Fixes to sorting in ReferencePosition
Merge pull request #8 from genomebridge/fixOptionSorting

Fixes to sorting in ReferencePosition
Modified reads2ref code to fix performance issue. Also, broke code up to add reads2pileups function.
Add vcf2adam command. Add ADAMVariant to schema.
Adding in implicit conversion functions for going between Java and Scala types. Makes pushing data between Scala/Java/Avro a bit cleaner.
Moved record field name enum over to the projections package.
Merge pull request #10 from bigdatagenomics/moving-record-enum

Moved record field name enum over to the projections package.
Missing brackets in VcfConverter.getType

There were missing brackets, I believe, in the method getType in the class VcfConverter,
which caused the VariantType.SV never to be returned correctly.

I've added a test to make sure that all the types are accessible to the getType method, and
I've moved the method itself to an object (since it depends on none of the fields of the
VcfConverter class itself).
Merge pull request #11 from genomebridge/vcfconverter-typo

Missing brackets in VcfConverter.getType
Fixed a bug in AdamContext.adamLoad

See the comment there -- basically, we weren't testing for a subclass
relationship between the type parameter T and ADAMRecord in the right way,
I think?

Added a test to make sure that we can load SAM files correctly.
Merge pull request #12 from genomebridge/subclass-error

Subclass testing bug in AdamContext.adamLoad
Adding in implicit conversion functions for going between Java and Scala types. Makes pushing data between Scala/Java/Avro a bit cleaner.
Adding indel realignment transform. Composed of several steps:
- Targets for realignment are generated
- Realignment candidates are generated using Smith-Waterman
- If candidates lead to a sufficient improvement, reads are realigned
Added body of indel realignment code.
Completed indel realignment feature. Now to test and debug.
Adding command for running local realignment.
Cleaning up merge issues.:
Clean compile of indel realigner with new pulls merged in.
Rebasing to master.
Adding documentation to newly added code.