cmpcmd

var Command = &command.Command{
	Usage: `cmp --got <file> --want <file>
	--trees <file> [-o|--output <file>]
	[--plot <file>]
	[--bound <value>]
	<project>`,
	Short: "compare two reconstructions",
	Long: `
Command cmp read two reconstructions and report the number of pixels in a
reconstruction that are present in a reference reconstruction.

The flag --got is required and indicates the file that contains the pixels to
be evaluated. The flag --want is required and indicates the file that contains
the reference reconstruction.

The flag --trees, is required and defines the file with the simulated trees.

The flag --output, or -o, defines the name of the file with the amount of
shared pixels. If no name is given, it will use '<project>-pixel-results.tab'.

By default, when reading a KDE reconstruction, it will only map the pixels in
the 0.95 of the CDF. Use the flag --bound to change this bound value.

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

The comparison is restricted to cladogenetic (or split) nodes. Intermediate
nodes (i.e., nodes inserted when branches pass several time stages), as well
as terminal nodes, are ignored.

If the flag --plot is defined, a plot with the proportion of nodes in which
the number of correct pixels is greater than the 45%, will be saved in the
indicated file.
	`,
	SetFlags: setFlags,
	Run:      run,
}