MauricioCarneiro/PairHMM — pull request #32 by MauricioCarneiro (2014-02-27 22:10:36+00:00)
Title: Simplify API before SSE implementation

Remove .hpp implementations
Move update method inside diagonals and now unused zero() method
Move diagonals to it's own class with all relevant operations
Move constants to it's own class with all relevant operations
Make padded_reads a private member of PairhmmImpl
Move make test to top-level makefile
Add 'make test' to Travis automated ci

Although I fully appreciate the effort of reducing compilation time,
the hpp split is not reasonable. The hpp is not a compilable standalone
unit and coding in it is a nightmare (without syntax checking). We need
a better standard. For now, let's keep it all in the .h

Fixes #31
Fixes #27
Fixes #26