Eric Banks d6277b70d8 Forgot to consider the optimized case in hasAllele		2012-04-24 11:32:28 -04:00
..
Allele.java	Added support for breakpoint alleles	2012-02-23 12:14:48 -05:00
CommonInfo.java	Bugfix for pError not being checked correctly in CommonInfo	2011-11-19 15:58:59 -05:00
Genotype.java	Damn you, Mark	2012-02-28 10:09:09 -05:00
GenotypeLikelihoods.java	Slightly better error message	2012-04-23 09:37:28 -04:00
GenotypesContext.java	Bug fix for incorrect logic in subsetSamples	2011-12-14 16:14:26 -05:00
LazyGenotypesContext.java	GenotypesContext now updates cached data for add, set, replace operations when possible	2011-11-22 08:40:48 -05:00
VariantContext.java	Forgot to consider the optimized case in hasAllele	2012-04-24 11:32:28 -04:00
VariantContextBuilder.java	Major restructuring of HaplotypeCaller's LikelihoodCalculationEngine and GenotypingEngine. We no longer create an ugly event dictionary and genotype events found on haplotypes independently by finding the haplotype with the max likelihood. Lots of code has been rewritten to be much cleaner.	2012-03-14 12:05:05 -04:00
VariantContextUtils.java	If we are subsetting alleles in the UG (either because there were too many or because some were not polymorphic), then we may need to trim the alleles (because the original VariantContext may have had to pad at the end). Thanks to Ryan for reporting this. Only one of the integration tests had even partially covered this case, so I added one that did.	2012-04-20 17:00:05 -04:00
VariantJEXLContext.java	Change interface to getNegLog10PError to getLog10PError	2011-11-18 21:07:30 -05:00