BioJulia / Bio.jl

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia
http://biojulia.dev
MIT License
261 stars 63 forks source link

fix some Bio.Var tests #432

Closed bicycle1885 closed 7 years ago

bicycle1885 commented 7 years ago

I didn't notice but large amounts of tests of Bio.Var are inside a block comment. This seems to be introduced in this commit: https://github.com/BioJulia/Bio.jl/commit/3ed91d20d140b2385aa5673bbf949700eb62fec8. Unfortunately, some tests didn't pass and I'm not sure how I should fix them. So, I narrowed the range of the comment and fixed a few test I could.

@Ward9250 Could you take care of that after change?

codecov-io commented 7 years ago

Codecov Report

Merging #432 into master will increase coverage by 7.57%. The diff coverage is n/a.

@@            Coverage Diff             @@
##           master     #432      +/-   ##
==========================================
+ Coverage   70.95%   78.52%   +7.57%     
==========================================
  Files         125      125              
  Lines        9140     9146       +6     
==========================================
+ Hits         6485     7182     +697     
+ Misses       2655     1964     -691
Impacted Files Coverage Δ
src/intervals/interval.jl 91.89% <0%> (-1.36%) :arrow_down:
src/var/vcf/reader.jl 6.48% <0%> (+6.48%) :arrow_up:
src/var/bcf/record.jl 84.95% <0%> (+84.95%) :arrow_up:
src/var/vcf/record.jl 85.21% <0%> (+85.21%) :arrow_up:
src/var/vcf/metainfo.jl 88.76% <0%> (+88.76%) :arrow_up:
src/var/bcf/reader.jl 88.88% <0%> (+88.88%) :arrow_up:
src/var/vcf/header.jl 92.59% <0%> (+92.59%) :arrow_up:
src/var/bcf/writer.jl 94.44% <0%> (+94.44%) :arrow_up:
src/var/vcf/writer.jl 100% <0%> (+100%) :arrow_up:

Continue to review full report at Codecov.

Legend - Click here to learn more Δ = absolute <relative> (impact), ø = not affected, ? = missing data Powered by Codecov. Last update 2aebb14...461b007. Read the comment docs.

TransGirlCodes commented 7 years ago

@bicycle1885 Yes this should relate to distance computation methods which are currently not exported until I deal with them to make them compatible with new site counting api in Var.

The thing is, I've come to see some of the site counting code in Var, should be in Seq, with Var extending it a bit by adding new site types. Additionally, in an older branch in which I was working on bit-flipping methods to count mutations in a bit parallel manner, I see scope for extending the Seq code for doing the bitpar_mismatches. So as my bit_parallel mutation counting methods can slot in there! So there's a few loose ends of this little bit of my postdoc I have to tie together soon.