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Add FASTA-TwoBit converter #117

Merged
merged 3 commits into from Oct 25, 2017
Merged

Add FASTA-TwoBit converter #117

merged 3 commits into from Oct 25, 2017

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totakke
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@totakke totakke commented Oct 25, 2017

Adds FASTA-TwoBit conversion, and test cases also.

As known issue, it is hard to convert a large reference file such as hg38.fa because of memory consumption. The reason is that cljam.io.fasta.reader/sequential-read-string is non-lazy and cljam.io.twobit.reader/read-all-sequences realizes some sequences by chunking. I plan on fixing them on another branch.

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codecov bot commented Oct 25, 2017

Codecov Report

Merging #117 into master will increase coverage by 0.12%.
The diff coverage is 94.44%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #117      +/-   ##
==========================================
+ Coverage    85.4%   85.53%   +0.12%     
==========================================
  Files          62       62              
  Lines        4104     4113       +9     
  Branches      401      401              
==========================================
+ Hits         3505     3518      +13     
+ Misses        198      194       -4     
  Partials      401      401
Impacted Files Coverage Δ
src/cljam/algo/convert.clj 78.57% <100%> (+7.6%) ⬆️
src/cljam/tools/cli.clj 53.66% <66.66%> (-0.36%) ⬇️
src/cljam/io/twobit/reader.clj 79.38% <0%> (+0.76%) ⬆️
src/cljam/io/sequence.clj 100% <0%> (+2.7%) ⬆️
src/cljam/io/fasta/core.clj 94.64% <0%> (+3.57%) ⬆️

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@alumi alumi merged commit 9b6cf23 into master Oct 25, 2017
@alumi alumi deleted the feature/fasta-twobit-convert branch October 25, 2017 15:39
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alumi commented Oct 25, 2017

LGTM 👍

I plan on fixing them on another branch.

And thank you for working on the memory issue!

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2 participants