Fix documentation of sequenceRead
Merge pull request #24 from hammerlab/doc_fix_pileup_element

Fix documentation of sequenceRead
Fix a bug where unsorted reads were accepted, plus a test.
makeRead alignment
Remove tests which are written already.
Merge pull request #25 from hammerlab/sliding-test-sorted

Fix a bug where unsorted reads were accepted, plus a test.
Fix 2 assumptions regarding `RichADAMRecord.end`

This follows up on #23.
Merge pull request #26 from hammerlab/fix_more_end_read_assumptions

Fix 2 assumptions regarding `RichADAMRecord.end`
Check text of the exceptions that are thrown
Use "should include" for string matching
made algebraic datatype called Alignment in Pileup which combines the cigar operator and sequenceRead and statically captures the invariant that deletions have an empty sequenceRead, and Match/Mismatch have only one character

rename chr/seq to base/bases
Fix off by one bug, lots of debug code
remove debug code
Merge pull request #28 from hammerlab/check-exceptions

More tests for SlidingWindow
Add a test for halfWindowSize=1
Merge pull request #29 from hammerlab/hws=1

Add a test for SlidingWindow with halfWindowSize=1
rebase off master
Merge pull request #27 from hammerlab/cigar_adt

made algebraic datatype called Alignment in Pileup which combines the...
add LociMap, refactor LociSet to use it
lots of half-complete refactoring of distribution code