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arXiv · 2408.04537

Faster run-length compressed suffix arrays

Nathaniel K. Brown·Travis Gagie·Giovanni Manzini·Gonzalo Navarro·Marinella Sciortino
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Abstract

We first review how we can store a run-length compressed suffix array (RLCSA) for a text $T$ of length $n$ over an alphabet of size $\sigma$ whose Burrows-Wheeler Transform (BWT) consists of $r$ runs in $O \left( \rule{0ex}{2ex} r \log (n / r) + r \log \sigma + \sigma \right)$ bits such that later, given character $a$ and the suffix array interval for $P$, we can find the suffix-array (SA) interval for $a P$ in $O (\log r_a + \log \log n)$ time, where $r_a$ is the number of runs of copies of $a$ in the BWT. We then show how to modify the RLCSA such that we find the SA interval for $a P$ in only $O (\log r_a)$ time, without increasing its asymptotic space bound. Our key idea is applying a result by Nishimoto and Tabei (ICALP 2021) and then replacing rank queries on sparse bitvectors by a constant number of select queries. We also review two-level indexing and discuss how our faster RLCSA may be useful in improving it. Finally, we briefly discuss how two-level indexing may speed up a recent heuristic for finding maximal exact matches of a pattern with respect to an indexed text.

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BibTeXRIS

Nathaniel K. Brown, Travis Gagie, Giovanni Manzini, Gonzalo Navarro, Marinella Sciortino. 2024-08-08. Faster run-length compressed suffix arrays. https://arxiv.org/abs/2408.04537

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