PROGRAM: pbsDecode

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

DESCRIPTION: 

    Decode a binary encoding of a probabilistic biological sequence
    (PBS).  Outputs a table with a row for each position in the
    sequence and a column for each base, such that the (i,j)th value
    is the probability of base j at position i.  The same codefile
    that was used to encode the sequence should be given.

    This program performs the inverse function of pbsEncode.

EXAMPLE:

    Decode an encoded ancestral sequence:
        pbsDecode anc.human-mouse.bin mammal.code > anc.human-mouse.probs

    where "anc.human-mouse.bin" is a binary encoding of an ancestral
    sequence produced by pbsEncode or prequel, and "mammal.code" is a
    codefile produced by pbsTrain.

OPTIONS:

    --start, -s <sidx>
	Decode only the subsequence starting at position <sidx>.
	Indexing starts with 1.

    --end, -e <eidx>
	Decode only the subsequence ending at position <eidx>.
	Indexing starts with 1.

    --discard-gaps, -G
	Do not report gaps in the PBS.  

    --help, -h
	Produce this help message.