Package: STITCH
Type: Package
Title: STITCH - Sequencing To Imputation Through Constructing
        Haplotypes
Version: 1.7.0
Date: 2024-07-18
Author: Robert William Davies
Maintainer: Robert William Davies <robertwilliamdavies@gmail.com>
Description: STITCH performs imputation of individuals sequenced to low coverage
    in a read aware fashion without a reference panel.
Installation: To install, first install dependencies, then run the
        install.packages command, pointing to the downloaded tarball
        (STITCH.tar.gz)
Getting started: A minimum run requires the following options to be
        set: the chromosome being run (chr); a path to a file with a
        set of bi-allelic SNP sites (posfile); a choice of K, the
        number of internally modelled haplotypes (K); a path to an
        output directory (outputdir); a path to a temporary directory,
        ideally on fast disks or a RAM disk (tempdir); a list of bam
        files (bamlist); and the number of generations since founding
        (nGen), which can be approximated from a choice of K for wild
        populations from 4 * Ne / K. Additional useful options relate
        to what region to impute (regionStart, regionEnd, buffer),
        whether to use validation data to benchmark imputation
        (genfile), the number of cores to use (nCores), whether
        imputation is run on a server or cluster (environment), the
        number of EM iterations (niterations), whether to run in
        diploid or pseudoHaploid mode (method), and if run in
        pseudoHaploid mode, what iteration to switch from pseudoHaploid
        to diploid (switchModelIteration).
Depends: parallel
Imports: Rcpp, data.table
Suggests: testthat, rrbgen (>= 0.0.4)
Remotes: github::rwdavies/rrbgen/rrbgen
LinkingTo: Rcpp, RcppArmadillo
Packaged: 2024-07-18 16:06:37 UTC; zilong
RoxygenNote: 7.3.1
License: GPL | file LICENSE
SystemRequirements: C++11
NeedsCompilation: yes
Built: R 4.3.3; x86_64-conda-linux-gnu; 2024-08-18 13:56:05 UTC; unix
