gatk3的最后一个经典版本3.8

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
public	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
settings	Updated the tribble jar -- this should fix most of the integration test	2011-06-29 01:11:03 -04:00
LICENSE	One last test...	2011-06-28 19:18:17 -04:00
build.xml	Fix up gsalib target to work with new public/private directory structure.	2011-06-29 14:48:10 -04:00
ivy.xml	A prototype script and library dependencies to extract a BAM list from a	2011-06-22 22:53:45 +00:00