Mark DePristo bd7ed0d028 Enable efficient parallel output of BCF2 ... -- Previous IO stub was hardcoded to write VCF. So when you ran -nt 2 -o my.bcf you actually created intermediate VCF files that were then encoded single threaded as BCF. Now we emit natively per thread BCF, and use the fast mergeInfo code to read BCF -> write BCF. Upcoming optimizations to avoid decoding genotype data unnecessarily will enable us to really quickly process BCF2 in parallel -- VariantContextWriterStub forces BCF output for intermediate files -- Nicer debug log message in BCF2Codec -- Turn off debug logging of BCF2LazyGenotypesDecoder -- BCF2FieldWriterManager now uses .debug not .info, so you won't see all of that field manager debugging info with BCF2 any longer -- VariantContextWriterFactory.isBCFOutput now has version that accepts just a file path, not path + options		2012-08-15 21:13:15 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Enable efficient parallel output of BCF2	2012-08-15 21:13:15 -04:00
test	Clean, documented implementation of ThreadFactory that monitors running / blocking / waiting time of threads it creates	2012-08-15 21:13:15 -04:00