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Use ncls as default. Note: The two-pointer sweep needs work, as it doesn't behave as expected in testing.
Fix returning empty 'var' for anndata object.
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Implemented
PETrackII.return_anndatato use a single non-overlapping sweep method. The method now copies and merges input regions once, then builds the barcode × peak matrix with a vectorized two-pointer/searchsortedapproach over cached NumPy start/end/count arrays, using dense barcode-to-row indexing and chunked CSR assembly.This is faster because the method no longer spends time in Python-level per-overlap branching and repeated structured-array field access. Instead, it computes overlap ranges in bulk with
np.searchsorted, expands only the required triplets with NumPy operations, and constructs the sparse matrix directly from contiguous integer buffers.