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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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	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
test	By default, IndelLengthHistogram won't collapse large events into the last bin, as it produces weird looking plots	2012-04-04 18:48:03 -04:00