make sure peel-transmat gets columns in same order as counts file

petrelharp / context

Context-dependent mutation rate inference machinery.

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Closed petrelharp closed 9 years ago

petrelharp commented 9 years ago

... and refactor to precompute the tree traversal.

petrelharp commented 9 years ago

In fa10f036c6efd28393de5324456325a1c35f5c66 :

peel.transmat refactored into peel.transmat.setup and peel.transmat.compute to do this; and also
test of the resulting transition matrix in testing-code/tree-tests.R

In 76927b85660a56e3ca4fbb4db55b955b7bd8016b :