Port germline filter from M2

[davidbenjamin]

This requires reading in copy number segmentation from the M2 pipeline into some sort of interval data structure and porting the M2 germline probability model to M3.

However, this doesn't just mean that the germline filter becomes the responsibility of M3 instead of M2. Rather, it means integrating the germline model into the M3 posterior classifier, just as we have already done for sequencing error.