commit ef7a9140e1b553894218238feea1cf719cca0a6249ca7ae33bb54a312cf3b3f3 Author: Atri Bhattacharya Date: Mon May 2 09:30:00 2022 +0000 Accepting request 971254 from home:susnux:branches:science Required for libhts OBS-URL: https://build.opensuse.org/request/show/971254 OBS-URL: https://build.opensuse.org/package/show/science/htscodecs?expand=0&rev=1 diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..9b03811 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,23 @@ +## Default LFS +*.7z filter=lfs diff=lfs merge=lfs -text +*.bsp filter=lfs diff=lfs merge=lfs -text +*.bz2 filter=lfs diff=lfs merge=lfs -text +*.gem filter=lfs diff=lfs merge=lfs -text +*.gz filter=lfs diff=lfs merge=lfs -text +*.jar filter=lfs diff=lfs merge=lfs -text +*.lz filter=lfs diff=lfs merge=lfs -text +*.lzma filter=lfs diff=lfs merge=lfs -text +*.obscpio filter=lfs diff=lfs merge=lfs -text +*.oxt filter=lfs diff=lfs merge=lfs -text +*.pdf filter=lfs diff=lfs merge=lfs -text +*.png filter=lfs diff=lfs merge=lfs -text +*.rpm filter=lfs diff=lfs merge=lfs -text +*.tbz filter=lfs diff=lfs merge=lfs -text +*.tbz2 filter=lfs diff=lfs merge=lfs -text +*.tgz filter=lfs diff=lfs merge=lfs -text +*.ttf filter=lfs diff=lfs merge=lfs -text +*.txz filter=lfs diff=lfs merge=lfs -text +*.whl filter=lfs diff=lfs merge=lfs -text +*.xz filter=lfs diff=lfs merge=lfs -text +*.zip filter=lfs diff=lfs merge=lfs -text +*.zst filter=lfs diff=lfs merge=lfs -text diff --git a/baselibs.conf b/baselibs.conf new file mode 100644 index 0000000..8bbc8db --- /dev/null +++ b/baselibs.conf @@ -0,0 +1 @@ +libhtscodecs2 diff --git a/htscodecs-1.2.2.tar.gz b/htscodecs-1.2.2.tar.gz new file mode 100644 index 0000000..7f4eb80 --- /dev/null +++ b/htscodecs-1.2.2.tar.gz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:d17d7a505da3fc79dcced320c132c5492b5dc78ee70d9ca8218b927070f183ca +size 3044356 diff --git a/htscodecs.changes b/htscodecs.changes new file mode 100644 index 0000000..a84a371 --- /dev/null +++ b/htscodecs.changes @@ -0,0 +1,5 @@ +------------------------------------------------------------------- +Wed Apr 20 19:45:48 UTC 2022 - Ferdinand Thiessen + +- Created initial package for libhts + diff --git a/htscodecs.spec b/htscodecs.spec new file mode 100644 index 0000000..f30b037 --- /dev/null +++ b/htscodecs.spec @@ -0,0 +1,83 @@ +# +# spec file for package htscodecs +# +# Copyright (c) 2022 SUSE LLC +# +# All modifications and additions to the file contributed by third parties +# remain the property of their copyright owners, unless otherwise agreed +# upon. The license for this file, and modifications and additions to the +# file, is the same license as for the pristine package itself (unless the +# license for the pristine package is not an Open Source License, in which +# case the license is the MIT License). An "Open Source License" is a +# license that conforms to the Open Source Definition (Version 1.9) +# published by the Open Source Initiative. + +# Please submit bugfixes or comments via https://bugs.opensuse.org/ +# + + +%define sonum 2 +Name: htscodecs +Version: 1.2.2 +Release: 0 +Summary: C library for custom compression for CRAM and other formats +License: MIT +Group: Productivity/Scientific/Other +URL: https://github.com/samtools/htscodecs +Source0: https://github.com/samtools/htscodecs/releases/download/v%{version}/htscodecs-%{version}.tar.gz +Source100: baselibs.conf +BuildRequires: gcc-c++ +BuildRequires: pkgconfig +BuildRequires: pkgconfig(bzip2) +BuildRequires: pkgconfig(zlib) + +%description +htscodecs provides an API to access CRAM codecs used for "EXTERNAL" block types. +These consist of two variants of the rANS codec (8-bit and 16-bit renormalisation, +with run-length encoding and bit-packing also supported in the latter), +a dynamic arithmetic coder, and custom codecs for name/ID compression +and quality score compression derived from fqzcomp. + +%package -n lib%{name}%{sonum} +Summary: C library for custom compression for CRAM and other formats +Group: System/Libraries + +%description -n lib%{name}%{sonum} +htscodecs provides an API to access CRAM codecs used for "EXTERNAL" block types. +These consist of two variants of the rANS codec (8-bit and 16-bit renormalisation, +with run-length encoding and bit-packing also supported in the latter), +a dynamic arithmetic coder, and custom codecs for name/ID compression +and quality score compression derived from fqzcomp. + +%package devel +Summary: Header files and libraries for compiling against %{name} +Group: Development/Libraries/C and C++ +Requires: lib%{name}%{sonum} = %{version} + +%description devel +Header files and libraries of the samtools project for compiling against %{name}. + +%prep +%setup -q + +%build +%configure --disable-static +%make_build + +%install +%make_install +rm %{buildroot}%{_libdir}/lib%{name}.la + +%post -n lib%{name}%{sonum} -p /sbin/ldconfig +%postun -n lib%{name}%{sonum} -p /sbin/ldconfig + +%files -n lib%{name}%{sonum} +%license LICENSE.md +%{_libdir}/lib%{name}.so.* + +%files devel +%doc README.md NEWS +%{_includedir}/htscodecs +%{_libdir}/lib%{name}.so + +%changelog