minimap2 0.2.25.1 → 0.2.26.0

Sign up to get free protection for your applications and to get access to all the features.
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
@@ -1,112 +0,0 @@
1
- /* Permission is hereby granted, free of charge, to any person
2
- * obtaining a copy of this software and associated documentation
3
- * files (the "Software"), to deal in the Software without
4
- * restriction, including without limitation the rights to use, copy,
5
- * modify, merge, publish, distribute, sublicense, and/or sell copies
6
- * of the Software, and to permit persons to whom the Software is
7
- * furnished to do so, subject to the following conditions:
8
- *
9
- * The above copyright notice and this permission notice shall be
10
- * included in all copies or substantial portions of the Software.
11
- *
12
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
13
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
14
- * MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
15
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
16
- * BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
17
- * ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
18
- * CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
19
- * SOFTWARE.
20
- *
21
- * Copyright:
22
- * 2020 Evan Nemerson <evan@nemerson.com>
23
- */
24
-
25
- #if !defined(SIMDE__AVX512VL_H)
26
- #define SIMDE__AVX512VL_H
27
- #include "avx512bw.h"
28
-
29
- HEDLEY_DIAGNOSTIC_PUSH
30
- SIMDE_DISABLE_UNWANTED_DIAGNOSTICS
31
-
32
- #if defined(SIMDE_AVX512VL_NATIVE)
33
- #undef SIMDE_AVX512VL_NATIVE
34
- #endif
35
- #if defined(SIMDE_ARCH_X86_AVX512VL) && !defined(SIMDE_AVX512VL_NO_NATIVE) && !defined(SIMDE_NO_NATIVE)
36
- #define SIMDE_AVX512VL_NATIVE
37
- #elif defined(SIMDE_ARCH_ARM_NEON) && !defined(SIMDE_AVX512VL_NO_NEON) && !defined(SIMDE_NO_NEON)
38
- #define SIMDE_AVX512VL_NEON
39
- #elif defined(SIMDE_ARCH_POWER_ALTIVEC)
40
- #define SIMDE_AVX512VL_POWER_ALTIVEC
41
- #endif
42
-
43
- #if defined(SIMDE_AVX512VL_NATIVE)
44
- #include <immintrin.h>
45
- #endif
46
-
47
- #if defined(SIMDE_AVX512VL_POWER_ALTIVEC)
48
- #include <altivec.h>
49
- #endif
50
-
51
- #if !defined(SIMDE_AVX512VL_NATIVE) && defined(SIMDE_ENABLE_NATIVE_ALIASES)
52
- #define SIMDE_AVX512VL_ENABLE_NATIVE_ALIASES
53
- #endif
54
- SIMDE__BEGIN_DECLS
55
-
56
- SIMDE__FUNCTION_ATTRIBUTES
57
- simde__m128i
58
- simde_mm_cvtsepi16_epi8 (simde__m128i a) {
59
- #if defined(SIMDE_AVX512VL_NATIVE) && defined(SIMDE_AVX512BW_NATIVE)
60
- return _mm_cvtsepi16_epi8(a);
61
- #else
62
- simde__m128i_private r_ = simde__m128i_to_private(simde_mm_setzero_si128());;
63
- simde__m128i_private a_ = simde__m128i_to_private(a);
64
-
65
- SIMDE__VECTORIZE
66
- for (size_t i = 0 ; i < (sizeof(a_.i16) / sizeof(a_.i16[0])) ; i++) {
67
- r_.i8[i] =
68
- (a_.i16[i] < INT8_MIN)
69
- ? (INT8_MIN)
70
- : ((a_.i16[i] > INT8_MAX)
71
- ? (INT8_MAX)
72
- : HEDLEY_STATIC_CAST(int8_t, a_.i16[i]));
73
- }
74
-
75
- return simde__m128i_from_private(r_);
76
- #endif
77
- }
78
- #if defined(SIMDE_AVX512VL_ENABLE_NATIVE_ALIASES)
79
- #define _mm_cvtsepi16_epi8(a) simde_mm_cvtsepi16_epi8(a)
80
- #endif
81
-
82
- SIMDE__FUNCTION_ATTRIBUTES
83
- simde__m128i
84
- simde_mm256_cvtsepi16_epi8 (simde__m256i a) {
85
- #if defined(SIMDE_AVX512VL_NATIVE) && defined(SIMDE_AVX512BW_NATIVE)
86
- return _mm256_cvtsepi16_epi8(a);
87
- #else
88
- simde__m128i_private r_;
89
- simde__m256i_private a_ = simde__m256i_to_private(a);
90
-
91
- SIMDE__VECTORIZE
92
- for (size_t i = 0 ; i < (sizeof(r_.i8) / sizeof(r_.i8[0])) ; i++) {
93
- r_.i8[i] =
94
- (a_.i16[i] < INT8_MIN)
95
- ? (INT8_MIN)
96
- : ((a_.i16[i] > INT8_MAX)
97
- ? (INT8_MAX)
98
- : HEDLEY_STATIC_CAST(int8_t, a_.i16[i]));
99
- }
100
-
101
- return simde__m128i_from_private(r_);
102
- #endif
103
- }
104
- #if defined(SIMDE_AVX512VL_ENABLE_NATIVE_ALIASES)
105
- #define _mm256_cvtsepi16_epi8(a) simde_mm256_cvtsepi16_epi8(a)
106
- #endif
107
-
108
- SIMDE__END_DECLS
109
-
110
- HEDLEY_DIAGNOSTIC_POP
111
-
112
- #endif /* !defined(SIMDE__AVX512VL_H) */