minimap2 0.2.25.0 → 0.2.25.1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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 +1,112 @@
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) */