pbsDecode1

Overview

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.

Examples

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.