Mark DePristo 17fbd103d0 Smarter infrastructure to decode genotypes in BCF ... -- Eliminated the large intermediate map from field name to list of list<Integer> values needed to create genotypes without the GenotypeBuilder. The new code is cleaner and simply fills in an array of GenotypeBuilders as it moves through the column layout in BCF2 -- Now we create once decoders specialized for each GT field (GT, AD, etc) that can be optimized for putting data into the GenotypeBuilder. In a subsequent commit these will actually use lower level BCF2 decoders to create the low-level ints and int[], avoiding the intermediate List<Integer> form -- Reduced the amount of data further to be computed in the DiffEngine. The DiffEngine algorithm needs to be rethought to be efficient...		2012-06-14 16:42:25 -04:00
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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	Efficient Genotype object Intermediate commit	2012-06-14 16:42:24 -04:00
jna	Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000.	2012-05-29 11:18:22 -04:00
utils	Finalizing new Genotype object and associated routines	2012-06-14 16:42:25 -04:00
BaseTest.java	Updated hard limit MathUtils.MAXN number of samples from 11,000 to 50,000.	2012-05-29 11:18:22 -04:00
MD5DB.java	Smarter infrastructure to decode genotypes in BCF	2012-06-14 16:42:25 -04:00
MD5Mismatch.java	Final updates to integration tests for BCF2	2012-05-24 10:58:59 -04:00
StingTextReporter.java	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
WalkerTest.java	First step towards an efficient Genotype object	2012-06-14 16:42:23 -04:00