An Optimal-Time RLBWT Construction in BWT-runs Bounded Space

Takaaki Nishimoto; Shunsuke Kanda; Yasuo Tabei

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arXiv · 2202.07885

An Optimal-Time RLBWT Construction in BWT-runs Bounded Space

Takaaki Nishimoto·Shunsuke Kanda·Yasuo Tabei

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Abstract

The compression of highly repetitive strings (i.e., strings with many repetitions) has been a central research topic in string processing, and quite a few compression methods for these strings have been proposed thus far. Among them, an efficient compression format gathering increasing attention is the run-length Burrows--Wheeler transform (RLBWT), which is a run-length encoded BWT as a reversible permutation of an input string on the lexicographical order of suffixes. State-of-the-art construction algorithms of RLBWT have a serious issue with respect to (i) non-optimal computation time or (ii) a working space that is linearly proportional to the length of an input string. In this paper, we present \emph{r-comp}, the first optimal-time construction algorithm of RLBWT in BWT-runs bounded space. That is, the computational complexity of r-comp is $O(n + r \log{r})$ time and $O(r\log{n})$ bits of working space for the length $n$ of an input string and the number $r$ of equal-letter runs in BWT. The computation time is optimal (i.e., $O(n)$) for strings with the property $r=O(n/\log{n})$, which holds for most highly repetitive strings. Experiments using a real-world dataset of highly repetitive strings show the effectiveness of r-comp with respect to computation time and space.

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BibTeX RIS

Takaaki Nishimoto, Shunsuke Kanda, Yasuo Tabei. 2022-02-16. An Optimal-Time RLBWT Construction in BWT-runs Bounded Space. https://arxiv.org/abs/2202.07885

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