bigdatagenomics/adam — pull request #310 by tdanford (2014-07-13 18:22:27+00:00)
Title: Upgrade to bdg formats 0.1.2

In particular, making the following changes:
* updating the (deprecated) uses of Record.end to Record.getEnd
* changing Variant.get/setPosition to Variant.get/setStart
* changing Variant.get/setVariantAllele to Variant.get/setAlterateAllele

The tests still aren't passing, this is mostly due to Indel realignment tests
and I'm not sure why they're not working. @fnothaft, can you help out a bit here?