BQSR cleanups and fixes
Add BQSR debug flags
Remove attempted emulation of GATK 1.6
style and naming fixes
Add CycleCovariate
remove tabs in pom.xml
Update SAM to ADAM conversion

Parse out the OQ (original quality) common attribute and populate the ADAMRecord with it
(if it exists).
Clarify BQSR debug flags
Merge pull request #213 from jey/bqsr-updates

BQSR updates
Merge pull request #220 from hammerlab/parse-origQual-from-sam

Update SAM to ADAM conversion
Cleanup and optimize basic variant conversion
Sites-only multi-allelic variant conversion
Basic multi-allelic conversion of genotypes
Now with scalariform...
Migrate from reference ids to reference names

We decided that using RefSeq names for our contigs was better practice
than minting our own IDs and handling complicated sequence dictionary
merges.
Merge pull request #217 from hammerlab/ref-id-to-name

Stop using reference IDs and use reference names instead
Use SparkConf object to configure SparkContext

The new Spark SparkConf object replaces the old configuration system that uses
Java system properties and environment variables. SparkConf is thread-safe and
self-contained. For now, SparkConf is constructed to honor the old system and
environment properties. With time, we should change this behavior.

One effect of this move to SparkConf is to prevent errors around binding a port
for the SparkContext in each test case.

This commit also fixes a race condition in GenotypePredicatesSuites.
Merge pull request #223 from massie/sparkconf

Use SparkConf object to configure SparkContext
build up reference information during cigar processing