Guillermo del Angel 3dfb60a46e Fixing up and refactoring usage of indel categories. On a variant context, isInsertion() and isDeletion() are now removed because behavior before was wrong in case of multiallelic sites. Now, methods isSimpleInsertion() and isSimpleDeletion() will return true only if sites are biallelic. For multiallelic sites, isComplex() will return true in all cases. ... VariantEval module CountVariants is corrected and an additional column is added so that we log mixed events and complex indels separately (before they were being conflated). VariantEval module IndelStatistics is considerably simplified as the sample stratification was wrong and redundant, now it should work with the VE-generic Sample stratification. Several columns are renamed or removed since they're not really useful		2011-08-18 16:17:38 -04:00
..
baq	Removed a public -> private dependency in our test suite.	2011-08-12 17:29:10 -04:00
bed	…
codecs	Renaming the HapMap codec and feature to RawHapMap so that we don't get esoteric errors when trying to bind a rod with the name 'hapmap' (since it was also a feature).	2011-08-12 11:11:56 -04:00
collections	…
fasta	Long-delayed change to CachingIndexedFastaSequenceFile. Made the cache	2011-07-01 16:04:30 -04:00
genotype	Darn, forgot to update unit tests.	2011-08-03 12:31:08 -04:00
interval	…
pileup	…
report	…
sam	…
text	GATKReport v0.2:	2011-08-03 00:24:47 -04:00
threading	Removed GATK use of distributed parallelism framework.	2011-07-20 16:26:09 -04:00
variantcontext	Fixing up and refactoring usage of indel categories. On a variant context, isInsertion() and isDeletion() are now removed because behavior before was wrong in case of multiallelic sites. Now, methods isSimpleInsertion() and isSimpleDeletion() will return true only if sites are biallelic. For multiallelic sites, isComplex() will return true in all cases.	2011-08-18 16:17:38 -04:00
BaseUtilsUnitTest.java	…
GenomeLocParserUnitTest.java	…
GenomeLocSortedSetUnitTest.java	…
GenomeLocUnitTest.java	…
MWUnitTest.java	…
MathUtilsUnitTest.java	…
PathUtilsUnitTest.java	…
ReadUtilsUnitTest.java	…
ReservoirDownsamplerUnitTest.java	…
SimpleTimerUnitTest.java	…
UtilsUnitTest.java	…