minimap2 0.2.24.3 → 0.2.24.6

data/ext/minimap2/lib/simde/test/x86/test-avx.h

@@ -0,0 +1,16 @@
+#include "../../simde/x86/avx.h"
+
+#include "test-sse2.h"
+
+#if !defined(SIMDE_TEST_X86_AVX)
+#define SIMDE_TEST_X86_AVX
+
+SIMDE_TEST_DEFINE_ASSERT_VEC_CLOSE(m256, f32)
+SIMDE_TEST_DEFINE_ASSERT_VEC_CLOSE(m256d, f64)
+
+#define simde_assert_m256_close(a, b, precision) \
+  simde_assert_m256_f32_close_ex(__LINE__, __FILE__, a, b, precision)
+#define simde_assert_m256d_close(a, b, precision) \
+  simde_assert_m256d_f64_close_ex(__LINE__, __FILE__, a, b, precision)
+
+#endif /* !defined(SIMDE_TEST_X86_AVX) */

data/ext/minimap2/lib/simde/test/x86/test-avx512.h

@@ -0,0 +1,25 @@
+#include "../../simde/x86/avx512f.h"
+
+#include "test-avx.h"
+
+#if !defined(SIMDE_TEST_X86_AVX512)
+#define SIMDE_TEST_X86_AVX512
+
+SIMDE_TEST_DEFINE_ASSERT_VEC_CLOSE(m512, f32)
+SIMDE_TEST_DEFINE_ASSERT_VEC_CLOSE(m512d, f64)
+
+#define simde_assert_m512_close(a, b, precision) \
+  simde_assert_m512_f32_close_ex(__LINE__, __FILE__, a, b, precision)
+#define simde_assert_m512d_close(a, b, precision) \
+  simde_assert_m512d_f64_close_ex(__LINE__, __FILE__, a, b, precision)
+
+#define simde_assert_mmask8(a, op, b) \
+  munit_assert_uint8(HEDLEY_STATIC_CAST(uint8_t, a), op, HEDLEY_STATIC_CAST(uint8_t, b))
+#define simde_assert_mmask16(a, op, b) \
+  munit_assert_uint16(HEDLEY_STATIC_CAST(uint16_t, a), op, HEDLEY_STATIC_CAST(uint16_t, b))
+#define simde_assert_mmask32(a, op, b) \
+  munit_assert_uint32(HEDLEY_STATIC_CAST(uint32_t, a), op, HEDLEY_STATIC_CAST(uint32_t, b))
+#define simde_assert_mmask64(a, op, b) \
+  munit_assert_uint64(HEDLEY_STATIC_CAST(uint64_t, a), op, HEDLEY_STATIC_CAST(uint64_t, b))
+
+#endif /* !defined(SIMDE_TEST_X86_AVX512) */

data/ext/minimap2/lib/simde/test/x86/test-mmx.h

@@ -0,0 +1,13 @@
+#include "../../simde/x86/mmx.h"
+
+#include "test-x86-internal.h"
+
+#if !defined(SIMDE_TEST_X86_MMX)
+#define SIMDE_TEST_X86_MMX
+
+SIMDE_TEST_DEFINE_ASSERT_VEC_CLOSE(m64, f32)
+
+#define simde_assert_m64_close(a, b, precision) \
+  simde_assert_m64_f32_close_ex(__LINE__, __FILE__, a, b, precision)
+
+#endif /* !defined(SIMDE_TEST_X86_MMX) */

data/ext/minimap2/lib/simde/test/x86/test-sse.h

@@ -0,0 +1,13 @@
+#include "../../simde/x86/sse.h"
+
+#include "test-mmx.h"
+
+#if !defined(SIMDE_TEST_X86_SSE)
+#define SIMDE_TEST_X86_SSE
+
+SIMDE_TEST_DEFINE_ASSERT_VEC_CLOSE(m128, f32)
+
+#define simde_assert_m128_close(a, b, precision) \
+  simde_assert_m128_f32_close_ex(__LINE__, __FILE__, a, b, precision)
+
+#endif /* !defined(SIMDE_TEST_X86_SSE) */

data/ext/minimap2/lib/simde/test/x86/test-sse2.h

@@ -0,0 +1,13 @@
+#include "../../simde/x86/sse2.h"
+
+#include "test-sse.h"
+
+#if !defined(SIMDE_TEST_X86_SSE2)
+#define SIMDE_TEST_X86_SSE2
+
+SIMDE_TEST_DEFINE_ASSERT_VEC_CLOSE(m128d, f64)
+
+#define simde_assert_m128d_close(a, b, precision) \
+  simde_assert_m128d_f64_close_ex(__LINE__, __FILE__, a, b, precision)
+
+#endif /* !defined(SIMDE_TEST_X86_SSE2) */

data/ext/minimap2/lib/simde/test/x86/test-x86-internal.h

@@ -0,0 +1,196 @@
+#if !defined(SIMDE_TESTS_X86_INTERNAL_H)
+#define SIMDE_TESTS_CURRENT_ARCH x86
+
+#include "../run-tests.h"
+
+/* Assert that two vectors are bit-identical without worring about the
+   underlying type. */
+#define simde_assert_vec_equal(a, b, T) do { \
+    const T##_private simde_a_ = T##_to_private(a); \
+    const T##_private simde_b_ = T##_to_private(b); \
+    for (int simde_i_ = 0 ; simde_i_ < HEDLEY_STATIC_CAST(int, (sizeof(simde_a_.u32f) / sizeof(simde_a_.u32f[0]))) ; simde_i_++) { \
+      if (HEDLEY_UNLIKELY(simde_a_.u32f[simde_i_] != simde_b_.u32f[simde_i_])) { \
+        munit_errorf("assertion failed: " #a ".u32f[%d] (%" PRIxFAST32 ") != " #b ".u32f[%d] (%" PRIxFAST32 ")", \
+            simde_i_, simde_a_.u32f[simde_i_], \
+            simde_i_, simde_b_.u32f[simde_i_]); \
+      } \
+    } \
+  } while(0)
+#define simde_assert_m64_equal(a, b) \
+  simde_assert_vec_equal(a, b, simde__m64)
+#define simde_assert_m128_equal(a, b) \
+  simde_assert_vec_equal(a, b, simde__m128)
+#define simde_assert_m128i_equal(a, b) \
+  simde_assert_vec_equal(a, b, simde__m128i)
+#define simde_assert_m128d_equal(a, b) \
+  simde_assert_vec_equal(a, b, simde__m128d)
+#define simde_assert_m256_equal(a, b) \
+  simde_assert_vec_equal(a, b, simde__m256)
+#define simde_assert_m256i_equal(a, b) \
+  simde_assert_vec_equal(a, b, simde__m256i)
+#define simde_assert_m256d_equal(a, b) \
+  simde_assert_vec_equal(a, b, simde__m256d)
+
+/* Assert that every integer in two vectors are equal */
+#define simde_assert_vec_i(a, op, b, T, accessor, fmt) do { \
+      const T##_private simde_a_ = T##_to_private(a); \
+      const T##_private simde_b_ = T##_to_private(b); \
+      for (int simde_i_ = 0 ; simde_i_ < HEDLEY_STATIC_CAST(int, (sizeof(simde_a_.accessor) / sizeof(simde_a_.accessor[0]))) ; simde_i_++) { \
+        if (HEDLEY_UNLIKELY(!(simde_a_.accessor[simde_i_] op simde_b_.accessor[simde_i_]))) { \
+          munit_errorf("assertion failed: " #a "." #accessor "[%d] " #op " " #b "." #accessor "[%d] (%" fmt " " #op " %" fmt ")", \
+              simde_i_, simde_i_, simde_a_.accessor[simde_i_], simde_b_.accessor[simde_i_]); \
+        } \
+      } \
+    } while (0)
+#define simde_assert_m512i_i8(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m512i,  i8,  PRId8)
+#define simde_assert_m512i_i16(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m512i, i16, PRId16)
+#define simde_assert_m512i_i32(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m512i, i32, PRId32)
+#define simde_assert_m512i_i64(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m512i, i64, PRId64)
+#define simde_assert_m512i_u8(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m512i,  u8,  PRIu8)
+#define simde_assert_m512i_u16(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m512i, u16, PRIu16)
+#define simde_assert_m512i_u32(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m512i, u32, PRIu32)
+#define simde_assert_m512i_u64(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m512i, u64, PRIu64)
+#define simde_assert_m256i_i8(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m256i,  i8,  PRId8)
+#define simde_assert_m256i_i16(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m256i, i16, PRId16)
+#define simde_assert_m256i_i32(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m256i, i32, PRId32)
+#define simde_assert_m256i_i64(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m256i, i64, PRId64)
+#define simde_assert_m256i_u8(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m256i,  u8,  PRIu8)
+#define simde_assert_m256i_u16(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m256i, u16, PRIu16)
+#define simde_assert_m256i_u32(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m256i, u32, PRIu32)
+#define simde_assert_m256i_u64(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m256i, u64, PRIu64)
+#define simde_assert_m128i_i8(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m128i,  i8,  PRId8)
+#define simde_assert_m128i_i16(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m128i, i16, PRId16)
+#define simde_assert_m128i_i32(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m128i, i32, PRId32)
+#define simde_assert_m128i_i64(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m128i, i64, PRId64)
+#define simde_assert_m128i_u8(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m128i,  u8,  PRIu8)
+#define simde_assert_m128i_u16(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m128i, u16, PRIu16)
+#define simde_assert_m128i_u32(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m128i, u32, PRIu32)
+#define simde_assert_m128i_u64(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m128i, u64, PRIu64)
+#define simde_assert_m64_i8(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m64,  i8,  PRId8)
+#define simde_assert_m64_i16(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m64, i16, PRId16)
+#define simde_assert_m64_i32(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m64, i32, PRId32)
+#define simde_assert_m64_i64(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m64, i64, PRId64)
+#define simde_assert_m64_u8(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m64,  u8,  PRIu8)
+#define simde_assert_m64_u16(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m64, u16, PRIu16)
+#define simde_assert_m64_u32(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m64, u32, PRIu32)
+#define simde_assert_m64_u64(a, op, b) \
+  simde_assert_vec_i(a, op, b, simde__m64, u64, PRIu64)
+
+/* Assert that the integer values in each vector are approximately equal. */
+#define simde_assert_vec_i_close(a, b, precision, T, accessor, fmt) do { \
+      const T##_private simde_a_ = T##_to_private(a); \
+      const T##_private simde_b_ = T##_to_private(b); \
+      for (int simde_i_ = 0 ; simde_i_ < HEDLEY_STATIC_CAST(int, (sizeof(simde_a_.accessor) / sizeof(simde_a_.accessor[0]))) ; simde_i_++) { \
+        if (!((simde_a_.accessor[simde_i_] <= (simde_b_.accessor[simde_i_] + precision)) && (simde_a_.accessor[simde_i_] >= (simde_b_.accessor[simde_i_] - precision)))) { \
+          munit_errorf("assertion failed: " #a "." #accessor "[%d] " SIMDE_ALMOST_EQUAL_TO " " #b "." #accessor "[%d] (%" fmt " " SIMDE_ALMOST_EQUAL_TO " %" fmt ")", \
+              simde_i_, simde_i_, simde_a_.accessor[simde_i_], simde_b_.accessor[simde_i_]); \
+        } \
+      } \
+    } while(0)
+
+#define simde_assert_m64_i8_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m64, i8, PRId8)
+#define simde_assert_m64_i16_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m64, i16, PRId16)
+#define simde_assert_m64_i32_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m64, i32, PRId32)
+#define simde_assert_m64_i64_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m64, i64, PRId64)
+#define simde_assert_m64_u8_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m64, u8, PRIu8)
+#define simde_assert_m64_u16_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m64, u16, PRIu16)
+#define simde_assert_m64_u32_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m64, u32, PRIu32)
+#define simde_assert_m64_u64_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m64, u64, PRIu64)
+#define simde_assert_m128i_i8_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m128i, i8, PRId8)
+#define simde_assert_m128i_i16_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m128i, i16, PRId16)
+#define simde_assert_m128i_i32_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m128i, i32, PRId32)
+#define simde_assert_m128i_i64_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m128i, i64, PRId64)
+#define simde_assert_m128i_u8_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m128i, u8, PRIu8)
+#define simde_assert_m128i_u16_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m128i, u16, PRIu16)
+#define simde_assert_m128i_u32_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m128i, u32, PRIu32)
+#define simde_assert_m128i_u64_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m128i, u64, PRIu64)
+#define simde_assert_m256i_i8_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m256i, i8, PRId8)
+#define simde_assert_m256i_i16_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m256i, i16, PRId16)
+#define simde_assert_m256i_i32_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m256i, i32, PRId32)
+#define simde_assert_m256i_i64_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m256i, i64, PRId64)
+#define simde_assert_m256i_u8_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m256i, u8, PRIu8)
+#define simde_assert_m256i_u16_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m256i, u16, PRIu16)
+#define simde_assert_m256i_u32_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m256i, u32, PRIu32)
+#define simde_assert_m256i_u64_close(a, b, precision) \
+  simde_assert_vec_i_close(a, b, precision, simde__m256i, u64, PRIu64)
+
+HEDLEY_BEGIN_C_DECLS
+
+#define SIMDE_TESTS_GENERATE_SUITE_GETTERS(isax) \
+  MunitSuite* SIMDE_TESTS_GENERATE_SYMBOL_FULL(suite, SIMDE_TESTS_CURRENT_ARCH, isax, native, c)(void); \
+  MunitSuite* SIMDE_TESTS_GENERATE_SYMBOL_FULL(suite, SIMDE_TESTS_CURRENT_ARCH, isax, native, cpp)(void); \
+  MunitSuite* SIMDE_TESTS_GENERATE_SYMBOL_FULL(suite, SIMDE_TESTS_CURRENT_ARCH, isax, emul,   c)(void); \
+  MunitSuite* SIMDE_TESTS_GENERATE_SYMBOL_FULL(suite, SIMDE_TESTS_CURRENT_ARCH, isax, emul,   cpp)(void)
+
+SIMDE_TESTS_GENERATE_SUITE_GETTERS(mmx);
+SIMDE_TESTS_GENERATE_SUITE_GETTERS(sse);
+SIMDE_TESTS_GENERATE_SUITE_GETTERS(sse2);
+SIMDE_TESTS_GENERATE_SUITE_GETTERS(sse3);
+SIMDE_TESTS_GENERATE_SUITE_GETTERS(ssse3);
+SIMDE_TESTS_GENERATE_SUITE_GETTERS(sse4_1);
+SIMDE_TESTS_GENERATE_SUITE_GETTERS(sse4_2);
+SIMDE_TESTS_GENERATE_SUITE_GETTERS(avx);
+SIMDE_TESTS_GENERATE_SUITE_GETTERS(fma);
+SIMDE_TESTS_GENERATE_SUITE_GETTERS(avx2);
+SIMDE_TESTS_GENERATE_SUITE_GETTERS(avx512f);
+SIMDE_TESTS_GENERATE_SUITE_GETTERS(avx512bw);
+SIMDE_TESTS_GENERATE_SUITE_GETTERS(avx512vl);
+SIMDE_TESTS_GENERATE_SUITE_GETTERS(svml);
+
+HEDLEY_END_C_DECLS
+
+#endif /* !defined(SIMDE_TESTS_X86_INTERNAL_H) */

data/ext/minimap2/lib/simde/test/x86/test-x86.c

@@ -0,0 +1,48 @@
+#include "test-x86.h"
+#include "test-x86-internal.h"
+
+#include <stdio.h>
+
+#if defined(SIMDE_BUILD_CPP_TESTS)
+#define SUITES_PER_ISAX 4
+#define SET_CHILDREN_FOR_ARCH(isax) \
+  children[i++] = *SIMDE_TESTS_GENERATE_SYMBOL_FULL(suite, SIMDE_TESTS_CURRENT_ARCH, isax, native, c)(); \
+  children[i++] = *SIMDE_TESTS_GENERATE_SYMBOL_FULL(suite, SIMDE_TESTS_CURRENT_ARCH, isax, emul,   c)(); \
+  children[i++] = *SIMDE_TESTS_GENERATE_SYMBOL_FULL(suite, SIMDE_TESTS_CURRENT_ARCH, isax, native, cpp)(); \
+  children[i++] = *SIMDE_TESTS_GENERATE_SYMBOL_FULL(suite, SIMDE_TESTS_CURRENT_ARCH, isax, emul,   cpp)()
+#else
+#define SUITES_PER_ISAX 2
+#define SET_CHILDREN_FOR_ARCH(isax) \
+  children[i++] = *SIMDE_TESTS_GENERATE_SYMBOL_FULL(suite, SIMDE_TESTS_CURRENT_ARCH, isax, native, c)(); \
+  children[i++] = *SIMDE_TESTS_GENERATE_SYMBOL_FULL(suite, SIMDE_TESTS_CURRENT_ARCH, isax, emul,   c)()
+#endif
+
+MunitSuite*
+simde_tests_x86_get_suite(void) {
+  static MunitSuite children[(14 * SUITES_PER_ISAX) + 1];
+  static MunitSuite suite = { "/x86", NULL, children, 1, MUNIT_SUITE_OPTION_NONE };
+  static const MunitSuite empty = { NULL, NULL, NULL, 1, MUNIT_SUITE_OPTION_NONE };
+
+  size_t i = 0;
+
+  SET_CHILDREN_FOR_ARCH(mmx);
+  SET_CHILDREN_FOR_ARCH(sse);
+  SET_CHILDREN_FOR_ARCH(sse2);
+  SET_CHILDREN_FOR_ARCH(sse3);
+  SET_CHILDREN_FOR_ARCH(ssse3);
+  SET_CHILDREN_FOR_ARCH(sse4_1);
+  SET_CHILDREN_FOR_ARCH(sse4_2);
+  SET_CHILDREN_FOR_ARCH(avx);
+  SET_CHILDREN_FOR_ARCH(fma);
+  SET_CHILDREN_FOR_ARCH(avx2);
+  SET_CHILDREN_FOR_ARCH(avx512f);
+  SET_CHILDREN_FOR_ARCH(avx512bw);
+  SET_CHILDREN_FOR_ARCH(avx512vl);
+  SET_CHILDREN_FOR_ARCH(svml);
+
+  children[i++] = empty;
+
+  munit_assert_size(i, <=, sizeof(children) / sizeof(children[0]));
+
+  return &suite;
+}

data/ext/minimap2/lib/simde/test/x86/test-x86.h

@@ -0,0 +1,8 @@
+#include "../../simde/hedley.h"
+#include "../munit/munit.h"
+
+HEDLEY_BEGIN_C_DECLS
+
+MunitSuite* simde_tests_x86_get_suite(void);
+
+HEDLEY_END_C_DECLS

data/lib/minimap2/aligner.rb

@@ -80,8 +80,8 @@ module Minimap2
         map_opt[:b] = scoring[1]
         map_opt[:q] = scoring[2]
         map_opt[:e] = scoring[3]
-        map_opt[:q2] = map_opt.q
-        map_opt[:e2] = map_opt.e
+        map_opt[:q2] = map_opt[:q]
+        map_opt[:e2] = map_opt[:e]
         if scoring.size >= 6
           map_opt[:q2] = scoring[4]
           map_opt[:e2] = scoring[5]

data/lib/minimap2/ffi/constants.rb

@@ -136,8 +136,11 @@ module Minimap2
         :mid_occ_frac,         :float,   # only used by mm_mapopt_update(); see below
         :q_occ_frac,           :float,
         :min_mid_occ,          :int32,
+        :max_mid_occ,          :int32,
         :mid_occ,              :int32, # ignore seeds with occurrences above this threshold
         :max_occ,              :int32,
+        :max_max_occ,          :int32,
+        :occ_dist,             :int32,
         :mini_batch_size,      :int64_t, # size of a batch of query bases to process in parallel
         :max_sw_mat,           :int64_t,
         :cap_kalloc,           :int64_t,

data/lib/minimap2/version.rb

@@ -2,5 +2,5 @@
 
 module Minimap2
   #  Minimap2-2.24 (r1122)
-  VERSION = "0.2.24.3"
+  VERSION = "0.2.24.6"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: minimap2
 version: !ruby/object:Gem::Version
-  version: 0.2.24.3
+  version: 0.2.24.6
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-04-26 00:00:00.000000000 Z
+date: 2023-04-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: ffi
@@ -87,6 +87,102 @@ files:
 - ext/minimap2/kthread.h
 - ext/minimap2/kvec.h
 - ext/minimap2/lchain.c
+- ext/minimap2/lib/simde/CONTRIBUTING.md
+- ext/minimap2/lib/simde/COPYING
+- ext/minimap2/lib/simde/README.md
+- ext/minimap2/lib/simde/amalgamate.py
+- ext/minimap2/lib/simde/meson.build
+- ext/minimap2/lib/simde/netlify.toml
+- ext/minimap2/lib/simde/simde/arm/neon.h
+- ext/minimap2/lib/simde/simde/arm/neon/float32x2.h
+- ext/minimap2/lib/simde/simde/arm/neon/float32x4.h
+- ext/minimap2/lib/simde/simde/arm/neon/float64x1.h
+- ext/minimap2/lib/simde/simde/arm/neon/float64x2.h
+- ext/minimap2/lib/simde/simde/arm/neon/int16x4.h
+- ext/minimap2/lib/simde/simde/arm/neon/int16x8.h
+- ext/minimap2/lib/simde/simde/arm/neon/int32x2.h
+- ext/minimap2/lib/simde/simde/arm/neon/int32x4.h
+- ext/minimap2/lib/simde/simde/arm/neon/int64x1.h
+- ext/minimap2/lib/simde/simde/arm/neon/int64x2.h
+- ext/minimap2/lib/simde/simde/arm/neon/int8x16.h
+- ext/minimap2/lib/simde/simde/arm/neon/int8x8.h
+- ext/minimap2/lib/simde/simde/arm/neon/uint16x4.h
+- ext/minimap2/lib/simde/simde/arm/neon/uint16x8.h
+- ext/minimap2/lib/simde/simde/arm/neon/uint32x2.h
+- ext/minimap2/lib/simde/simde/arm/neon/uint32x4.h
+- ext/minimap2/lib/simde/simde/arm/neon/uint64x1.h
+- ext/minimap2/lib/simde/simde/arm/neon/uint64x2.h
+- ext/minimap2/lib/simde/simde/arm/neon/uint8x16.h
+- ext/minimap2/lib/simde/simde/arm/neon/uint8x8.h
+- ext/minimap2/lib/simde/simde/check.h
+- ext/minimap2/lib/simde/simde/debug-trap.h
+- ext/minimap2/lib/simde/simde/hedley.h
+- ext/minimap2/lib/simde/simde/simde-arch.h
+- ext/minimap2/lib/simde/simde/simde-common.h
+- ext/minimap2/lib/simde/simde/x86/avx.h
+- ext/minimap2/lib/simde/simde/x86/avx2.h
+- ext/minimap2/lib/simde/simde/x86/avx512bw.h
+- ext/minimap2/lib/simde/simde/x86/avx512f.h
+- ext/minimap2/lib/simde/simde/x86/avx512vl.h
+- ext/minimap2/lib/simde/simde/x86/fma.h
+- ext/minimap2/lib/simde/simde/x86/mmx.h
+- ext/minimap2/lib/simde/simde/x86/sse.h
+- ext/minimap2/lib/simde/simde/x86/sse2.h
+- ext/minimap2/lib/simde/simde/x86/sse3.h
+- ext/minimap2/lib/simde/simde/x86/sse4.1.h
+- ext/minimap2/lib/simde/simde/x86/sse4.2.h
+- ext/minimap2/lib/simde/simde/x86/ssse3.h
+- ext/minimap2/lib/simde/simde/x86/svml.h
+- ext/minimap2/lib/simde/test/CMakeLists.txt
+- ext/minimap2/lib/simde/test/arm/meson.build
+- ext/minimap2/lib/simde/test/arm/neon/meson.build
+- ext/minimap2/lib/simde/test/arm/neon/skel.c
+- ext/minimap2/lib/simde/test/arm/neon/test-neon-internal.h
+- ext/minimap2/lib/simde/test/arm/neon/test-neon.c
+- ext/minimap2/lib/simde/test/arm/neon/test-neon.h
+- ext/minimap2/lib/simde/test/arm/neon/vadd.c
+- ext/minimap2/lib/simde/test/arm/neon/vdup_n.c
+- ext/minimap2/lib/simde/test/arm/neon/vmul.c
+- ext/minimap2/lib/simde/test/arm/neon/vsub.c
+- ext/minimap2/lib/simde/test/arm/test-arm-internal.h
+- ext/minimap2/lib/simde/test/arm/test-arm.c
+- ext/minimap2/lib/simde/test/arm/test-arm.h
+- ext/minimap2/lib/simde/test/cmake/AddCompilerFlags.cmake
+- ext/minimap2/lib/simde/test/cmake/ExtraWarningFlags.cmake
+- ext/minimap2/lib/simde/test/meson.build
+- ext/minimap2/lib/simde/test/munit/COPYING
+- ext/minimap2/lib/simde/test/munit/Makefile
+- ext/minimap2/lib/simde/test/munit/README.md
+- ext/minimap2/lib/simde/test/munit/example.c
+- ext/minimap2/lib/simde/test/munit/meson.build
+- ext/minimap2/lib/simde/test/munit/munit.c
+- ext/minimap2/lib/simde/test/munit/munit.h
+- ext/minimap2/lib/simde/test/run-tests.c
+- ext/minimap2/lib/simde/test/run-tests.h
+- ext/minimap2/lib/simde/test/x86/avx.c
+- ext/minimap2/lib/simde/test/x86/avx2.c
+- ext/minimap2/lib/simde/test/x86/avx512bw.c
+- ext/minimap2/lib/simde/test/x86/avx512f.c
+- ext/minimap2/lib/simde/test/x86/avx512vl.c
+- ext/minimap2/lib/simde/test/x86/fma.c
+- ext/minimap2/lib/simde/test/x86/meson.build
+- ext/minimap2/lib/simde/test/x86/mmx.c
+- ext/minimap2/lib/simde/test/x86/skel.c
+- ext/minimap2/lib/simde/test/x86/sse.c
+- ext/minimap2/lib/simde/test/x86/sse2.c
+- ext/minimap2/lib/simde/test/x86/sse3.c
+- ext/minimap2/lib/simde/test/x86/sse4.1.c
+- ext/minimap2/lib/simde/test/x86/sse4.2.c
+- ext/minimap2/lib/simde/test/x86/ssse3.c
+- ext/minimap2/lib/simde/test/x86/svml.c
+- ext/minimap2/lib/simde/test/x86/test-avx.h
+- ext/minimap2/lib/simde/test/x86/test-avx512.h
+- ext/minimap2/lib/simde/test/x86/test-mmx.h
+- ext/minimap2/lib/simde/test/x86/test-sse.h
+- ext/minimap2/lib/simde/test/x86/test-sse2.h
+- ext/minimap2/lib/simde/test/x86/test-x86-internal.h
+- ext/minimap2/lib/simde/test/x86/test-x86.c
+- ext/minimap2/lib/simde/test/x86/test-x86.h
 - ext/minimap2/main.c
 - ext/minimap2/map.c
 - ext/minimap2/minimap.h
@@ -164,7 +260,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.4.10
+rubygems_version: 3.4.1
 signing_key: 
 specification_version: 4
 summary: minimap2