Better documentation in HasReferenceRegion

Closes #255.
Fix SlidingWindow.nextLocusWithRegions

 * Add test case that exposed a bug in slidingWindow.nextLocusWithRegions. Upon
   initialization of a slidingWindow, currentLocus=-1, which can confuse
   nextLocusWithRegions into having an assertion error when the first read's start
   is <= halfWindowSize.
 * Fixed the bug in SlidingWindow.scala. Also added some more comments.
Merge pull request #256 from hammerlab/sliding-window-nextLocusWithRegions-fix

Sliding window next locus with regions fix