bigdatagenomics/avocado — pull request #53 by arahuja (2014-04-25 02:11:17+00:00)
Title: Use function from ADAM to create reference sequence

In ReadCallAssemblyCaller a function was written that creates a reference sequence, when a function for this exists in ADAM. I've removed that function.

In doing so, many of the functions now take RichADAMRecord instead of ADAMRecord since we need to the conversion to access the mdTag (it was being done anyways, now it is just done explicitly upfront).