diff --git a/pyfastani/_fasta.pyx b/pyfastani/_fasta.pyx
index c4381ea79399721d2cc2f00f0a84c9e4da48d499..394ba0846c068f01ed6d5ea579ee4bd2a0dd2dc8 100644
--- a/pyfastani/_fasta.pyx
+++ b/pyfastani/_fasta.pyx
@@ -11,7 +11,7 @@ from libc.errno cimport errno
from libc.string cimport strlen, memcpy, memset
from _unicode cimport PyUnicode_1BYTE_KIND, PyUnicode_FromKindAndData
-from _simd cimport copy_upper
+from _sequtils cimport copy_upper
cdef extern from "<ctype.h>" nogil:
cdef int toupper(int c)
diff --git a/pyfastani/_fastani.pyx b/pyfastani/_fastani.pyx
index 2afb2633b2a5526cb62fe19e5063e438f8e2c41f..663ed817b6e370980ebd0f18f37d10af7024aa04 100644
--- a/pyfastani/_fastani.pyx
+++ b/pyfastani/_fastani.pyx
@@ -46,8 +46,9 @@ from fastani.map.base_types cimport (
# HACK: we need kseq_t* as a template argument, which is not supported by
# Cython at the moment, so we just `typedef kseq_t* kseq_ptr_t` in
# an external C++ header to make Cython happy
-from _utils cimport kseq_ptr_t, toupper, complement, distance
+from _utils cimport kseq_ptr_t, toupper, distance
from _unicode cimport *
+from _sequtils cimport copy_upper, reverse_complement
# --- Python imports ---------------------------------------------------------
@@ -88,10 +89,17 @@ cdef ssize_t _read_nucl(
else:
length = 0
- for j in range(length):
- nuc = toupper(<int> PyUnicode_READ(kind, data, i + j))
- fwd[_MAX_KMER_SIZE + j] = nuc
- bwd[_MAX_KMER_SIZE - j - 1] = complement(nuc)
+ # if UCS-1, bytes are next to each other, so we can use the SIMD
+ # implementations to copy into uppercase
+ if kind == PyUnicode_1BYTE_KIND:
+ copy_upper(&fwd[_MAX_KMER_SIZE], &(<char*> data)[i], length)
+ else:
+ for j in range(length):
+ fwd[_MAX_KMER_SIZE + j] = toupper(<int> PyUnicode_READ(kind, data, i + j))
+
+ # reverse complement in backward buffer
+ reverse_complement(&bwd[_MAX_KMER_SIZE - length], &fwd[_MAX_KMER_SIZE], length)
+
return length
diff --git a/pyfastani/_sequtils/__init__.pxd b/pyfastani/_sequtils/__init__.pxd
new file mode 100644
index 0000000000000000000000000000000000000000..2ef1acee34702888c3b0f4f98117d044615bce87
--- /dev/null
+++ b/pyfastani/_sequtils/__init__.pxd
@@ -0,0 +1,4 @@
+cdef extern from "sequtils.h" nogil:
+ char complement(char base)
+ void copy_upper(char*, const char*, size_t)
+ void reverse_complement(char*, const char*, size_t)
diff --git a/pyfastani/_sequtils/complement.h b/pyfastani/_sequtils/complement.h
new file mode 100644
index 0000000000000000000000000000000000000000..2a3ccb84ac93001e49ef4a41f5bba95bbae997b6
--- /dev/null
+++ b/pyfastani/_sequtils/complement.h
@@ -0,0 +1,28 @@
+#ifndef __SEQUTILS_COMPLEMENT_H
+#define __SEQUTILS_COMPLEMENT_H
+
+// efficient nucleotide complement with a lookup table
+static const char COMPLEMENT_LOOKUP[128] = {
+ '\x00', '\x01', '\x02', '\x03', '\x04', '\x05', '\x06', '\x07',
+ '\x08', '\t', '\n', '\x0', '\x0c', '\r', '\x0e', '\x0f',
+ '\x10', '\x11', '\x12', '\x13', '\x14', '\x15', '\x16', '\x17',
+ '\x18', '\x19', '\x1a', '\x1', '\x1c', '\x1d', '\x1e', '\x1f',
+ ' ', '!', '"', '#', '$', '%', '&', '\'',
+ '(', ')', '*', '+', ',', '-', '.', '/',
+ '0', '1', '2', '3', '4', '5', '6', '7',
+ '8', '9', ':', ';', '<', '=', '>', '?',
+ '@', 'T', 'V', 'G', 'H', 'E', 'F', 'C',
+ 'D', 'I', 'J', 'M', 'L', 'K', 'N', 'O',
+ 'P', 'Q', 'Y', 'S', 'A', 'U', 'B', 'W',
+ 'X', 'R', 'Z', '[', '\\', ']', '^', '_',
+ '`', 't', 'v', 'g', 'h', 'e', 'f', 'c',
+ 'd', 'i', 'j', 'm', 'l', 'k', 'n', 'o',
+ 'p', 'q', 'y', 's', 'a', 'u', 'b', 'w',
+ 'x', 'r', 'z', '{', '|', '}', '~', '\x7f'
+};
+
+static char complement(char base) {
+ return COMPLEMENT_LOOKUP[(size_t) (base & 0x7F)];
+}
+
+#endif
diff --git a/pyfastani/_sequtils/sequtils.h b/pyfastani/_sequtils/sequtils.h
new file mode 100644
index 0000000000000000000000000000000000000000..8bc1edfdceaa61692b4cb06a94b3a70f46f1dfa8
--- /dev/null
+++ b/pyfastani/_sequtils/sequtils.h
@@ -0,0 +1,29 @@
+#ifndef __SEQUTILS_H
+#define __SEQUTILS_H
+
+#include "complement.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+void default_copy_upper(char*, const char*, size_t);
+#ifdef SSE2_BUILD_SUPPORTED
+void sse2_copy_upper(char*, const char*, size_t);
+#endif
+#ifdef NEON_BUILD_SUPPORTED
+void neon_copy_upper(char* dst, const char* src, size_t len);
+#endif
+void copy_upper(char*, const char*, size_t);
+
+void default_reverse_complement(char*, const char*, size_t);
+#ifdef SSSE3_BUILD_SUPPORTED
+extern void ssse3_reverse_complement(char* dst, const char* src, size_t len);
+#endif
+void reverse_complement(char*, const char*, size_t);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
diff --git a/pyfastani/_simd.c b/pyfastani/_simd.c
deleted file mode 100644
index 5114c65343d7ed4aade13164229149aea6c3d806..0000000000000000000000000000000000000000
--- a/pyfastani/_simd.c
+++ /dev/null
@@ -1,87 +0,0 @@
-#include <ctype.h>
-#include <stddef.h>
-#ifdef __SSE2__
-#include <x86intrin.h>
-#endif
-#ifdef __ARM_NEON__
-#include <arm_neon.h>
-#endif
-
-#include "_simd.h"
-
-void default_copy_upper(char* dst, const char* src, size_t len) {
- while (len-- > 0) {
- *dst = toupper(*src);
- src++;
- dst++;
- }
-}
-
-#ifdef __SSE2__
-void sse2_copy_upper(char* dst, const char* src, size_t len) {
-
- const __m128i ascii_a = _mm_set1_epi8('a' - 1);
- const __m128i ascii_z = _mm_set1_epi8('z');
- const __m128i offset = _mm_set1_epi8('a' - 'A');
-
- while (len >= sizeof(__m128i)) {
- __m128i inp = _mm_loadu_si128((__m128i*) src);
- __m128i greater_than_a = _mm_cmpgt_epi8(inp, ascii_a);
- __m128i less_equal_z = _mm_cmpgt_epi8(ascii_z, inp);
- __m128i mask = _mm_and_si128(greater_than_a, less_equal_z);
- __m128i diff = _mm_and_si128(mask, offset);
- __m128i added = _mm_sub_epi8(inp, diff);
- _mm_storeu_si128((__m128i *) dst, added);
- len -= sizeof(__m128i);
- src += sizeof(__m128i);
- dst += sizeof(__m128i);
- }
-
- default_copy_upper(dst, src, len);
-}
-#endif
-#ifdef __ARM_NEON__
-void neon_copy_upper(char* dst, const char* src, size_t len) {
-
- const int8x16_t ascii_a = vdupq_n_s8('a' - 1);
- const int8x16_t ascii_z = vdupq_n_s8('z');
- const int8x16_t offset = vdupq_n_s8('a' - 'A');
-
- while (len >= sizeof(int8x16_t)) {
- int8x16_t inp = vld1q_u8((int8_t*) src);
- int8x16_t greater_than_a = vcgtq_s8(inp, ascii_a);
- int8x16_t less_equal_z = vcgtq_s8(ascii_z, inp);
- int8x16_t mask = vandq_s8(greater_than_a, less_equal_z);
- int8x16_t diff = vandq_s8(mask, offset);
- int8x16_t added = vsubq_s8(inp, diff);
- vst1q_s8((int8_t*) dst, added);
- len -= sizeof(int8x16_t);
- src += sizeof(int8x16_t);
- dst += sizeof(int8x16_t);
- }
-
- default_copy_upper(dst, src, len);
-}
-#endif
-
-void (*resolve_copy_upper (void))(char*, const char*, size_t)
-{
- // ifunc resolvers fire before constructors, explicitly call the init
- // function.
-#ifdef __SSE2__
- __builtin_cpu_init ();
- if (__builtin_cpu_supports ("sse2"))
- return sse2_copy_upper; // fast copying plus upper.
- else
-#endif
-#ifdef __ARM_NEON__
-__builtin_cpu_init ();
-if (__builtin_cpu_supports ("neon"))
- return neon_copy_upper; // fast copying plus upper.
-else
-#endif
- return default_copy_upper;
-}
-
-void copy_upper(char*, const char*, size_t)
- __attribute__ ((ifunc ("resolve_copy_upper")));
diff --git a/pyfastani/_simd.h b/pyfastani/_simd.h
deleted file mode 100644
index 1eeac380693c0b7dc81ad2daf87ab4c9d27641d6..0000000000000000000000000000000000000000
--- a/pyfastani/_simd.h
+++ /dev/null
@@ -1,21 +0,0 @@
-#ifndef __SIMD_H
-#define __SIMD_H
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-void default_copy_upper(char*, const char*, size_t);
-#ifdef __SSE2__
-void sse_copy_upper(char*, const char*, size_t);
-#endif
-#ifdef __ARM_NEON__
-void neon_copy_upper(char* dst, const char* src, size_t len);
-#endif
-void copy_upper(char*, const char*, size_t);
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif
diff --git a/pyfastani/_simd.pxd b/pyfastani/_simd.pxd
deleted file mode 100644
index f545df43d38f279ff71b2e1b2802dfa82ef3580b..0000000000000000000000000000000000000000
--- a/pyfastani/_simd.pxd
+++ /dev/null
@@ -1,2 +0,0 @@
-cdef extern from "_simd.h" nogil:
- void copy_upper(char*, const char*, size_t)
diff --git a/pyfastani/_utils.cpp b/pyfastani/_utils.cpp
index af2065688a01fce3675f30d8b223d2b82390c13a..8170735b0b1bdbcdec9230636455af6b8b09ed9b 100644
--- a/pyfastani/_utils.cpp
+++ b/pyfastani/_utils.cpp
@@ -1,14 +1,6 @@
-#include "omp.h"
+#include <zlib.h>
#include "_utils.hpp"
-int omp_get_thread_num(void) {
- return 1; // Make the logger shut up.
-}
-
-int omp_get_num_threads(void) {
- return 1;
-}
-
ZEXTERN gzFile ZEXPORT gzdopen(int fd, const char* mode) {
return NULL;
}
diff --git a/pyfastani/_utils.hpp b/pyfastani/_utils.hpp
index 0c113608cfcff73cb74d795d46519b185ff4ac6f..6b9b317414e14e4a4af1f9a7fc70359c044e889b 100644
--- a/pyfastani/_utils.hpp
+++ b/pyfastani/_utils.hpp
@@ -14,34 +14,8 @@
#include "map/include/winSketch.hpp"
extern "C" {
-
// compatibility layer for Cython
typedef kseq_t* kseq_ptr_t;
-
- // efficient nucleotide complement with a lookup table
- static const char COMPLEMENT_LOOKUP[128] = {
- '\x00', '\x01', '\x02', '\x03', '\x04', '\x05', '\x06', '\x07',
- '\x08', '\t', '\n', '\x0', '\x0c', '\r', '\x0e', '\x0f',
- '\x10', '\x11', '\x12', '\x13', '\x14', '\x15', '\x16', '\x17',
- '\x18', '\x19', '\x1a', '\x1', '\x1c', '\x1d', '\x1e', '\x1f',
- ' ', '!', '"', '#', '$', '%', '&', '\'',
- '(', ')', '*', '+', ',', '-', '.', '/',
- '0', '1', '2', '3', '4', '5', '6', '7',
- '8', '9', ':', ';', '<', '=', '>', '?',
- '@', 'T', 'V', 'G', 'H', 'E', 'F', 'C',
- 'D', 'I', 'J', 'M', 'L', 'K', 'N', 'O',
- 'P', 'Q', 'Y', 'S', 'A', 'U', 'B', 'W',
- 'X', 'R', 'Z', '[', '\\', ']', '^', '_',
- '`', 't', 'v', 'g', 'h', 'e', 'f', 'c',
- 'd', 'i', 'j', 'm', 'l', 'k', 'n', 'o',
- 'p', 'q', 'y', 's', 'a', 'u', 'b', 'w',
- 'x', 'r', 'z', '{', '|', '}', '~', '\x7f'
- };
-
- inline char complement(char base) {
- return COMPLEMENT_LOOKUP[(size_t) (base & 0x7F)];
- }
-
}
-#endif // ifdef __UTILS_HPP
+#endif
diff --git a/pyfastani/_utils.pxd b/pyfastani/_utils.pxd
index a630ee114bb9c7ac76cf15dc98e69cd796a617a8..11500d8402a1dd1d7d70624d8deef37ff319edd0 100644
--- a/pyfastani/_utils.pxd
+++ b/pyfastani/_utils.pxd
@@ -24,20 +24,18 @@ cdef extern from "<iterator>" namespace "std" nogil:
cdef ssize_t distance[I](I first, I last);
-cdef extern from "<zlib.h>" nogil:
- cdef struct gzFile_s:
- pass
-
- ctypedef gzFile_s* gzFile
-
- gzFile gzopen(int fd, const char* mode)
- gzFile gzopen64(const char* path, const char* mode)
- int gzread(gzFile file, void* buf, unsigned int len)
- int gzclose(gzFile file)
+# cdef extern from "<zlib.h>" nogil:
+# cdef struct gzFile_s:
+# pass
+#
+# ctypedef gzFile_s* gzFile
+#
+# gzFile gzopen(int fd, const char* mode)
+# gzFile gzopen64(const char* path, const char* mode)
+# int gzread(gzFile file, void* buf, unsigned int len)
+# int gzclose(gzFile file)
cdef extern from "_utils.hpp" nogil:
ctypedef kseq_t* kseq_ptr_t
-
- int complement(int)
diff --git a/pyfastani/omp.cpp b/pyfastani/omp.cpp
index e670dd613d92b68c246869ddb9e59b50005d8f61..f6c68896fc6f483c2718c0b403f3ce734f4c1c0a 100644
--- a/pyfastani/omp.cpp
+++ b/pyfastani/omp.cpp
@@ -2,5 +2,10 @@
// not needed anywhere except in `cgi::correctRefGenomeIds` so we can just
// patch these functions to disable logging
-extern int omp_get_thread_num(void);
-extern int omp_get_num_threads(void);
+int omp_get_thread_num(void) {
+ return 1; // Make the logger shut up.
+}
+
+int omp_get_num_threads(void) {
+ return 1;
+}