Suffix sorting via matching statistics

TL;DR

This paper presents a novel algorithm for efficiently constructing the generalized suffix array of similar strings by leveraging compressed matching statistics, resulting in faster performance on such collections.

Contribution

The paper introduces a new method that uses compressed matching statistics to improve suffix array construction for highly similar string collections.

Findings

Constructed suffix arrays faster than existing methods on similar strings

Developed a heuristic for quick matching statistics computation

Prototype implementation 'sacamats' demonstrates competitive performance

Abstract

We introduce a new algorithm for constructing the generalized suffix array of a collection of highly similar strings. As a first step, we construct a compressed representation of the matching statistics of the collection with respect to a reference string. We then use this data structure to distribute suffixes into a partial order, and subsequently to speed up suffix comparisons to complete the generalized suffix array. Our experimental evidence with a prototype implementation (a tool we call sacamats) shows that on string collections with highly similar strings we can construct the suffix array in time competitive with or faster than the fastest available methods. Along the way, we describe a heuristic for fast computation of the matching statistics of two strings, which may be of independent interest.