fungalrelease() {
local CMD="java $EOOM $EA $EOOM $z $z2 -cp $CP jgi.FungalRelease $@"
echo $CMD >&2
eval $CMD
}
fungalrelease "$@"
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