ratschlab · adamant-pwn · May 5, 2025 · Mar 21, 2025 · Mar 21, 2025 · May 5, 2025
diff --git a/metagraph/CMakeLists.txt b/metagraph/CMakeLists.txt
@@ -334,6 +334,8 @@ target_compile_options(zlib
     -Wno-implicit-fallthrough
     -Wno-deprecated-non-prototype
     -Wno-unknown-warning-option
+    -Wno-unused-parameter
+    -Wno-maybe-uninitialized
 )
 
 add_library(progress_bar STATIC

diff --git a/metagraph/CMakeListsKMC.txt.in b/metagraph/CMakeListsKMC.txt.in
@@ -2,7 +2,11 @@ cmake_minimum_required(VERSION 2.8.12)
 
 project(KMC)
 
-add_compile_options(-Wall -O3 -m64 -pthread -std=c++11)
+if(CMAKE_SYSTEM_PROCESSOR MATCHES "^(arm|aarch64|arm64)")
+  add_compile_options(-Wall -O3 -pthread -std=c++11)
+else()
+  add_compile_options(-Wall -O3 -m64 -pthread -std=c++11)
+endif()
 
 if(@BUILD_STATIC@)
 string(APPEND CMAKE_CXX_FLAGS " -static ")

diff --git a/metagraph/external-libraries/KMC b/metagraph/external-libraries/KMC
diff --git a/metagraph/external-libraries/sdsl-lite b/metagraph/external-libraries/sdsl-lite
diff --git a/metagraph/external-libraries/zlib b/metagraph/external-libraries/zlib
diff --git a/metagraph/src/common/bloom_filter.cpp b/metagraph/src/common/bloom_filter.cpp
@@ -110,7 +110,8 @@ batch_insert_avx2(BloomFilter &bloom,
     for (; hashes_begin + 4 <= hashes_end; hashes_begin += 4) {
         simde__m256i block_indices
             = restrict_to_mask_epi64(hashes_begin, size, block_mask_out);
-        const uint64_t *block_index_array = reinterpret_cast<const uint64_t*>(&block_indices);
+        alignas(32) uint64_t block_index_array[4];
+        simde_mm256_store_si256(reinterpret_cast<simde__m256i*>(block_index_array), block_indices);
 
         if (num_hash_functions_ > 1) {
             for (size_t j = 0; j < 4; ++j) {
@@ -211,13 +212,13 @@ batch_check_avx2(const BloomFilter &bloom,
     const simde__m256i add = simde_mm256_setr_epi64x(0, 1, 2, 3);
     const simde__m256i numhash = simde_mm256_set1_epi64x(num_hash_functions_);
 
-    simde__m256i block_indices;
-    const uint64_t *block_index_array = reinterpret_cast<const uint64_t*>(&block_indices);
-
     // check four input elements (represented by hashes) at a time
     size_t i = 0;
     for (; hashes_begin + 4 <= hashes_end; hashes_begin += 4) {
-        block_indices = restrict_to_mask_epi64(hashes_begin, size, block_mask_out);
+        simde__m256i block_indices = restrict_to_mask_epi64(hashes_begin, size, block_mask_out);
+        alignas(32) uint64_t block_index_array[4];
+        simde_mm256_store_si256(reinterpret_cast<simde__m256i*>(block_index_array), block_indices);
+
 
         if (num_hash_functions_ > 1) {
             for (size_t j = 0; j < 4; ++j) {

diff --git a/metagraph/src/common/serialization.cpp b/metagraph/src/common/serialization.cpp
@@ -22,6 +22,7 @@
 
 #endif
 
+#include <boost/locale.hpp>
 #include <tsl/hopscotch_map.h>
 #include <sdsl/int_vector.hpp>
 
@@ -171,9 +172,7 @@ template bool load_number_vector<bool>(std::istream &in, std::vector<bool> *);
 void encode_utf8(uint32_t num, std::ostream &out) {
     if (num > 0x7FFFFFFF)
         throw std::runtime_error("Encoding value out of range for code.");
-
-    std::string enc = std::wstring_convert<std::codecvt_utf8<char32_t>,
-                                           char32_t>().to_bytes(num);
+    std::string enc = boost::locale::conv::utf_to_utf<char>(std::u32string(1, num));
     out.write(enc.c_str(), enc.size());
 }
 

diff --git a/metagraph/src/seq_io/sequence_io.cpp b/metagraph/src/seq_io/sequence_io.cpp
@@ -5,6 +5,8 @@
 #include <fstream>
 #include <thread>
 
+#include <unistd.h>
+
 #include "common/seq_tools/reverse_complement.hpp"
 #include "common/utils/string_utils.hpp"
 #include "vcf_parser.hpp"

diff --git a/metagraph/tests/test_utils.cpp b/metagraph/tests/test_utils.cpp
@@ -102,15 +102,15 @@ TEST(Utils, TempFileCheckStateFlow) {
     {
         utils::TempFile tmp;
         ASSERT_TRUE(tmp.ifstream().good());
-        EXPECT_DEBUG_DEATH(tmp.ofstream().good(), "Can't write after reading");
+        EXPECT_DEBUG_DEATH((void)tmp.ofstream().good(), "Can't write after reading");
     }
     {
         utils::TempFile tmp;
         ASSERT_TRUE(tmp.ofstream().good());
         ASSERT_TRUE(tmp.ofstream().good());
         ASSERT_TRUE(tmp.ifstream().good());
         ASSERT_TRUE(tmp.ifstream().good());
-        EXPECT_DEBUG_DEATH(tmp.ofstream().good(), "Can't write after reading");
+        EXPECT_DEBUG_DEATH((void)tmp.ofstream().good(), "Can't write after reading");
     }
 }
+1 −1		kmc_api/kmer_api.cpp
+1 −1		kmc_api/kmer_api.h
+4 −4		kmer_counter/splitter.cpp
+6 −2		.github/workflows/cmake.yml
+3 −1		.github/workflows/make.yml
+19 −0		.github/workflows/rust.yml
+24 −0		.github/workflows/semgrep.yml
+4 −0		.gitignore
+42 −26		CMakeLists.txt
+27 −0		Cargo.toml
+4 −4		ChangeLog
+1 −1		FAQ
+22 −0		LICENSE
+13 −7		Makefile.in
+11 −9		README
+9 −0		README.md
+12 −27		adler32.c
+1 −1		amiga/Makefile.sas
+0 −215		as400/bndsrc
+0 −110		as400/compile.clp
+0 −115		as400/readme.txt
+0 −451		as400/zlib.inc
+52 −0		benches/bench.rs
+74 −1		chunkcopy.h
+29 −34		compress.c
+132 −23		configure
+46 −67		crc32.c
+90 −159		deflate.c
+2 −2		deflate.h
+6 −6		doc/txtvsbin.txt
+5 −0		examples/README.examples
+385 −360		examples/enough.c
+3 −3		examples/fitblk.c
+11 −11		examples/gun.c
+3 −3		examples/gzappend.c
+5 −3		examples/gzlog.c
+1 −1		examples/gzlog.h
+470 −0		examples/gznorm.c
+15 −11		examples/zlib_how.html
+164 −94		examples/zran.c
+40 −0		examples/zran.h
+1 −3		gzclose.c
+42 −38		gzguts.h
+39 −84		gzlib.c
+31 −64		gzread.c
+115 −105		gzwrite.c
+31 −40		infback.c
+20 −23		inffast.c
+1 −1		inffast.h
+61 −42		inffast_chunk.c
+22 −6		inffast_chunk.h
+104 −125		inflate.c
+6 −4		inflate.h
+13 −20		inftrees.c
+4 −4		inftrees.h
+3 −3		make_vms.com
+1 −1		msdos/Makefile.dj2
+1 −1		msdos/Makefile.emx
+1 −1		old/Makefile.emx
+1 −1		old/os2/Makefile.os2
+6 −0		rust/README.md
+125 −0		rust/build.rs
+246 −0		rust/lib.rs
+ −		rust/test_files/test1
+47 −78		test/example.c
+12 −11		test/infcover.c
+39 −81		test/minigzip.c
+1 −1		treebuild.xml
+79 −133		trees.c
+6 −13		uncompr.c
+0 −1		win32/Makefile.bor
+1 −6		win32/Makefile.gcc
+1 −1		win32/README-WIN32.txt
+1 −1		win32/zlib1.rc
+26 −26		zconf.h
+24 −24		zconf.h.cmakein
+24 −24		zconf.h.in
+409 −353		zlib.h
+0 −152		zlib2ansi
+21 −52		zutil.c
+44 −53		zutil.h