NAME
pbsDecode - Decode a binary encoding of a probabilistic biological sequence
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.
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This program performs the inverse function of pbsEncode.
EXAMPLE
Decode an encoded ancestral sequence:
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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>
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Decode only the subsequence starting at position <sidx>. Indexing starts with 1.
--end, -e <eidx>
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Decode only the subsequence ending at position <eidx>. Indexing starts with 1.
--discard-gaps, -G Do not report gaps in the PBS.
--help, -h
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Produce this help message.