TASK-5318 - Implement custom annotator to allow clients private files #262
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jtarraga
changed the title
j-coll
changed the title
j-coll
reviewed
Jun 5, 2024
| return new SequenceOntologyTerm(ConsequenceTypeMappings.getSoAccessionString(name), name); | ||
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| public static String buildVariantId(String chromosome, int start, String reference, String alternate) { |
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Unused method. This method is intended to be used to create an _id for mongodb. It should not be here
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This includes appendChromosome(..) and SEPARATOR_CHAR
j-coll
requested changes
Jun 5, 2024
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| public static final char SEPARATOR_CHAR = ':'; | ||
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| public static final String THREEPRIME_OVERLAPPING_NCRNA = "3prime_overlapping_ncrna"; |
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Most of these constant values should be enums
| public static final String TRANSLATED_UNPROCESSED_PSEUDOGENE = "translated_unprocessed_pseudogene"; | ||
| public static final String LRG_GENE = "LRG_gene"; | ||
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| public static final String INTERGENIC_VARIANT = "intergenic_variant"; |
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These values here are partially duplicated with values from ConsequenceTypeMappings
…bly match, #TASK-5913, #TASK-5318 On branch TASK-5318 Changes to be committed: modified: biodata-formats/src/main/java/org/opencb/biodata/formats/variant/cosmic/CosmicParser.java modified: biodata-formats/src/test/java/org/opencb/biodata/formats/variant/cosmic/CosmicParserTest.java
On branch TASK-5318 Changes to be committed: modified: biodata-models/src/main/java/org/opencb/biodata/models/sequence/SequenceLocation.java
j-coll
approved these changes
Aug 9, 2024
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Implement COSMIC parser
TASK-5318