minimap2 0.2.25.0 → 0.2.25.1

data/ext/minimap2/options.c

@@ -8,7 +8,7 @@ void mm_idxopt_init(mm_idxopt_t *opt)
 	opt->k = 15, opt->w = 10, opt->flag = 0;
 	opt->bucket_bits = 14;
 	opt->mini_batch_size = 50000000;
-	opt->batch_size = 4000000000ULL;
+	opt->batch_size = 8000000000ULL;
 }
 
 void mm_mapopt_init(mm_mapopt_t *opt)

data/ext/minimap2/pyproject.toml

@@ -0,0 +1,2 @@
+[build-system]
+requires = ["setuptools", "wheel", "Cython"]

data/ext/minimap2/python/mappy.pyx

@@ -3,7 +3,7 @@ from libc.stdlib cimport free
 cimport cmappy
 import sys
 
-__version__ = '2.24'
+__version__ = '2.25'
 
 cmappy.mm_reset_timer()
 
@@ -172,6 +172,7 @@ cdef class Aligner:
 		cdef cmappy.mm_mapopt_t map_opt
 
 		if self._idx == NULL: return
+		if ((self.map_opt.flag & 4) and (self._idx.flag & 2)): return
 		map_opt = self.map_opt
 		if max_frag_len is not None: map_opt.max_frag_len = max_frag_len
 		if extra_flags is not None: map_opt.flag |= extra_flags
@@ -217,6 +218,7 @@ cdef class Aligner:
 		cdef int l
 		cdef char *s
 		if self._idx == NULL: return
+		if ((self.map_opt.flag & 4) and (self._idx.flag & 2)): return
 		s = cmappy.mappy_fetch_seq(self._idx, name.encode(), start, end, &l)
 		if l == 0: return None
 		r = s[:l] if isinstance(s, str) else s[:l].decode()

data/ext/minimap2/seed.c

@@ -7,7 +7,7 @@ void mm_seed_mz_flt(void *km, mm128_v *mv, int32_t q_occ_max, float q_occ_frac)
 	mm128_t *a;
 	size_t i, j, st;
 	if (mv->n <= q_occ_max || q_occ_frac <= 0.0f || q_occ_max <= 0) return;
-	KMALLOC(km, a, mv->n);
+	a = Kmalloc(km, mm128_t, mv->n);
 	for (i = 0; i < mv->n; ++i)
 		a[i].x = mv->a[i].x, a[i].y = i;
 	radix_sort_128x(a, a + mv->n);

data/ext/minimap2/setup.py

@@ -1,29 +1,40 @@
 try:
 	from setuptools import setup, Extension
+	from setuptools.command.build_ext import build_ext
 except ImportError:
 	from distutils.core import setup
 	from distutils.extension import Extension
+	from distutils.command.build_ext import build_ext
 
-import sys, platform
+import sys, platform, subprocess
 
-sys.path.append('python')
-
-extra_compile_args = ['-DHAVE_KALLOC']
-include_dirs = ["."]
-
-if platform.machine() in ["aarch64", "arm64"]:
-	include_dirs.append("sse2neon/")
-	extra_compile_args.extend(['-ftree-vectorize', '-DKSW_SSE2_ONLY', '-D__SSE2__'])
-else:
-	extra_compile_args.append('-msse4.1') # WARNING: ancient x86_64 CPUs don't have SSE4
 
 def readme():
 	with open('python/README.rst') as f:
 		return f.read()
 
+
+class LibMM2Build(build_ext):
+	# Uses Makefile to build library, avoids duplicating logic
+	# determining which objects to compile but does require
+	# end users to have Make (since precompiled wheels are not
+	# distributed on PyPI).
+	def run(self):
+		def compile_libminimap2(*args, **kwargs):
+			cmd = ['make', 'libminimap2.a'] + list(args)
+			subprocess.check_call(cmd)
+		options = []
+		if platform.machine() in ["aarch64", "arm64"]:
+			options = ["arm_neon=1", "aarch64=1"]
+		self.execute(
+			compile_libminimap2, options,
+			'Compiling libminimap2 using Makefile')
+		build_ext.run(self)
+
+
 setup(
 	name = 'mappy',
-	version = '2.24',
+	version = '2.25',
 	url = 'https://github.com/lh3/minimap2',
 	description = 'Minimap2 python binding',
 	long_description = readme(),
@@ -32,16 +43,15 @@ setup(
 	license = 'MIT',
 	keywords = 'sequence-alignment',
 	scripts = ['python/minimap2.py'],
-	ext_modules = [Extension('mappy',
-		sources = ['python/mappy.pyx', 'align.c', 'bseq.c', 'lchain.c', 'seed.c', 'format.c', 'hit.c', 'index.c', 'pe.c', 'options.c',
-				   'ksw2_extd2_sse.c', 'ksw2_exts2_sse.c', 'ksw2_extz2_sse.c', 'ksw2_ll_sse.c',
-				   'kalloc.c', 'kthread.c', 'map.c', 'misc.c', 'sdust.c', 'sketch.c', 'esterr.c', 'splitidx.c'],
-		depends = ['minimap.h', 'bseq.h', 'kalloc.h', 'kdq.h', 'khash.h', 'kseq.h', 'ksort.h',
-				   'ksw2.h', 'kthread.h', 'kvec.h', 'mmpriv.h', 'sdust.h',
-				   'python/cmappy.h', 'python/cmappy.pxd'],
-		extra_compile_args = extra_compile_args,
-		include_dirs = include_dirs,
-		libraries = ['z', 'm', 'pthread'])],
+	cmdclass = {'build_ext': LibMM2Build},
+	ext_modules = [
+		Extension(
+			'mappy',
+			sources = ['python/mappy.pyx'],
+			depends = ['python/cmappy.h', 'python/cmappy.pxd'],
+			include_dirs = ['.'],
+			extra_objects = ['libminimap2.a'],
+			libraries = ['z', 'm', 'pthread'])],
 	classifiers = [
 		'Development Status :: 5 - Production/Stable',
 		'License :: OSI Approved :: MIT License',

data/lib/minimap2/version.rb

@@ -2,5 +2,5 @@
 
 module Minimap2
   # Minimap2-2.25 (r1173)
-  VERSION = "0.2.25.0"
+  VERSION = "0.2.25.1"
 end

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: minimap2
 version: !ruby/object:Gem::Version
-  version: 0.2.25.0
+  version: 0.2.25.1
 platform: ruby
 authors:
 - kojix2
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2023-04-27 00:00:00.000000000 Z
+date: 2023-05-01 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
@@ -98,6 +194,7 @@ files:
 - ext/minimap2/mmpriv.h
 - ext/minimap2/options.c
 - ext/minimap2/pe.c
+- ext/minimap2/pyproject.toml
 - ext/minimap2/python/README.rst
 - ext/minimap2/python/cmappy.h
 - ext/minimap2/python/cmappy.pxd
@@ -164,7 +261,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubygems_version: 3.4.1
+rubygems_version: 3.4.6
 signing_key: 
 specification_version: 4
 summary: minimap2