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https://doi.org/10.1109/dcc526...
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RLBWT Tricks

Authors: Nathaniel K. Brown; Travis Gagie; Massimiliano Rossi 0001;
Abstract

Until recently, most experts would probably have agreed we cannot backwards-step in constant time with a run-length compressed Burrows-Wheeler Transform (RLBWT), since doing so relies on rank queries on sparse bitvectors and those inherit lower bounds from predecessor queries. At ICALP '21, however, Nishimoto and Tabei described a new, simple and constant-time implementation. For a permutation $π$, it stores an $O (r)$-space table -- where $r$ is the number of positions $i$ where either $i = 0$ or $π(i + 1) \neq π(i) + 1$ -- that enables the computation of successive values of $π(i)$ by table look-ups and linear scans. Nishimoto and Tabei showed how to increase the number of rows in the table to bound the length of the linear scans such that the query time for computing $π(i)$ is constant while maintaining $O (r)$-space. In this paper we refine Nishimoto and Tabei's approach, including a time-space tradeoff, and experimentally evaluate different implementations demonstrating the practicality of part of their result. We show that even without adding rows to the table, in practice we almost always scan only a few entries during queries. We propose a decomposition scheme of the permutation $π$ corresponding to the LF-mapping that allows an improved compression of the data structure, while limiting the query time. We tested our implementation on real-world genomic datasets and found that without compression of the table, backward-stepping is drastically faster than with sparse bitvector implementations but, unfortunately, also uses drastically more space. After compression, backward-stepping is competitive both in time and space with the best existing implementations.

15 pages, 8 figures. New edition with expanded experimental results after poster acceptance at earlier conference. Section 4 removed, sections added for implementation details

Country
Germany
Keywords

FOS: Computer and information sciences, Compressed String Indexes, Repetitive Text Collections, Computer Science - Data Structures and Algorithms, Data Structures and Algorithms (cs.DS), Burrows-Wheeler Transform, 004, ddc: ddc:004

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
2
Average
Average
Average
Green
gold