Changed referenceBases to silently fail and emit a single warning if there is no reference #3299
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Codecov Report
@@ Coverage Diff @@
## master #3299 +/- ##
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+ Coverage 80.366% 80.374% +0.008%
- Complexity 17666 17673 +7
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Files 1178 1179 +1
Lines 63864 63880 +16
Branches 9930 9930
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+ Hits 51325 51343 +18
+ Misses 8584 8582 -2
Partials 3955 3955
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| @Override | ||
| public List<String> getKeyNames() { return Collections.singletonList(REFERENCE_BASES_KEY); } | ||
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| @Override | ||
| public Map<String, Object> annotate(final ReferenceContext ref, | ||
| final VariantContext vc, | ||
| final ReadLikelihoods<Allele> likelihoods) { | ||
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| if (ref==null) { |
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I though that #2799 suggest to throw an UserException, which actually makes sense if the user provides an annotation that couldn't be apply because the requirements are not met...
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The warning seems good for now, and consistent with existing behavior in the annotation classes -- we can open a separate ticket to discuss whether there should be a mode in which GATK throws in these cases.
…exsist and added a one time logger functionality
| * A logger wrapper class which only outputs the first warning provided to it | ||
| */ | ||
| public class OneShotLogger { | ||
| Logger logger; |
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Mark as @VisibleForTesting
| @Override | ||
| public List<String> getKeyNames() { return Collections.singletonList(REFERENCE_BASES_KEY); } | ||
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| @Override | ||
| public Map<String, Object> annotate(final ReferenceContext ref, | ||
| final VariantContext vc, | ||
| final ReadLikelihoods<Allele> likelihoods) { | ||
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| if (ref==null) { |
There was a problem hiding this comment.
The warning seems good for now, and consistent with existing behavior in the annotation classes -- we can open a separate ticket to discuss whether there should be a mode in which GATK throws in these cases.
jamesemery
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