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Fix exon annotation not showing #484

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merged 2 commits into from
Jan 10, 2025
Merged

Fix exon annotation not showing #484

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5b1eee8
Fix exon annotation not showing
calvinlu3 Dec 19, 2024
8a7a01b
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calvinlu3 Jan 9, 2025
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7 changes: 3 additions & 4 deletions src/main/java/org/mskcc/oncokb/curation/service/MainService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -214,6 +214,9 @@ public AlterationAnnotationStatus annotateAlteration(ReferenceGenome referenceGe
alteration.setName(alteration.getAlteration());
}

alterationWithStatus.setMessage(alterationWithEntityStatus.getMessage());
alterationWithStatus.setType(alterationWithEntityStatus.getType());

// update reference genome
if (alteration.getGenes().size() > 0 && PROTEIN_CHANGE.equals(alteration.getType())) {
Gene gene = alteration.getGenes().iterator().next();
Expand Down Expand Up @@ -241,17 +244,13 @@ public AlterationAnnotationStatus annotateAlteration(ReferenceGenome referenceGe
"The reference allele does not match with the transcript. It's supposed to be " + refRe
);
alterationWithStatus.setType(EntityStatusType.WARNING);
return alterationWithStatus;
}
}
}
}
}
}

alterationWithStatus.setMessage(alterationWithEntityStatus.getMessage());
alterationWithStatus.setType(alterationWithEntityStatus.getType());

// Provide annotation for the alteration
// 1. check whether alteration is hotspot
AnnotationDTO annotationDTO = new AnnotationDTO();
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7 changes: 2 additions & 5 deletions src/main/java/org/mskcc/oncokb/curation/util/parser/ProteinChangeParser.java
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Expand Up @@ -139,11 +139,8 @@ public static ParsingStatus<Alteration> parseInframe(String proteinChange) {
Alteration alteration = new Alteration();
String revisedProteinChange = "";
MutationConsequence term = UNKNOWN;
if (m.group(1) != null && m.group(3) == null) {
// we only want to specify reference when it's one position ins/del
alteration.setRefResidues(m.group(1).toUpperCase());
revisedProteinChange += alteration.getRefResidues();
}
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This change requires discussion. Is Y770_G772dup or 770_G772dup valid?

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According to hgvs nomenclature, the reference allele can be include for multi position change

alteration.setRefResidues(m.group(1).toUpperCase());
revisedProteinChange += alteration.getRefResidues();
alteration.setStart(Integer.valueOf(m.group(2)));
revisedProteinChange += alteration.getStart();
if (m.group(3) != null) {
Expand Down
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