Eric Banks c07a577ba3 Significant restructuring of the Exact model, as discussed within the dev group last week. There is no more marginalizing over alternate alleles, and we now keep track of the MLE and MAP. Important notes: 1) integration tests change because the previous marginalization wasn't done correctly (as pointed out by Guillermo) and our confidences were too high for many multi-allelic sites; 2) there is a major TO-DO item that needs to be discussed within the dev group (so they should expect a follow up email); 3) this code is still in flux as I am awaiting feedback from Ryan now on its performance with the Haplotype Caller (the good news, Ryan, is that we recover that site that we were losing previously).		2012-03-27 00:27:44 -05:00
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datasources	Avoid buffer underflow in GATKBAMIndex by detecting premature EOF in BAM indices	2012-03-08 15:30:44 -05:00
executive	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
filters	Taking care of bad cigars in the GATK	2012-03-20 14:32:57 -04:00
iterators	a) Bug fix in calling new functions that give indel bases and length from regular pileup in LocusIteratorByState, b) Added unit test to cover these.	2012-02-25 13:57:28 -05:00
refdata	Merge with master	2011-11-19 09:56:06 -05:00
report	GATK Report code cleanup	2012-03-19 11:53:57 -04:00
samples	Added UnitTests for getFamilies() and getChildrenWithParents()	2011-12-09 15:57:07 +01:00
traversals	First pass of the asynchronous block loader.	2011-11-18 15:02:59 -05:00
walkers	Significant restructuring of the Exact model, as discussed within the dev group last week. There is no more marginalizing over alternate alleles, and we now keep track of the MLE and MAP. Important notes: 1) integration tests change because the previous marginalization wasn't done correctly (as pointed out by Guillermo) and our confidences were too high for many multi-allelic sites; 2) there is a major TO-DO item that needs to be discussed within the dev group (so they should expect a follow up email); 3) this code is still in flux as I am awaiting feedback from Ryan now on its performance with the Haplotype Caller (the good news, Ryan, is that we recover that site that we were losing previously).	2012-03-27 00:27:44 -05:00
EngineFeaturesIntegrationTest.java	HierarchicalMicroScheduler no longer attempts to wrap exceptions	2012-03-23 11:27:21 -04:00
GenomeAnalysisEngineUnitTest.java	Allow processing of empty intervals, but warn user when this case is encountered.	2011-10-28 12:12:14 -04:00
WalkerManagerUnitTest.java	Moving more tools over to use the standard VC arg collection. Also, while I'm in there, I removed all of the empty references to @Requires given that it's no longer relevant.	2011-08-10 12:20:18 -04:00