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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net/sf	Removed annoying FastaSequenceIndexBuilderProgressListener infrastructure that was just a boolean switch on whether to print progress or not.	2011-07-27 22:06:23 -04:00
org/broadinstitute/sting	Removed lots of old, and not to be used, HMM options	2011-09-27 10:08:40 -04:00