Add support for the TP (topology) tag in the sequence dictionary

[nh13]

See https://github.com/samtools/hts-specs/pull/405

[cmnbroad]

Holding off until samtools/hts-specs#405 is merged.

[jmarshall]

From the commit message:

as well as if the start (or mate start) is off the end.

Um… not sure anyone has made a case for allowing this?

[nh13]

@jmarshall

Um… not sure anyone has made a case for allowing this?

That's definitely my mistake. I think what I want is to say that it's ok for the mate's start to be past the end of the reference as long as the current start is not. So we can have a template span the origin, but not have a template that goes past it. If that makes sense, I'll fix the implementation.

[yfarjoun]

I suggest the non-controversial parts be extracted into a separate PR.

[yfarjoun]

note that testLongReferenceQuery is failing in Travis.