{"doi":"10.48550/arxiv.2408.04537","title":"Faster run-length compressed suffix arrays","abstract":"We first review how we can store a run-length compressed suffix array (RLCSA) for a text $T$ of length $n$ over an alphabet of size $σ$ whose Burrows-Wheeler Transform (BWT) consists of $r$ runs in $O \\left( \\rule{0ex}{2ex} r \\log (n / r) + r \\log σ+ σ\\right)$ bits such that later, given character $a$ and the suffix array interval for $P$, we can find the suffix-array (SA) interval for $a P$ in $O (\\log r_a + \\log \\log n)$ time, where $r_a$ is the number of runs of copies of $a$ in the BWT. We then show how to modify the RLCSA such that we find the SA interval for $a P$ in only $O (\\log r_a)$ time, without increasing its asymptotic space bound. Our key idea is applying a result by Nishimoto and Tabei (ICALP 2021) and then replacing rank queries on sparse bitvectors by a constant number of select queries. We also review two-level indexing and discuss how our faster RLCSA may be useful in improving it. Finally, we briefly discuss how two-level indexing may speed up a recent heuristic for finding maximal exact matches of a pattern with respect to an indexed text.","journal":"arXiv (Cornell University)","year":2024,"id":503082,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9559,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":662070,"name":"Travis Gagie","orcid":"0000-0003-3689-327X","position":1,"is_corresponding":false},{"id":805393,"name":"Giovanni Manzini","orcid":"0000-0002-5047-0196","position":2,"is_corresponding":false},{"id":805394,"name":"Gonzalo Navarro","orcid":"0000-0002-2286-741X","position":3,"is_corresponding":false},{"id":1165216,"name":"Marinella Sciortino","orcid":"0000-0001-6928-0168","position":4,"is_corresponding":false},{"id":1353034,"name":"Brown, Nathaniel K.","orcid":null,"position":0,"is_corresponding":true}],"reference_count":0,"raw_metadata":null,"created_at":"2026-07-19T02:10:27.781502Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}