minimap2 0.2.25.0 → 0.2.25.1
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- checksums.yaml +4 -4
- data/README.md +2 -3
- data/ext/minimap2/Makefile +6 -2
- data/ext/minimap2/NEWS.md +38 -0
- data/ext/minimap2/README.md +9 -3
- data/ext/minimap2/align.c +5 -3
- data/ext/minimap2/cookbook.md +2 -2
- data/ext/minimap2/format.c +7 -4
- data/ext/minimap2/kalloc.c +20 -1
- data/ext/minimap2/kalloc.h +13 -2
- data/ext/minimap2/ksw2.h +1 -0
- data/ext/minimap2/ksw2_extd2_sse.c +1 -1
- data/ext/minimap2/ksw2_exts2_sse.c +79 -40
- data/ext/minimap2/ksw2_extz2_sse.c +1 -1
- data/ext/minimap2/lchain.c +15 -16
- data/ext/minimap2/lib/simde/CONTRIBUTING.md +114 -0
- data/ext/minimap2/lib/simde/COPYING +20 -0
- data/ext/minimap2/lib/simde/README.md +333 -0
- data/ext/minimap2/lib/simde/amalgamate.py +58 -0
- data/ext/minimap2/lib/simde/meson.build +33 -0
- data/ext/minimap2/lib/simde/netlify.toml +20 -0
- data/ext/minimap2/lib/simde/simde/arm/neon/float32x2.h +140 -0
- data/ext/minimap2/lib/simde/simde/arm/neon/float32x4.h +137 -0
- data/ext/minimap2/lib/simde/simde/arm/neon/float64x1.h +142 -0
- data/ext/minimap2/lib/simde/simde/arm/neon/float64x2.h +145 -0
- data/ext/minimap2/lib/simde/simde/arm/neon/int16x4.h +140 -0
- data/ext/minimap2/lib/simde/simde/arm/neon/int16x8.h +145 -0
- data/ext/minimap2/lib/simde/simde/arm/neon/int32x2.h +140 -0
- data/ext/minimap2/lib/simde/simde/arm/neon/int32x4.h +143 -0
- data/ext/minimap2/lib/simde/simde/arm/neon/int64x1.h +137 -0
- data/ext/minimap2/lib/simde/simde/arm/neon/int64x2.h +141 -0
- data/ext/minimap2/lib/simde/simde/arm/neon/int8x16.h +147 -0
- data/ext/minimap2/lib/simde/simde/arm/neon/int8x8.h +141 -0
- data/ext/minimap2/lib/simde/simde/arm/neon/uint16x4.h +134 -0
- data/ext/minimap2/lib/simde/simde/arm/neon/uint16x8.h +138 -0
- data/ext/minimap2/lib/simde/simde/arm/neon/uint32x2.h +134 -0
- data/ext/minimap2/lib/simde/simde/arm/neon/uint32x4.h +137 -0
- data/ext/minimap2/lib/simde/simde/arm/neon/uint64x1.h +131 -0
- data/ext/minimap2/lib/simde/simde/arm/neon/uint64x2.h +135 -0
- data/ext/minimap2/lib/simde/simde/arm/neon/uint8x16.h +141 -0
- data/ext/minimap2/lib/simde/simde/arm/neon/uint8x8.h +135 -0
- data/ext/minimap2/lib/simde/simde/arm/neon.h +97 -0
- data/ext/minimap2/lib/simde/simde/check.h +267 -0
- data/ext/minimap2/lib/simde/simde/debug-trap.h +83 -0
- data/ext/minimap2/lib/simde/simde/hedley.h +1899 -0
- data/ext/minimap2/lib/simde/simde/simde-arch.h +445 -0
- data/ext/minimap2/lib/simde/simde/simde-common.h +697 -0
- data/ext/minimap2/lib/simde/simde/x86/avx.h +5385 -0
- data/ext/minimap2/lib/simde/simde/x86/avx2.h +2402 -0
- data/ext/minimap2/lib/simde/simde/x86/avx512bw.h +391 -0
- data/ext/minimap2/lib/simde/simde/x86/avx512f.h +3389 -0
- data/ext/minimap2/lib/simde/simde/x86/avx512vl.h +112 -0
- data/ext/minimap2/lib/simde/simde/x86/fma.h +659 -0
- data/ext/minimap2/lib/simde/simde/x86/mmx.h +2210 -0
- data/ext/minimap2/lib/simde/simde/x86/sse.h +3696 -0
- data/ext/minimap2/lib/simde/simde/x86/sse2.h +5991 -0
- data/ext/minimap2/lib/simde/simde/x86/sse3.h +343 -0
- data/ext/minimap2/lib/simde/simde/x86/sse4.1.h +1783 -0
- data/ext/minimap2/lib/simde/simde/x86/sse4.2.h +105 -0
- data/ext/minimap2/lib/simde/simde/x86/ssse3.h +1053 -0
- data/ext/minimap2/lib/simde/simde/x86/svml.h +543 -0
- data/ext/minimap2/lib/simde/test/CMakeLists.txt +166 -0
- data/ext/minimap2/lib/simde/test/arm/meson.build +4 -0
- data/ext/minimap2/lib/simde/test/arm/neon/meson.build +23 -0
- data/ext/minimap2/lib/simde/test/arm/neon/skel.c +871 -0
- data/ext/minimap2/lib/simde/test/arm/neon/test-neon-internal.h +134 -0
- data/ext/minimap2/lib/simde/test/arm/neon/test-neon.c +39 -0
- data/ext/minimap2/lib/simde/test/arm/neon/test-neon.h +10 -0
- data/ext/minimap2/lib/simde/test/arm/neon/vadd.c +1260 -0
- data/ext/minimap2/lib/simde/test/arm/neon/vdup_n.c +873 -0
- data/ext/minimap2/lib/simde/test/arm/neon/vmul.c +1084 -0
- data/ext/minimap2/lib/simde/test/arm/neon/vsub.c +1260 -0
- data/ext/minimap2/lib/simde/test/arm/test-arm-internal.h +18 -0
- data/ext/minimap2/lib/simde/test/arm/test-arm.c +20 -0
- data/ext/minimap2/lib/simde/test/arm/test-arm.h +8 -0
- data/ext/minimap2/lib/simde/test/cmake/AddCompilerFlags.cmake +171 -0
- data/ext/minimap2/lib/simde/test/cmake/ExtraWarningFlags.cmake +68 -0
- data/ext/minimap2/lib/simde/test/meson.build +64 -0
- data/ext/minimap2/lib/simde/test/munit/COPYING +21 -0
- data/ext/minimap2/lib/simde/test/munit/Makefile +55 -0
- data/ext/minimap2/lib/simde/test/munit/README.md +54 -0
- data/ext/minimap2/lib/simde/test/munit/example.c +351 -0
- data/ext/minimap2/lib/simde/test/munit/meson.build +37 -0
- data/ext/minimap2/lib/simde/test/munit/munit.c +2055 -0
- data/ext/minimap2/lib/simde/test/munit/munit.h +535 -0
- data/ext/minimap2/lib/simde/test/run-tests.c +20 -0
- data/ext/minimap2/lib/simde/test/run-tests.h +260 -0
- data/ext/minimap2/lib/simde/test/x86/avx.c +13752 -0
- data/ext/minimap2/lib/simde/test/x86/avx2.c +9977 -0
- data/ext/minimap2/lib/simde/test/x86/avx512bw.c +2664 -0
- data/ext/minimap2/lib/simde/test/x86/avx512f.c +10416 -0
- data/ext/minimap2/lib/simde/test/x86/avx512vl.c +210 -0
- data/ext/minimap2/lib/simde/test/x86/fma.c +2557 -0
- data/ext/minimap2/lib/simde/test/x86/meson.build +33 -0
- data/ext/minimap2/lib/simde/test/x86/mmx.c +2878 -0
- data/ext/minimap2/lib/simde/test/x86/skel.c +2984 -0
- data/ext/minimap2/lib/simde/test/x86/sse.c +5121 -0
- data/ext/minimap2/lib/simde/test/x86/sse2.c +9860 -0
- data/ext/minimap2/lib/simde/test/x86/sse3.c +486 -0
- data/ext/minimap2/lib/simde/test/x86/sse4.1.c +3446 -0
- data/ext/minimap2/lib/simde/test/x86/sse4.2.c +101 -0
- data/ext/minimap2/lib/simde/test/x86/ssse3.c +2084 -0
- data/ext/minimap2/lib/simde/test/x86/svml.c +1545 -0
- data/ext/minimap2/lib/simde/test/x86/test-avx.h +16 -0
- data/ext/minimap2/lib/simde/test/x86/test-avx512.h +25 -0
- data/ext/minimap2/lib/simde/test/x86/test-mmx.h +13 -0
- data/ext/minimap2/lib/simde/test/x86/test-sse.h +13 -0
- data/ext/minimap2/lib/simde/test/x86/test-sse2.h +13 -0
- data/ext/minimap2/lib/simde/test/x86/test-x86-internal.h +196 -0
- data/ext/minimap2/lib/simde/test/x86/test-x86.c +48 -0
- data/ext/minimap2/lib/simde/test/x86/test-x86.h +8 -0
- data/ext/minimap2/main.c +13 -6
- data/ext/minimap2/map.c +0 -5
- data/ext/minimap2/minimap.h +40 -31
- data/ext/minimap2/minimap2.1 +19 -5
- data/ext/minimap2/misc/paftools.js +545 -24
- data/ext/minimap2/options.c +1 -1
- data/ext/minimap2/pyproject.toml +2 -0
- data/ext/minimap2/python/mappy.pyx +3 -1
- data/ext/minimap2/seed.c +1 -1
- data/ext/minimap2/setup.py +32 -22
- data/lib/minimap2/version.rb +1 -1
- metadata +100 -3
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#if !defined(SIMDE_TESTS_NEON_INTERNAL_H)
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#define SIMDE_TESTS_CURRENT_ARCH arm
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#define SIMDE_TESTS_CURRENT_ISAX neon
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#include "../../run-tests.h"
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#include "../../../simde/arm/neon.h"
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HEDLEY_BEGIN_C_DECLS
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#define SIMDE_TESTS_GENERATE_SUITE_GETTERS(op) \
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MunitSuite* SIMDE_TESTS_GENERATE_SYMBOL_FULL(op, SIMDE_TESTS_CURRENT_ARCH, neon, native, c) (void); \
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MunitSuite* SIMDE_TESTS_GENERATE_SYMBOL_FULL(op, SIMDE_TESTS_CURRENT_ARCH, neon, native, cpp)(void); \
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MunitSuite* SIMDE_TESTS_GENERATE_SYMBOL_FULL(op, SIMDE_TESTS_CURRENT_ARCH, neon, emul, c) (void); \
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MunitSuite* SIMDE_TESTS_GENERATE_SYMBOL_FULL(op, SIMDE_TESTS_CURRENT_ARCH, neon, emul, cpp)(void)
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#define SIMDE_TESTS_NEON_GENERATE_INTRIN_FULL(vtype, variant) HEDLEY_CONCAT(v, SIMDE_TESTS_CONCAT3(HEDLEY_CONCAT(SIMDE_TESTS_CURRENT_NEON_OP, vtype), _, variant))
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#define SIMDE_TESTS_NEON_GENERATE_INTRIN(vtype, variant) HEDLEY_CONCAT(v, SIMDE_TESTS_CONCAT3(SIMDE_TESTS_CURRENT_NEON_OP, _, variant))
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#define SIMDE_TESTS_NEON_DEFINE_TEST_FULL(vtype, variant) \
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{ (char*) HEDLEY_STRINGIFY(vtype) "_" HEDLEY_STRINGIFY(variant) "/" HEDLEY_STRINGIFY(SIMDE_TESTS_CURRENT_NATIVE) "/" HEDLEY_STRINGIFY(SIMDE_TESTS_CURRENT_LANG), HEDLEY_CONCAT(test_simde_, SIMDE_TESTS_NEON_GENERATE_INTRIN_FULL(vtype, variant)), NULL, NULL, MUNIT_TEST_OPTION_NONE, NULL }
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#define SIMDE_TESTS_NEON_DEFINE_TEST(variant) \
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{ (char*) "_" HEDLEY_STRINGIFY(variant) "/" HEDLEY_STRINGIFY(SIMDE_TESTS_CURRENT_NATIVE) "/" HEDLEY_STRINGIFY(SIMDE_TESTS_CURRENT_LANG), HEDLEY_CONCAT(test_simde_, SIMDE_TESTS_NEON_GENERATE_INTRIN(vtype, variant)), NULL, NULL, MUNIT_TEST_OPTION_NONE, NULL }
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SIMDE_TESTS_GENERATE_SUITE_GETTERS(add);
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SIMDE_TESTS_GENERATE_SUITE_GETTERS(dup);
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SIMDE_TESTS_GENERATE_SUITE_GETTERS(mul);
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SIMDE_TESTS_GENERATE_SUITE_GETTERS(sub);
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#define simde_neon_assert_int8x8(a, op, b) \
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simde_assert_typev(int8_t, PRId8, (sizeof(a) / sizeof(int8_t)), (const int8_t*) &(a), op, (const int8_t*) &(b))
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#define simde_neon_assert_int16x4(a, op, b) \
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simde_assert_typev(int16_t, PRId16, (sizeof(a) / sizeof(int16_t)), (const int16_t*) &(a), op, (const int16_t*) &(b))
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#define simde_neon_assert_int32x2(a, op, b) \
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simde_assert_typev(int32_t, PRId32, (sizeof(a) / sizeof(int32_t)), (const int32_t*) &(a), op, (const int32_t*) &(b))
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#define simde_neon_assert_int64x1(a, op, b) \
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simde_assert_typev(int64_t, PRId64, (sizeof(a) / sizeof(int64_t)), (const int64_t*) &(a), op, (const int64_t*) &(b))
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#define simde_neon_assert_uint8x8(a, op, b) \
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simde_assert_typev(uint8_t, PRId8, (sizeof(a) / sizeof(uint8_t)), (const uint8_t*) &(a), op, (const uint8_t*) &(b))
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#define simde_neon_assert_uint16x4(a, op, b) \
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simde_assert_typev(uint16_t, PRId16, (sizeof(a) / sizeof(uint16_t)), (const uint16_t*) &(a), op, (const uint16_t*) &(b))
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#define simde_neon_assert_uint32x2(a, op, b) \
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simde_assert_typev(uint32_t, PRId32, (sizeof(a) / sizeof(uint32_t)), (const uint32_t*) &(a), op, (const uint32_t*) &(b))
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#define simde_neon_assert_uint64x1(a, op, b) \
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simde_assert_typev(uint64_t, PRId64, (sizeof(a) / sizeof(uint64_t)), (const uint64_t*) &(a), op, (const uint64_t*) &(b))
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#define simde_neon_assert_float32x2(a, op, b) \
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simde_assert_typev(simde_float32, "f", (sizeof(a) / sizeof(simde_float32)), (const simde_float32*) &(a), op, (const simde_float32*) &(b))
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#define simde_neon_assert_float32x2_equal(a, b, precision) \
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simde_assert_f32v_equal(simde_float32, (sizeof(a) / sizeof(simde_float32)), (const simde_float32*) &(a), (const simde_float32*) &(b), precision)
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#define simde_neon_assert_float64x1(a, op, b) \
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simde_assert_typev(simde_float64, "f", (sizeof(a) / sizeof(simde_float64)), (const simde_float64*) &(a), op, (const simde_float64*) &(b))
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#define simde_neon_assert_float64x1_equal(a, b, precision) \
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simde_assert_f32v_equal(simde_float64, (sizeof(a) / sizeof(simde_float64)), (const simde_float64*) &(a), (const simde_float64*) &(b), precision)
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#define simde_neon_assert_int8x16(a, op, b) \
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simde_assert_typev(int8_t, PRId8, (sizeof(a) / sizeof(int8_t)), (const int8_t*) &(a), op, (const int8_t*) &(b))
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#define simde_neon_assert_int16x8(a, op, b) \
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simde_assert_typev(int16_t, PRId16, (sizeof(a) / sizeof(int16_t)), (const int16_t*) &(a), op, (const int16_t*) &(b))
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#define simde_neon_assert_int32x4(a, op, b) \
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simde_assert_typev(int32_t, PRId32, (sizeof(a) / sizeof(int32_t)), (const int32_t*) &(a), op, (const int32_t*) &(b))
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#define simde_neon_assert_int64x2(a, op, b) \
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simde_assert_typev(int64_t, PRId64, (sizeof(a) / sizeof(int64_t)), (const int64_t*) &(a), op, (const int64_t*) &(b))
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#define simde_neon_assert_uint8x16(a, op, b) \
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simde_assert_typev(uint8_t, PRId8, (sizeof(a) / sizeof(uint8_t)), (const uint8_t*) &(a), op, (const uint8_t*) &(b))
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#define simde_neon_assert_uint16x8(a, op, b) \
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simde_assert_typev(uint16_t, PRId16, (sizeof(a) / sizeof(uint16_t)), (const uint16_t*) &(a), op, (const uint16_t*) &(b))
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#define simde_neon_assert_uint32x4(a, op, b) \
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simde_assert_typev(uint32_t, PRId32, (sizeof(a) / sizeof(uint32_t)), (const uint32_t*) &(a), op, (const uint32_t*) &(b))
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#define simde_neon_assert_uint64x2(a, op, b) \
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simde_assert_typev(uint64_t, PRId64, (sizeof(a) / sizeof(uint64_t)), (const uint64_t*) &(a), op, (const uint64_t*) &(b))
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#define simde_neon_assert_float32x4(a, op, b) \
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simde_assert_typev(simde_float32, "f", (sizeof(a) / sizeof(simde_float32)), (const simde_float32*) &(a), op, (const simde_float32*) &(b))
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#define simde_neon_assert_float32x4_equal(a, b, precision) \
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simde_assert_f32v_equal(simde_float32, (sizeof(a) / sizeof(simde_float32)), (const simde_float32*) &(a), (const simde_float32*) &(b), precision)
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#define simde_neon_assert_float64x2(a, op, b) \
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simde_assert_typev(simde_float64, "f", (sizeof(a) / sizeof(simde_float64)), (const simde_float64*) &(a), op, (const simde_float64*) &(b))
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#define simde_neon_assert_float64x2_equal(a, b, precision) \
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simde_assert_f32v_equal(simde_float64, (sizeof(a) / sizeof(simde_float64)), (const simde_float64*) &(a), (const simde_float64*) &(b), precision)
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#include <math.h>
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#define SIMDE_NEON_GEN_RAND_ARRAY_FUNC(L, N, V) \
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SIMDE__FUNCTION_ATTRIBUTES \
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simde_float##L##x##N##_t \
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simde_neon_random_float##L##x##N(void) { \
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simde_float##L v[sizeof(simde_float##L##x##N##_t) / sizeof(simde_float##L)]; \
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for (size_t i = 0 ; i < sizeof(v) / sizeof(v[0]) ; i++) { \
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v[i] = (simde_float##L) (round(random_f64_range(-1000.0, 1000.0) * 100.0) / 100.0); \
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} \
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return simde_vld1##V##_f##L(v); \
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}
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SIMDE__FUNCTION_ATTRIBUTES
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simde_float32x2_t
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simde_neon_random_float32x2(void) {
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simde_float32 v[sizeof(simde_float32x2_t) / sizeof(simde_float32)];
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for (size_t i = 0 ; i < sizeof(v) / sizeof(v[0]) ; i++) {
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v[i] = (simde_float32) (round(random_f64_range(-1000.0, 1000.0) * 100.0) / 100.0);
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}
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return simde_vld1_f32(v);
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}
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SIMDE__FUNCTION_ATTRIBUTES
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simde_float64x1_t
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simde_neon_random_float64x1(void) {
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simde_float64 v[sizeof(simde_float64x1_t) / sizeof(simde_float64)];
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for (size_t i = 0 ; i < sizeof(v) / sizeof(v[0]) ; i++) {
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v[i] = (simde_float64) (round(random_f64_range(-1000.0, 1000.0) * 100.0) / 100.0);
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}
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+
return simde_vld1_f64(v);
|
110
|
+
}
|
111
|
+
|
112
|
+
SIMDE__FUNCTION_ATTRIBUTES
|
113
|
+
simde_float32x4_t
|
114
|
+
simde_neon_random_float32x4(void) {
|
115
|
+
simde_float32 v[sizeof(simde_float32x4_t) / sizeof(simde_float32)];
|
116
|
+
for (size_t i = 0 ; i < sizeof(v) / sizeof(v[0]) ; i++) {
|
117
|
+
v[i] = (simde_float32) (round(random_f64_range(-1000.0, 1000.0) * 100.0) / 100.0);
|
118
|
+
}
|
119
|
+
return simde_vld1q_f32(v);
|
120
|
+
}
|
121
|
+
|
122
|
+
SIMDE__FUNCTION_ATTRIBUTES
|
123
|
+
simde_float64x2_t
|
124
|
+
simde_neon_random_float64x2(void) {
|
125
|
+
simde_float64 v[sizeof(simde_float64x2_t) / sizeof(simde_float64)];
|
126
|
+
for (size_t i = 0 ; i < sizeof(v) / sizeof(v[0]) ; i++) {
|
127
|
+
v[i] = (simde_float64) (round(random_f64_range(-1000.0, 1000.0) * 100.0) / 100.0);
|
128
|
+
}
|
129
|
+
return simde_vld1q_f64(v);
|
130
|
+
}
|
131
|
+
|
132
|
+
HEDLEY_END_C_DECLS
|
133
|
+
|
134
|
+
#endif /* !defined(SIMDE_TESTS_NEON_INTERNAL_H) */
|
@@ -0,0 +1,39 @@
|
|
1
|
+
#include "test-neon.h"
|
2
|
+
#include "test-neon-internal.h"
|
3
|
+
|
4
|
+
#include <stdio.h>
|
5
|
+
|
6
|
+
#if defined(SIMDE_BUILD_CPP_TESTS)
|
7
|
+
#define CHILD_GROUP_LEN 4
|
8
|
+
#define SET_CHILDREN_FOR_OP(op) \
|
9
|
+
children[i++] = *SIMDE_TESTS_GENERATE_SYMBOL_FULL(op, SIMDE_TESTS_CURRENT_ARCH, neon, native, c) (); \
|
10
|
+
children[i++] = *SIMDE_TESTS_GENERATE_SYMBOL_FULL(op, SIMDE_TESTS_CURRENT_ARCH, neon, emul, c) (); \
|
11
|
+
children[i++] = *SIMDE_TESTS_GENERATE_SYMBOL_FULL(op, SIMDE_TESTS_CURRENT_ARCH, neon, native, cpp)(); \
|
12
|
+
children[i++] = *SIMDE_TESTS_GENERATE_SYMBOL_FULL(op, SIMDE_TESTS_CURRENT_ARCH, neon, emul, cpp)()
|
13
|
+
#else
|
14
|
+
#define CHILD_GROUP_LEN 2
|
15
|
+
#define SET_CHILDREN_FOR_OP(op) \
|
16
|
+
children[i++] = *SIMDE_TESTS_GENERATE_SYMBOL_FULL(op, SIMDE_TESTS_CURRENT_ARCH, neon, native, c) (); \
|
17
|
+
children[i++] = *SIMDE_TESTS_GENERATE_SYMBOL_FULL(op, SIMDE_TESTS_CURRENT_ARCH, neon, emul, c) ()
|
18
|
+
|
19
|
+
#endif
|
20
|
+
|
21
|
+
MunitSuite*
|
22
|
+
simde_tests_arm_neon_get_suite(void) {
|
23
|
+
static MunitSuite children[(4 * CHILD_GROUP_LEN) + 1];
|
24
|
+
static MunitSuite suite = { "/neon", NULL, children, 1, MUNIT_SUITE_OPTION_NONE };
|
25
|
+
static const MunitSuite empty = { NULL, NULL, NULL, 1, MUNIT_SUITE_OPTION_NONE };
|
26
|
+
|
27
|
+
size_t i = 0;
|
28
|
+
|
29
|
+
SET_CHILDREN_FOR_OP(add);
|
30
|
+
SET_CHILDREN_FOR_OP(dup);
|
31
|
+
SET_CHILDREN_FOR_OP(mul);
|
32
|
+
SET_CHILDREN_FOR_OP(sub);
|
33
|
+
|
34
|
+
children[i++] = empty;
|
35
|
+
|
36
|
+
munit_assert_size(i, ==, sizeof(children) / sizeof(children[0]));
|
37
|
+
|
38
|
+
return &suite;
|
39
|
+
}
|