Mark DePristo e99ff3caae Removed lots of old, and not to be used, HMM options ... -- resulted in massive code cleanup -- GdA will integrate his new banded algorithm here -- Removed: DO_CONTEXT_DEPENDENT_PENALTIES, GET_GAP_PENALTIES_FROM_DATA, INDEL_RECAL_FILE, dovit, GSA_PRODUCTION_ONLY		2011-09-27 10:08:40 -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	Removed lots of old, and not to be used, HMM options	2011-09-27 10:08:40 -04:00
test	Refactored reduced read utilities	2011-09-26 12:58:31 -04:00