Package: seqtrie
Title: Radix Tree and Trie-Based String Distances
Version: 0.4.0
Date: 2026-06-02
Authors@R: c(
    person("Travers", "Ching", email = "traversc@gmail.com", role = c("aut", "cre", "cph")),
    person("Martin", "Moene", role = c("ctb", "cph"), comment = "span-lite C++ library"),
    person("Steve", "Hanov", role = c("ctb"), comment = "Trie levenshtein implementation in Python"),
    person("Martin", "Leitner-Ankerl", role = c("ctb"), comment = "Ankerl unordered dense hashmap"),
    person("Eduard", "Zorita", role = "ctb", comment = "Starcode algorithm and publication"),
    person("Pol", "Cuscó", role = "ctb", comment = "Starcode algorithm and publication"),
    person("Guillaume J.", "Filion", role = "ctb", comment = "Starcode algorithm and publication")
	)
Description: A collection of Radix Tree and Trie algorithms for finding similar sequences and calculating sequence distances (Levenshtein and other distance metrics). This work was inspired by a trie implementation in Python: "Fast and Easy Levenshtein distance using a Trie." Hanov (2011) <https://stevehanov.ca/blog/index.php?id=114>. It also includes a modified version of the Starcode all-pairs search algorithm (Zorita, Cuscó, and Filion 2015) <doi:10.1093/bioinformatics/btv053>.
License: GPL-3
Biarch: true
Encoding: UTF-8
Depends: R (>= 3.5.0)
LazyData: true
SystemRequirements: GNU make, C++17
LinkingTo: Rcpp, RcppParallel
Imports: Rcpp (>= 0.12.18.3), RcppParallel (>= 5.1.3), R6, S7
Suggests: knitr, rmarkdown, pwalign, igraph, ggplot2
VignetteBuilder: knitr
RoxygenNote: 7.3.3
Copyright: This package includes code from the 'span-lite' library
        owned by Martin Moene under Boost Software License 1.0; see
        inst/licenses/span-lite-BSL-1.0-LICENSE. This package includes
        code from the 'ankerl' library owned by Martin Leitner-Ankerl
        under MIT License. This package includes a modified version of
        the Starcode all-pairs search algorithm described by Eduard
        Zorita, Pol Cuscó, and Guillaume J. Filion (2015). See
        inst/licenses/starcode-GPL-3-LICENSE. This package contains
        data derived from Adaptive Biotechnologies "ImmuneCODE" dataset
        under Creative Commons Attribution 4.0.
URL: https://github.com/traversc/seqtrie
BugReports: https://github.com/traversc/seqtrie/issues
NeedsCompilation: yes
Packaged: 2026-06-03 02:39:08 UTC; ted
Author: Travers Ching [aut, cre, cph],
  Martin Moene [ctb, cph] (span-lite C++ library),
  Steve Hanov [ctb] (Trie levenshtein implementation in Python),
  Martin Leitner-Ankerl [ctb] (Ankerl unordered dense hashmap),
  Eduard Zorita [ctb] (Starcode algorithm and publication),
  Pol Cuscó [ctb] (Starcode algorithm and publication),
  Guillaume J. Filion [ctb] (Starcode algorithm and publication)
Maintainer: Travers Ching <traversc@gmail.com>
Repository: CRAN
Date/Publication: 2026-06-03 08:20:08 UTC
Built: R 4.5.3; x86_64-w64-mingw32; 2026-08-25 23:05:32 UTC; windows
Archs: x64
