jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified September 13, 2019
jpayne@69: 
jpayne@69: Description:  Uses mapped paired reads to generate scaffolds from contigs.
jpayne@69: Designed for use with ordinary paired-end Illumina libraries.
jpayne@69: 
jpayne@69: Usage:  lilypad.sh in=mapped.sam ref=contigs.fa out=scaffolds.fa
jpayne@69: 
jpayne@69: Standard parameters:
jpayne@69: in=<file>       Reads mapped to the reference; should be sam or bam.
jpayne@69: ref=<file>      Reference; may be fasta or fastq.
jpayne@69: out=<file>      Modified reference; should be fasta.
jpayne@69: overwrite=f     (ow) Set to false to force the program to abort rather than
jpayne@69:                 overwrite an existing file.
jpayne@69: 
jpayne@69: Processing parameters:
jpayne@69: gap=10          Pad gaps with a minimum of this many Ns.
jpayne@69: mindepth=4      Minimum spanning read pairs to join contigs.
jpayne@69: maxinsert=3000  Maximum allowed insert size for proper pairs.
jpayne@69: mincontig=200   Ignore contigs under this length if there is a 
jpayne@69:                 longer alternative.
jpayne@69: minwr=0.8       (minWeightRatio) Minimum fraction of outgoing edges 
jpayne@69:                 pointing to the same contig.  Lower values will increase
jpayne@69:                 continuity at a risk of misassemblies.
jpayne@69: minsr=0.8       (minStrandRatio) Minimum fraction of outgoing edges 
jpayne@69:                 indicating the same orientation.  Lower values will increase
jpayne@69:                 continuity at a possible risk of inversions.
jpayne@69: passes=8        More passes may increase continuity.
jpayne@69: samestrandpairs=f  Read pairs map to the same strand.  Currently untested.
jpayne@69: 
jpayne@69: Java Parameters:
jpayne@69: -Xmx            This will set Java's memory usage, overriding autodetection.
jpayne@69:                 -Xmx20g will specify 20 gigs of RAM, and -Xmx200m will
jpayne@69:                 specify 200 megs. The max is typically 85% of physical memory.
jpayne@69: -eoom           This flag will cause the process to exit if an out-of-memory
jpayne@69:                 exception occurs.  Requires Java 8u92+.
jpayne@69: -da             Disable assertions.
jpayne@69: 
jpayne@69: Please contact Brian Bushnell at bbushnell@lbl.gov if you encounter any problems.
jpayne@69: "
jpayne@69: }
jpayne@69: 
jpayne@69: #This block allows symlinked shellscripts to correctly set classpath.
jpayne@69: pushd . > /dev/null
jpayne@69: DIR="${BASH_SOURCE[0]}"
jpayne@69: while [ -h "$DIR" ]; do
jpayne@69:   cd "$(dirname "$DIR")"
jpayne@69:   DIR="$(readlink "$(basename "$DIR")")"
jpayne@69: done
jpayne@69: cd "$(dirname "$DIR")"
jpayne@69: DIR="$(pwd)/"
jpayne@69: popd > /dev/null
jpayne@69: 
jpayne@69: #DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )/"
jpayne@69: CP="$DIR""current/"
jpayne@69: 
jpayne@69: z="-Xmx4g"
jpayne@69: z2="-Xms4g"
jpayne@69: set=0
jpayne@69: 
jpayne@69: if [ -z "$1" ] || [[ $1 == -h ]] || [[ $1 == --help ]]; then
jpayne@69: 	usage
jpayne@69: 	exit
jpayne@69: fi
jpayne@69: 
jpayne@69: calcXmx () {
jpayne@69: 	source "$DIR""/calcmem.sh"
jpayne@69: 	setEnvironment
jpayne@69: 	parseXmx "$@"
jpayne@69: 	if [[ $set == 1 ]]; then
jpayne@69: 		return
jpayne@69: 	fi
jpayne@69: 	freeRam 4000m 84
jpayne@69: 	z="-Xmx${RAM}m"
jpayne@69: 	z2="-Xms${RAM}m"
jpayne@69: }
jpayne@69: calcXmx "$@"
jpayne@69: 
jpayne@69: lilypad() {
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP consensus.Lilypad $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: lilypad "$@"