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Reportable Shortcuts with RLBWTs
Travis Gagie
Backward search over a run-length compressed Burrows--Wheeler transform (RLBWT) takes one step per pattern character, even when long stretches of the pattern match material that re…
Parse indexing for discarding short pseudo-MEMs safely
Travis Gagie
Brown et al.\ (2025) described a pre-processing step, called -mer based breaking (KeBaB), that speeds up searching for long maximal exact matches (MEMs) between a pattern an…
Faster PBWT prefix-array access via batching
Travis Gagie
The positional Burrows-Wheeler Transform (PBWT) is commonly used to store haplotype panels compactly in such a way that, given a query haplotype, we can quickly find the set maxima…
Merging RLBWTs adaptively
Travis Gagie
We show how to merge two run-length compressed Burrows-Wheeler Transforms (RLBWTs) into a run-length compressed extended Burrows-Wheeler Transform (eBWT) in space and $O ((…
r*-indexing
Travis Gagie
Let be a text over an alphabet of size , let be the sum of the numbers of runs in the Burrows-Wheeler Transforms of and its reverse,…
Tag arrays
Travis Gagie
The Burrows-Wheeler Transform (BWT) moves characters with similar contexts in a text together, where a character's context consists of the characters immediately following it. We s…