minimap2 0.2.25.1 → 0.2.26.0

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Files changed (109) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +9 -0
  3. data/ext/Rakefile +2 -2
  4. data/ext/minimap2/NEWS.md +9 -0
  5. data/ext/minimap2/README.md +2 -2
  6. data/ext/minimap2/cookbook.md +2 -2
  7. data/ext/minimap2/minimap.h +1 -1
  8. data/ext/minimap2/minimap2.1 +1 -1
  9. data/ext/minimap2/misc/paftools.js +1 -1
  10. data/ext/minimap2/python/mappy.pyx +1 -1
  11. data/ext/minimap2/setup.py +22 -32
  12. data/lib/minimap2/version.rb +1 -1
  13. metadata +1 -97
  14. data/ext/minimap2/lib/simde/CONTRIBUTING.md +0 -114
  15. data/ext/minimap2/lib/simde/COPYING +0 -20
  16. data/ext/minimap2/lib/simde/README.md +0 -333
  17. data/ext/minimap2/lib/simde/amalgamate.py +0 -58
  18. data/ext/minimap2/lib/simde/meson.build +0 -33
  19. data/ext/minimap2/lib/simde/netlify.toml +0 -20
  20. data/ext/minimap2/lib/simde/simde/arm/neon/float32x2.h +0 -140
  21. data/ext/minimap2/lib/simde/simde/arm/neon/float32x4.h +0 -137
  22. data/ext/minimap2/lib/simde/simde/arm/neon/float64x1.h +0 -142
  23. data/ext/minimap2/lib/simde/simde/arm/neon/float64x2.h +0 -145
  24. data/ext/minimap2/lib/simde/simde/arm/neon/int16x4.h +0 -140
  25. data/ext/minimap2/lib/simde/simde/arm/neon/int16x8.h +0 -145
  26. data/ext/minimap2/lib/simde/simde/arm/neon/int32x2.h +0 -140
  27. data/ext/minimap2/lib/simde/simde/arm/neon/int32x4.h +0 -143
  28. data/ext/minimap2/lib/simde/simde/arm/neon/int64x1.h +0 -137
  29. data/ext/minimap2/lib/simde/simde/arm/neon/int64x2.h +0 -141
  30. data/ext/minimap2/lib/simde/simde/arm/neon/int8x16.h +0 -147
  31. data/ext/minimap2/lib/simde/simde/arm/neon/int8x8.h +0 -141
  32. data/ext/minimap2/lib/simde/simde/arm/neon/uint16x4.h +0 -134
  33. data/ext/minimap2/lib/simde/simde/arm/neon/uint16x8.h +0 -138
  34. data/ext/minimap2/lib/simde/simde/arm/neon/uint32x2.h +0 -134
  35. data/ext/minimap2/lib/simde/simde/arm/neon/uint32x4.h +0 -137
  36. data/ext/minimap2/lib/simde/simde/arm/neon/uint64x1.h +0 -131
  37. data/ext/minimap2/lib/simde/simde/arm/neon/uint64x2.h +0 -135
  38. data/ext/minimap2/lib/simde/simde/arm/neon/uint8x16.h +0 -141
  39. data/ext/minimap2/lib/simde/simde/arm/neon/uint8x8.h +0 -135
  40. data/ext/minimap2/lib/simde/simde/arm/neon.h +0 -97
  41. data/ext/minimap2/lib/simde/simde/check.h +0 -267
  42. data/ext/minimap2/lib/simde/simde/debug-trap.h +0 -83
  43. data/ext/minimap2/lib/simde/simde/hedley.h +0 -1899
  44. data/ext/minimap2/lib/simde/simde/simde-arch.h +0 -445
  45. data/ext/minimap2/lib/simde/simde/simde-common.h +0 -697
  46. data/ext/minimap2/lib/simde/simde/x86/avx.h +0 -5385
  47. data/ext/minimap2/lib/simde/simde/x86/avx2.h +0 -2402
  48. data/ext/minimap2/lib/simde/simde/x86/avx512bw.h +0 -391
  49. data/ext/minimap2/lib/simde/simde/x86/avx512f.h +0 -3389
  50. data/ext/minimap2/lib/simde/simde/x86/avx512vl.h +0 -112
  51. data/ext/minimap2/lib/simde/simde/x86/fma.h +0 -659
  52. data/ext/minimap2/lib/simde/simde/x86/mmx.h +0 -2210
  53. data/ext/minimap2/lib/simde/simde/x86/sse.h +0 -3696
  54. data/ext/minimap2/lib/simde/simde/x86/sse2.h +0 -5991
  55. data/ext/minimap2/lib/simde/simde/x86/sse3.h +0 -343
  56. data/ext/minimap2/lib/simde/simde/x86/sse4.1.h +0 -1783
  57. data/ext/minimap2/lib/simde/simde/x86/sse4.2.h +0 -105
  58. data/ext/minimap2/lib/simde/simde/x86/ssse3.h +0 -1053
  59. data/ext/minimap2/lib/simde/simde/x86/svml.h +0 -543
  60. data/ext/minimap2/lib/simde/test/CMakeLists.txt +0 -166
  61. data/ext/minimap2/lib/simde/test/arm/meson.build +0 -4
  62. data/ext/minimap2/lib/simde/test/arm/neon/meson.build +0 -23
  63. data/ext/minimap2/lib/simde/test/arm/neon/skel.c +0 -871
  64. data/ext/minimap2/lib/simde/test/arm/neon/test-neon-internal.h +0 -134
  65. data/ext/minimap2/lib/simde/test/arm/neon/test-neon.c +0 -39
  66. data/ext/minimap2/lib/simde/test/arm/neon/test-neon.h +0 -10
  67. data/ext/minimap2/lib/simde/test/arm/neon/vadd.c +0 -1260
  68. data/ext/minimap2/lib/simde/test/arm/neon/vdup_n.c +0 -873
  69. data/ext/minimap2/lib/simde/test/arm/neon/vmul.c +0 -1084
  70. data/ext/minimap2/lib/simde/test/arm/neon/vsub.c +0 -1260
  71. data/ext/minimap2/lib/simde/test/arm/test-arm-internal.h +0 -18
  72. data/ext/minimap2/lib/simde/test/arm/test-arm.c +0 -20
  73. data/ext/minimap2/lib/simde/test/arm/test-arm.h +0 -8
  74. data/ext/minimap2/lib/simde/test/cmake/AddCompilerFlags.cmake +0 -171
  75. data/ext/minimap2/lib/simde/test/cmake/ExtraWarningFlags.cmake +0 -68
  76. data/ext/minimap2/lib/simde/test/meson.build +0 -64
  77. data/ext/minimap2/lib/simde/test/munit/COPYING +0 -21
  78. data/ext/minimap2/lib/simde/test/munit/Makefile +0 -55
  79. data/ext/minimap2/lib/simde/test/munit/README.md +0 -54
  80. data/ext/minimap2/lib/simde/test/munit/example.c +0 -351
  81. data/ext/minimap2/lib/simde/test/munit/meson.build +0 -37
  82. data/ext/minimap2/lib/simde/test/munit/munit.c +0 -2055
  83. data/ext/minimap2/lib/simde/test/munit/munit.h +0 -535
  84. data/ext/minimap2/lib/simde/test/run-tests.c +0 -20
  85. data/ext/minimap2/lib/simde/test/run-tests.h +0 -260
  86. data/ext/minimap2/lib/simde/test/x86/avx.c +0 -13752
  87. data/ext/minimap2/lib/simde/test/x86/avx2.c +0 -9977
  88. data/ext/minimap2/lib/simde/test/x86/avx512bw.c +0 -2664
  89. data/ext/minimap2/lib/simde/test/x86/avx512f.c +0 -10416
  90. data/ext/minimap2/lib/simde/test/x86/avx512vl.c +0 -210
  91. data/ext/minimap2/lib/simde/test/x86/fma.c +0 -2557
  92. data/ext/minimap2/lib/simde/test/x86/meson.build +0 -33
  93. data/ext/minimap2/lib/simde/test/x86/mmx.c +0 -2878
  94. data/ext/minimap2/lib/simde/test/x86/skel.c +0 -2984
  95. data/ext/minimap2/lib/simde/test/x86/sse.c +0 -5121
  96. data/ext/minimap2/lib/simde/test/x86/sse2.c +0 -9860
  97. data/ext/minimap2/lib/simde/test/x86/sse3.c +0 -486
  98. data/ext/minimap2/lib/simde/test/x86/sse4.1.c +0 -3446
  99. data/ext/minimap2/lib/simde/test/x86/sse4.2.c +0 -101
  100. data/ext/minimap2/lib/simde/test/x86/ssse3.c +0 -2084
  101. data/ext/minimap2/lib/simde/test/x86/svml.c +0 -1545
  102. data/ext/minimap2/lib/simde/test/x86/test-avx.h +0 -16
  103. data/ext/minimap2/lib/simde/test/x86/test-avx512.h +0 -25
  104. data/ext/minimap2/lib/simde/test/x86/test-mmx.h +0 -13
  105. data/ext/minimap2/lib/simde/test/x86/test-sse.h +0 -13
  106. data/ext/minimap2/lib/simde/test/x86/test-sse2.h +0 -13
  107. data/ext/minimap2/lib/simde/test/x86/test-x86-internal.h +0 -196
  108. data/ext/minimap2/lib/simde/test/x86/test-x86.c +0 -48
  109. data/ext/minimap2/lib/simde/test/x86/test-x86.h +0 -8
@@ -1,105 +0,0 @@
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- /* Copyright (c) 2017 Evan Nemerson <evan@nemerson.com>
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- *
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- * Permission is hereby granted, free of charge, to any person
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- * obtaining a copy of this software and associated documentation
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- * files (the "Software"), to deal in the Software without
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- * restriction, including without limitation the rights to use, copy,
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- * modify, merge, publish, distribute, sublicense, and/or sell copies
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- * of the Software, and to permit persons to whom the Software is
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- * furnished to do so, subject to the following conditions:
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- *
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- * The above copyright notice and this permission notice shall be
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- * included in all copies or substantial portions of the Software.
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- *
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- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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- * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
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- * BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
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- * ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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- * CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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- * SOFTWARE.
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- */
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-
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- #if !defined(SIMDE__SSE4_2_H)
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- # if !defined(SIMDE__SSE4_2_H)
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- # define SIMDE__SSE4_2_H
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- # endif
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- # include "sse4.1.h"
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-
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- HEDLEY_DIAGNOSTIC_PUSH
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- SIMDE_DISABLE_UNWANTED_DIAGNOSTICS
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-
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- # if defined(SIMDE_SSE4_2_NATIVE)
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- # undef SIMDE_SSE4_2_NATIVE
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- # endif
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- # if defined(SIMDE_ARCH_X86_SSE4_2) && !defined(SIMDE_SSE4_2_NO_NATIVE) && !defined(SIMDE_NO_NATIVE)
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- # define SIMDE_SSE4_2_NATIVE
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- # elif defined(SIMDE_ARCH_ARM_NEON) && !defined(SIMDE_SSE4_2_NO_NEON) && !defined(SIMDE_NO_NEON)
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- # define SIMDE_SSE4_2_NEON
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- # elif defined(SIMDE_ARCH_POWER_ALTIVEC)
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- # define SIMDE_SSE4_2_POWER_ALTIVEC
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- # endif
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-
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- # if defined(SIMDE_SSE4_2_NATIVE) && !defined(SIMDE_SSE4_1_NATIVE)
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- # if defined(SIMDE_SSE4_2_FORCE_NATIVE)
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- # error Native SSE4.2 support requires native SSE4.1 support
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- # else
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- HEDLEY_WARNING("Native SSE4.2 support requires native SSE4.1 support, disabling")
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- # undef SIMDE_SSE4_2_NATIVE
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- # endif
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- # elif defined(SIMDE_SSE4_2_NEON) && !defined(SIMDE_SSE4_1_NEON)
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- HEDLEY_WARNING("SSE4.2 NEON support requires SSE4.1 NEON support, disabling")
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- # undef SIMDE_SSE4_2_NEON
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- # endif
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-
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- # if defined(SIMDE_SSE4_2_NATIVE)
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- # include <nmmintrin.h>
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- # else
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- # if defined(SIMDE_SSE4_1_NEON)
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- # include <arm_neon.h>
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- # endif
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- # endif
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-
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- # if !defined(SIMDE_SSE4_2_NATIVE) && defined(SIMDE_ENABLE_NATIVE_ALIASES)
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- # define SIMDE_SSE4_2_ENABLE_NATIVE_ALIASES
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- # endif
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-
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- SIMDE__BEGIN_DECLS
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-
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- SIMDE__FUNCTION_ATTRIBUTES
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- simde__m128i
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- simde_mm_cmpgt_epi64 (simde__m128i a, simde__m128i b) {
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- #if defined(SIMDE_SSE4_2_NATIVE)
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- return _mm_cmpgt_epi64(a, b);
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- #else
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- simde__m128i_private
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- r_,
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- a_ = simde__m128i_to_private(a),
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- b_ = simde__m128i_to_private(b);
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-
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- #if defined(SIMDE_SSE4_2_NEON) && defined(SIMDE_ARCH_AARCH64)
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- r_.neon_i64 = vreinterpretq_s64_u64(vcgtq_s64(a_.neon_i64, b_.neon_i64));
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- #elif defined(SIMDE_SSE4_2_POWER_ALTIVEC)
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- r_.altivec_i64 = (vector signed long long) vec_cmpgt(a_.altivec_i64, b_.altivec_i64);
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- #elif defined(SIMDE_VECTOR_SUBSCRIPT_OPS)
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- r_.i64 = HEDLEY_STATIC_CAST(__typeof__(r_.i64), a_.i64 > b_.i64);
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- #else
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- SIMDE__VECTORIZE
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- for (size_t i = 0 ; i < (sizeof(r_.i64) / sizeof(r_.i64[0])) ; i++) {
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- r_.i64[i] = (a_.i64[i] > b_.i64[i]) ? ~INT64_C(0) : INT64_C(0);
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- }
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- #endif
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-
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- return simde__m128i_from_private(r_);
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- #endif
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- }
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- #if defined(SIMDE_SSE2_ENABLE_NATIVE_ALIASES)
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- # define _mm_cmpgt_epi64(a, b) simde_mm_cmpgt_epi64(a, b)
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- #endif
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-
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- SIMDE__END_DECLS
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-
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- HEDLEY_DIAGNOSTIC_POP
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-
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- #endif /* !defined(SIMDE__SSE4_2_H) */