codecov[bot]
commented
3 years ago Codecov Report
Merging #5 (c87d478) into master (f2d0654) will increase coverage by
0.14%. The diff coverage is93.39%.
@@ Coverage Diff @@
## master #5 +/- ##
==========================================
+ Coverage 93.07% 93.21% +0.14%
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Files 8 8
Lines 982 2108 +1126
==========================================
+ Hits 914 1965 +1051
- Misses 68 143 +75 | Flag | Coverage Δ | |
|---|---|---|
| CPython | 93.21% <93.39%> (+0.14%) |
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| Linux | 93.21% <93.39%> (+0.14%) |
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| OSX | 93.21% <93.39%> (+0.14%) |
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| PyPy | 98.07% <ø> (ø) |
|
| Windows | 99.73% <ø> (ø) |
|
| v3.5 | 93.14% <93.39%> (+0.22%) |
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| v3.6 | 93.19% <93.39%> (+0.16%) |
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| v3.7 | 93.19% <93.39%> (+0.16%) |
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| v3.8 | 93.21% <93.39%> (+0.14%) |
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| v3.9 | 93.21% <93.39%> (+0.14%) |
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| Impacted Files | Coverage Δ | |
|---|---|---|
| pyrodigal/_pyrodigal.pyx | 91.82% <93.39%> (+2.79%) |
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The original Prodigal implementation uses bitmaps to store the input sequences, which allows storing both strands in the usual indexing order, and reduces overall memory consumption by 35% (using a 2-bitmap for the forward strand, a 2-bitmap for the reverse strand, and a 1-bitmap to mark unknown characters). However this approach also comes with sensible drawbacks: testing a bitmap takes more time and prevents SIMD implementation.
This PR reimplements most of the functions in the Prodigal C code as Cython function that work with a sequence stored in a contiguous
uint8_tarray instead of bitmaps, among other things.