avoid java serialization through spark broadcast
Merge pull request #43 from hammerlab/serialize-set

Avoid java serialization through spark broadcast
add breaking LociSet serialization case. Strangly, we can make an RDD[LociSet] fine, but attemping to use a LociSet in a closure results in a serialization error.
more LociSet serialization tests
disabling the closure LociSet serialization test for now
Merge pull request #44 from hammerlab/serialization-debug

A few more tests for Kryo-based (i.e. not from a closure) LociSet serialization
drop newReads from SlidingReadWindow
minor comment cleanup
LociMap Builder now coalesces adjacent intervals with the same value. Started DistributedUtilSuite
Add tests for Pileup (issue #2)

This a work-in-progress and the last test is currently disabled because
it depends on #30 being implemented.
Merge pull request #45 from hammerlab/pileup_testing_i2_seb

Add tests for Pileup (issue #2)
HDFS support

Followed changes here: https://github.com/hammerlab/avocado/commit/9d942e9956d933e24c70a253f6450cdf7eeb3762#commitcomment-6059717
Drop support for -parallelism=0.

Set default parallelism to 1. No need to have a separate code path for parallelism=0. Closes #40.
Project all CIGAR ops onto Pileup.Element.Alignment

This is a first fix for #30. It also re-enables the “read 5” test of
PileupSuite (#2).

The “long names” of `CigarOperator` are not enough
(c.f.
[net/sf/samtools/CigarOperator.java](https://github.com/nh13/picard/blob/master/src/java/net/sf/samtools/CigarOperator.java)
and
[documentation](http://picard.sourceforge.net/javadoc/net/sf/samtools/CigarOperator.html))
so I went back to the “one-letter” ones.

The assumptions are taken from this [wikipage about
SAM](http://davetang.org/wiki/tiki-index.php?page=SAM) and
Matt's
[blog post](http://zenfractal.com/2013/06/19/playing-with-matches/).
Merge pull request #46 from hammerlab/fix_i30_seb

Project all CIGAR operations onto our Pileup.Element.Alignment
optimization for collecting all loci with mapped reads in Common.loci
change locuspredicate to unique read mapped predicate
Merge pull request #47 from hammerlab/change-predicate

Change locuspredicate to unique read mapped predicate
test threshold caller
Merge pull request #49 from hammerlab/threshold-caller-tests

Simple tests for Threshold variant caller