Add extra column Hgvs_Offset and extend Additional_Transcripts - #301
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leexgh wants to merge 7 commits into
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Add extra column Hgvs_Offset and extend Additional_Transcripts#301leexgh wants to merge 7 commits into
leexgh wants to merge 7 commits into
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- Bump genome-nexus-java-api-client to b43dccc7fa, which adds TranscriptConsequence.hgvsOffset (needed to read hgvs_offset from Genome Nexus responses; the previously pinned client never exposed it). - Add HGVS_Offset column under --mode extended, resolved by matching the canonical transcript against the raw transcriptConsequences list. - Fix minimal_example_with_additional_columns.txt, which went stale after RefSeq was added to Additional_Transcripts entries and was never regenerated, breaking the extended-mode integration test.
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Production upgraded from v2.1.3 to v2.2.1 (crossing genome-nexus#861's canonical transcript / splice consequence changes), which changed HGVSp resolution for intronic splice-region and synonymous-splice variants (e.g. blank/"p.X###_splice" -> "p.Leu###="/"p.*###*"). Regenerated all affected fixtures against the live server; verified each diff was consistent with this one underlying behavior change before accepting.
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…mutation so the protein change is different (since 2.2.1)
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Summary
HGVS_Offsetcolumn, populated under--mode extended(alongsideAdditional_Transcripts), resolved from the canonical transcript'shgvs_offsetin the raw Genome NexustranscriptConsequencesresponse.genome-nexus-java-api-clientfromc8ba14d555tob43dccc7fa, which is required to readhgvs_offsetat all — the previously pinned client never deserialized that field (confirmed viajavapbefore making any code changes).minimal_example_with_additional_columns.txtwent stale after RefSeq was added toAdditional_Transcriptsentries and was never regenerated, soSpringBatchIntegrationTest#check_if_output_contains_additional_transcripts_when_extendedMode_is_truewas failing on this branch. Regenerated againstwww.genomenexus.organd confirmed the only diff was the missingRefSeqfield.Details
AnnotationUtil.resolveHgvsOffset(...)matches the canonical transcript bytranscriptIdagainst the rawtranscriptConsequenceslist (the summarizedTranscriptConsequenceSummaryused for HGVSc/HGVSp doesn't exposehgvs_offset).GenomeNexusImpl/AnnotatedRecordfollow the exact same pattern asAdditional_Transcripts(extended-mode gated, header only grows when the field is actually set).AnnotationUtilTestunit tests cover the matching logic directly, sincewww.genomenexus.orgdoesn't computehgvs_offsetyet (still pre-genome-nexus#861, confirmed via direct API check) — the field reads blank in the live integration test fixture for that reason, not a bug.Test plan
mvn clean testpasses (full suite)AnnotationUtilTestcovers match found / null offset / no match / null transcript list / null canonical transcriptTranscriptConsequence.getHgvsOffset()exists in the new client jar viajavapbefore wiring it in