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arXiv · 2605.15819

Faster PBWT prefix-array access via batching

Travis Gagie
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Abstract

The positional Burrows-Wheeler Transform (PBWT) is commonly used to store haplotype panels compactly in such a way that, given a query haplotype, we can quickly find the set maximal exact matches (SMEMs) between the query and the haplotypes in a panel. There are generally two steps in this process: first we find the maximal substrings of the query that occur in the same positions in haplotypes in the panel and then, for each such substring, report the haplotypes in the panel in which the substring occurs in the same position as in the query. Very recently, Bonizzoni, Gagie and Gao (2026) gave two time-space tradeoffs for the second step: they use either $O ((r + h) \log n)$ bits and $O (\log \log \min (h, \ell) + k)$ time to report $k$ haplotypes in the panel, or $O (r \log h + h \log n)$ bits and $O (k \log \log h)$ time, where $r$ is the number of runs in the panel's PBWT and $h$, $\ell$ and $n = h \ell$ are the panel's height, length and size, respectively. We observe here that if we can batch queries until we have found $r \lg (h) / \lg r$ such substrings and we report an average of at least $\lg (r) / \lg h$ haplotypes in the panel per substring, for example, then for the second step we can easily use $O (r \log h)$ bits and constant time to report each haplotype. Our approach is based on an algorithm for constructing the prefix arrays quickly from the PBWT, which may be of independent interest.

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Travis Gagie. 2026-05-15. Faster PBWT prefix-array access via batching. https://arxiv.org/abs/2605.15819

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