Closed standage closed 5 years ago
Merging #350 into master will increase coverage by
0.03%
. The diff coverage is100%
.
@@ Coverage Diff @@
## master #350 +/- ##
==========================================
+ Coverage 95.06% 95.09% +0.03%
==========================================
Files 48 48
Lines 3039 3055 +16
Branches 570 574 +4
==========================================
+ Hits 2889 2905 +16
Misses 108 108
Partials 42 42
Impacted Files | Coverage Δ | |
---|---|---|
kevlar/simlike.py | 96.48% <100%> (+0.25%) |
:arrow_up: |
kevlar/cli/simlike.py | 100% <100%> (ø) |
:arrow_up: |
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This update adds a new filter to the
simlike
module to discard outlier high abundance k-mers at the ends of a variant-spanning window. As described in #349, a single bad k-mer with high abundance in all 3 samples can throw off the likelihood score, even if the rest of the k-mers show good separation (high abundance in proband, 0 abundance in parents).This filter is disabled by default, since there are some cases in which using this filter will increase the number of false positives substantially.
Closes #349.