Closed standage closed 5 years ago
Merging #354 into master will decrease coverage by
0.08%
. The diff coverage is100%
.
@@ Coverage Diff @@
## master #354 +/- ##
==========================================
- Coverage 97.13% 97.05% -0.08%
==========================================
Files 48 48
Lines 2894 2886 -8
Branches 532 533 +1
==========================================
- Hits 2811 2801 -10
- Misses 51 52 +1
- Partials 32 33 +1
Impacted Files | Coverage Δ | |
---|---|---|
kevlar/cli/varfilter.py | 100% <ø> (ø) |
:arrow_up: |
kevlar/intervalforest.py | 77.42% <100%> (-4.06%) |
:arrow_down: |
kevlar/vcf.py | 96% <100%> (+0.03%) |
:arrow_up: |
kevlar/varfilter.py | 100% <100%> (ø) |
:arrow_up: |
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The difference in runtime is tremendous: 3 minutes vs 30+ minutes before.
I don't know if the biggest factor is the difference in building vs querying an interval tree, or Python's object overhead, or what. In any case, storing a much smaller amount of data in memory and streaming the "big" data is always the better idea and should have been my first thought.
Testing out a complete rewrite of the varfilter module. Should drastically reduce memory requirements. Run time comparison in progress.