freq

var Command = &command.Command{
	Usage: `freq [--kde <value>] [--cpu <number>]
	-i|--input <file> [-o|--output <file>] <project-file>`,
	Short: "calculate pixel frequencies",
	Long: `
Command freq reads a file from a stochastic mapping reconstruction for the
nodes of one or more trees in a project and produces an equivalent file with
pixel frequencies.

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

The flag --input, or -i, is required and indicates the input file.

By default, the ranges are taken as given. If the flag --kde is defined, a
kernel density estimation using a spherical normal will be used to smooth the
results with the indicated concentration parameter (in 1/radians^2). As
calculating the KDE can be computationally expensive, this procedure is run in
parallel using all available processors. Use the flag --cpu to change the
number of processors.

By default, the output file will have the name of the input file with the
prefix "freq" or "kde" if the --kde flag is used. With the flag --output, or
-o, a different prefix can be defined.
	`,
	SetFlags: setFlags,
	Run:      run,
}