jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified January 26, 2021
jpayne@69: 
jpayne@69: Description:  Mutates a reference by applying a set of variants.
jpayne@69: When 2 variants overlap, the one with the higher allele count is used.
jpayne@69: 
jpayne@69: Usage:  applyvariants.sh in=<input file> vcf=<vcf file> out=<output file>
jpayne@69: 
jpayne@69: Standard parameters:
jpayne@69: in=<file>       Reference fasta.
jpayne@69: vcf=<file>      Variants.
jpayne@69: basecov=<file>  Optional per-base coverage from BBMap or Pileup.
jpayne@69: out=<file>      Output 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: ziplevel=2      (zl) Set to 1 (lowest) through 9 (max) to change compression
jpayne@69:                 level; lower compression is faster.
jpayne@69: 
jpayne@69: Processing parameters:		
jpayne@69: mincov=0        If positive and depth is below this, change ref to N.
jpayne@69:                 Requires a coverage file.
jpayne@69: maxindel=-1     If positive, ignore indels longer than this.
jpayne@69: noframeshifts=f Ignore indels that are not a multiple of 3 in length.
jpayne@69: 
jpayne@69: Renaming:
jpayne@69: name=           Optionally rename sequences to this.
jpayne@69: addnumbers=f    Add _1 and so forth to ensure sequence names are unique.
jpayne@69: prefix=t        Use the name as a prefix to the old name, instead of replacing
jpayne@69:                 the old name.
jpayne@69: delimiter=_     Symbol to place between parts of the new name.
jpayne@69:                 For space or tab, use the literal word.
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: applyvariants() {
jpayne@69: 	local CMD="java $EA $EOOM $z -cp $CP var2.ApplyVariants $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: applyvariants "$@"