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#!/bin/bash
usage(){
echo "
Written by Brian Bushnell
Last modified September 13, 2019
Description: Uses mapped paired reads to generate scaffolds from contigs.
Designed for use with ordinary paired-end Illumina libraries.
Usage: lilypad.sh in=mapped.sam ref=contigs.fa out=scaffolds.fa
Standard parameters:
in=<file> Reads mapped to the reference; should be sam or bam.
ref=<file> Reference; may be fasta or fastq.
out=<file> Modified reference; should be fasta.
overwrite=f (ow) Set to false to force the program to abort rather than
overwrite an existing file.
Processing parameters:
gap=10 Pad gaps with a minimum of this many Ns.
mindepth=4 Minimum spanning read pairs to join contigs.
maxinsert=3000 Maximum allowed insert size for proper pairs.
mincontig=200 Ignore contigs under this length if there is a
longer alternative.
minwr=0.8 (minWeightRatio) Minimum fraction of outgoing edges
pointing to the same contig. Lower values will increase
continuity at a risk of misassemblies.
minsr=0.8 (minStrandRatio) Minimum fraction of outgoing edges
indicating the same orientation. Lower values will increase
continuity at a possible risk of inversions.
passes=8 More passes may increase continuity.
samestrandpairs=f Read pairs map to the same strand. Currently untested.
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${RAM}m"
}
calcXmx "$@"
lilypad() {
local CMD="java $EA $EOOM $z -cp $CP consensus.Lilypad $@"
echo $CMD >&2
eval $CMD
}
lilypad "$@"
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