Create MongoDBManager, which keeps track of connections based on Locator class. Locators can be instantiated directly, or read from JSON files (NA12878DBArgumentCollection uses the GSon library)
0. Add additional create method to MongoVariantContext as convenience, if we want a custom TruthStatus (and change "type" to less ambiguous "truthStatus")
1. Have NA12878KnowledgeBase return WriteResults from insert methods, so caller can know if there's an error
2. Provide constructors for NA12878DBArgumentCollection, since we need to be able to create this class for NA12878DBKnowledgeBase
-- Cleaned up code for SiteIterator.
-- Added a generic error handling system for the SiteIterator. Created approaches to simply throw errors when invalid records are found, to log them, and to remove them from the sites collection.
-- By default getCalls() produces a SiteIterator that removes incorrectly formatted records from the DB
-- Created NA12878KnowledgeBaseServer GATK walker that (1) continually finds newly added records to the sites database and rebuilds the consensus as needed and (2) archives the reviewed sites to a VCF file upon server termination
-- More, better unit tests everywhere
-- Adding infrastructure to find only newly added sites to the NA12878KnowledgeBase. Uses mongos ordering of _id to obtain the records (and the sites) of variants newly added to the sites collection. This is essential infrastructure to write a NA12878KnowledgeBase server that continually keeps the consensus records updated as new sites are added to the database
-- Multi-allelic variants are split into their bi-allelic version, trimmed, and we attempt to provide a meaningful genotype for NA12878 here. It's not perfect and needs some discussion on how to handle het/alt variants
-- Adding splitInBiallelic funtion to VariantContextUtils as well as extensive unit tests that also indirectly test reverseTrimAlleles (which worked perfectly FYI)
-- MongoVariantContexts and MongoGenotype have a validate() function that ensures that the information is consistent, in anticipation of potential problems with the data coming in from reviews via IGV
-- Divide the world into production, development, and test DB, via the NA12878DBArgumentCollection
Guillermo del Angel
Chris Hartl
Mark DePristo
Menachem Fromer
Jacob Silterra
Mauricio Carneiro
Eric Banks
Joel Thibault
Ryan Poplin