Guillermo del Angel c44c7b9a97 Restored optimization in Pair HMM only to compute HMM matrices starting in index where haplotypes start to diverge - saves about 15-20% of runtime which is what we lost by disabling banding in latest version, so runtime should be now about the same as what it was before refactoring. Output is bit-true to previous commit		2012-04-19 19:39:43 -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	Restored optimization in Pair HMM only to compute HMM matrices starting in index where haplotypes start to diverge - saves about 15-20% of runtime which is what we lost by disabling banding in latest version, so runtime should be now about the same as what it was before refactoring. Output is bit-true to previous commit	2012-04-19 19:39:43 -04:00
test	Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable	2012-04-19 12:50:29 -04:00