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.