VCF-53: Fix read_variant_stats() segfault when region is empty#871
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alancleary merged 4 commits intomainfrom Jan 22, 2026
Merged
VCF-53: Fix read_variant_stats() segfault when region is empty#871alancleary merged 4 commits intomainfrom
alancleary merged 4 commits intomainfrom
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These edge cases are to handle when the buffers returned by a dataset read are empty. Specifically, an array's offsets must still contain the initial 0 value even when there's no data, and a string array must always have 3 buffers, even when there's no data.
…rrow tables Previously the allele count binding would be return None and the variant stats binding would try to parse the empty buffers returned by the reader, causing a segmentation fault.
…nt() These tests ensure that both methods return an empty DataFrame when the regions are empty or don't match the constraints of the query.
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Note that the CLI failure will be fixed by PR #870. |
jp-dark
approved these changes
Jan 22, 2026
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The issue was caused by the code that converts VCF read buffers into Arrow arrays assuming that the buffers would not be empty.
read_variant_stats()now returns an empty Arrow Table with the correct schema if the read buffers are empty. Theread_allele_count()method was updated to do the same. Previously it returnedNonewhen the read buffers are empty, which needlessly complicates downstream parsing and aggregation.