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On Elias-Fano for Rank Queries in FM-indexes

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Citation Author(s):
Danyang Ma, Simon J. Puglisi, Rajeev Raman, Bella Zhukova
Submitted by:
Bella Zhukova
Last updated:
2 March 2021 - 2:37pm
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Presentation Slides
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Presenters Name:
Bella Zhukova
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Abstract 

Abstract: 

We describe methods to support fast rank queries on the Burrows-Wheeler transform (BWT) string S of an input string T on alphabet Σ, in order to support pattern counting queries. Our starting point is an approach previously adopted by several authors, which is to represent S as |Σ| bitvectors, where the bitvector for symbol c has a 1 at position i if and only if S[i] = c, with the bitvec- tors stored in Elias-Fano (EF) encodings, to enable binary rank queries. We first show that the clustering of symbols induced by the BWT makes standard implementations of EF unattractive. We then engineer several improvements to EF that go some way to alleviating this problem, and go on to describe two new EF-inspired bitvectors that have superior practical performance.

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