A bloated FM-index reducing the number of cache misses during the search

Abstract

The FM-index is a well-known compressed full-text index, based on the Burrows-Wheeler transform (BWT). During a pattern search, the BWT sequence is accessed at "random" locations, which is cache-unfriendly. In this paper, we are interested in speeding up the FM-index by working on $q$-grams rather than individual characters, at the cost of using more space. The first presented variant is related to an inverted index on $q$-grams, yet the occurrence lists in our solution are in the sorted suffix order rather than text order in a traditional inverted index. This variant obtains $O(m/|CL|+\log n\log m)$ cache misses in the worst case, where $n$ and $m$ are the text and pattern lengths, respectively, and $|CL|$ is the CPU cache line size, in symbols (typically 64 in modern hardware). This index is often several times faster than the fastest known FM-indexes (especially for long patterns), yet the space requirements are enormous, $O(n{\log }^{2}n)$ bits in theory and about $80n$-$95n$ bytes in practice. For this reason, we dub our approach FM-bloated. The second presented variant requires $O(n\log n)$ bits of space.

5 figures

References in corpus (1)

• KMC 2: Fast and resource-frugal $k$-mer counting