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|
Author: Andreas Tille <tille@debian.org>
Description: Use Debian packaged streamvbyte library
Reviewed-By: Étienne Mollier <emollier@debian.org>
Last-Update: 2024-07-24
Forwarded: not-needed
--- libslow5lib.orig/CMakeLists.txt
+++ libslow5lib/CMakeLists.txt
@@ -38,7 +38,6 @@
# include_directories(${PROJECT_SOURCE_DIR}/src)
# include_directories(${PROJECT_SOURCE_DIR}/test)
# include_directories(${PROJECT_SOURCE_DIR}/include)
-# include_directories(${PROJECT_SOURCE_DIR}/thirdparty/streamvbyte/include)
set(slow5_ src/slow5.c)
set(slow5_idx src/slow5_idx.c)
@@ -54,7 +53,6 @@
# set(openmp_get_reads examples/random_read_openmp.c)
# add_executable(slow5exmp ${openmp_get_reads})
-add_subdirectory(thirdparty/streamvbyte)
option(SLOW5_LINK_STATIC "libslow5 will create a static lib" OFF) #OFF by default
if(SLOW5_LINK_STATIC)
@@ -67,7 +65,7 @@
unset(SLOW5_LINK_STATIC CACHE)
target_include_directories(slow5 PUBLIC ${PROJECT_SOURCE_DIR}/include)
-target_link_libraries(slow5 streamvbyte_slow5)
+target_link_libraries(slow5)
# Build a static lib
#add_library(slow5 STATIC ${slow5_} ${slow5_idx} ${slow5_misc} ${slow5_press})
--- libslow5lib.orig/test/Makefile
+++ libslow5lib/test/Makefile
@@ -4,7 +4,7 @@
CPPFLAGS += -I ../include/ -I $(SRC)/
#CFLAGS += -g -Wall -Werror -Wpedantic -std=c99
CFLAGS += -g -Wall -Werror -std=gnu99
-LDFLAGS += $(LIB)/libslow5.a -lm -lz
+LDFLAGS += $(LIB)/libslow5.a -lm -lz -lstreamvbyte
ifeq ($(zstd),1)
CFLAGS += -DSLOW5_USE_ZSTD
LDFLAGS += -lzstd
--- libslow5lib.orig/src/slow5_press.c
+++ libslow5lib/src/slow5_press.c
@@ -1062,7 +1062,7 @@
static uint8_t *ptr_compress_svb(const uint32_t *ptr, size_t count, size_t *n) {
uint32_t length = count / sizeof *ptr;
- size_t max_n = __slow5_streamvbyte_max_compressedbytes(length);
+ size_t max_n = streamvbyte_max_compressedbytes(length);
uint8_t *out = (uint8_t *) malloc(max_n + sizeof length);
if (!out) {
SLOW5_MALLOC_ERROR();
@@ -1070,7 +1070,7 @@
return NULL;
}
- *n = __slow5_streamvbyte_encode(ptr, length, out + sizeof length);
+ *n = streamvbyte_encode(ptr, length, out + sizeof length);
memcpy(out, &length, sizeof length); /* copy original length of ptr (needed for depress) */
*n = *n + sizeof length;
SLOW5_LOG_DEBUG("max svb bytes=%zu\nsvb bytes=%zu\n",
@@ -1103,7 +1103,7 @@
slow5_errno = SLOW5_ERR_MEM;
return NULL;
}
- __slow5_zigzag_delta_encode(in, diff, length, 0);
+ zigzag_delta_encode(in, diff, length, 0);
SLOW5_LOG_DEBUG("orig bytes=%zu\n", count); /* TESTING */
@@ -1127,7 +1127,7 @@
}
size_t bytes_read;
- if ((bytes_read = __slow5_streamvbyte_decode(ptr + sizeof length, out, length)) != count - sizeof length) {
+ if ((bytes_read = streamvbyte_decode(ptr + sizeof length, out, length)) != count - sizeof length) {
SLOW5_ERROR("Expected streamvbyte_decode to read '%zu' bytes, instead read '%zu' bytes.",
count - sizeof length, bytes_read);
slow5_errno = SLOW5_ERR_PRESS;
@@ -1152,14 +1152,14 @@
}
uint32_t length = *n / sizeof *diff;
- int16_t *orig = (int16_t *) malloc(length * sizeof *orig);
+ int32_t *orig = (int32_t *) malloc(length * sizeof *orig);
if (!orig) {
SLOW5_MALLOC_ERROR();
free(diff);
slow5_errno = SLOW5_ERR_MEM;
return NULL;
}
- __slow5_zigzag_delta_decode(diff, orig, length, 0);
+ zigzag_delta_decode(diff, orig, length, 0);
// int16_t *orig = (int16_t *) malloc(length * sizeof *orig);
// for (int64_t i = 0; i < length; ++ i) {
@@ -1169,7 +1169,7 @@
*n = length * sizeof *orig;
free(diff);
//free(out);
- return orig;
+ return (int16_t*)orig; /* /o\ */
}
@@ -1346,7 +1346,7 @@
return -1;
}
- nr_press_tmp = __slow5_streamvbyte_max_compressedbytes(nex);
+ nr_press_tmp = streamvbyte_max_compressedbytes(nex);
ex_pos_press = (uint8_t *)malloc(nr_press_tmp);
if(!ex_pos_press){
free(ex_pos_delta);
@@ -1357,7 +1357,7 @@
return -1;
}
- nr_press_tmp=__slow5_streamvbyte_encode(ex_pos_delta, nex, ex_pos_press);
+ nr_press_tmp=streamvbyte_encode(ex_pos_delta, nex, ex_pos_press);
free(ex_pos_delta);
nex_pos_press = (uint32_t) nr_press_tmp;
SLOW5_ASSERT(nex_pos_press > 0);
@@ -1372,7 +1372,7 @@
offset += nex_pos_press;
//actual exceptions
- nr_press_tmp = __slow5_streamvbyte_max_compressedbytes(nex);
+ nr_press_tmp = streamvbyte_max_compressedbytes(nex);
ex_press = (uint8_t *)malloc(nr_press_tmp);
if(!ex_press){
free(ex_pos);
@@ -1382,7 +1382,7 @@
return -1;
}
- nr_press_tmp=__slow5_streamvbyte_encode(ex, nex, ex_press);
+ nr_press_tmp=streamvbyte_encode(ex, nex, ex_press);
nex_press = (uint32_t) nr_press_tmp;
SLOW5_ASSERT(nex_press > 0);
@@ -1486,7 +1486,7 @@
(void) memcpy(ex_pos_press, in + offset, nex_pos_press);
offset += nex_pos_press;
- int ret = __slow5_streamvbyte_decode(ex_pos_press, ex_pos, nex);
+ int ret = streamvbyte_decode(ex_pos_press, ex_pos, nex);
if (ret !=nex_pos_press){
SLOW5_ERROR("Expected streamvbyte_decode to read '%d' bytes, instead read '%d' bytes.",
nex_pos_press, ret);
@@ -1516,7 +1516,7 @@
offset += nex_press;
- ret = __slow5_streamvbyte_decode(ex_press, ex, nex);
+ ret = streamvbyte_decode(ex_press, ex, nex);
if (ret != nex_press){
SLOW5_ERROR("Expected streamvbyte_decode to read '%d' bytes, instead read '%d' bytes.",
nex_press, ret);
--- libslow5lib.orig/setup.py
+++ libslow5lib/setup.py
@@ -18,9 +18,9 @@
# for the install.
try:
import numpy as np
- include_dirs = ['include/', np.get_include(), 'thirdparty/streamvbyte/include']
+ include_dirs = ['include/', np.get_include() ]
except ImportError:
- include_dirs = ['include/', 'thirdparty/streamvbyte/include']
+ include_dirs = ['include/']
def np(*args, ** kwargs ):
import numpy as np
return np(*args, ** kwargs)
@@ -38,12 +38,12 @@
sources=['python/pyslow5.pyx', 'src/slow5.c', 'src/slow5_press.c', 'src/slow5_misc.c', 'src/slow5_idx.c',
'src/slow5_mt.c',
- 'thirdparty/streamvbyte/src/streamvbyte_zigzag.c', 'thirdparty/streamvbyte/src/streamvbyte_decode.c', 'thirdparty/streamvbyte/src/streamvbyte_encode.c']
+ ]
depends=['python/pyslow5.pxd', 'python/pyslow5.h',
'slow5/slow5.h', 'slow5/slow5_defs.h', 'slow5/slow5_error.h', 'slow5/slow5_press.h', 'slow5/slow5_lazymt.h',
'slow5/klib/khash.h', 'slow5/klib/kvec.h',
'src/slow5_extra.h', 'src/slow5_idx.h', 'src/slow5_misc.h', 'src/klib/ksort.h',
- 'thirdparty/streamvbyte/include/streamvbyte.h', 'thirdparty/streamvbyte/include/streamvbyte_zigzag.h']
+ ]
extra_compile_args = ['-g', '-Wall', '-O2', '-std=c99', '-DSLOW5_ENABLE_MT=1' ]
# extra_compile_args = []
# os.environ["CFLAGS"] = '-g -Wall -O2 -std=c99'
@@ -58,8 +58,8 @@
extra_compile_args.extend(['-DSTREAMVBYTE_SSSE3=1', '-mssse3']) # WARNING: ancient x86_64 CPUs don't have SSSE3
# note that on macos, for now we just let it compile without simd
-# include_dirs = ['include/', np.get_include(), 'thirdparty/streamvbyte/include']
-libraries = ['m', 'z']
+# include_dirs = ['include/', np.get_include() ]
+libraries = ['m', 'z', 'streamvbyte']
library_dirs = ['.']
# a nasty hack to provide option to build with zstd
|
