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
Adding ADAMContig back to ADAMVariant.
Merge pull request #245 from fnothaft/variant-avdl

Adding ADAMContig back to ADAMVariant.
Making sample ID field in genotype nullable.
Merge pull request #246 from fnothaft/genotype-fix-sample-id

Making sample ID field in genotype nullable.
fix for issue244; fragments were incorrect order and only took first fragment off of a sequence
Merge pull request #247 from hammerlab/issue-244

For #244, Fragments were incorrect order and incomplete
Cosmetic changes to FastaConverter and FastaConverterSuite.

Just making a few little cosmetic changes to FastaConverter, to make part of the code more readable.

Also, added a second condition to one of the tests in FastaConverterSuite, to check that the reassembled
sequence (which had been created, but wasn't being used) matched what was in the original file.
CHANGES.md is updated at release instead of per pull request
Merge pull request #251 from massie/chachachanges

CHANGES.md is updated at release instead of per pull request
Added a note about rebasing-off-master to CONTRIBUTING.md

Contributors should rebase their feature branches off of master (and
moderators should double-check that this is the case) before the feature
branch can (will be) merged.
Adding utilities for read trimming.
Merge pull request #249 from genomebridge/cosmetic-changes

Cosmetic changes to FastaConverter and FastaConverterSuite.
Merge pull request #252 from genomebridge/rererebase

Added a note about rebasing-off-master to CONTRIBUTING.md
Merge pull request #248 from fnothaft/read-trimming

Adding utilities for read trimming.