Package: genoaligner
Type: Package
Title: GPU-Portable Pairwise and Codon-Aware Multiple Sequence
        Alignment
Version: 2.0.0.9000
Authors@R: 
    person("Angel", "Robles-Fernandez", role = c("aut", "cre"),
           email = "a.l.robles.fernandez@gmail.com")
Description: Sequence alignment from one portable C++17 core:
        edit-distance (Levenshtein / WFA-equivalent) and Smith-Waterman
        local pairwise alignment with score and CIGAR reconstruction,
        plus multiple sequence alignment in DNA, protein and
        codon-aware modes (MACSE-class: whole-codon indels that
        preserve the reading frame, optional frameshift refinement).
        The core builds and runs anywhere (it is the CPU backend, so it
        needs no GPU toolchain); the wavefront/GPU backend (ROCm/CUDA)
        computes the same results with acceleration and is tracked in
        the sibling C++ repository. A batch API aligns many pairs in
        one call and reports how many were resolved, so silent
        under-serving is impossible. Designed to slot into
        data.frame/tibble pipelines.
URL: https://github.com/alrobles/genoaligner-r,
        https://alrobles.github.io/genoaligner-r/
BugReports: https://github.com/alrobles/genoaligner-r/issues
License: MIT + file LICENSE
Encoding: UTF-8
Language: en-US
Depends: R (>= 4.1.0)
Imports: Rcpp
LinkingTo: Rcpp
Suggests: testthat (>= 3.0.0), knitr, rmarkdown, spelling, ape
VignetteBuilder: knitr
SystemRequirements: C++17
NeedsCompilation: yes
Config/testthat/edition: 3
Roxygen: list(markdown = TRUE)
Config/roxygen2/version: 8.0.0
LazyData: true
Repository: https://alrobles.r-universe.dev
Date/Publication: 2026-09-28 13:25:40 UTC
RemoteUrl: https://github.com/alrobles/genoaligner-r
RemoteRef: HEAD
RemoteSha: d7a0767e8605f0537deb2b15a683bc5ae49d22e3
Packaged: 2026-10-11 11:14:04 UTC; root
Author: Angel Robles-Fernandez [aut, cre]
Maintainer: Angel Robles-Fernandez <a.l.robles.fernandez@gmail.com>