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%global _empty_manifest_terminate_build 0
Name: python-cyvcf2
Version: 0.30.18
Release: 1
Summary: fast vcf parsing with cython + htslib
License: MIT
URL: https://github.com/brentp/cyvcf2/
Source0: https://mirrors.nju.edu.cn/pypi/web/packages/8e/b1/31b20c3453944fda0eb43d519787bcce4178b6f3b29c94a6286a801fbad3/cyvcf2-0.30.18.tar.gz
BuildArch: noarch
Requires: python3-numpy
Requires: python3-coloredlogs
Requires: python3-click
%description
Note: cyvcf2 versions < 0.20.0 require htslib < 1.10. cyvcf2 versions >= 0.20.0 require htslib >= 1.10
<!-- ghp-import -p docs/build/html/ -->
The latest documentation for cyvcf2 can be found here:
[](http://brentp.github.io/cyvcf2/)
If you use cyvcf2, please cite the [paper](https://academic.oup.com/bioinformatics/article/2971439/cyvcf2)
Fast python **(2 and 3)** parsing of VCF and BCF including region-queries.
[](https://github.com/brentp/cyvcf2/actions?query=workflow%3ABuild)
cyvcf2 is a cython wrapper around [htslib](https://github.com/samtools/htslib) built for fast parsing of [Variant Call Format](https://en.m.wikipedia.org/wiki/Variant_Call_Format) (VCF) files.
Attributes like `variant.gt_ref_depths` return a numpy array directly so they are immediately ready for downstream use.
**note** that the array is backed by the underlying C data, so, once `variant` goes out of scope. The array will contain nonsense.
To persist a copy, use: `cpy = np.array(variant.gt_ref_depths)` instead of just `arr = variant.gt_ref_depths`.
%package -n python3-cyvcf2
Summary: fast vcf parsing with cython + htslib
Provides: python-cyvcf2
BuildRequires: python3-devel
BuildRequires: python3-setuptools
BuildRequires: python3-pip
%description -n python3-cyvcf2
Note: cyvcf2 versions < 0.20.0 require htslib < 1.10. cyvcf2 versions >= 0.20.0 require htslib >= 1.10
<!-- ghp-import -p docs/build/html/ -->
The latest documentation for cyvcf2 can be found here:
[](http://brentp.github.io/cyvcf2/)
If you use cyvcf2, please cite the [paper](https://academic.oup.com/bioinformatics/article/2971439/cyvcf2)
Fast python **(2 and 3)** parsing of VCF and BCF including region-queries.
[](https://github.com/brentp/cyvcf2/actions?query=workflow%3ABuild)
cyvcf2 is a cython wrapper around [htslib](https://github.com/samtools/htslib) built for fast parsing of [Variant Call Format](https://en.m.wikipedia.org/wiki/Variant_Call_Format) (VCF) files.
Attributes like `variant.gt_ref_depths` return a numpy array directly so they are immediately ready for downstream use.
**note** that the array is backed by the underlying C data, so, once `variant` goes out of scope. The array will contain nonsense.
To persist a copy, use: `cpy = np.array(variant.gt_ref_depths)` instead of just `arr = variant.gt_ref_depths`.
%package help
Summary: Development documents and examples for cyvcf2
Provides: python3-cyvcf2-doc
%description help
Note: cyvcf2 versions < 0.20.0 require htslib < 1.10. cyvcf2 versions >= 0.20.0 require htslib >= 1.10
<!-- ghp-import -p docs/build/html/ -->
The latest documentation for cyvcf2 can be found here:
[](http://brentp.github.io/cyvcf2/)
If you use cyvcf2, please cite the [paper](https://academic.oup.com/bioinformatics/article/2971439/cyvcf2)
Fast python **(2 and 3)** parsing of VCF and BCF including region-queries.
[](https://github.com/brentp/cyvcf2/actions?query=workflow%3ABuild)
cyvcf2 is a cython wrapper around [htslib](https://github.com/samtools/htslib) built for fast parsing of [Variant Call Format](https://en.m.wikipedia.org/wiki/Variant_Call_Format) (VCF) files.
Attributes like `variant.gt_ref_depths` return a numpy array directly so they are immediately ready for downstream use.
**note** that the array is backed by the underlying C data, so, once `variant` goes out of scope. The array will contain nonsense.
To persist a copy, use: `cpy = np.array(variant.gt_ref_depths)` instead of just `arr = variant.gt_ref_depths`.
%prep
%autosetup -n cyvcf2-0.30.18
%build
%py3_build
%install
%py3_install
install -d -m755 %{buildroot}/%{_pkgdocdir}
if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi
if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi
if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi
if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi
pushd %{buildroot}
if [ -d usr/lib ]; then
find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/lib64 ]; then
find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/bin ]; then
find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst
fi
if [ -d usr/sbin ]; then
find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst
fi
touch doclist.lst
if [ -d usr/share/man ]; then
find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst
fi
popd
mv %{buildroot}/filelist.lst .
mv %{buildroot}/doclist.lst .
%files -n python3-cyvcf2 -f filelist.lst
%dir %{python3_sitelib}/*
%files help -f doclist.lst
%{_docdir}/*
%changelog
* Sun Apr 23 2023 Python_Bot <Python_Bot@openeuler.org> - 0.30.18-1
- Package Spec generated
|
