Eric Banks 7519484a38 Refactored PairHMM.initialize to first take haplotype max length and then the read max length so that it is consistent with other PairHMM methods.		2013-02-25 15:04:23 -05:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Refactored PairHMM.initialize to first take haplotype max length and then the read max length so that it is consistent with other PairHMM methods.	2013-02-25 15:04:23 -05:00
test	Replace Smith-Waterman alignment with the bubble traversal.	2013-02-22 15:42:16 -05:00