feat: add the 'ea' tag to bwa aln in case the search exits early #111
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In some cases, bwa aln may exit its search early, even when asked to do so exhaustively in cases when the stack gets too large (see -m). In this case, we add the 'ea' flag to flag alignments where an alignment is returned but the search was stopped short. This is important when using pybwa for primer design and exhaustive search.
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Jun 4, 2025
| assert rec.query_name == "test" | ||
| if should_fail: | ||
| assert rec.is_unmapped is True | ||
| print(rec) |
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In some cases, bwa aln may exit its search early, even when asked to do so exhaustively in cases when the stack gets too large (see -m). In this case, we add the 'ea' flag to flag alignments where an alignment is returned but the search was stopped short. This is important when using pybwa for primer design and exhaustive search.
📚 Documentation preview 📚: https://pybwa--111.org.readthedocs.build/en/111/