Guillermo del Angel a05a7f287d TMP: disable checking of whether on the fly index is equal to index after run completed		2012-03-16 21:14:45 -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	TMP: disable checking of whether on the fly index is equal to index after run completed	2012-03-16 21:14:45 -04:00