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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simde_test_x86_sources = [
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'mmx.c',
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'sse.c',
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'sse2.c',
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'sse3.c',
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'ssse3.c',
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'sse4.1.c',
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'sse4.2.c',
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'avx.c',
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'avx2.c',
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'fma.c',
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'avx512f.c',
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'avx512bw.c',
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'avx512vl.c',
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'svml.c'
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]
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foreach src : simde_test_x86_sources
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simde_test_x86_sources += configure_file(input: src, output: src + 'pp', copy: true)
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endforeach
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simde_tests_x86_emul = static_library('simde-tests-x86-emul', simde_test_x86_sources,
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c_args: simde_c_args + simde_c_defs + simde_native_c_flags + ['-DSIMDE_NO_NATIVE'],
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cpp_args: simde_cxx_args + simde_cxx_defs + simde_native_cxx_flags + ['-DSIMDE_NO_NATIVE'],
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include_directories: simde_include_dir)
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simde_tests_x86_native = static_library('simde-tests-x86-native', simde_test_x86_sources,
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c_args: simde_c_args + simde_c_defs + simde_native_c_flags,
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cpp_args: simde_cxx_args + simde_cxx_defs + simde_native_cxx_flags,
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include_directories: simde_include_dir)
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simde_tests_x86 = static_library('simde-tests-x86', 'test-x86.c',
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link_with: [simde_tests_x86_emul, simde_tests_x86_native])
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