Modifying conversion code to resolve #112.

[fnothaft]

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 SAMRecordConverter: ensure internal consistency of flags #112.

[AmplabJenkins]

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/352/

[tdanford]

I merged another of your PR's, so don't forget to rebase this one!

[fnothaft]

@tdanford rebased!

[AmplabJenkins]

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/356/

[tdanford]

If I read the code above correctly, your new "secondaryAlignment" flag is equivalent to "mapped, but not primary or supplementary." Is that right? If so, can you clarify the description in the comment block above?

Also, is there any interaction here with the code in ReadBucket and SingleReadBucket? In particular, there are already fields in those classes with particles like "secondary" in their names -- do they match the use of this "secondaryAlignment" flag?

[fnothaft]

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?

[AmplabJenkins]

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/359/

[tdanford]

Thanks, Frank!