# The value of Makefile LIBHTS_SOVERSION.
%global so_version 2

Name: htslib
Version: 1.9
Release: 4%{?dist}
Summary: C library for high-throughput sequencing data formats

# The entire source code is MIT/Expat except cram/ which is Modified-BSD.
# But as there is no "Expat" license in short name list, set "MIT".
# Expat license is same with MIT license.
# https://lists.fedoraproject.org/archives/list/legal@lists.fedoraproject.org/thread/C5AHVIW3F6LF5CYLR2PSHNANFYKP327P/
License: MIT and BSD
URL: http://www.htslib.org
Source0: https://github.com/samtools/%{name}/releases/download/%{version}/%{name}-%{version}.tar.bz2

BuildRequires: gcc
BuildRequires: bzip2-devel
BuildRequires: libcurl-devel
BuildRequires: openssl-devel
BuildRequires: xz-devel
BuildRequires: zlib-devel
# It's used in make test.
BuildRequires: perl-interpreter
BuildRequires: perl-Data-Dumper
BuildRequires: perl-Getopt-Long

%description
HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM, CRAM and VCF, used for high-throughput sequencing data,
and is the core library used by samtools and bcftools.


%package devel
Summary: Development files for %{name}
Requires: %{name}%{?_isa} = %{version}-%{release}
# zlib-devel is required for 1.9; remove when bumping to next HTSlib release.
# See <https://github.com/samtools/htslib/commit/7a215862ccfeffac12584d754836f66ce2641a47>
Requires: zlib-devel

%description devel
The %{name}-devel package contains libraries and header files for
developing applications that use %{name}.


%package tools
Summary: Additional htslib-based tools
Requires: %{name}%{?_isa} = %{version}-%{release}

%description tools
Includes the popular tabix indexer, which indexes both .tbi and .csi formats,
the htsfile identifier tool, and the bgzip compression utility.


%prep
%setup -q

%build
%configure CFLAGS="%{optflags}" LDFLAGS="%{build_ldflags}" \
    --prefix=%{_prefix} \
    --libdir=%{_libdir} \
    --enable-plugins \
    --with-plugin-path='%{_usr}/local/libexec/htslib:$(plugindir)' \
    --enable-gcs \
    --enable-libcurl \
    --enable-s3
%make_build

# As we don't install libhts.a, the .private keywords are irrelevant.
sed -i -E '/^(Libs|Requires)\.private:/d' htslib.pc.tmp

%install
%make_install
pushd %{buildroot}/%{_libdir}
chmod 755 libhts.so.%{version}
popd

find %{buildroot} -name '*.la' -delete
rm -f %{buildroot}/%{_libdir}/libhts.a

%check
make test

%ldconfig_scriptlets

%files
%license LICENSE
%doc NEWS
%{_libdir}/libhts.so.%{version}
%{_libdir}/libhts.so.%{so_version}
# The plugin so files should be in the main package,
# as they are loaded when libhts.so.%%{so_version} is used.
%dir %{_libexecdir}/%{name}
%{_libexecdir}/%{name}/hfile_gcs.so
%{_libexecdir}/%{name}/hfile_libcurl.so
%{_libexecdir}/%{name}/hfile_s3.so
# The man5 pages are aimed at users.
%{_mandir}/man5/faidx.5*
%{_mandir}/man5/sam.5*
%{_mandir}/man5/vcf.5*

%files devel
%dir %{_includedir}/%{name}
%{_includedir}/%{name}/*.h
%{_libdir}/libhts.so
%{_libdir}/pkgconfig/htslib.pc

%files tools
%{_bindir}/bgzip
%{_bindir}/htsfile
%{_bindir}/tabix
%{_mandir}/man1/bgzip.1*
%{_mandir}/man1/htsfile.1*
%{_mandir}/man1/tabix.1*


%changelog
* Tue Nov 05 2019 John Marshall <jmarshall@users.sourceforge.net> - 1.9-4
- Remove unneeded pkg-config keywords for static linking, which generated
  unnecessary htslib-devel dependencies.
- Explicitly list zlib-devel dependency, needed for htslib-1.9.
- Align the field delimiter as 1 space.
- Add check section and "make test" in it.

* Sun Oct 27 2019 Jun Aruga <jaruga@redhat.com> - 1.9-3
- Fix a bug that %%{_libexecdir}/%%{name} directory is not removed,
  when uninstalling the package "rpm -e htslib".
- Add %%dir to directories to verify the files in the directory.

* Tue Oct 22 2019 Jun Aruga <jaruga@redhat.com> - 1.9-2
- Add configure script.
- Enable separately-compiled plugins.
- Enable support for Google Cloud Storage URLs.
- Enable libcurl-based support for http/https/etc URLs.
- Enable support for Amazon AWS S3 URLs.
- Move the man5 page files to main package.

* Fri Sep 06 2019 Jun Aruga <jaruga@redhat.com> - 1.9-1
- Update for htslib version 1.9

* Thu Jun 2 2016 Sam Nicholls <sam@samnicholls.net> - 1.3.1-4
- Fix changelog
- Add comment RE:bzip2/lzma support

* Sat May 28 2016 Sam Nicholls <sam@samnicholls.net> - 1.3.1-3
- Add LICENSE and NEWS to doc
- Remove unnecessary DESTDIR from call to make_install macro
- Remove explicit Provides

* Thu Apr 28 2016 Sam Nicholls <sam@samnicholls.net> - 1.3.1-1
- Alter permissions of SO to permit strip

* Tue Apr 26 2016 Sam Nicholls <sam@samnicholls.net> - 1.3.1-0
- Update for htslib version 1.3.1

* Tue Apr 12 2016 Sam Nicholls <sam@samnicholls.net> - 1.3.0-0
- Initial version