Name:		minimap2
Version:	2.30
Release:	1%{?dist}
Summary:	A versatile pairwise aligner for genomic and spliced nucleotide sequences

License:	MIT
URL:		https://lh3.github.io/minimap2/
Source0:	https://github.com/lh3/%{name}/archive/refs/tags/v%{version}.tar.gz
# Set up SIMDe capable compilation
# https://salsa.debian.org/med-team/minimap2/-/blob/f763aafa692e1fb1effda1900bb73f060f9015d8/debian/patches/simde
Patch0:		minimap2-2.30-simde.patch
# Patch1:		python-sse4-arch.patch
Patch1:		python-sse4.patch

BuildRequires:	make
BuildRequires:	gcc
BuildRequires:	zlib-devel
BuildRequires:	simde-devel

# For creating minimap2.pdf
BuildRequires:	gnuplot perl-interpreter texlive-epstopdf ghostscript
BuildRequires:	texlive-latex texlive-crop texlive-latex-amsmath-dev
BuildRequires:	texlive-amsfonts texlive-sttools texlive-amscls
BuildRequires:	texlive-changepage texlive-algorithm2e texlive-times
BuildRequires:	texlive-epstopdf-pkg texlive-helvetic texlive-dvips

Requires:	k8
BuildRequires:	python3-devel python3-setuptools python3-pip python3-distutils-extra tox
BuildRequires:  python3-cython


%description
Minimap2 is a versatile sequence alignment program that aligns DNA or
mRNA sequences against a large reference database. Typical use cases
include: (1) mapping PacBio or Oxford Nanopore genomic reads to the
human genome; (2) finding overlaps between long reads with error rate
up to ~15%; (3) splice-aware alignment of PacBio Iso-Seq or Nanopore
cDNA or Direct RNA reads against a reference genome; (4) aligning
Illumina single- or paired-end reads; (5) assembly-to-assembly
alignment; (6) full-genome alignment between two closely related
species with divergence below ~15%.


%prep
%autosetup


%build
%ifarch x86_64
  %make_build
%else
  CFLAGS="%{optflags} -fopenmp-simd -O3 -DSIMDE_ENABLE_OPENMP"
  %ifarch aarch64
    %make_build -f Makefile.simde arm_neon=1 aarch64=1
  %else
    %make_build -f Makefile.simde
  %endif
%endif

# Build Mappy, Minimap2 Python binding
%pyproject_wheel

# Build minimap2.pdf documentation
cd tex
%make_build


%install
rm -rf %{buildroot}
mkdir -p %{buildroot}%{_bindir}
install -m 0755 minimap2 %{buildroot}%{_bindir}

mkdir -p %{buildroot}%{_mandir}/man1
install -m 0644 minimap2.1 %{buildroot}%{_mandir}/man1/

%pyproject_install
%pyproject_save_files -l mappy

%package -n python3-mappy
Summary: Python bindings for minimap2
%{?python_provide:%python_provide python3-mappy}

%description -n python3-mappy
Python bindings (mappy) for minimap2.


%files
%license LICENSE.txt
%doc cookbook.md FAQ.md misc NEWS.md README.md test tex/minimap2.pdf
%{_bindir}/minimap2
%{_mandir}/man1/minimap2.1.gz


%files -n python3-mappy -f %{pyproject_files}
%{_bindir}/minimap2.py


%changelog
* Mon Feb  9 2026 Rasmus Ory Nielsen <ron@ron.dk> - 2.30-1
- Initial build