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Precompute row and column counts #2

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Precompute row and column counts #2

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dmbates
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@dmbates dmbates commented Nov 2, 2018

  • At the time that a .bed file is memory-mapped, compute the column and row counts
  • Provide views of the column and row counts as Vector{SVector{4,Int}}
  • Modify summary statistics (mean, var, maf, minorallele, missingrate) to use the cached column or row counts.
  • I attempted to create a new version of the grm calculation but it didn't go well. The original from @Hua-Zhou performs better. Mine is called newgrm and not exported. For some reason it allocates about 10 times as much memory as the earlier version.
  • It is not clear that the work on precomputing the row and column counts is worthwhile. For one thing, they only work properly with files opened read-only. If an element of the data array is modified the cached values will no longer be valid.

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coveralls commented Nov 2, 2018

Pull Request Test Coverage Report for Build 27

  • 58 of 115 (50.43%) changed or added relevant lines in 3 files are covered.
  • 1 unchanged line in 1 file lost coverage.
  • Overall coverage increased (+1.9%) to 27.857%

Changes Missing Coverage Covered Lines Changed/Added Lines %
src/bedfile.jl 8 19 42.11%
src/summarystats.jl 50 68 73.53%
src/grm.jl 0 28 0.0%
Files with Coverage Reduction New Missed Lines %
src/bedfile.jl 1 14.75%
Totals Coverage Status
Change from base Build 18: 1.9%
Covered Lines: 78
Relevant Lines: 280

💛 - Coveralls

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codecov bot commented Nov 2, 2018

Codecov Report

Merging #2 into master will increase coverage by 1.94%.
The diff coverage is 50.43%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master       #2      +/-   ##
==========================================
+ Coverage   25.91%   27.85%   +1.94%     
==========================================
  Files           2        4       +2     
  Lines         247      280      +33     
==========================================
+ Hits           64       78      +14     
- Misses        183      202      +19
Impacted Files Coverage Δ
src/BEDFiles.jl 100% <ø> (ø) ⬆️
src/grm.jl 0% <0%> (ø)
src/bedfile.jl 14.75% <42.1%> (-10.86%) ⬇️
src/summarystats.jl 73.52% <73.52%> (ø)

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