Modifying conversion code to resolve #112.

Resolves #112. Specifically:

* Adds code to SAM->ADAM conversion to only set mapping flags if the record is mapped.
* Adds fields to the ADAMRecord to disambiguate secondary vs. supplementary alignments
* Adds accompanying code to the ADAM->SAM conversion to ensure that secondary vs. supplementary alignments are properly converted back to SAM.
* Updates DecadentRead to add the requirement statement that was removed because of #112.
I've updated the comment. I'm not going to touch the ReadBucket/SingleReadBucket code. I think primary/secondary there maps to primary/(secondary || supplemental), but it's not clear. @massie, can you clarify?