Eric Banks 5c3ddec4c2 Large refactoring of the genotyping codebase. Deprecated several of the old classes that had the wrong allele ordering and made new better copies with the correct ordering; eventually we'll push the new ones into the place of the old ones but for now we'll give users a chance to update their code. Also, removed (or deprecated as needed) the genotype priors classes since we never use them and all they serve to do is make reading the code more complicated. I expect to finish this refactoring in GATK 1.7 (or 2.0?) so that should give Kristian ample time to update.		2012-04-05 10:49:08 -04:00
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net/sf	Merged bug fix from Stable into Unstable	2012-02-13 16:37:11 -05:00
org/broadinstitute/sting	Large refactoring of the genotyping codebase. Deprecated several of the old classes that had the wrong allele ordering and made new better copies with the correct ordering; eventually we'll push the new ones into the place of the old ones but for now we'll give users a chance to update their code. Also, removed (or deprecated as needed) the genotype priors classes since we never use them and all they serve to do is make reading the code more complicated. I expect to finish this refactoring in GATK 1.7 (or 2.0?) so that should give Kristian ample time to update.	2012-04-05 10:49:08 -04:00