Abstract
Run-length encoding Burrows-Wheeler Transformed strings, resulting in Run-Length BWT (RLBWT), is a powerful tool for processing highly repetitive strings. We propose a new algorithm for online RLBWT working in run-compressed space, which runs in \(O(n\lg r)\) time and \(O(r\lg n)\) bits of space, where n is the length of input string S received so far and r is the number of runs in the BWT of the reversed S. We improve the state-of-the-art algorithm for online RLBWT in terms of empirical construction time. Adopting the dynamic list for maintaining a total order, we can replace rank queries in a dynamic wavelet tree on a run-length compressed string by the direct comparison of labels in a dynamic list. The empirical result for various benchmarks show the efficiency of our algorithm, especially for highly repetitive strings.
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Notes
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Or appending a character but constructing BWT for reversed string.
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The basic idea of the algorithm originates from the work of RLFM+ index in [12].
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See http://pizzachili.dcc.uchile.cl/repcorpus/statistics.pdf for statistics of the datasets.
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Acknowledgments
This work was supported by JST CREST (Grant Number JPMJCR1402), and KAKENHI (Grant Numbers 17H01791 and 16K16009).
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Ohno, T., Takabatake, Y., I, T., Sakamoto, H. (2018). A Faster Implementation of Online Run-Length Burrows-Wheeler Transform. In: Brankovic, L., Ryan, J., Smyth, W. (eds) Combinatorial Algorithms. IWOCA 2017. Lecture Notes in Computer Science(), vol 10765. Springer, Cham. https://doi.org/10.1007/978-3-319-78825-8_33
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