Allow open-ended intervals in loadIndexedBam

[ryan-williams]

Intervals' start and end has to be specified in a ReferenceRegion before being passed to loadIndexedBam.

It would be nice to allow intervals of the form [N,∞) without resorting to making callers use Long.MaxValue or the like.

The right model would be a sort of ReferenceRegion-precursor, shaped like (String, Long, Option[Long]), that basically only exists ephemerally in the course of loading subsets of indexed BAMs.

Guacamole has some code that does basically this here, allowing open-ended intervals, whole contigs, and "all" and "none" keywords, then resolving things into concrete ReferenceRegions once contig-lengths are available, after parsing a BAM header.

[heuermh]

I've suggested before using Range from Guava, which handles bounded and unbounded ranges. It is well-designed and well-tested.

I abuse it for genomics here https://github.com/heuermh/dishevelled-bio/tree/master/range/src/main/java/org/dishevelled/bio/range