Succinct Suffix Arrays Based on Run-Length Encoding

A succinct full-text self-index is a data structure built on a text T = t1t2 . . . tn, which takes little space (ideally close to that of the compressed text), permits efficient search for the occurrences of a pattern P = p1p2 . . . pm in T , and is able to reproduce any text substring, so the self-index replaces the text. Several remarkable self-indexes have been developed in recent years. They usually take O(nH0) or O(nHk) bits, being Hk the kth order empirical entropy of T . The time to count how many times does P occur in T ranges from O(m) to O(m log n). We present a new self-index, called run-length FM-index (RLFM index), that counts the occurrences of P in T in O(m) time when the alphabet size is σ = O(polylog(n)). The index requires nHk log2 σ +O(n) bits of space for small k. We then show how to implement the RLFM index in practice, and obtain in passing another implementation with different space-time tradeoffs. We empirically compare ours against the best existing implementations of other indexes and show that ours are fastest among indexes taking less space than the text.