jpayne@69: #!/bin/bash
jpayne@69: 
jpayne@69: usage(){
jpayne@69: echo "
jpayne@69: Written by Brian Bushnell
jpayne@69: Last modified August 6, 2019
jpayne@69: 
jpayne@69: Description:  Creates a mutant version of a genome.
jpayne@69: 
jpayne@69: Usage:  mutate.sh in=<input file> out=<output file> id=<identity>
jpayne@69: 
jpayne@69: I/O parameters:
jpayne@69: in=<file>       Input genome.
jpayne@69: out=<file>      Output mutant genome.
jpayne@69: vcf=<file>      Output VCF file showing variations added.
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: subrate=0       Substitution rate, 0 to 1.     
jpayne@69: indelrate=0     Indel rate, 0 to 1.
jpayne@69: maxindel=1      Max indel length.
jpayne@69: indelspacing=10 Minimum distance between subsequent indels.
jpayne@69: id=1            Target identity, 0 to 1; 1 means 100%.
jpayne@69:                 If this is used it will override subrate and indelrate;
jpayne@69:                 99% of the mutations will be substitutions, and 1% indels.
jpayne@69: fraction=1      Genome fraction, 0 to 1; 1 means 100%.  A lower fraction
jpayne@69:                 will randomly select that fraction on a per-sequence basis,
jpayne@69:                 possibly incurring one chimeric junction per sequence.
jpayne@69:                 Not compatible with VCF output.
jpayne@69: period=-1       If positive, place exactly one mutation every X bases.
jpayne@69: prefix=         Set this flag to rename the new contigs with this prefix
jpayne@69:                 and a number.
jpayne@69: amino=f         Treat the input as amino acid sequence.
jpayne@69: ploidy=1        Set the ploidy.  ploidy>1 allows heterozygous mutations.
jpayne@69:                 This will create one copy of each input sequence per ploidy.
jpayne@69: hetrate=0.5     If polyploid, fraction of mutations that are heterozygous.
jpayne@69: nohomopolymers=f  If true, prevent indels in homopolymers that lead to
jpayne@69:                 ambiguous variant calls.  For example, inserting A between
jpayne@69:                 AC or deleting T from TTTT.  This is mainly for grading 
jpayne@69:                 purposes.  It does not fully solve the problem, but greatly
jpayne@69:                 improves concordance (reducing disagreements by 70%).
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: mutate() {
jpayne@69: 	local CMD="java $EA $EOOM $z $z2 -cp $CP jgi.MutateGenome $@"
jpayne@69: 	echo $CMD >&2
jpayne@69: 	eval $CMD
jpayne@69: }
jpayne@69: 
jpayne@69: mutate "$@"