Annotation manifest - #164
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…F3 validation Add annotation context (-context annotation) for submitting GFF3 annotations against existing ENA assemblies using analysis_type DECOUPLED_ANNOTATION. Rebased onto master as a single clean commit. Includes: - AnnotationManifestReader: parses NAME, GFF3, ANALYSIS_TYPE, PRIMARY_ID, ANALYSIS_ATTRIBUTE fields - AnnotationXmlWriter: writes PRIMARY_ID, DECOUPLED_ANNOTATION analysis type, GFF3 file elements, custom analysis attributes - Gff3Validator: structural GFF3 validation via gff3tools (no FASTA cross-check — sequences referenced via PRIMARY_ID and resolved server-side in webin-gff3-stages). GFF3_UNDEFINED_SEQID errors downgraded to warnings; TRANSLATION_COMPARISON rule disabled. - AnnotationSubmissionValidator: delegates to SubmissionValidator then runs Gff3Validator on GFF3 files - WebinCliContext.annotation enum entry - build.gradle: gff3tools + fastareader dependencies - Tests: manifest reader, XML writer, GFF3 validation - Test resources: valid.gff3.gz, invalid.gff3.gz Replaces the reverted annotation commits on master (faf9951, cb159a2) with a clean implementation that includes GFF3 validation.
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