Atri Bhattacharya
be257a4acf
* Extend annot-tsv with several new command line options.
* Allow annot-tsv -a to rename annotations.
* Extend annot-tsv --overlap to be able to specify the overlap
fraction separately for source and target.
* Added new APIs to facilitate low-level CRAM container
manipulations, used by the new samtools cat region
filtering code.
* Some speed improvements.
For a complete list of changes, see
https://github.com/samtools/htslib/releases/tag/1.21
OBS-URL: https://build.opensuse.org/package/show/science/libhts?expand=0&rev=21
160 lines
6.0 KiB
RPMSpec
160 lines
6.0 KiB
RPMSpec
#
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# spec file for package libhts
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#
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# Copyright (c) 2025 SUSE LLC
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#
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# All modifications and additions to the file contributed by third parties
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# remain the property of their copyright owners, unless otherwise agreed
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# upon. The license for this file, and modifications and additions to the
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# file, is the same license as for the pristine package itself (unless the
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# license for the pristine package is not an Open Source License, in which
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# case the license is the MIT License). An "Open Source License" is a
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# license that conforms to the Open Source Definition (Version 1.9)
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# published by the Open Source Initiative.
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# Please submit bugfixes or comments via https://bugs.opensuse.org/
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#
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# Upstream does not bump htscodecs SOVERSION on backwards incompatible changes
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%define htscodecsminversion 1.6.1
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Name: libhts
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Version: 1.21
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Release: 0
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%define sonum 3
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Summary: C library for high-throughput sequencing data formats
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License: MIT
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Group: Productivity/Scientific/Other
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URL: https://github.com/samtools/htslib/
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Source0: https://github.com/samtools/htslib/releases/download/%{version}/htslib-%{version}.tar.bz2
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Source100: baselibs.conf
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BuildRequires: gcc-c++
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BuildRequires: htscodecs-devel >= %{htscodecsminversion}
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BuildRequires: pkgconfig(bzip2)
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BuildRequires: pkgconfig(libcurl)
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BuildRequires: pkgconfig(liblzma)
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BuildRequires: pkgconfig(zlib)
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%description
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HTSlib is an implementation of a unified C library for accessing common file formats, such as
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SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by
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samtools and bcftools.
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HTSlib implements a generalized BAM index, with file extension .csi (coordinate-sorted index).
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The HTSlib file reader first looks for the new index and then for the old if the new index is absent.
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This project also includes the popular tabix indexer, which indexes both .tbi and .csi formats, and
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the bgzip compression utility.
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%package -n libhts%{sonum}
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Summary: C library for high-throughput sequencing data formats
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Group: System/Libraries
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Requires: libhtscodecs2 >= %{htscodecsminversion}
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%description -n libhts%{sonum}
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HTSlib is an implementation of a unified C library for accessing common file formats, such as
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SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by
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samtools and bcftools.
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HTSlib implements a generalized BAM index, with file extension .csi (coordinate-sorted index).
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The HTSlib file reader first looks for the new index and then for the old if the new index is absent.
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%package -n bgzip
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Summary: Block compression/decompression utility from the HTSlib project
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Group: Productivity/Scientific/Other
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Requires: libhts%{sonum} = %{version}
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Requires: tabix = %{version}
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%description -n bgzip
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HTSlib is an implementation of a unified C library for accessing common file formats, such as
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SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by
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samtools and bcftools.
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HTSlib implements a generalized BAM index, with file extension .csi (coordinate-sorted index).
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The HTSlib file reader first looks for the new index and then for the old if the new index is absent.
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This project also includes the popular tabix indexer, which indexes both .tbi and .csi formats, and
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the bgzip compression utility.
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%package -n tabix
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Summary: Generic indexer for TAB-delimited genome position files from the HTSlib project
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Group: Productivity/Scientific/Other
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Requires: bgzip = %{version}
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Requires: libhts%{sonum} = %{version}
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%description -n tabix
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HTSlib is an implementation of a unified C library for accessing common file formats, such as
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SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by
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samtools and bcftools.
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HTSlib implements a generalized BAM index, with file extension .csi (coordinate-sorted index).
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The HTSlib file reader first looks for the new index and then for the old if the new index is absent.
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This project also includes the popular tabix indexer, which indexes both .tbi and .csi formats, and
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the bgzip compression utility.
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%package -n htsfile
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Summary: Identify high-throughput sequencing data files from the HTSlib project
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Group: Productivity/Scientific/Other
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Requires: libhts%{sonum} = %{version}
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%description -n htsfile
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HTSlib is an implementation of a unified C library for accessing common file formats, such as
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SAM, CRAM and VCF, used for high-throughput sequencing data, and is the core library used by
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samtools and bcftools.
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HTSlib implements a generalized BAM index, with file extension .csi (coordinate-sorted index).
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The HTSlib file reader first looks for the new index and then for the old if the new index is absent.
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This project also includes the popular tabix indexer, which indexes both .tbi and .csi formats, and
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the bgzip compression utility.
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%package devel
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Summary: Header files and libraries for compiling against %{name}
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Group: Development/Libraries/C and C++
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Requires: libhts%{sonum} = %{version}
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Requires: pkgconfig(bzip2)
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Requires: pkgconfig(libcurl)
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Requires: pkgconfig(liblzma)
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Requires: pkgconfig(zlib)
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%description devel
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Header files and libraries of the HTSlib project for compiling against %{name}.
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%prep
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%setup -q -n htslib-%{version}
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%build
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%configure --with-external-htscodecs --disable-static
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%make_build
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%install
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%make_install
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# remove static library
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rm %{buildroot}%{_libdir}/libhts.a
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# fix permissions
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chmod 0755 %{buildroot}%{_libdir}/libhts.so.*
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%post -n libhts%{sonum} -p /sbin/ldconfig
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%postun -n libhts%{sonum} -p /sbin/ldconfig
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%files -n libhts%{sonum}
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%{_libdir}/libhts.so.*
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%files -n bgzip
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%{_bindir}/bgzip
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%{_mandir}/man1/bgzip*
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%files -n tabix
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%{_bindir}/tabix
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%{_mandir}/man1/tabix*
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%files -n htsfile
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%license LICENSE
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%doc NEWS README
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%{_bindir}/htsfile
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%{_bindir}/annot-tsv
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%{_mandir}/man1/htsfile*
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%{_mandir}/man1/annot-tsv*
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%{_mandir}/man5/*
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%{_mandir}/man7/*
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%files devel
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%{_includedir}/htslib
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%{_libdir}/libhts.so
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%{_libdir}/pkgconfig/htslib.pc
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%changelog
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