Closed standage closed 5 years ago
Merging #339 into master will increase coverage by
0.04%
. The diff coverage is100%
.
@@ Coverage Diff @@
## master #339 +/- ##
==========================================
+ Coverage 95.01% 95.05% +0.04%
==========================================
Files 48 48
Lines 3005 3029 +24
Branches 563 570 +7
==========================================
+ Hits 2855 2879 +24
Misses 108 108
Partials 42 42
Impacted Files | Coverage Δ | |
---|---|---|
kevlar/call.py | 88.32% <ø> (ø) |
:arrow_up: |
kevlar/simlike.py | 96.35% <100%> (+0.31%) |
:arrow_up: |
kevlar/cli/simlike.py | 100% <100%> (ø) |
:arrow_up: |
kevlar/cli/call.py | 100% <100%> (ø) |
:arrow_up: |
kevlar/vcf.py | 95.96% <100%> (+0.01%) |
:arrow_up: |
kevlar/varmap.py | 99.02% <100%> (+0.01%) |
:arrow_up: |
Continue to review full report at Codecov.
Legend - Click here to learn more
Δ = absolute <relative> (impact)
,ø = not affected
,? = missing data
Powered by Codecov. Last update d9f0838...4536b99. Read the comment docs.
Also in this PR: changed some recently added hard-coded filters to configurable/disableable parameters/options.
It is often unreasonable to expect that all k-mers spanning the variant in the proband will be high abundance, and so kevlar has never required that all spanning k-mers are "interesting" or putatively novel. Even filtering based on the number of spanning k-mers that are "interesting" has been problematic, since some true variants sometimes have few spanning k-mers that meet the required thresholds.
However, kevlar has never filtered calls based on what is not expected in the k-mer spanning the variant in the proband. While it is common to have low abundance k-mers intermittently, it is very rare to have long stretches of low abundance k-mers spanning the variant in a true variant.
This update introduces a new filter that will discard a variant prediction if there are 5 or more low-abundance k-mers spanning the variant call. Based on observations, this will eliminate many false positives, while having little to no effect on true calls.