Fix reported bug where no-call genotypes with no reads get genotype #5667
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
posterior probabilities and calls
Codecov Report
@@ Coverage Diff @@
## master #5667 +/- ##
==============================================
- Coverage 87.05% 64.421% -22.63%
+ Complexity 31700 15093 -16607
==============================================
Files 1938 1204 -734
Lines 146097 70364 -75733
Branches 16128 11343 -4785
==============================================
- Hits 127178 45329 -81849
- Misses 13033 20294 +7261
+ Partials 5886 4741 -1145
|
| return false; | ||
| } | ||
| if (genotype.hasDP() && genotype.getDP() == 0) { | ||
| int[] pls = genotype.getPL(); |
There was a problem hiding this comment.
How about return MathUtils.max(genotype.getPL()) > 0?
| @Test | ||
| public void testGenotypesWithNoDataDoNotChange() { | ||
| final GenotypeBuilder gb = new GenotypeBuilder("s1"); | ||
| gb.alleles(Arrays.asList(Allele.NO_CALL, Allele.NO_CALL)).DP(0).AD(new int[]{0,0}).GQ(0).PL(new int[]{0,0,0}); |
There was a problem hiding this comment.
How about chaining .alleles etc with the previous line?
| public void testGenotypesWithNoDataDoNotChange() { | ||
| final GenotypeBuilder gb = new GenotypeBuilder("s1"); | ||
| gb.alleles(Arrays.asList(Allele.NO_CALL, Allele.NO_CALL)).DP(0).AD(new int[]{0,0}).GQ(0).PL(new int[]{0,0,0}); | ||
| final VariantContext vc = makeVC("noCall", Arrays.asList(Allele.create("A",true), Allele.create("T")), gb.make()); |
There was a problem hiding this comment.
Allele.create("A", true) can be replaced with the pre-defined Allele.REF_A.
davidbenjamin
requested changes
Feb 14, 2019
|
Back to you @davidbenjamin |
|
Good to merge! 👍 |
davidbenjamin
approved these changes
Feb 14, 2019
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
posterior probabilities and calls
Closes #5666