Added in a VcfFuncotationFactory. #4593
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Fixes #4375 Need to release new copy of data sources along with this.
LeeTL1220
reviewed
Mar 27, 2018
| @@ -812,7 +813,7 @@ private String createProgramGroupID(final SAMFileHeader header) { | |||
| final String name, | |||
| final Class<? extends Feature> featureType) { | |||
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| final FeatureInput<? extends Feature> featureInput = new FeatureInput<>(name + ":" + filePath); | |||
| final FeatureInput<? extends Feature> featureInput = new FeatureInput<>(name + FEATURE_ARGUMENT_TAG_DELIMITER + filePath); | |||
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Minor... Can you change this to FeatureInput.FEATURE_ARGUMENT_TAG_DELIMITER and change the import statement above?
| * @param gencodeFuncotations {@link List} of {@link GencodeFuncotation} that have already been created for the given {@code variant}/{@code referenceContext}/{@code featureContext}. | ||
| * @return {@link List} of {@link Funcotation} given the {@code variant}, {@code referenceContext}, and {@code featureContext}. This should never be empty. | ||
| */ | ||
| public List<Funcotation> createFuncotations(final VariantContext variant, final ReferenceContext referenceContext, final Map<String, List<Feature>> featureSourceMap, final List<GencodeFuncotation> gencodeFuncotations) { |
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Can you combine this method with the one above to leverage shared code? If a data source needs gencode info, but createFuncotation(...) is called without Gencode, will an exception be thrown?
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Ha! Yeah - I forgot to combine them.
Yeah - I'll add that in.
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Yeah - the exception gets thrown in the concrete classes implementations of createFuncotations
| VCF("vcf") { | ||
| @Override | ||
| public void assertConfigFilePropertiesAreValid(final Properties configFileProperties, final Path configFilePath) { | ||
| // There is no special check required for vcf files. |
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Can you add a sentence of "why not" ?
| @@ -191,13 +197,13 @@ public String getName() { | |||
| * This method should never be called on a {@link CosmicFuncotationFactory} - knowledge of the applied | |||
| * {@link GencodeFuncotation}s is required to create a {@link Funcotation} from here. | |||
| */ | |||
| public List<Funcotation> createFuncotations(final VariantContext variant, final ReferenceContext referenceContext, final List<Feature> featureList) { | |||
| protected List<Funcotation> createFuncotationsOnVariant(final VariantContext variant, final ReferenceContext referenceContext, final List<Feature> featureList) { | |||
| // TODO: this should be allowed, but with a warning to the user that only annotations with good Genome Positions can be used. | |||
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Not yet.
Added as issue #4594
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OK @LeeTL1220 - first round comments addressed. |
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@jonn-smith OK by me to merge then. |
Codecov Report
@@ Coverage Diff @@
## master #4593 +/- ##
===============================================
- Coverage 79.839% 79.837% -0.002%
- Complexity 16958 16995 +37
===============================================
Files 1062 1063 +1
Lines 61680 61802 +122
Branches 9983 10008 +25
===============================================
+ Hits 49245 49341 +96
- Misses 8540 8556 +16
- Partials 3895 3905 +10
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cwhelan
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to cwhelan/gatk-linked-reads
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May 25, 2018
* Added in a VcfFuncotationFactory. Fixes broadinstitute#4357 (in conjunction with a new data sources release)
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Fixes #4357
Need to release new copy of data sources along with this.