minimap2 0.2.25.0 → 0.2.25.1

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Files changed (123) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +2 -3
  3. data/ext/minimap2/Makefile +6 -2
  4. data/ext/minimap2/NEWS.md +38 -0
  5. data/ext/minimap2/README.md +9 -3
  6. data/ext/minimap2/align.c +5 -3
  7. data/ext/minimap2/cookbook.md +2 -2
  8. data/ext/minimap2/format.c +7 -4
  9. data/ext/minimap2/kalloc.c +20 -1
  10. data/ext/minimap2/kalloc.h +13 -2
  11. data/ext/minimap2/ksw2.h +1 -0
  12. data/ext/minimap2/ksw2_extd2_sse.c +1 -1
  13. data/ext/minimap2/ksw2_exts2_sse.c +79 -40
  14. data/ext/minimap2/ksw2_extz2_sse.c +1 -1
  15. data/ext/minimap2/lchain.c +15 -16
  16. data/ext/minimap2/lib/simde/CONTRIBUTING.md +114 -0
  17. data/ext/minimap2/lib/simde/COPYING +20 -0
  18. data/ext/minimap2/lib/simde/README.md +333 -0
  19. data/ext/minimap2/lib/simde/amalgamate.py +58 -0
  20. data/ext/minimap2/lib/simde/meson.build +33 -0
  21. data/ext/minimap2/lib/simde/netlify.toml +20 -0
  22. data/ext/minimap2/lib/simde/simde/arm/neon/float32x2.h +140 -0
  23. data/ext/minimap2/lib/simde/simde/arm/neon/float32x4.h +137 -0
  24. data/ext/minimap2/lib/simde/simde/arm/neon/float64x1.h +142 -0
  25. data/ext/minimap2/lib/simde/simde/arm/neon/float64x2.h +145 -0
  26. data/ext/minimap2/lib/simde/simde/arm/neon/int16x4.h +140 -0
  27. data/ext/minimap2/lib/simde/simde/arm/neon/int16x8.h +145 -0
  28. data/ext/minimap2/lib/simde/simde/arm/neon/int32x2.h +140 -0
  29. data/ext/minimap2/lib/simde/simde/arm/neon/int32x4.h +143 -0
  30. data/ext/minimap2/lib/simde/simde/arm/neon/int64x1.h +137 -0
  31. data/ext/minimap2/lib/simde/simde/arm/neon/int64x2.h +141 -0
  32. data/ext/minimap2/lib/simde/simde/arm/neon/int8x16.h +147 -0
  33. data/ext/minimap2/lib/simde/simde/arm/neon/int8x8.h +141 -0
  34. data/ext/minimap2/lib/simde/simde/arm/neon/uint16x4.h +134 -0
  35. data/ext/minimap2/lib/simde/simde/arm/neon/uint16x8.h +138 -0
  36. data/ext/minimap2/lib/simde/simde/arm/neon/uint32x2.h +134 -0
  37. data/ext/minimap2/lib/simde/simde/arm/neon/uint32x4.h +137 -0
  38. data/ext/minimap2/lib/simde/simde/arm/neon/uint64x1.h +131 -0
  39. data/ext/minimap2/lib/simde/simde/arm/neon/uint64x2.h +135 -0
  40. data/ext/minimap2/lib/simde/simde/arm/neon/uint8x16.h +141 -0
  41. data/ext/minimap2/lib/simde/simde/arm/neon/uint8x8.h +135 -0
  42. data/ext/minimap2/lib/simde/simde/arm/neon.h +97 -0
  43. data/ext/minimap2/lib/simde/simde/check.h +267 -0
  44. data/ext/minimap2/lib/simde/simde/debug-trap.h +83 -0
  45. data/ext/minimap2/lib/simde/simde/hedley.h +1899 -0
  46. data/ext/minimap2/lib/simde/simde/simde-arch.h +445 -0
  47. data/ext/minimap2/lib/simde/simde/simde-common.h +697 -0
  48. data/ext/minimap2/lib/simde/simde/x86/avx.h +5385 -0
  49. data/ext/minimap2/lib/simde/simde/x86/avx2.h +2402 -0
  50. data/ext/minimap2/lib/simde/simde/x86/avx512bw.h +391 -0
  51. data/ext/minimap2/lib/simde/simde/x86/avx512f.h +3389 -0
  52. data/ext/minimap2/lib/simde/simde/x86/avx512vl.h +112 -0
  53. data/ext/minimap2/lib/simde/simde/x86/fma.h +659 -0
  54. data/ext/minimap2/lib/simde/simde/x86/mmx.h +2210 -0
  55. data/ext/minimap2/lib/simde/simde/x86/sse.h +3696 -0
  56. data/ext/minimap2/lib/simde/simde/x86/sse2.h +5991 -0
  57. data/ext/minimap2/lib/simde/simde/x86/sse3.h +343 -0
  58. data/ext/minimap2/lib/simde/simde/x86/sse4.1.h +1783 -0
  59. data/ext/minimap2/lib/simde/simde/x86/sse4.2.h +105 -0
  60. data/ext/minimap2/lib/simde/simde/x86/ssse3.h +1053 -0
  61. data/ext/minimap2/lib/simde/simde/x86/svml.h +543 -0
  62. data/ext/minimap2/lib/simde/test/CMakeLists.txt +166 -0
  63. data/ext/minimap2/lib/simde/test/arm/meson.build +4 -0
  64. data/ext/minimap2/lib/simde/test/arm/neon/meson.build +23 -0
  65. data/ext/minimap2/lib/simde/test/arm/neon/skel.c +871 -0
  66. data/ext/minimap2/lib/simde/test/arm/neon/test-neon-internal.h +134 -0
  67. data/ext/minimap2/lib/simde/test/arm/neon/test-neon.c +39 -0
  68. data/ext/minimap2/lib/simde/test/arm/neon/test-neon.h +10 -0
  69. data/ext/minimap2/lib/simde/test/arm/neon/vadd.c +1260 -0
  70. data/ext/minimap2/lib/simde/test/arm/neon/vdup_n.c +873 -0
  71. data/ext/minimap2/lib/simde/test/arm/neon/vmul.c +1084 -0
  72. data/ext/minimap2/lib/simde/test/arm/neon/vsub.c +1260 -0
  73. data/ext/minimap2/lib/simde/test/arm/test-arm-internal.h +18 -0
  74. data/ext/minimap2/lib/simde/test/arm/test-arm.c +20 -0
  75. data/ext/minimap2/lib/simde/test/arm/test-arm.h +8 -0
  76. data/ext/minimap2/lib/simde/test/cmake/AddCompilerFlags.cmake +171 -0
  77. data/ext/minimap2/lib/simde/test/cmake/ExtraWarningFlags.cmake +68 -0
  78. data/ext/minimap2/lib/simde/test/meson.build +64 -0
  79. data/ext/minimap2/lib/simde/test/munit/COPYING +21 -0
  80. data/ext/minimap2/lib/simde/test/munit/Makefile +55 -0
  81. data/ext/minimap2/lib/simde/test/munit/README.md +54 -0
  82. data/ext/minimap2/lib/simde/test/munit/example.c +351 -0
  83. data/ext/minimap2/lib/simde/test/munit/meson.build +37 -0
  84. data/ext/minimap2/lib/simde/test/munit/munit.c +2055 -0
  85. data/ext/minimap2/lib/simde/test/munit/munit.h +535 -0
  86. data/ext/minimap2/lib/simde/test/run-tests.c +20 -0
  87. data/ext/minimap2/lib/simde/test/run-tests.h +260 -0
  88. data/ext/minimap2/lib/simde/test/x86/avx.c +13752 -0
  89. data/ext/minimap2/lib/simde/test/x86/avx2.c +9977 -0
  90. data/ext/minimap2/lib/simde/test/x86/avx512bw.c +2664 -0
  91. data/ext/minimap2/lib/simde/test/x86/avx512f.c +10416 -0
  92. data/ext/minimap2/lib/simde/test/x86/avx512vl.c +210 -0
  93. data/ext/minimap2/lib/simde/test/x86/fma.c +2557 -0
  94. data/ext/minimap2/lib/simde/test/x86/meson.build +33 -0
  95. data/ext/minimap2/lib/simde/test/x86/mmx.c +2878 -0
  96. data/ext/minimap2/lib/simde/test/x86/skel.c +2984 -0
  97. data/ext/minimap2/lib/simde/test/x86/sse.c +5121 -0
  98. data/ext/minimap2/lib/simde/test/x86/sse2.c +9860 -0
  99. data/ext/minimap2/lib/simde/test/x86/sse3.c +486 -0
  100. data/ext/minimap2/lib/simde/test/x86/sse4.1.c +3446 -0
  101. data/ext/minimap2/lib/simde/test/x86/sse4.2.c +101 -0
  102. data/ext/minimap2/lib/simde/test/x86/ssse3.c +2084 -0
  103. data/ext/minimap2/lib/simde/test/x86/svml.c +1545 -0
  104. data/ext/minimap2/lib/simde/test/x86/test-avx.h +16 -0
  105. data/ext/minimap2/lib/simde/test/x86/test-avx512.h +25 -0
  106. data/ext/minimap2/lib/simde/test/x86/test-mmx.h +13 -0
  107. data/ext/minimap2/lib/simde/test/x86/test-sse.h +13 -0
  108. data/ext/minimap2/lib/simde/test/x86/test-sse2.h +13 -0
  109. data/ext/minimap2/lib/simde/test/x86/test-x86-internal.h +196 -0
  110. data/ext/minimap2/lib/simde/test/x86/test-x86.c +48 -0
  111. data/ext/minimap2/lib/simde/test/x86/test-x86.h +8 -0
  112. data/ext/minimap2/main.c +13 -6
  113. data/ext/minimap2/map.c +0 -5
  114. data/ext/minimap2/minimap.h +40 -31
  115. data/ext/minimap2/minimap2.1 +19 -5
  116. data/ext/minimap2/misc/paftools.js +545 -24
  117. data/ext/minimap2/options.c +1 -1
  118. data/ext/minimap2/pyproject.toml +2 -0
  119. data/ext/minimap2/python/mappy.pyx +3 -1
  120. data/ext/minimap2/seed.c +1 -1
  121. data/ext/minimap2/setup.py +32 -22
  122. data/lib/minimap2/version.rb +1 -1
  123. metadata +100 -3
@@ -0,0 +1,101 @@
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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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+ #define SIMDE_TESTS_CURRENT_ISAX sse4_2
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+ #include <test/x86/test-x86-internal.h>
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+ #include <simde/x86/sse4.2.h>
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+
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+ #if defined(SIMDE_SSE4_2_NATIVE) || defined(SIMDE_NO_NATIVE) || defined(SIMDE_ALWAYS_BUILD_NATIVE_TESTS)
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+
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+ static MunitResult
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+ test_simde_mm_cmpgt_epi64(const MunitParameter params[], void* data) {
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+ (void) params;
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+ (void) data;
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+
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+ const struct {
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+ simde__m128i a;
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+ simde__m128i b;
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+ simde__m128i r;
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+ } test_vec[8] = {
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+ { simde_mm_set_epi64x(INT64_C(-2149331112921330677), INT64_C( 3189038460188560982)),
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+ simde_mm_set_epi64x(INT64_C( -996047549682722220), INT64_C(-3995545326609437904)),
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+ simde_mm_set_epi64x( INT64_C(0), ~INT64_C(0)) },
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+ { simde_mm_set_epi64x(INT64_C( 3213898448913237846), INT64_C( 9188286366666087308)),
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+ simde_mm_set_epi64x(INT64_C( 2918885787365950970), INT64_C( 6780053140456787494)),
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+ simde_mm_set_epi64x(~INT64_C(0), ~INT64_C(0)) },
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+ { simde_mm_set_epi64x(INT64_C(-6480415937191367948), INT64_C( 6434069133602920016)),
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+ simde_mm_set_epi64x(INT64_C( 8054577307931165184), INT64_C( 2226222084862743618)),
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+ simde_mm_set_epi64x( INT64_C(0), ~INT64_C(0)) },
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+ { simde_mm_set_epi64x(INT64_C(-6197561420805751907), INT64_C( 4778870285233423339)),
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+ simde_mm_set_epi64x(INT64_C( 1839658993612937599), INT64_C( -902367911293731861)),
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+ simde_mm_set_epi64x( INT64_C(0), ~INT64_C(0)) },
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+ { simde_mm_set_epi64x(INT64_C( 5091127324004768664), INT64_C(-2002251908801446460)),
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+ simde_mm_set_epi64x(INT64_C(-9056506211008935561), INT64_C(-6487933609077704174)),
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+ simde_mm_set_epi64x(~INT64_C(0), ~INT64_C(0)) },
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+ { simde_mm_set_epi64x(INT64_C(-4743149223868910453), INT64_C(-4137271544350199785)),
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+ simde_mm_set_epi64x(INT64_C( 4762909370147937560), INT64_C( 6560801355595049799)),
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+ simde_mm_set_epi64x( INT64_C(0), INT64_C(0)) },
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+ { simde_mm_set_epi64x(INT64_C( 913044205052582612), INT64_C(-2362244502684338485)),
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+ simde_mm_set_epi64x(INT64_C( -603710511502052754), INT64_C(-3179203207537477667)),
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+ simde_mm_set_epi64x(~INT64_C(0), ~INT64_C(0)) },
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+ { simde_mm_set_epi64x(INT64_C( 6753725813089147170), INT64_C( 7031124288307654085)),
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+ simde_mm_set_epi64x(INT64_C( 5046765831366456160), INT64_C( 6981054579474564569)),
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+ simde_mm_set_epi64x(~INT64_C(0), ~INT64_C(0)) }
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+ };
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+
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+ for (size_t i = 0 ; i < (sizeof(test_vec) / sizeof(test_vec[0])); i++) {
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+ simde__m128i r = simde_mm_cmpgt_epi64(test_vec[i].a, test_vec[i].b);
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+ simde_assert_m128i_i64(r, ==, test_vec[i].r);
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+ }
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+
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+ return MUNIT_OK;
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+ }
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+
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+ #endif /* defined(SIMDE_SSE4_2_NATIVE) || defined(SIMDE_NO_NATIVE) || defined(SIMDE_ALWAYS_BUILD_NATIVE_TESTS) */
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+
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+ HEDLEY_DIAGNOSTIC_PUSH
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+ HEDLEY_DIAGNOSTIC_DISABLE_CAST_QUAL
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+
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+ static MunitTest test_suite_tests[] = {
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+ #if defined(SIMDE_SSE4_2_NATIVE) || defined(SIMDE_NO_NATIVE) || defined(SIMDE_ALWAYS_BUILD_NATIVE_TESTS)
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+ SIMDE_TESTS_DEFINE_TEST(mm_cmpgt_epi64),
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+ #endif /* defined(SIMDE_SSE4_2_NATIVE) || defined(SIMDE_NO_NATIVE) || defined(SIMDE_ALWAYS_BUILD_NATIVE_TESTS) */
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+
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+ { NULL, NULL, NULL, NULL, MUNIT_TEST_OPTION_NONE, NULL }
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+ };
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+
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+ HEDLEY_C_DECL MunitSuite* SIMDE_TESTS_GENERATE_SYMBOL(suite)(void) {
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+ static MunitSuite suite = { (char*) "/" HEDLEY_STRINGIFY(SIMDE_TESTS_CURRENT_ISAX), test_suite_tests, NULL, 1, MUNIT_SUITE_OPTION_NONE };
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+
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+ return &suite;
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+ }
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+
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+ #if defined(SIMDE_TESTS_SINGLE_ISAX)
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+ int main(int argc, char* argv[HEDLEY_ARRAY_PARAM(argc + 1)]) {
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+ static MunitSuite suite = { "", test_suite_tests, NULL, 1, MUNIT_SUITE_OPTION_NONE };
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+
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+ return munit_suite_main(&suite, NULL, argc, argv);
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+ }
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+ #endif /* defined(SIMDE_TESTS_SINGLE_ISAX) */
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+
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+ HEDLEY_DIAGNOSTIC_POP