gatk3的最后一个经典版本3.8

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
public	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
settings	The tribble dependency is now handled through ivy. Revved tribble to r18 and removed obsolete build targets in build.xml	2011-08-11 16:38:29 -04:00
LICENSE	One last test...	2011-06-28 19:18:17 -04:00
build.xml	Fixing the javadoc/scaladoc targets in build.xml	2011-08-11 19:24:41 -04:00
ivy.xml	The tribble dependency is now handled through ivy. Revved tribble to r18 and removed obsolete build targets in build.xml	2011-08-11 16:38:29 -04:00