Mark DePristo 64d4238e2f 99% working version of BCF2 encoder / decoder ... -- fixed final bugs with PL encoding / decoding -- Ready for testing by other members of the group -- Current performance numbers aren't so great, but they will improve in the next phase of BCF2 optimizations -- Fixed a nasty bug in the filter field -- Not that some (many?) GATK tools won't work with BCF because they internally assume values are Strings not their true types Read 1500 genotypes file in VCF -> VCF : 11 seconds Read 1500 genotypes file in VCF -> BCF : 9.5 seconds VariantEval 1500 genotypes file in VCF : 3 seconds VariantEval 1500 genotypes file in BCF : 3 seconds		2012-05-24 10:57:05 -04:00
..
alignment	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
commandline	Added ability to specify arguments in files via -args/--arg_file	2011-10-24 15:58:34 -04:00
gatk	Killed two more resource leakers that ignored requests to close wrapped file pointers, and added Unit Tests for each.	2012-05-21 15:41:56 -04:00
jna	When using bam list mode in HSP deriving VCF name from bam list instead of requiring an additional parameter.	2011-12-16 18:09:25 -05:00
utils	99% working version of BCF2 encoder / decoder	2012-05-24 10:57:05 -04:00
BaseTest.java	Testing of BCF codec	2012-05-24 10:57:01 -04:00
MD5DB.java	Merged bug fix from Stable into Unstable	2011-10-13 18:02:06 -04:00
MedianUnitTest.java	Adding more unit tests and contracts to PairHMM util class. Updating HaplotypeCaller to use the new PairHMM util class. Now that the HMM result isn't dependent on the length of the haplotype there is no reason to ensure all haplotypes have the save length which simplifies the code considerably.	2012-03-05 08:28:42 -05:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	Rev'ing Tribble from 53 to 94	2012-05-03 07:31:47 -04:00