IntervalWalker, VariantWalker enhancements, and GenomeLoc -> SimpleInterval migration in the engine

[droazen]

-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).

-Moved shared arguments/code from Walker classes up into GATKTool. Still some issues
related to marking engine-wide arguments as optional/required on a per-traversal or
per-tool basis, but tickets have been created for these.

-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.

Resolves #109

[coveralls]

Coverage increased (+0.1%) to 75.04% when pulling f1a0bc8293137afb737bc82e0aaa1e30a1cd9d3b on dr_interval_walker into ae98b8c on master.

[coveralls]

Coverage increased (+0.08%) to 75.03% when pulling 61cb9e15970383ed11b35449f7a8dc055838b2e2 on dr_interval_walker into ae98b8c on master.

[droazen]

Comments addressed, ready for a second round of review. Two new commits: one for the trivial changes, and another to satisfy the request to push more functionality up into GATKTool. Currently there is still a bit of awkwardness (engine-wide input arguments are nominally marked as optional, and traversal types and/or individual tools override methods like requiresReads() to indicate input requirements), but I feel it's at least a step in the right direction.

[coveralls]

Coverage increased (+0.11%) to 75.03% when pulling fa873e6c3d88d0f8eadace5bd323ac57b3829eb3 on dr_interval_walker into db029de on master.

[coveralls]

Coverage increased (+0.11%) to 75.03% when pulling 6cb4dc27cda2bd4843ac4feb4025ee9dfa8eca15 on dr_interval_walker into db029de on master.

[coveralls]

Coverage increased (+0.11%) to 75.03% when pulling 6cb4dc27cda2bd4843ac4feb4025ee9dfa8eca15 on dr_interval_walker into db029de on master.

[coveralls]

Coverage increased (+0.11%) to 75.03% when pulling 1508c9a634fd458e82d34eb37da75c3bcd83d1df on dr_interval_walker into db029de on master.

[coveralls]

Coverage increased (+0.11%) to 75.03% when pulling d814052 on dr_interval_walker into db029de on master.

[droazen]

All comments addressed -- merging!