capture reference base, cigar element, and cigar offset during cigar processing; remove reference location in favor of reference position
Merge pull request #233 from hammerlab/refpos-reconcile

Build up reference information during cigar processing
Make ADAMVCFOutputFormat public

This commit makes the ADAMVCFOutputFormat defined in
ADAMVariationContext public and moves it to its own source file.
The alternate definition of ADAMVCFOutputFormat (unused) is
deleted.
Merge pull request #239 from massie/vcfout

Make ADAMVCFOutputFormat public
Fixes to FASTA code to properly handle indices.
Merge pull request #241 from fnothaft/fasta-long

Fixes to FASTA code to properly handle indices.
Upgrade to Parquet 1.4.3

Note that Parqeut 1.4.3 handles default values differently
than in the past. If a record field is *not* part of the specified
projection, it will be set to the default value (if it exists)
instead of null.
Merge pull request #242 from massie/parquet-upgrade

Upgrade to Parquet 1.4.3
Update CHANGES.md in preparation for 0.10.0 release
[maven-release-plugin] prepare release adam-parent-0.10.0
[maven-release-plugin] prepare for next development iteration
Implement contig-to-RefSeq translation, refactor SequenceDictionary with RefSeq information (and without numeric IDs) and prepare ADAMGenotype for incorporating reference model information.
Further implement reference model in variant conversion and address comments in PR re: incorporation of RefSeq IDs into SequenceDictioanry
Further address comments in PR re: incorporation of RefSeq IDs into SequenceDictioanry
Rebase work onto master
Merge pull request #243 from massie/pr238

Rebase PR#238 onto master