Release 2026.2.0#98
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bencap merged 19 commits intomavedb-mainfrom May 8, 2026
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- Add `build_ref_identical_allele` and `translate_ref_identical_to_vrs` to `lookup.py` to represent HGVS `.=` variants as VRS Alleles with a `ReferenceLengthExpression` state - Handle `.=` variants explicitly in `_construct_vrs_allele` and `_create_post_mapped_hgvs_strings` instead of silently skipping them - Remove `len(hgvs) == 3` guards from validity predicates and early-exit checks; the reference-identical case is now handled directly - Fix `is_intronic_variant` to return False for position-less variants - Skip `vrs_ref_allele_seq` annotation for `ReferenceLengthExpression` alleles to avoid redundant and expensive full-sequence lookups
…ilure when valid hgvs nt mapping exists
- Introduce `AlignmentQc` schema capturing per-alignment BLAT quality metrics (identity, CIGAR, mismatch positions, gap intervals) with in-memory-only position lists excluded from serialization - Add `TargetMapping` schema representing a per-(target, layer) mapping row with variant counts, tool parameters, and preferred-layer flag - Add `VrsMapResult` NamedTuple to pair VRS mappings with their `TargetMapping` rows from `vrs_map` - Rename `annotation_layer` → `alignment_level` on `MappedScore` / `ScoreAnnotation` to align with new terminology - Rename `ident_pct` → `percent_identity` on `AlignmentResult`; add `score`, `next_best_score`, `alignment_qc`, `aligner_parameters`, and `reference_assembly` fields - Implement `build_scoreset_mapping` in `annotate.py` to assemble `ScoresetMapping` with populated `target_mappings` list, per-variant locus-quality flags (`at_mismatched_locus`, `near_gap`), and reference sequence metadata - Restore canonical BLAT PSL scoring (`matches - misMatches - qNumInsert - tNumInsert`) in `_get_best_hsp`; previous BioPython port used raw identity count, causing noisy alignments to outrank clean ones - Update JSON schema, API router, CI workflow, and README to reflect new output shape - Add `test_annotate_target_mapping.py` and expand `test_align.py` / `test_annotate.py` with unit tests for new logic Co-authored-by: Copilot <copilot@github.com>
…alignment_qc - protein-vs-DNA (-q=prot -t=dnax) BLAT runs store target coords in nucleotide space and query coords in amino-acid space (3:1 ratio); minus-strand target blocks have ts > te, making seq[ts:te] return "". Comparison was crashing with ValueError from zip(strict=True); the per-base mismatch loop is now skipped entirely for this mode, setting mismatch_positions_unavailable=True so at_mismatched_locus is correctly left as None (not evaluated) rather than a false False. The preferred layer for protein scoresets is PROTEIN, flagged from the downstream protein-to-protein alignment, so no signal is lost. - For nucleotide-vs-nucleotide runs, replace the bare zip(strict=True) with an explicit length-mismatch guard that logs a WARNING and falls through to zip(strict=False), preserving all mismatches in the overlapping prefix rather than crashing or discarding the block.
…s for better matching This is mostly useful in multi-word target names where gene information is available but not in the first word of the target name.
…and adjust related annotations Co-authored-by: Copilot <copilot@github.com>
…-identical-vrs feat(vrs_map): add VRS mapping support for reference-identical variants
…-generated-unnecessarily Fix protein layer generation and error handling in vrs_map
…or-visibility feat(logging): improve error visibility and logging across application
…vel-mapping-metadata feat: Target level mapping metadata
- Exclude `notebooks/` directory from linting (1,299 noise errors) - Remove deprecated `ANN101` rule from configuration - Fix invalid noqa directive format in vrs_map.py (`:` vs `. `) - Update deprecated rule codes: `ASYNC101` → `ASYNC221` in main.py - Migrate `str + Enum` to `StrEnum` in schemas.py (Python 3.11+) - Fix subprocess S603 noqa placement in align.py - Wrap `NamedTemporaryFile` in context manager (SIM115) - Fix operator precedence with parentheses in annotate.py (RUF021) - Sort `__all__` exports in lookup.py and mavedb_data.py (RUF022) - Add `# noqa: A004` for unavoidable `map` builtin shadowing - Auto-fix pytest decorator style: `@pytest.fixture()` → `@pytest.fixture`
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