More RLBWT Tricks
Travis Gagie
原文摘要
Backward search over the run-length compressed Burrows-Wheeler transform (RLBWT) of a pangenome takes one step per character of the pattern, even when long stretches of the pattern match material that occurs many times in the collection. Two-level indexing also indexes a parse of the collection, so that a search can take one step per phrase. We parse at closed syncmers, whose phrases are prefix-free, and add blocks of continuations: when each phrase of a stretch of the pattern is the smallest phrase that follows the previous one anywhere in the collection, the search crosses the whole stretch in one step, on the BWT of a sequence of block symbols. We prove that the three BWTs stay in the same order, so the search still returns exactly the BWT interval of every match, and we bound the extra space by terms that depend on the length of the collection only through the number of distinct closed syncmers. On chromosome 19 haplotypes from the Human Pangenome Reference Consortium, finding the maximal exact matches of length at least 1000 of two haplotypes, on both strands, takes 5.5 to 5.7 seconds with 16, 32 or 64 other individuals, while backward search on a run-length compressed suffix array of the same collection takes 40 to 60 seconds and grows with the collection. We compare this with suffix-tree path decompositions (STPDs): over the parse, an STPD is no faster and needs about twice the memory; over the text it is about 1.7 times faster but needs the whole text in memory, about five times the space; and the published STPD-index, which compresses its text with relative Lempel-Ziv, is 8 to 10 times slower. Keeping a toehold through all three kinds of steps lets the search also list every occurrence of every MEM, for about 2 more seconds.
cs.DS