minimap2 0.2.25.0 → 0.2.25.1
Sign up to get free protection for your applications and to get access to all the features.
- 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
@@ -0,0 +1,105 @@
|
|
1
|
+
/* Copyright (c) 2017 Evan Nemerson <evan@nemerson.com>
|
2
|
+
*
|
3
|
+
* Permission is hereby granted, free of charge, to any person
|
4
|
+
* obtaining a copy of this software and associated documentation
|
5
|
+
* files (the "Software"), to deal in the Software without
|
6
|
+
* restriction, including without limitation the rights to use, copy,
|
7
|
+
* modify, merge, publish, distribute, sublicense, and/or sell copies
|
8
|
+
* of the Software, and to permit persons to whom the Software is
|
9
|
+
* furnished to do so, subject to the following conditions:
|
10
|
+
*
|
11
|
+
* The above copyright notice and this permission notice shall be
|
12
|
+
* included in all copies or substantial portions of the Software.
|
13
|
+
*
|
14
|
+
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
15
|
+
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
|
16
|
+
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
17
|
+
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
|
18
|
+
* BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
|
19
|
+
* ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
|
20
|
+
* CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
|
21
|
+
* SOFTWARE.
|
22
|
+
*/
|
23
|
+
|
24
|
+
#if !defined(SIMDE__SSE4_2_H)
|
25
|
+
# if !defined(SIMDE__SSE4_2_H)
|
26
|
+
# define SIMDE__SSE4_2_H
|
27
|
+
# endif
|
28
|
+
# include "sse4.1.h"
|
29
|
+
|
30
|
+
HEDLEY_DIAGNOSTIC_PUSH
|
31
|
+
SIMDE_DISABLE_UNWANTED_DIAGNOSTICS
|
32
|
+
|
33
|
+
# if defined(SIMDE_SSE4_2_NATIVE)
|
34
|
+
# undef SIMDE_SSE4_2_NATIVE
|
35
|
+
# endif
|
36
|
+
# if defined(SIMDE_ARCH_X86_SSE4_2) && !defined(SIMDE_SSE4_2_NO_NATIVE) && !defined(SIMDE_NO_NATIVE)
|
37
|
+
# define SIMDE_SSE4_2_NATIVE
|
38
|
+
# elif defined(SIMDE_ARCH_ARM_NEON) && !defined(SIMDE_SSE4_2_NO_NEON) && !defined(SIMDE_NO_NEON)
|
39
|
+
# define SIMDE_SSE4_2_NEON
|
40
|
+
# elif defined(SIMDE_ARCH_POWER_ALTIVEC)
|
41
|
+
# define SIMDE_SSE4_2_POWER_ALTIVEC
|
42
|
+
# endif
|
43
|
+
|
44
|
+
# if defined(SIMDE_SSE4_2_NATIVE) && !defined(SIMDE_SSE4_1_NATIVE)
|
45
|
+
# if defined(SIMDE_SSE4_2_FORCE_NATIVE)
|
46
|
+
# error Native SSE4.2 support requires native SSE4.1 support
|
47
|
+
# else
|
48
|
+
HEDLEY_WARNING("Native SSE4.2 support requires native SSE4.1 support, disabling")
|
49
|
+
# undef SIMDE_SSE4_2_NATIVE
|
50
|
+
# endif
|
51
|
+
# elif defined(SIMDE_SSE4_2_NEON) && !defined(SIMDE_SSE4_1_NEON)
|
52
|
+
HEDLEY_WARNING("SSE4.2 NEON support requires SSE4.1 NEON support, disabling")
|
53
|
+
# undef SIMDE_SSE4_2_NEON
|
54
|
+
# endif
|
55
|
+
|
56
|
+
# if defined(SIMDE_SSE4_2_NATIVE)
|
57
|
+
# include <nmmintrin.h>
|
58
|
+
# else
|
59
|
+
# if defined(SIMDE_SSE4_1_NEON)
|
60
|
+
# include <arm_neon.h>
|
61
|
+
# endif
|
62
|
+
# endif
|
63
|
+
|
64
|
+
# if !defined(SIMDE_SSE4_2_NATIVE) && defined(SIMDE_ENABLE_NATIVE_ALIASES)
|
65
|
+
# define SIMDE_SSE4_2_ENABLE_NATIVE_ALIASES
|
66
|
+
# endif
|
67
|
+
|
68
|
+
SIMDE__BEGIN_DECLS
|
69
|
+
|
70
|
+
SIMDE__FUNCTION_ATTRIBUTES
|
71
|
+
simde__m128i
|
72
|
+
simde_mm_cmpgt_epi64 (simde__m128i a, simde__m128i b) {
|
73
|
+
#if defined(SIMDE_SSE4_2_NATIVE)
|
74
|
+
return _mm_cmpgt_epi64(a, b);
|
75
|
+
#else
|
76
|
+
simde__m128i_private
|
77
|
+
r_,
|
78
|
+
a_ = simde__m128i_to_private(a),
|
79
|
+
b_ = simde__m128i_to_private(b);
|
80
|
+
|
81
|
+
#if defined(SIMDE_SSE4_2_NEON) && defined(SIMDE_ARCH_AARCH64)
|
82
|
+
r_.neon_i64 = vreinterpretq_s64_u64(vcgtq_s64(a_.neon_i64, b_.neon_i64));
|
83
|
+
#elif defined(SIMDE_SSE4_2_POWER_ALTIVEC)
|
84
|
+
r_.altivec_i64 = (vector signed long long) vec_cmpgt(a_.altivec_i64, b_.altivec_i64);
|
85
|
+
#elif defined(SIMDE_VECTOR_SUBSCRIPT_OPS)
|
86
|
+
r_.i64 = HEDLEY_STATIC_CAST(__typeof__(r_.i64), a_.i64 > b_.i64);
|
87
|
+
#else
|
88
|
+
SIMDE__VECTORIZE
|
89
|
+
for (size_t i = 0 ; i < (sizeof(r_.i64) / sizeof(r_.i64[0])) ; i++) {
|
90
|
+
r_.i64[i] = (a_.i64[i] > b_.i64[i]) ? ~INT64_C(0) : INT64_C(0);
|
91
|
+
}
|
92
|
+
#endif
|
93
|
+
|
94
|
+
return simde__m128i_from_private(r_);
|
95
|
+
#endif
|
96
|
+
}
|
97
|
+
#if defined(SIMDE_SSE2_ENABLE_NATIVE_ALIASES)
|
98
|
+
# define _mm_cmpgt_epi64(a, b) simde_mm_cmpgt_epi64(a, b)
|
99
|
+
#endif
|
100
|
+
|
101
|
+
SIMDE__END_DECLS
|
102
|
+
|
103
|
+
HEDLEY_DIAGNOSTIC_POP
|
104
|
+
|
105
|
+
#endif /* !defined(SIMDE__SSE4_2_H) */
|