- Update to 1.6.1:

* Changes + Improve warning levels by the compiler in CI. + Switch to GitHub actions for some CI builds. + Add configure check for cpuid systems. * Bug fixes + Use unsigned chars for ctype macros in the name tokeniser. On many systems this was already mitigated against, but on some OSes a char > 128 could trigger a buffer underrun. + Improve AVX512 compiler support. + Fix -std=c99 -pendantic pedantry (#117) OBS-URL: https://build.opensuse.org/package/show/science/htscodecs?expand=0&rev=9
2025-04-01 21:16:17 +00:00
commit 76b1455620
7 changed files with 212 additions and 0 deletions
--- a/.gitattributes
+++ 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
--- a/.gitignore
+++ b/.gitignore
@@ -0,0 +1 @@
+.osc
--- a/baselibs.conf
+++ b/baselibs.conf
@@ -0,0 +1 @@
+libhtscodecs2
--- a/htscodecs-1.6.0.tar.gz
+++ b/htscodecs-1.6.0.tar.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:4b4abb6dfa192f179386c1d49256892a134297ecb4dd25ad4c346e9dde1108c0
+size 3715332
--- a/htscodecs-1.6.1.tar.gz
+++ b/htscodecs-1.6.1.tar.gz
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:5821b171c9ba5d2a616cedc98db9f4cc8b384fd5efd55a5a0935528646122659
+size 3715406
--- a/htscodecs.changes
+++ b/htscodecs.changes
@@ -0,0 +1,97 @@
+-------------------------------------------------------------------
+Fri Mar 28 10:35:16 UTC 2025 - Stefan Brüns <stefan.bruens@rwth-aachen.de>
+
+- Update to 1.6.1:
+  * Changes
+    + Improve warning levels by the compiler in CI.
+    + Switch to GitHub actions for some CI builds.
+    + Add configure check for cpuid systems.
+  * Bug fixes
+    + Use unsigned chars for ctype macros in the name tokeniser.
+      On many systems this was already mitigated against, but on
+      some OSes a char > 128 could trigger a buffer underrun.
+    + Improve AVX512 compiler support.
+    + Fix -std=c99 -pendantic pedantry (#117)
+
+-------------------------------------------------------------------
+Wed Jan  3 01:32:19 UTC 2024 - Stefan Brüns <stefan.bruens@rwth-aachen.de>
+
+- Update to 1.6.0:
+  * Changes
+    + Replaced the rANS codec SIMD gathers with simulated gathers
+      via scalar memory fetches. This helps AMD Zen4, but
+      importantly it also fixes a disastrous performance regression
+      caused by Intel's DownFall microcode fix.
+    + There is an impact on pre-DownFall speeds, but we should
+      focus on patched CPUs as a priority.
+    + A small speed up to the rans_F_to_s3 function used by
+      order-0 rans decode.
+    + Small speed up to SIMD rans32x16 order-1 encoder by reducing
+      cache misses. Also sped up the rans4x8 order-1 encoder,
+      particularly on AMD Zen4.
+    + Now supports building with "zig cc"
+  * Bug fixes
+    + Improve robustness of name tokeniser when given non 7-bit
+      ASCII and on machines where "char" defaults to unsigned.
+    + Also fixed a 1 byte buffer read-overrun in name tokeniser.
+    + Fix name tokeniser encoder failure with some duplicated
+      streams.
+    + Fixed rans_set_cpu to work multiple times, as well as
+      reinstating the ability to change decode and encode side
+      independently (accidentally lost in commit 958032c). No
+      effect on usage, but it improves the test coverage.
+    + Added a round-trip fuzz tester to test the ability to
+      encode. The old fuzz testing was decode streams only.
+    + Fixed bounds checking in rans_uncompress_O0_32x16_avx2,
+      fixing buffer read overruns.
+    + Removed undefined behaviour in transpose_and_copy(),
+      fixing zig cc builds.
+
+-------------------------------------------------------------------
+Thu May  4 14:47:16 UTC 2023 - Andrea Manzini <andrea.manzini@suse.com>
+
+- Update to 1.5.0:
+  * Significant speed ups to the fqzcomp codec via code restructuring
+    and use of memory prefetch instructions. Encode is 30-40% faster
+    and decode 5-8% faster.
+  * Remove unused ax_with_libdeflate.m4 file from build system
+
+- removed patch fix_ix86_build.patch already merged in upstream
+
+- Update to 1.4.0:
+  * This is almost entirely minor bug fixing with a few small updates.
+  * Optimise compression / speed of the name tokeniser
+  * Improvements for Intel -m32 builds, including better AVX2 validation
+  * Detect Neon capability at runtime via operating system APIs.
+  * Update hts_pack to operate in line with CRAMcodecs spec, where the number of symbols > 16.
+  * Fixed too-stringent buffer overflow checking in O1 rans decoder.
+
+
+-------------------------------------------------------------------
+Thu Sep  8 21:52:47 UTC 2022 - Stefan Brüns <stefan.bruens@rwth-aachen.de>
+
+- Update to 1.3.0:
+  * The primary change in this release is a new SIMD enabled
+    rANS codec.
+    There is a 32-way unrolled rANS implementation. This is accessed
+    using the existing rans 4x16 API with the RANS_ORDER_X32 bit set.
+  * Improved memory allocation via a new htscodecs_tls_alloc function.
+  * Some external functions have been renamed, with the old ones
+    still existing in a deprecated fashion.
+  * Improved test framework with an "entropy" tool that iterates
+    over all entropy encoders.
+  * Reworked fuzzing infrastructure.
+  * Small speed improvements to various rANS encoders and decoders.
+  * Substantial memory reduction to the name tokeniser (tok3).
+  * Fixed undefined behaviour in our use of _builtin_clz().
+  * Fixed a few redundant #includes.
+  * Work around strict aliasing bugs, uncovered with gcc -O2.
+  * Fixed an issue with encoding data blocks close to 2GB in size.
+  * Fix encode error with large blocks using RANS_ORDER_STRIPE.
+- Add fix_ix86_build.patch
+
+-------------------------------------------------------------------
+Wed Apr 20 19:45:48 UTC 2022 - Ferdinand Thiessen <rpm@fthiessen.de>
+
+- Created initial package for libhts
+
--- a/htscodecs.spec
+++ b/htscodecs.spec
@@ -0,0 +1,84 @@
+#
+# spec file for package htscodecs
+#
+# Copyright (c) 2025 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:        1.6.1
+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:  autoconf
+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
+%autosetup -p1
+
+%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.md
+%{_includedir}/htscodecs
+%{_libdir}/lib%{name}.so
+
+%changelog