GoogleAPI progress
checkpoint
Abstract sam format alignment class from Picard (sam-jdk) implementation.
Refactoring to support parsing SAM type records from the "global api".
Fix failing unit test (GenomeSpace tool rename)
Picard / samtools package migration
Update gatk jar (na12878)
Add new picard jars
Picard / samtools package migration (reverted from commit 9d4e30b6c250e7ab63227467ae5116c57e7c0d1c)
Update gatk package names, etc
Changed package names to new htsjdk and GATK names.
- net.sf.samtools -> htsjdk.samtools
- org.broad.tribble -> htsjdk.tribble
- org.broadinstitute.variant -> htsjdk.variant
- org.broadinstitute.sting.gatk.walkers -> org.broadinstitute.gatk.tools
Restored MongoVCFVariant from 9d4e30b6c250e7ab63227467ae5116c57e7c0d1c^, with updates to gatk package names.
Merge pull request #91 from kshakir/ks_GlobalAPI_package_updates

Changed mongovariant package names to new htsjdk and GATK names.
Merge pull request #92 from broadinstitute/GlobalAPI

Global api