Author: Andreas Tille Description: Use Debian packaged streamvbyte library Reviewed-By: Étienne Mollier 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