Fixed MapCodonOntoAA in chooseGeneticCode to handle ambigs
Merge branch 'master' of github.com:veg/hyphy
put REWIND in all fscanf calls in ReadDelimitedFiles
Fixed chooseGeneticCode to let translateCodonToAA use - translations
Modified Tree + operation; can now supply branch length arguments and also directly attach to parent (instead of always splitting the branch)
Merge branch 'master' of github.com:veg/hyphy
Added the option to tree + AVL to allow the splitting of an A-B branch into A-C-B, by passing a non-empty PARENT and an empty (or missing) NAME
Adding the old 'examples' directory
"If a friend declaration specifies a default argument expression,
that declaration shall be a definition and shall be the only declaration
of the function or function template in the translation unit."
Fixed unwanted formula bindings in HXB2Mapper.bf
Merge branch 'master' of github.com:veg/hyphy
Fixing obsolete and broken _cdn_alignment_cleanup in SeqAlignmentCodonShared
Added the calculation of (i) actual LRT rejection levels; (ii) regularized CI when a parameter boundary is hit to profile likelihood calculations
Merge branch 'master' of github.com:veg/hyphy
Revised how LHC handles hitting parameter space boundaries
* Adding CMake items to gitignore
* Reverting Test.bf UnitTest
* Removing CMake files in gtest directory from repo