broadinstitute / hellbender / 641 / 1
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droazen 
IntervalWalker, VariantWalker enhancements, and GenomeLoc -> SimpleInterval migration in the engine

-Created a new class of tool, IntervalWalker, that processes a single interval at a time,
 with the ability to query optional overlapping sources of reads, reference data, and/or
 features/variants. Current implementation is simple/naive with no special caching;
 performance issues will be addressed once we port this traversal type to dataflow.

-Added the ability for VariantWalkers to access contextual reads/reference/feature data.

-To enable the above changes, migrated most of the engine to use SimpleIntervals rather
 than GenomeLocs. This allows for the creation of Context objects in traversals where there
 is not necessarily a sequence dictionary available (eg., VariantWalker).

-Since there isn't yet an htsjdk release that contains SimpleInterval, temporarily
 checked a copy of it into our repo, which we can remove the next time we
 rev htsjdk.

TODOs:

-We currently still require a sequence dictionary to actually parse intervals in
 IntervalArgumentCollection. This is due entirely to our support of intervals without
 specific stop positions (eg., "chr1" and "chr1:1+") -- for these intervals we must
 look up the stop position in a sequence dictionary. This means that IntervalWalkers
 currently require at least one input that contains a sequence dictionary (although
 VariantWalkers do not). We should look into ways of relaxing this restriction.

-Need to find a way to share common arguments and data source initialization code across
 traversal types, while still allowing customization on a per-traversal and/or per-tool
 basis (eg., for IntervalWalkers, -L should be required rather than optional).

Resolves #109

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Source Files on job 641.1 (TERM=dumb)