Eric Banks 70ba851478 Might as well check for the illegal state and throw an exception		2011-06-29 15:59:10 -04:00
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analyzecovariates	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
commandline	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
datasources/pipeline	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
gatk	Might as well check for the illegal state and throw an exception	2011-06-29 15:59:10 -04:00
jna	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
queue	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
utils	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