Eric Banks 1f19afe1d9 Fixed bug in the IndelRealigner: now that variants are correctly typed in VariantContext, it is possible that a variant can be an indel but neither an insertion or a deletion; added a isComplexIndel() method and now we check for such an event in the realigner (we don't use them to generate alternate consenses). Also, added a isMNP() method while I was there so that it would be consistent with other variant types.		2011-06-29 15:54:09 -04:00
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chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Fixed bug in the IndelRealigner: now that variants are correctly typed in VariantContext, it is possible that a variant can be an indel but neither an insertion or a deletion; added a isComplexIndel() method and now we check for such an event in the realigner (we don't use them to generate alternate consenses). Also, added a isMNP() method while I was there so that it would be consistent with other variant types.	2011-06-29 15:54:09 -04:00
packages	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
scala	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
testdata	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00