TASK-7549 - Include new annotation data: ACMG and variant context

[jtarraga]

No description provided.

[Copilot]

Pull Request Overview

This PR introduces two new annotation features: integrating genomic sequence context annotation and ACMG classification into the variant annotation workflow, along with a minor checkstyle configuration update.

• Updated checkstyle.xml to increase the maximum method length.
• Modified test expectations in VariantAnnotationCalculatorTest.java to accommodate changes in the ConsequenceType constructor.
• Added FutureGenomicSequenceContextAnnotator to generate genomic sequence context annotations and integrated ACMG classification in VariantAnnotationCalculator.java.

Reviewed Changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated no comments.

File	Description
checkstyle.xml	Increased the max value for MethodLength from 250 to 300, updating coding style constraints.
cellbase-lib/src/test/java/org/opencb/cellbase/lib/impl/core/VariantAnnotationCalculatorTest.java	Updated test cases to reflect the additional parameter in ConsequenceType instantiation.
cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/futures/FutureGenomicSequenceContextAnnotator.java	Introduced a new annotator implementation to fetch genomic sequence context asynchronously.
cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java	Integrated genomic sequence context processing and added ACMG classification for consequence types.

Comments suppressed due to low confidence (1)

cellbase-lib/src/main/java/org/opencb/cellbase/lib/variant/annotation/VariantAnnotationCalculator.java:699

• Ensure that 'java.util.stream.Collectors' is imported to support the usage of 'Collectors.toList()'.

consequenceType.setAcmg(acmgs.stream().map(ClinicalAcmg::getClassification).collect(Collectors.toList()));