Refactored SequenceDictionary aggregation to eliminate replication between RDD extensions, and to improve speed. Additionally, refactored SequenceDictionary class to reduce GC overhead and to make class immutable.
mpileup cleanup
variant context converter refactor
Upgraded to Hadoop-BAM 0.6.2/Picard 1.107.
update maven-surefire-plugin dependency version to 2.17, also create an entry in pluginManagement for git-commit-id-plugin
Merge pull request #169 from hammerlab/mpileup-update

Cleaning up mpileup command
Merge pull request #175 from hammerlab/variant-converter-refactor

VariantContext converter refactor
bqsr read from vcf
Merge pull request #179 from heuermh/surefire-2_17

Update maven-surefire-plugin dependency version to 2.17, also create an ...
Merge pull request #180 from hammerlab/bqsr-vcf

BQSR using vcf loader
Merge pull request #162 from fnothaft/sequence-dictionary-rdd-funcs

Refactored SequenceDictionary
vcf parsing for annotations
Merge pull request #173 from hammerlab/vcfanno

Parse annotations out of vcf files
Merge pull request #178 from fnothaft/hadoop-bam-0.6.2

Upgraded to Hadoop-BAM 0.6.2/Picard 1.107.