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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bqsr	Updating tests to handle bad validation data files (that used the wrong qual score encoding); overrides push from stable.	2012-12-03 22:01:07 -05:00
compression/reducereads	Co-Reduction implementation in ReduceReads	2012-11-14 10:33:21 -05:00
genotyper	Actual working version of unflushing VCFWriter	2012-12-13 16:15:08 -05:00
haplotypecaller	Related bug fixes to GGA mode in the HC: some variants (especially MNPs) were causing problems because they don't have to start at the current location to match the allele being genotyped. Fixed.	2012-12-10 14:47:04 -05:00