%global __brp_check_rpaths %{nil}
%global __requires_exclude ^libmpi
%global packname  RZooRoH
%global packver   0.4.2
%global rlibdir   /usr/local/lib/R/library

Name:             R-CRAN-%{packname}
Version:          0.4.2
Release:          1%{?dist}%{?buildtag}
Summary:          Partitioning of Individual Autozygosity into Multiple Homozygous-by-Descent Classes

License:          GPL-3
URL:              https://cran.r-project.org/package=%{packname}
Source0:          %{url}&version=%{packver}#/%{packname}_%{packver}.tar.gz


BuildRequires:    R-devel >= 3.5.0
Requires:         R-core >= 3.5.0
BuildRequires:    R-methods 
BuildRequires:    R-CRAN-foreach 
BuildRequires:    R-CRAN-doParallel 
BuildRequires:    R-parallel 
BuildRequires:    R-CRAN-data.table 
BuildRequires:    R-CRAN-RColorBrewer 
BuildRequires:    R-CRAN-iterators 
Requires:         R-methods 
Requires:         R-CRAN-foreach 
Requires:         R-CRAN-doParallel 
Requires:         R-parallel 
Requires:         R-CRAN-data.table 
Requires:         R-CRAN-RColorBrewer 
Requires:         R-CRAN-iterators 

%description
Functions to identify Homozygous-by-Descent (HBD) segments associated with
runs of homozygosity (ROH) and to estimate individual autozygosity (or
inbreeding coefficient). HBD segments and autozygosity are assigned to
multiple HBD classes with a model-based approach relying on a mixture of
exponential distributions. The rate of the exponential distribution is
distinct for each HBD class and defines the expected length of the HBD
segments. This rate is called the "rate of coancestry change". The HBD
classes are therefore related to the age of the segments (longer segments
and smaller rates for recent autozygosity / recent common ancestor). The
functions allow to estimate the parameters of the model (rates of the
exponential distributions called also rates of coancestry change; mixing
proportions related to the inbreeding rate per layer or generation), to
estimate global and local autozygosity probabilities and to identify HBD
segments with the Viterbi decoding. Functions also allow to compute
identity-by-descent (IBD) between pairs of haplotypes, to estimate kinship
between pairs of individuals and to predict inbreeding in the future
progeny of a genotyped couple. The current model is fully described in
Druet and Gautier (2022) <doi:10.1016/j.tpb.2022.03.001>. The model and
its properties were originally presented in Druet and Gautier (2017)
<doi:10.1111/mec.14324>. Extension to IBD and kinship analyses is
described in Forneris et al. (2025) <doi:10.1111/1755-0998.14068>.

%prep
%setup -q -c -n %{packname}

# fix end of executable files
find -type f -executable -exec grep -Iq . {} \; -exec sed -i -e '$a\' {} \;
# prevent binary stripping
[ -d %{packname}/src ] && find %{packname}/src -type f -exec \
  sed -i 's@/usr/bin/strip@/usr/bin/true@g' {} \; || true
[ -d %{packname}/src ] && find %{packname}/src/Make* -type f -exec \
  sed -i 's@-g0@@g' {} \; || true
# don't allow local prefix in executable scripts
find -type f -executable -exec sed -Ei 's@#!( )*/usr/local/bin@#!/usr/bin@g' {} \;

%build

%install

mkdir -p %{buildroot}%{rlibdir}
%{_bindir}/R CMD INSTALL -l %{buildroot}%{rlibdir} %{packname}
test -d %{packname}/src && (cd %{packname}/src; rm -f *.o *.so)
rm -f %{buildroot}%{rlibdir}/R.css
# remove buildroot from installed files
find %{buildroot}%{rlibdir} -type f -exec sed -i "s@%{buildroot}@@g" {} \;

%files
%{rlibdir}/%{packname}