forked from pool/htscodecs
Accepting request 1002208 from home:StefanBruens:branches:science
- 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
OBS-URL: https://build.opensuse.org/request/show/1002208
OBS-URL: https://build.opensuse.org/package/show/science/htscodecs?expand=0&rev=3
This commit is contained in:
Git OBS Bridge
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commit
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99
fix_ix86_build.patch
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99
fix_ix86_build.patch
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@ -0,0 +1,99 @@
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From 843d4f63b1c64905881b4648916a4d027baa1a1c Mon Sep 17 00:00:00 2001
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From: James Bonfield <jkb@sanger.ac.uk>
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Date: Wed, 17 Aug 2022 15:27:04 +0100
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Subject: [PATCH] Improvements for intel -m32 builds.
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On this platform _mm256_extract_epi64 isn't defined, but the rest of
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AVX2 is. It needs to fail auto-detection.
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Also we get unaligned accesses in the SSE4 code with tbuf due to
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differing data alignment caused by 32-bit pointers instead of 64-bit.
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This exposes an underlying problem of using aligned SIMD writes on
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tbuf without explicitly asking for alignment. (The new code is also
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sometimes a little faster.)
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See also samtools/htslib#1500
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---
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configure.ac | 3 ++-
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htscodecs/rANS_static32x16pr_avx2.c | 2 +-
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htscodecs/rANS_static32x16pr_avx512.c | 2 +-
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htscodecs/rANS_static32x16pr_sse4.c | 2 +-
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m4/ax_check_compile_flag.m4 | 6 +++++-
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5 files changed, 10 insertions(+), 5 deletions(-)
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diff --git a/configure.ac b/configure.ac
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index 4c8ad54..eb2f44e 100644
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--- a/configure.ac
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+++ b/configure.ac
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@@ -165,7 +165,8 @@ AX_CHECK_COMPILE_FLAG([-mavx2], [
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]],[[
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__m256i a = _mm256_set_epi32(1, 2, 3, 4, 5, 6, 7, 8);
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__m256i b = _mm256_add_epi32(a, a);
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- return *((char *) &b);
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+ long long c = _mm256_extract_epi64(b, 0);
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+ return (int) c;
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]])
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])
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AM_CONDITIONAL([RANS_32x16_AVX2],[test "x$MAVX2" != "x"])
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diff --git a/htscodecs/rANS_static32x16pr_avx2.c b/htscodecs/rANS_static32x16pr_avx2.c
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index 2dd14f1..c36f23c 100644
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--- a/htscodecs/rANS_static32x16pr_avx2.c
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+++ b/htscodecs/rANS_static32x16pr_avx2.c
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@@ -1123,7 +1123,7 @@ unsigned char *rans_uncompress_O1_32x16_avx2(unsigned char *in,
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union {
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unsigned char tbuf[32][32];
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uint64_t tbuf64[32][4];
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- } u;
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+ } u __attribute__((aligned(32)));
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unsigned int tidx = 0;
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if (0) {
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diff --git a/htscodecs/rANS_static32x16pr_avx512.c b/htscodecs/rANS_static32x16pr_avx512.c
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index 0d1456f..e9cce46 100644
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--- a/htscodecs/rANS_static32x16pr_avx512.c
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+++ b/htscodecs/rANS_static32x16pr_avx512.c
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@@ -735,7 +735,7 @@ unsigned char *rans_uncompress_O1_32x16_avx512(unsigned char *in,
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union {
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unsigned char tbuf[32][32];
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uint64_t tbuf64[32][4];
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- } u;
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+ } u __attribute__((aligned(32)));
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#else
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uint32_t tbuf[32][32];
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#endif
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diff --git a/htscodecs/rANS_static32x16pr_sse4.c b/htscodecs/rANS_static32x16pr_sse4.c
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index fe0345f..88bcbe0 100644
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--- a/htscodecs/rANS_static32x16pr_sse4.c
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+++ b/htscodecs/rANS_static32x16pr_sse4.c
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@@ -1423,7 +1423,7 @@ unsigned char *rans_uncompress_O1_32x16_sse4(unsigned char *in,
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uint16_t *sp = (uint16_t *)ptr;
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const uint32_t mask = ((1u << TF_SHIFT_O1_FAST)-1);
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__m128i maskv = _mm_set1_epi32(mask); // set mask in all lanes
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- uint8_t tbuf[32][32];
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+ uint8_t tbuf[32][32] __attribute__((aligned(32)));
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int tidx = 0;
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LOAD128(Rv, R);
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LOAD128(Lv, l);
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diff --git a/m4/ax_check_compile_flag.m4 b/m4/ax_check_compile_flag.m4
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index bd753b3..c2bd2c6 100644
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--- a/m4/ax_check_compile_flag.m4
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+++ b/m4/ax_check_compile_flag.m4
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@@ -36,13 +36,17 @@
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#serial 6
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+# LOCAL modification; change AC_COMPILE_IFELSE to AC_LINK_IFELSE so
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+# _mm256_extract_epi64 tests on a x86_64 running under -m32 still
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+# fails. (Otherwise it compiles, but fails to link.)
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+
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AC_DEFUN([AX_CHECK_COMPILE_FLAG],
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[AC_PREREQ(2.64)dnl for _AC_LANG_PREFIX and AS_VAR_IF
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AS_VAR_PUSHDEF([CACHEVAR],[ax_cv_check_[]_AC_LANG_ABBREV[]flags_$4_$1])dnl
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AC_CACHE_CHECK([whether _AC_LANG compiler accepts $1], CACHEVAR, [
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ax_check_save_flags=$[]_AC_LANG_PREFIX[]FLAGS
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_AC_LANG_PREFIX[]FLAGS="$[]_AC_LANG_PREFIX[]FLAGS $4 $1"
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- AC_COMPILE_IFELSE([m4_default([$5],[AC_LANG_PROGRAM()])],
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+ AC_LINK_IFELSE([m4_default([$5],[AC_LANG_PROGRAM()])],
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[AS_VAR_SET(CACHEVAR,[yes])],
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[AS_VAR_SET(CACHEVAR,[no])])
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_AC_LANG_PREFIX[]FLAGS=$ax_check_save_flags])
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@ -1,3 +0,0 @@
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version https://git-lfs.github.com/spec/v1
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oid sha256:d17d7a505da3fc79dcced320c132c5492b5dc78ee70d9ca8218b927070f183ca
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size 3044356
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3
htscodecs-1.3.0.tar.gz
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3
htscodecs-1.3.0.tar.gz
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@ -0,0 +1,3 @@
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version https://git-lfs.github.com/spec/v1
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oid sha256:696c0affbfa7e59276e0dfc71dcba2f04b0a6db12998f30f1baf2fc21e9113f4
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size 3368716
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@ -1,3 +1,26 @@
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-------------------------------------------------------------------
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Thu Sep 8 21:52:47 UTC 2022 - Stefan Brüns <stefan.bruens@rwth-aachen.de>
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- Update to 1.3.0:
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* The primary change in this release is a new SIMD enabled
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rANS codec.
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There is a 32-way unrolled rANS implementation. This is accessed
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using the existing rans 4x16 API with the RANS_ORDER_X32 bit set.
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* Improved memory allocation via a new htscodecs_tls_alloc function.
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* Some external functions have been renamed, with the old ones
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still existing in a deprecated fashion.
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* Improved test framework with an "entropy" tool that iterates
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over all entropy encoders.
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* Reworked fuzzing infrastructure.
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* Small speed improvements to various rANS encoders and decoders.
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* Substantial memory reduction to the name tokeniser (tok3).
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* Fixed undefined behaviour in our use of _builtin_clz().
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* Fixed a few redundant #includes.
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* Work around strict aliasing bugs, uncovered with gcc -O2.
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* Fixed an issue with encoding data blocks close to 2GB in size.
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* Fix encode error with large blocks using RANS_ORDER_STRIPE.
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- Add fix_ix86_build.patch
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-------------------------------------------------------------------
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Wed Apr 20 19:45:48 UTC 2022 - Ferdinand Thiessen <rpm@fthiessen.de>
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@ -18,7 +18,7 @@
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%define sonum 2
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Name: htscodecs
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Version: 1.2.2
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Version: 1.3.0
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Release: 0
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Summary: C library for custom compression for CRAM and other formats
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License: MIT
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@ -26,6 +26,9 @@ Group: Productivity/Scientific/Other
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URL: https://github.com/samtools/htscodecs
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Source0: https://github.com/samtools/htscodecs/releases/download/v%{version}/htscodecs-%{version}.tar.gz
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Source100: baselibs.conf
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# PATCH-FIX-UPSTREAM
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Patch0: https://github.com/samtools/htscodecs/commit/843d4f63b1c64905881b4648916a4d027baa1a1c.patch#/fix_ix86_build.patch
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BuildRequires: autoconf
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BuildRequires: gcc-c++
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BuildRequires: pkgconfig
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BuildRequires: pkgconfig(bzip2)
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@ -58,9 +61,11 @@ Requires: lib%{name}%{sonum} = %{version}
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Header files and libraries of the samtools project for compiling against %{name}.
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%prep
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%setup -q
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%autosetup -p1
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%build
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# Rebuild configure script after Patch0
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autoconf
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%configure --disable-static
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%make_build
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@ -76,7 +81,7 @@ rm %{buildroot}%{_libdir}/lib%{name}.la
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%{_libdir}/lib%{name}.so.*
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%files devel
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%doc README.md NEWS
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%doc README.md NEWS.md
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%{_includedir}/htscodecs
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%{_libdir}/lib%{name}.so
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