particles

var Command = &command.Command{
	Usage: `particles [-p|--particles <number>]
	-i|--input <file> [-o|--output <file>]
	[--cpu <number>] [--nomat] <project-file>`,
	Short: "perform a stochastic mapping",
	Long: `
Command particles reads a file with the conditional likelihoods of one or more
trees in a project and writes the results of a stochastic mapping.

The argument of the command is the name of the project file.

By default, 1000 particles will be simulated for the stochastic mapping. The
number of particles can be changed with the flag --particles, or -p.

The flag --input, or -i, is required and indicates the input file. The input
file is a pixel probability file with stored log-likelihoods.

The prefix for the name of the output file will be the name of the project
file. To set a different prefix, use the flag --output, or -o. The full file
name will be the prefix, the tree name, the value of lambda, and the number of
particles.

The output file is a TSV file, indicating the name of the tree, the number of
the particle simulation, the node, the age of the node time stage, and the
pixel location of the particle at the beginning and end of the stage.

By default, all available CPUs will be used in the processing. Set the --cpu
flag to use a different number of CPUs.

By default, if the base pixelation is smaller than 500 pixels at the equator,
it will build a distance matrix to speed up the simulation. As this matrix
consumes a lot of memory, it can be disabled using the flag --nomat.
	`,
	SetFlags: setFlags,
	Run:      run,
}