bigdatagenomics/adam — pull request #182 by fnothaft (2014-03-19 04:37:30+00:00)
Title: Indel target cleanup

This PR is against the indel realigner cleanup target branch. This PR is focused on the front end of indel realignment: realignment target generation. Performance is improved by switching to generating targets off of the raw read data, which eliminates a conversion from reads to pileups. This saves compute time and is also more memory efficient.

Additionally, this PR adds more configuration flags to indel realignment, to make our indel realigner more harmonious with the GATK's. Specifically, we bring out the max indel length, max target length, log-odds threshold, and max consensus count flags.

This PR does not pass all tests. On this target branch, I expect to have several further PRs:

* One to add alternate consensus methods (Smith-Waterman #50, known indels)
* One to remove the current pileup code and clean up tests
* One to address back-end (realigner) performance; this may not be necessary, as that performance currently looks pretty good

This PR will clean up substantially after it's associated fast-forward to ToT merges in (#181).