Funcotator: add 5'/3' flank support, with tests #5403
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@jonn-smith and @LeeTL1220 please review. I still plan to add a few more tests (in particular, for overlapping genes and for all-transcripts mode), but I will add these during review rather than holding this branch up any longer. |
Codecov Report
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## master #5403 +/- ##
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+ Coverage 87.027% 87.085% +0.058%
- Complexity 30440 30468 +28
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Files 1852 1853 +1
Lines 140936 141335 +399
Branches 15508 15517 +9
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+ Hits 122652 123081 +429
+ Misses 12645 12614 -31
- Partials 5639 5640 +1
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| @@ -85,6 +85,20 @@ | |||
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| public List<String> annotationOverrides = new ArrayList<>(); | |||
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| @Argument( | |||
| fullName = FuncotatorArgumentDefinitions.FIVE_PRIME_FLANK_SIZE_NAME, | |||
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Can you update the documentation for these two inputs to refer to transcript rather than gene?
| .setTumorSeqAllele2(altAllele.getBaseString()) | ||
| .setGenomeChange(getGenomeChangeString(variant, altAllele)) | ||
| .setAnnotationTranscript(transcript.getTranscriptId()) | ||
| .setOtherTranscripts(gtfFeature.getTranscripts().stream().map(GencodeGtfTranscriptFeature::getTranscriptId).collect(Collectors.toList())) |
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You shouldn't need to set other transcripts here - it'll get populated in createGencodeFuncotationsByAllTranscripts in the call to populateOtherTranscriptsMapForFuncotation.
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| final GencodeFuncotation gencodeFuncotation = (GencodeFuncotation)funcotations.get(0); | ||
| Assert.assertEquals(gencodeFuncotation.getVariantClassification(), GencodeFuncotation.VariantClassification.IGR); | ||
| Assert.assertNull(gencodeFuncotation.getHugoSymbol()); |
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As we discussed in person it would be beneficial to make sure testCreateFuncotations is run with a non-zero flanking size for 5' and 3'.
See line 1475
(Putting this here because I can't put it lower in github.)
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Turned on both 5' and 3' flanks for testCreateFuncotations(), and all test cases are passing.
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Unfortunately I don't have time to implement the multi-gene test before I catch my flight, so I've spun it off into a separate issue to be addressed in a future PR: #5417 |
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@jonn-smith All comments (except for #5417) addressed, and the branch has been rebased onto your latest changes. If you give me a final thumbs up, I'll merge once tests pass. |
Added support for annotating 5'/3' flanks via new FIVE_PRIME_FLANK and THREE_PRIME_FLANK funcotations.
Added --five-prime-flank-size and --three-prime-flank-size arguments to control the size of each flanking region.
Refactored datasource classes to allow for padded/custom queries to make this feature possible.
We now emit IGR funcotations in more cases (in particular, when a gene has no basic transcripts, and when the basic transcripts do not fully span a gene and the flank size is small).
Added comprehensive unit tests, and updated integration test data.
Resolves #4771