Faster run-length compressed suffix arrays
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arXiv
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| Autores principales: | , , , , |
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| Formato: | Preprint |
| Publicado: |
2024
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| _version_ | 1866916697106022400 |
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| author | Brown, Nathaniel K. Gagie, Travis Manzini, Giovanni Navarro, Gonzalo Sciortino, Marinella |
| author_facet | Brown, Nathaniel K. Gagie, Travis Manzini, Giovanni Navarro, Gonzalo Sciortino, Marinella |
| contents | 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 $σ$ whose Burrows-Wheeler Transform (BWT) consists of $r$ runs in $O \left( \rule{0ex}{2ex} r \log (n / r) + r \log σ+ σ\right)$ 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. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2408_04537 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | Faster run-length compressed suffix arrays Brown, Nathaniel K. Gagie, Travis Manzini, Giovanni Navarro, Gonzalo Sciortino, Marinella Data Structures and Algorithms 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 $σ$ whose Burrows-Wheeler Transform (BWT) consists of $r$ runs in $O \left( \rule{0ex}{2ex} r \log (n / r) + r \log σ+ σ\right)$ 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. |
| title | Faster run-length compressed suffix arrays |
| topic | Data Structures and Algorithms |
| url | https://arxiv.org/abs/2408.04537 |