Improvements to NA12878KnowledgeBase system

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-- 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

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This commit is contained in:

Mark DePristo 2012-11-26 15:31:26 -05:00

parent 9bfe39411e

commit 4281498c2c

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