Guillermo del Angel aee66ab157 Big UG refactoring and intermediate commit to support indels in pool caller (not done yet). Lots of code pulled out of long spaghetti-like functions and modularized to be easily shareable. Add functionality in ErrorModel to count indel matches/mismatches (but left part disabled as not to change integration tests in this commit), add computation of pool genotype likelihoods for indels (not fully working yet in more realistic cases, only working in artificial nice pools). Lot's of TBD's still but existing UG and pool SNP functionality should be intact		2012-06-13 11:14:44 -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	Big UG refactoring and intermediate commit to support indels in pool caller (not done yet). Lots of code pulled out of long spaghetti-like functions and modularized to be easily shareable. Add functionality in ErrorModel to count indel matches/mismatches (but left part disabled as not to change integration tests in this commit), add computation of pool genotype likelihoods for indels (not fully working yet in more realistic cases, only working in artificial nice pools). Lot's of TBD's still but existing UG and pool SNP functionality should be intact	2012-06-13 11:14:44 -04:00
test	Drat, forgot the unit tests again	2012-06-12 19:00:47 -04:00