Switch default aligner to SweepGA #8
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These seqwish-* directories are temporary working files created by seqwish during graph construction runs. They were accidentally committed and are bloating the repository. Removed: - 36 files across 12 seqwish-* directories (~10MB total) - Files: .sqa, .sqi, .sqq (seqwish's intermediate sequence alignment data) Added to .gitignore: - seqwish-*/ pattern to prevent future commits - wfmash-*/ pattern (similar temp directories) These temporary directories are automatically created by seqwish and should never be tracked in version control.
SweepGA (FastGA + plane sweep filtering) is significantly faster for all-vs-all alignment of sequences ≥100bp, making it better suited as the default aligner for typical pangenome graph construction workflows. Changes: - Set default aligner to 'sweepga' (was 'allwave') - Updated README to reflect SweepGA as default - Updated build instructions to use --features use-sweepga - Fixed README citation (removed incorrect co-author) - Added SweepGA to acknowledgments AllWave remains available via --aligner allwave for shorter sequences or when wavefront alignment is specifically needed. Note: SweepGA uses PAF output from FastGA, so orientation detection happens natively in the FastGA alignment phase (strand column in PAF).
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SweepGA alignments were not producing good results for graph construction. Reverting back to AllWave as the default aligner. This reverts: - Switch default aligner to SweepGA (#8) - Fix SweepGA filtering: remove min_block_length for graph construction (#9) SweepGA work is preserved on the 'sweepga-default-experiment' branch for future investigation.
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Summary
Switch the default aligner from AllWave to SweepGA for better performance on typical pangenome graph construction workflows.
Rationale
SweepGA is faster for all-vs-all alignment of sequences ≥100bp:
AllWave remains available via
--aligner allwavefor:Changes
Code
Args:default_value = "sweepga"(was"allwave")Documentation (README.md)
--features use-sweepgaTechnical Note
SweepGA uses PAF output from FastGA, so orientation detection happens natively in the alignment phase (strand column in PAF). We parse the PAF into
AlignmentRecordobjects rather than using raw alignment objects.Testing
✅ Build successful with
--features use-sweepga✅ All tests pass
✅ Verified SweepGA is used by default (FastGA output in logs)
Impact
Users will get faster alignments by default. Those needing AllWave can explicitly specify
--aligner allwave.