Documentation

The primitive pieces for genotype calling: A position, a base represented as four likelihoods, an inserted sequence, and the length of a deleted sequence. The logic is that we look at a base followed by some indel, and all those indels are combined into a single insertion and a single deletion.

Represents our knowledge about a certain base, which consists of the base itself (A,C,G,T, encoded as 0..3; no Ns), the quality score (anything that isn't A,C,G,T becomes A with quality 0), and a substitution matrix representing post-mortem but pre-sequencing substitutions.

Unfortunately, none of this can be rolled into something more simple, because damage and sequencing error behave so differently.

Damage information is polymorphic. We might run with a simple version (a matrix) for calling, but we need more (a matrix and a mutable matrix, I think) for estimation.

Decomposes a BAM record into chunks suitable for piling up. We pick apart the CIGAR and MD fields, and combine them with sequence and quality as appropriate. Clipped bases are removed/skipped as needed. We also apply a substitution matrix to each base, which must be supplied along with the read.

Statistics about a genotype call. Probably only useful for filtering (so not very useful), but we keep them because it's easy to track them.

Map quality and a list of encountered bases, with damage information and reference base if known.

Map quality and a list of encountered indel variants. The deletion has the reference sequence, if known, an insertion has the inserted sequence with damage information.

Running pileup results in a series of piles. A Pile' has the basic statistics of a VarCall, but no likelihood values and a pristine list of variants instead of a proper call. We emit one pile with two BasePiles (one for each strand) and one IndelPile (the one immediately following) at a time.

Raw pile. Bases and indels are piled separately on forward and backward strands.

The pileup enumeratee takes BamRaws, dissects them, interleaves the pieces appropriately, and generates Pile's. The output will contain at most one BasePile and one IndelPile for each position, piles are sorted by position.

This top level driver receives BamRaws. Unaligned reads and duplicates are skipped (but not those merely failing quality checks). Processing stops when the first read with invalid br_rname is encountered or a t end of file.