bam pileup

[Peter]

I have a class that I think is mature enough to be included in yat. It takes a bam range provides interface to walk in to directions: 1) user can iterate along the genome position dimension, 2) for a given position iterate over reads that overlap with that position.

Similar functionality exists in libbam api, but iirc it uses void function pointers and similar, and there are three things I try to stay away from since they typically cause head ache: void pointers, perl, and terrorists.

[Peter]

(In [3310]) a first version of new class Pileup. refs #806

[Peter]

(In [3317]) refs #806 add test for Pileup class

[Peter]

(In [3327]) redefine Pileup::const_iterator so it avoids reads that do not overlap current position. refs #806

[Peter]

(In [3328]) avoid temporary variables; prefer initialization. refs #806

[Peter]

(In [3332]) In Pileup store reads in a std::list (rather than std::deque) to allow easy erase as soon as we are one passed last base. Erasing reads immediately implies we don't need a filter_iterator, but can use list::const_iterator directly.

Fix a bug in Pileup::Entry, which held a BamRead? and CigarIterator? and the latter is essentially a uint32_t* that is returned from BamRead::cigar(). This caused problems in copy/assignment since the BamRead? was copied by value and the CigarIterator? didn't point to BamRead? in this class but to BamRead? in rhs. The problem was solved by replacing the BamRead? by a shared_ptr<BamRead?>.

refs #806

[Peter]

(In [3333]) correct docs. refs #806

[Peter]

(In [3334]) Avoid stopping at position one passed a pile, instead fast forward to next locus with coverage.

refs #806

[Peter]

(In [3335]) closes #806