Build up reference information during cigar processing

[arahuja]

This PR is to track more reference information during the cigar processing.

Currently, RichADAMRecord parses the Cigar string to extract the reference position (as a Long).
This:

• Also captures the reference base, cigar element, and cigar offset (which will allow for us to not reparse the cigar string when building pileups)
• Change reference position to be an instance of ReferencePosition (and changes the overlaps function to check other ReferencePosition ensuring a contigName check (resolving RichADAMRecord: referencePosition methods ignore contig #113))

Also, this removes ReferenceLocation in favor of ReferencePosition as they had duplicate functionality

Noted issues:

• This has overlaps with Remove duplicate mdtag field #230 slightly
• This still uses the current Cigar processing from samtools, there was some talk of removing this dependency
• DecadentRead vs RichAdamRecord do we want to merge or distinguish these more?

[fnothaft]

How is this different from the contains(other: ReferencePosition) method above?

[arahuja]

It's not - didn't see that one, will update, thanks!

[fnothaft]

+1, looks good!

• This still uses the current Cigar processing from samtools, there was some talk of removing this dependency

I've been speaking with the UCSC folks about this. I'm hoping to have a design document/writeup for this approach by the end of the week.

[AmplabJenkins]

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/306/

[AmplabJenkins]

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/307/

[nealsid]

Sorry to be a commit history nag but can you move some of the PR description over to the git commit message?

[AmplabJenkins]

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/308/

[arahuja]

Rebased after #230 merged in.

[AmplabJenkins]

All automated tests passed.
Refer to this link for build results: https://amplab.cs.berkeley.edu/jenkins/job/ADAM-prb/317/

[massie]

Thanks, Arun!