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 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.
@InProceedings{nishimoto_et_al:LIPIcs.ICALP.2022.99, author = {Nishimoto, Takaaki and Kanda, Shunsuke and Tabei, Yasuo}, title = {{An Optimal-Time RLBWT Construction in BWT-Runs Bounded Space}}, booktitle = {49th International Colloquium on Automata, Languages, and Programming (ICALP 2022)}, pages = {99:1--99:20}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-235-8}, ISSN = {1868-8969}, year = {2022}, volume = {229}, editor = {Boja\'{n}czyk, Miko{\l}aj and Merelli, Emanuela and Woodruff, David P.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2022.99}, URN = {urn:nbn:de:0030-drops-164403}, doi = {10.4230/LIPIcs.ICALP.2022.99}, annote = {Keywords: lossless data compression, Burrows-Wheeler transform, highly repetitive text collections} }
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