4281498c2c
-- 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 |
||
|---|---|---|
| licensing | ||
| protected/java | ||
| public | ||
| settings | ||
| .gitignore | ||
| build.xml | ||
| intellij_example.tar.bz2 | ||
| ivy.xml | ||