Mauricio Carneiro 1085df8b7b Making the BQSR pipeline publicly available and supported. ... this is for all the Pacbio validation that is going on right no in the cancer group. They are all using this script, and I'm happy to support it.		2011-06-29 16:05:32 -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	Making the BQSR pipeline publicly available and supported.	2011-06-29 16:05:32 -04:00
testdata	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00