PROGRAM: pbsEncode

USAGE: pbsEncode [OPTIONS] input.probs codefile > output.bin

DESCRIPTION: 

    Produce an approximate binary encoding of a probabilistic
    biological sequence (PBS), as defined by a text file
    ("input.probs") with a row for each position in the sequence and a
    column for each base.  The (i,j)th value in this table should be
    the probability of base j at position i.  Columns should be
    white-space delimited.  The encoding will be as defined by
    "codefile", which should be in the format used by pbsTrain.

    This program performs the inverse function of pbsDecode.

EXAMPLE:

    Encode the probabilities in a file "anc.human-mouse.probs",
    produced by prequel, using a code file "mammals.code", produced by
    pbsTrain.

	pbsEncode anc.human-mouse.probs mammals.code > anc.human-mouse.bin

OPTIONS:

    --discard-gaps, -G
	Discard gaps in the PBS.  Gaps in the input data are assumed
	to be represented by rows consisting of a single "-" character.

    --help, -h
	Produce this help message.