Mark DePristo aeab932c63 Actual working version of unflushing VCFWriter ... -- Uses high-performance local writer backed by byte array that writes the entire VCF line in some write operation to the underlying output stream. -- Fixes problems with indexing of unflushed writes while still allowing efficient block zipping -- Same (or better) IO performance as previous implementation -- IndexingVariantContextWriter now properly closes the underlying output stream when it's closed -- Updated compressed VCF output file		2012-12-13 16:15:08 -05:00
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gatk	Actual working version of unflushing VCFWriter	2012-12-13 16:15:08 -05:00
utils/pairhmm	Refactoring the PairHMM util class to allow for multiple implementations which can be specified by the callers via an enum argument. Adding an optimized PairHMM implementation which caches per-read calculations as well as a logless implementation which drastically reduces the runtime of the HMM while also increasing the precision of the result. In the HaplotypeCaller we now lexicographically sort the haplotypes to take maximal benefit of the haplotype offset optimization which only recalculates the HMM matrices after the first differing base in the haplotype. Many thanks to Mauricio for all the initial groundwork for these optimizations. The change to the one HC integration test is in the fourth decimal of HaplotypeScore.	2012-10-20 16:38:18 -04:00