updated so that we pass around a BamChunkRead object which stores readName, nucleotides, alignment, forwardStrand (and anything else we care about). Required redefining some functions and some work to temporarily save alignments (such as RLE alignments or POA iterative alignments) to the object.. this doesn't feel like a great solution, but it works.
updated so that we pass around a BamChunkRead object which stores readName, nucleotides, alignment, forwardStrand (and anything else we care about). Required redefining some functions and some work to temporarily save alignments (such as RLE alignments or POA iterative alignments) to the object.. this doesn't feel like a great solution, but it works.
Tests pass (other than "can't find lastz" errors)