Test CL to use Hadoop 2.2 libraries from CDH5 repo, as well as protobuf 2.5
spacing
fix spacing
disambiguate isMismatchBase(), other small cleanups
Factor out SnpTable, fix crash in SNP handling
add some comments
Merge branch 'master' of https://github.com/bigdatagenomics/adam

Conflicts:
	adam-cli/pom.xml
Rewrite foldleft as aggregate to make it more parallel.
Update Spark to 0.8.1 and add hadoop2.2 profile
Add tests for reference position and fix refpos position off-by-one-error
Merge pull request #40 from arahuja/referenceend

Fixing reference position from offset implementation
Print a log message on startup to more easily tell runs apart
Improve BQSR performance by reducing GC pressure
Rename 'offset' to 'readOffset' and 'position' to 'referencePosition'
Merge pull request #38 from jey/bqsr

Small bugfixes and cleanups to BQSR
Just the start of reading VCF files.

-Bumped up picard version to 1.102.0 in order to get new VCFileReader classes (need to test to make sure our Hadoop-BAM works with this new version)
-Started filling in Vcf2Adam command class, as well as the additions to AdamContext class
Merge remote branch 'origin' into nested-variant
Load & print VCF headers using Picard
Fill in VCF reading using Hadoop-BAM
Merge branch 'hadoop2profile' of https://github.com/arahuja/adam into nested-variant

Conflicts:
	pom.xml