Made it possible to specify the mutation pattern (still G->A by default)
Version bump reflection in CHANGELOG
Added MutPattern class and associated simple tests
The heavily refactored hypermutation evaluation (with context) seems to, at the very least, be 'doing a thing'. Still have to get splitting functional again, do sanity checks, revisit tests, add options, and clean up various data output business.
Corrected header names in Set#write_analysis
Added another mut_pattern constant and some more careful lookahead regexing to deal with overlaps
Fixed bad mut_pattern negation and have a few more tests passing now
Woops - removing debugging code
Renamed a bunch of things for better consistency with new gestault
Having almost all tests passing again
Have all tests passing! (Had the wrong old_control_pattern)
Fixed some issues with regexp negation and such. New test making sure context based aproach is doing the right thing.
Added command line options for switching between different patterns
Versioning stuff
Fixed type mismatching between pattern names and patterns
Working implementation of the beta_rat dependent branch; complete with tests and, debugging printout and so on; still hangs sometimes on the beta_rat.pdf computation, but that needs to be fixed there.
Set up again for computing fisher pvalues and basing hm_pos off that.
Swapped out fisher; Fixed failing tests; Fixed splitting on no HM
Fixed broken analysis tests, altered A3 context patterns to disclude trinucleotide context
Removed the upper tail from analysis (should save time), and set right tail to 5% instead of 2.5%.