BioJulia / Bio.jl / 2033
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Evolutionary distance computation for BioSequence. (#228)

* Initial commit evo_dist

First draft of raw distance

count_differences & count_differences_pairdel

count_differences

Added drafts of is_ambiguous_strict, and is_ambiguous_leinient

Set up ambiguity tests in runtests.

Added substitution models to exports

Added isambiguous to using statement.

Changed signature of is_ambiguous_leinient

Added count types

Edits to mutation_counting and addition of parametric P and Raw distance types

* Swapped phylo and var order in Bio.jl file

* Added tests for N and P distance computations.

* Corrected exports from Phylo module

* Corrected using statements in phylo tests

* Corrected errors in docs

* Corrected error in two distance methods

* Added distance method for N_Mutations{TsTv} and corresponding test.

* Corrected a test

* Made distance method parametric on TsTv

* added K80 distance methods

* Added fix to JC69 distance method

* Added JC69 test

* Edited the JC69 methods, internal methods were redundant right now

* Fixed JC69 distance method to correct testing failure

* Added extra tests for JC69, P, and N distances

* Corrected dna sequences and expected results for tests

* Changed test to test approximately equal results

* Edited JC69 test

* Added tests for K80

* P_Distance now returns the length of the sequence as well as N_Mutations

* Edited tests and JC69 function

* Added docstrings to the exported methods

* Changes to distance type naming based on review comments.

* Bikeshedding: moved distance computation to Var module.

* Edited manual pages and docstrings for evolutionary distances

* More rename

* Typealiases gone

* Corrected tests

* Corrected line 132 of distances.jl

4910 of 5975 relevant lines covered (82.18%)

1001385.72 hits per line

Jobs
ID Job ID Ran Files Coverage
1 2033.1 0
82.18
 Travis Job 2033.1
3 2033.3 0
82.18
 Travis Job 2033.3
Source Files on build 2033
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