Online LZ77 parsing and matching statistics with RLBWTs

Hideo Bannai, Travis Gagie, Tomohiro I

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Citations (Scopus)

Abstract

Lempel-Ziv 1977 (LZ77) parsing, matching statistics and the Burrows-Wheeler Transform (BWT) are all fundamental elements of stringology. In a series of recent papers, Policriti and Prezza (DCC 2016 and Algorithmica, CPM 2017) showed how we can use an augmented run-length compressed BWT (RLBWT) of the reverse TR of a text T, to compute offline the LZ77 parse of T in O(n log r) time and O(r) space, where n is the length of T and r is the number of runs in the BWT of TR. In this paper we first extend a well-known technique for updating an unaugmented RLBWT when a character is prepended to a text, to work with Policriti and Prezza's augmented RLBWT. This immediately implies that we can build online the LZ77 parse of T while still using O(n log r) time and O(r) space; it also seems likely to be of independent interest. Our experiments, using an extension of Ohno, Takabatake, I and Sakamoto's (IWOCA 2017) implementation of updating, show our approach is both time- and space-efficient for repetitive strings. We then show how to augment the RLBWT further -albeit making it static again and increasing its space by a factor proportional to the size of the alphabet -such that later, given another string S and O(log log n)-time random access to T, we can compute the matching statistics of S with respect to T in O(|S| log log n) time.

Original languageEnglish
Title of host publication29th Annual Symposium on Combinatorial Pattern Matching, CPM 2018
EditorsBinhai Zhu, Gonzalo Navarro, David Sankoff
PublisherSchloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
Pages71-712
Number of pages642
ISBN (Electronic)9783959770743
DOIs
Publication statusPublished - May 1 2018
Event29th Annual Symposium on Combinatorial Pattern Matching, CPM 2018 - Qingdao, China
Duration: Jul 2 2018Jul 4 2018

Publication series

NameLeibniz International Proceedings in Informatics, LIPIcs
Volume105
ISSN (Print)1868-8969

Other

Other29th Annual Symposium on Combinatorial Pattern Matching, CPM 2018
CountryChina
CityQingdao
Period7/2/187/4/18

All Science Journal Classification (ASJC) codes

  • Software

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  • Cite this

    Bannai, H., Gagie, T., & I, T. (2018). Online LZ77 parsing and matching statistics with RLBWTs. In B. Zhu, G. Navarro, & D. Sankoff (Eds.), 29th Annual Symposium on Combinatorial Pattern Matching, CPM 2018 (pp. 71-712). (Leibniz International Proceedings in Informatics, LIPIcs; Vol. 105). Schloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing. https://doi.org/10.4230/LIPIcs.CPM.2018.7