Eric Banks 7424041a17 Updating integration tests to deal with the new GL framework. Now multi-allelic indel calls are correct.		2012-03-16 12:50:39 -04:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Add a conversion from the deprecated PL ordering to the new one. We need this for the DiploidSNPGenotypeLikelihoods which still use the old ordering. My intention is for this to be a temporary patch, but changing the ordering in DiploidSNPGenotypeLikelihoods is not appriopriate for committing to stable as it will break all of the external tools (e.g. MuTec) that are built on top of the class. We will have to talk to e.g. Kristian to see how disruptive this will be. Added unit tests to the GL conversions and indexing.	2012-03-16 11:14:37 -04:00
test	Updating integration tests to deal with the new GL framework. Now multi-allelic indel calls are correct.	2012-03-16 12:50:39 -04:00