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

TL;DR

This paper introduces r-comp, an optimal-time algorithm for constructing run-length BWT in space proportional to the number of runs, significantly improving efficiency for highly repetitive strings.

Contribution

The paper presents the first optimal-time RLBWT construction algorithm with space bounded by the number of BWT runs, addressing previous limitations.

Findings

Achieves $O(n + r \,\log r)$ time complexity

Uses $O(r \,\log n)$ bits of working space

Effective on real-world highly repetitive datasets

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.