DESCRIPTION

Package: kalis
Type: Package
Title: High Performance Li & Stephens Local Ancestry Inference
Version: 2.0.0
Authors@R: c(person("Louis", "Aslett", role = c("aut", "cre"),
                    email = "louis.aslett@durham.ac.uk",
                    comment = c(ORCID = "0000-0003-2211-233X")),
             person("Ryan", "Christ", role = "aut",
                    email = "rchrist@wustl.edu",
                    comment = c(ORCID = "0000-0002-2049-3389")))
Author: Louis Aslett [aut, cre],
  Ryan Christ [aut]
Maintainer: Louis Aslett <louis.aslett@durham.ac.uk>
Description: kalis <doi:10.1186/s12859-024-05688-8> provides a high performance 
  implementation of the Li & Stephens model <doi:10.1093/genetics/165.4.2213> 
  for local ancestry inference (local referring to a region of the genome). For 
  a set of N phased haplotypes, kalis computes the posterior marginal
  probability of each haplotype copying every other haplotype by running N
  hidden Markov models in parallel. This yields an N x N distance matrix that
  summarizes the recent local ancestry at each variant of interest. The package
  provides functionality for specifying a recombination map, site-specific
  mutation rates, and differing prior copying probabilities for each recipient
  haplotype. Extensive use is made of low level threading and CPU vector
  instructions.
License: GPL (>= 3)
BugReports: https://github.com/louisaslett/kalis/issues
URL: https://kalis.louisaslett.com/, https://github.com/louisaslett/kalis
LazyData: TRUE
Depends: R (>= 3.5.0)
Imports:
    utils,
    stats,
    parallel,
    dplyr,
    glue (>= 1.3.0),
    rlang,
    digest (>= 0.6.18),
    checkmate,
    grDevices,
    RColorBrewer,
    lobstr,
    prettyunits
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)
Suggests: 
    rhdf5,
    hdf5r,
    rstudioapi,
    knitr,
    rmarkdown,
    fastcluster,
    lattice,
    testthat (>= 3.0.0),
    data.table
VignetteBuilder: knitr
Encoding: UTF-8
Config/testthat/edition: 3