BioJulia / Bio.jl / 2298
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Improvements to mutation counting. (#287)

* Added a new composition method for tuples of nucleotides.

* Added consensus method

* Corrected a dumb mistake

* Corrected spelling error

* Added mostfrequent method in src/seq/composition.jl

* Corrected my moronic mistake

* added convert statement to mostfrequent

* Added 3 majority vote algorithms

* majorityvote

* Progress with majorityvote

* majorityvote draft

* moved majorityvote

* Restored branch_basics.jl

* added majorityvote2 for comparrison purposes

* removed now redundant composition code

* Added draft count_mutations for vectors of sequences

* Corrected typo

* Exported NucleotideAlphabets from Seq

* Corrected typo

* Added inbounds macro to outer loop

* inlined isambiguous

* inlined Base.count_ones for nucleotides

* Changed logical operators to not use short circuit eval

* Added is_mutation for transitions

* Parameterised count_mutations

* Added inline to istransition and in transversion

* Changed && in ispurine and ispyrimadine to non-short circuit &'s

* Edited ispurine and ispyrimadine

* corrected is_mutation for Transition mutations

* Added is_mutation for transversions

* Added count_mutations for both transitions and transversions together

* Added docstrings to new count_mutations methods

* More docstrings and manual edit

* Edited existing tests for counting mutations

* Corrected NucleotideAlphabets

* Corrected a, b to s1 and s2

* Moved types to first arguments of count_mutations

* Separated matrix operations into thir own count_mutations method

* Changed distance(::Count{T})

* Corrected is_mutation error

* Changed distance(Proportion{T})

* Added @inbounds to distance(Proportion{T})

* Edited error in proportion distance

* Added inbounds to jukes cantor and tests

* Edited jukescantor tests

* corrected error in variance signature

* Added K80 and tests

* Added docstrings for count_mutations(::Matrix) methods

* Added matrix methods

* Implemented @kdmurray's AnyMutation suggestion

* Added @kdmurray91's docstring shortening suggestion

* Edited docstrings

* Changed 2 AnyMutation in Phylo.jl

* Fixed conflicting variable and static parameter

* Corrected error in phylo/runtests.jl

* revert logical ops

* Added tests for distance(Matrix{Nucleotide})

7794 of 10982 relevant lines covered (70.97%)

2077972.94 hits per line

Jobs
ID Job ID Ran Files Coverage
1 2298.1 0
81.99
 Travis Job 2298.1
2 2298.2 0
70.3
 Travis Job 2298.2
3 2298.3 0
81.99
 Travis Job 2298.3
4 2298.4 0
70.29
 Travis Job 2298.4
Source Files on build 2298
Detailed source file information is not available for this build.