Updated GencodeGtfCodec to be more permissive. #7166
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- Now the GencodeGtfCodec no longer parses transcriptType and geneType into enums. They are now stored as strings. This allows for arbitrary values in these fields and will help to future-proof (and species proof) the GTF parser. - Fixes #7054
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droazen
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Apr 1, 2021
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@jonn-smith Back to you with a few minor comments. Go ahead and merge after addressing them.
src/main/java/org/broadinstitute/hellbender/tools/funcotator/TranscriptSelectionMode.java
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...roadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java
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...roadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java
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src/test/java/org/broadinstitute/hellbender/utils/codecs/gtf/GencodeGtfCodecUnitTest.java
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droazen
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Apr 2, 2021
...roadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java
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Now the
GencodeGtfCodecno longer parsestranscriptTypeandgeneTypeinto enums. These fields are now each stored as a
String. This allows for arbitraryvalues in these fields and will help to future-proof (and species proof) the GTF parser.
Fixes IndexFeatureFile Error to Run Funcotator with Mouse Ensembl GTF #7054