feat: Add coordinate_system_zero_based parameter to all table providers #36
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📊 Benchmark ResultsBenchmarks have been completed and stored for this PR. View Results: https://biodatageeks.org/datafusion-bio-formats/benchmark-comparison/
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This commit implements the coordinate system parameter for all bio format table providers (VCF, GFF, BAM, BED, CRAM) to support both 0-based and 1-based coordinate output. Changes: - Add `coordinate_system_zero_based: bool` parameter to all TableProvider constructors - Store coordinate system preference in Arrow schema metadata with key `bio.coordinate_system_zero_based` - Add `COORDINATE_SYSTEM_METADATA_KEY` constant in bio-format-core - Update position conversion in physical_exec.rs for each format: - When true (default): subtract 1 from noodles 1-based positions - When false: use noodles positions as-is (1-based) - Update all binaries, examples, and tests to pass the new parameter - Fix test assertions to expect 0-based coordinates (default) Breaking Change: All TableProvider::new() constructors now require an additional bool parameter as the last argument. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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📊 Benchmark ResultsBenchmarks have been completed and stored for this PR. View Results: https://biodatageeks.org/datafusion-bio-formats/benchmark-comparison/
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📊 Benchmark ResultsBenchmarks have been completed and stored for this PR. View Results: https://biodatageeks.org/datafusion-bio-formats/benchmark-comparison/
Raw data: https://biodatageeks.org/datafusion-bio-formats/benchmark-data/ |
- Add coordinate_system_zero_based parameter to BgzfGffTableProvider::try_new() - Pass parameter through to BgzfGffExec for coordinate conversion - Apply coordinate conversion at parse time (subtract 1 from start when zero_based=true) - Update binaries and tests to use new API 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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📊 Benchmark ResultsBenchmarks have been completed and stored for this PR. View Results: https://biodatageeks.org/datafusion-bio-formats/benchmark-comparison/
Raw data: https://biodatageeks.org/datafusion-bio-formats/benchmark-data/ |
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Summary
coordinate_system_zero_based: boolparameter to all TableProvider constructors (VCF, GFF, BAM, BED, CRAM)true(default), positions are converted from noodles' internal 1-based system to 0-based coordinatesbio.coordinate_system_zero_basedDetails
This change supports the polars-bio initiative (issue #259) to switch the default coordinate system from 1-based to 0-based for consistency with common bioinformatics tools and conventions.
Implementation
COORDINATE_SYSTEM_METADATA_KEYconstant in bio-format-corephysical_exec.rsnow converts positions when reading records:start = noodles_position.get() - 1whencoordinate_system_zero_based=trueFiles Changed
Test plan
🤖 Generated with Claude Code