Fix Funcotator transcript override functionality #9214
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- Correctly remove the version suffix from transcripts that include an underscore character - Allow ENSEMBL GTF files to use the --prefer-mane-transcripts option
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Github actions tests reported job failures from actions build 15832447462
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kachulis
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Jun 23, 2025
src/main/java/org/broadinstitute/hellbender/tools/funcotator/FuncotatorUtils.java
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...roadinstitute/hellbender/tools/funcotator/dataSources/gencode/GencodeFuncotationFactory.java
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kachulis
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Jun 24, 2025
| @@ -886,19 +886,25 @@ private List<GencodeFuncotation> createFuncotationsHelper(final VariantContext v | |||
| List<GencodeGtfTranscriptFeature> transcriptList; | |||
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| // Only get basic transcripts if we're using data from Gencode: | |||
| if ( gtfFeature.getGtfSourceFileType().equals(GencodeGtfCodec.GTF_FILE_TYPE_STRING) || | |||
| gtfFeature.getGtfSourceFileType().equals(EnsemblGtfCodec.GTF_FILE_TYPE_STRING)) { | |||
| if ( gtfFeature.getGtfSourceFileType().equals(GencodeGtfCodec.GTF_FILE_TYPE_STRING) ) { | |||
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why split this up like this instead of keeping in the same if block?
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Some of the newer GENCODE GTFs (at the very least GRCh37 liftovers of versions >v19) contain transcript IDs whose version numbers include a secondary number separated with an underscore, e.g. "ENST00000xxxxxx.yy_zz". The currently used regex only considers a single dot character followed by one or more digits and therefore fails to properly remove the version number. This PR should fix that.
Personal note: I don't like regexes in production code anyway, so instead of replacing it with one that works for now, I opted for a cleaner and more maintainable (in my opinion) alternative.
In addition, the recently introduced
--prefer-mane-transcriptsrequires the file to be strictly of the GENCODE GTF format, but the hg19 data source with GENCODE v43 (backmapped to GRCh37) contains a GTF in the ENSEMBL GTF format (actually GFF3), making this option unusable. This PR should also fix that.