Commits on Mar 14, 2015

1. IntervalWalker, VariantWalker enhancements, and GenomeLoc -> SimpleIn… …

   …terval 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).
   
   -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

   

   droazen committed Mar 14, 2015
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