comment typo
No more LociMap[Unit], just use LociMap[Long] in LociSet
comments for LociMap[Unit] change
Merge pull request #60 from hammerlab/boxedunit-debug

Don't use LociMap[Unit] in LociSet
fix cigar element offset processing
Merge pull request #61 from hammerlab/cigar-offset-tests

Cigar offsets incorrectly jumps full length of elements
update pileup element to handle insertions as a single element
Merge pull request #59 from hammerlab/pileup-insertion-tests

Tests for handling insertions in pileups
add tests for pileupflatmap
upgrade adam to 0.10 and move off snapshot release
Merge pull request #62 from hammerlab/adam-update

Upgrade ADAM to 0.10 and move off snapshot release
add function comment for getlocifromallcontigs
Merge pull request #57 from hammerlab/distributed-util-tests

Test for PileupFlatmap in Distributed Util
add quality score to pileup element; create pileup package
fixed comment; moved pileup.element to separate class PileupElement
Merge pull request #64 from hammerlab/pileup-quality

Add quality score to pileup element; create pileup package
sort reads locally on each task
remove count() operation in writeVariants
add take() method to LociSet and LociMap
Implement loci partitioning by approximate read depth.