codecov[bot]
commented
3 years ago Codecov Report
Merging #227 into develop will increase coverage by
10.71%. The diff coverage is100.00%.
@@ Coverage Diff @@
## develop #227 +/- ##
============================================
+ Coverage 80.48% 91.20% +10.71%
============================================
Files 52 52
Lines 9123 9126 +3
============================================
+ Hits 7343 8323 +980
+ Misses 1780 803 -977 | Flag | Coverage Δ | |
|---|---|---|
| #unittests | 91.20% <100.00%> (+10.71%) |
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| Impacted Files | Coverage Δ | |
|---|---|---|
| mavis/annotate/file_io.py | 88.73% <ø> (+2.25%) |
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| mavis/annotate/fusion.py | 96.02% <ø> (+0.33%) |
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| mavis/annotate/genomic.py | 93.12% <ø> (+1.03%) |
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| mavis/annotate/protein.py | 91.28% <ø> (+5.12%) |
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| mavis/assemble.py | 95.60% <ø> (+2.93%) |
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| mavis/blat.py | 90.27% <ø> (+1.85%) |
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| mavis/breakpoint.py | 95.00% <ø> (+1.53%) |
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| mavis/illustrate/elements.py | 96.37% <ø> (+1.69%) |
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| mavis/interval.py | 94.48% <ø> (ø) |
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| mavis/annotate/variant.py | 92.80% <100.00%> (+12.71%) |
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| ... and 27 more |
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Seems like when Annotation() is created, the breakpoint positions got swapped (due to sorting of positions) but the transcripts didn't, so the breakpoint positions and transcripts don't line up anymore. Fix is to check if breakpoints are in the right order, and swap them before Annotation() is created.