Closed standage closed 5 years ago
Merging #359 into master will decrease coverage by
0.27%
. The diff coverage is38.46%
.
@@ Coverage Diff @@
## master #359 +/- ##
==========================================
- Coverage 97.05% 96.79% -0.27%
==========================================
Files 48 48
Lines 2886 2895 +9
Branches 533 536 +3
==========================================
+ Hits 2801 2802 +1
- Misses 52 58 +6
- Partials 33 35 +2
Impacted Files | Coverage Δ | |
---|---|---|
kevlar/vcf.py | 93.31% <38.46%> (-2.69%) |
:arrow_down: |
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,? = missing data
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Merging #359 into master will decrease coverage by
0.27%
. The diff coverage is38.46%
.
@@ Coverage Diff @@
## master #359 +/- ##
==========================================
- Coverage 97.05% 96.79% -0.27%
==========================================
Files 48 48
Lines 2886 2895 +9
Branches 533 536 +3
==========================================
+ Hits 2801 2802 +1
- Misses 52 58 +6
- Partials 33 35 +2
Impacted Files | Coverage Δ | |
---|---|---|
kevlar/vcf.py | 93.31% <38.46%> (-2.69%) |
:arrow_down: |
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 c4d4ddd...a17fddf. Read the comment docs.
This update modifies kevlar's VCF parser so that it does not choke on VCF produced by scalpel or DiscoSnp++. In particular, it checks whether VCF
FILTER
strings matched the pre-defined filters used by kevlar. If not, it prints a warning message rather than throwing an exception. This warning message can be disabled by settingreader.suppress_filter_warnings
toTrue
.Closes #358.