Flawfinder version 2.0.10, (C) 2001-2019 David A. Wheeler. Number of rules (primarily dangerous function names) in C/C++ ruleset: 223 Examining data/idba-1.1.3/src/graph/hash_graph_path.h Examining data/idba-1.1.3/src/graph/hash_graph_branch_group.cpp Examining data/idba-1.1.3/src/graph/contig_graph_vertex.h Examining data/idba-1.1.3/src/graph/scaffold_graph.h Examining data/idba-1.1.3/src/graph/contig_info.h Examining data/idba-1.1.3/src/graph/hash_graph.h Examining data/idba-1.1.3/src/graph/contig_builder.h Examining data/idba-1.1.3/src/graph/hash_graph_vertex.h Examining data/idba-1.1.3/src/graph/contig_graph.h Examining data/idba-1.1.3/src/graph/vertex_status.h Examining data/idba-1.1.3/src/graph/contig_graph_branch_group.cpp Examining data/idba-1.1.3/src/graph/contig_graph_path.h Examining data/idba-1.1.3/src/graph/contig_graph_branch_group.h Examining data/idba-1.1.3/src/graph/hash_graph.cpp Examining data/idba-1.1.3/src/graph/scaffold_graph_vertex.h Examining data/idba-1.1.3/src/graph/hash_graph_branch_group.h Examining data/idba-1.1.3/src/graph/bit_edges.h Examining data/idba-1.1.3/src/graph/scaffold_graph_path.h Examining data/idba-1.1.3/src/graph/contig_graph.cpp Examining data/idba-1.1.3/src/graph/scaffold_graph.cpp Examining data/idba-1.1.3/src/graph/contig_info.cpp Examining data/idba-1.1.3/src/misc/hash_aligner.cpp Examining data/idba-1.1.3/src/misc/options_description.h Examining data/idba-1.1.3/src/misc/utils.h Examining data/idba-1.1.3/src/misc/utils.cpp Examining data/idba-1.1.3/src/misc/log.cpp Examining data/idba-1.1.3/src/misc/hash_aligner.h Examining data/idba-1.1.3/src/misc/blat_record.h Examining data/idba-1.1.3/src/misc/log.h Examining data/idba-1.1.3/src/misc/blat_record.cpp Examining data/idba-1.1.3/src/misc/options_description.cpp Examining data/idba-1.1.3/src/basic/hash.h Examining data/idba-1.1.3/src/basic/pool.h Examining data/idba-1.1.3/src/basic/histgram.h Examining data/idba-1.1.3/src/basic/math.h Examining data/idba-1.1.3/src/basic/bit_operation.h Examining data/idba-1.1.3/src/basic/math.cpp Examining data/idba-1.1.3/src/basic/kmer.h Examining data/idba-1.1.3/src/basic/functional.h Examining data/idba-1.1.3/src/basic/atomic_integer.h Examining data/idba-1.1.3/src/sequence/sequence_reader.h Examining data/idba-1.1.3/src/sequence/sequence_io.h Examining data/idba-1.1.3/src/sequence/sequence_writer.h Examining data/idba-1.1.3/src/sequence/sequence.h Examining data/idba-1.1.3/src/sequence/short_sequence.cpp Examining data/idba-1.1.3/src/sequence/compact_sequence.h Examining data/idba-1.1.3/src/sequence/sequence_reader.cpp Examining data/idba-1.1.3/src/sequence/read_library.h Examining data/idba-1.1.3/src/sequence/sequence_io.cpp Examining data/idba-1.1.3/src/sequence/compact_sequence.cpp Examining data/idba-1.1.3/src/sequence/sequence_writer.cpp Examining data/idba-1.1.3/src/sequence/short_sequence.h Examining data/idba-1.1.3/src/sequence/sequence.cpp Examining data/idba-1.1.3/src/tools/sample_reads.cpp Examining data/idba-1.1.3/src/tools/parallel_rna_blat.cpp Examining data/idba-1.1.3/src/tools/test.cpp Examining data/idba-1.1.3/src/tools/sort_reads.cpp Examining data/idba-1.1.3/src/tools/filter_contigs.cpp Examining data/idba-1.1.3/src/tools/filter_blat.cpp Examining data/idba-1.1.3/src/tools/scaffold.cpp Examining data/idba-1.1.3/src/tools/sort_psl.cpp Examining data/idba-1.1.3/src/tools/validate_reads_blat.cpp Examining data/idba-1.1.3/src/tools/validate_contigs_mummer.cpp Examining data/idba-1.1.3/src/tools/split_fa.cpp Examining data/idba-1.1.3/src/tools/validate_component.cpp Examining data/idba-1.1.3/src/tools/shuffle_reads.cpp Examining data/idba-1.1.3/src/tools/idba_tran_test.cpp Examining data/idba-1.1.3/src/tools/split_fq.cpp Examining data/idba-1.1.3/src/tools/validate_rna.cpp Examining data/idba-1.1.3/src/tools/fa2fq.cpp Examining data/idba-1.1.3/src/tools/print_graph.cpp Examining data/idba-1.1.3/src/container/hash_set.h Examining data/idba-1.1.3/src/container/hash_map.h Examining data/idba-1.1.3/src/container/hash_table.h Examining data/idba-1.1.3/src/container/managed_list.h Examining data/idba-1.1.3/src/assembly/assembly_utility.h Examining data/idba-1.1.3/src/assembly/local_assembler.h Examining data/idba-1.1.3/src/assembly/local_assembler.cpp Examining data/idba-1.1.3/src/assembly/assembly_utility.cpp Examining data/idba-1.1.3/src/release/split_scaffold.cpp Examining data/idba-1.1.3/src/release/fq2fa.cpp Examining data/idba-1.1.3/src/release/validate_contigs_blat.cpp Examining data/idba-1.1.3/src/release/parallel_blat.cpp Examining data/idba-1.1.3/src/release/idba_hybrid.cpp Examining data/idba-1.1.3/src/release/sim_reads_tran.cpp Examining data/idba-1.1.3/src/release/idba_ud.cpp Examining data/idba-1.1.3/src/release/filterfa.cpp Examining data/idba-1.1.3/src/release/idba_tran.cpp Examining data/idba-1.1.3/src/release/idba.cpp Examining data/idba-1.1.3/src/release/raw_n50.cpp Examining data/idba-1.1.3/src/release/sim_reads.cpp Examining data/idba-1.1.3/src/test/sequence_unittest.cpp Examining data/idba-1.1.3/src/test/histgram_unittest.cpp Examining data/idba-1.1.3/src/test/kmer_unittest.cpp Examining data/idba-1.1.3/src/test/bit_edges_unittest.cpp Examining data/idba-1.1.3/src/test/managed_list_unittest.cpp Examining data/idba-1.1.3/src/test/hash_table_unittest.cpp Examining data/idba-1.1.3/src/test/vertex_status_unittest.cpp Examining data/idba-1.1.3/src/test/short_sequence_unittest.cpp Examining data/idba-1.1.3/src/test/compact_sequence_unittest.cpp Examining data/idba-1.1.3/src/test/hash_set_unittest.cpp Examining data/idba-1.1.3/src/test/atomic_integer_unittest.cpp Examining data/idba-1.1.3/src/test/hash_map_unittest.cpp Examining data/idba-1.1.3/gtest_src/gtest/gtest_main.cc Examining data/idba-1.1.3/gtest_src/gtest/gtest-all.cc Examining data/idba-1.1.3/gtest_src/gtest/gtest.h FINAL RESULTS: data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:1440:10: [4] (format) vsnprintf: If format strings can be influenced by an attacker, they can be exploited, and note that sprintf variations do not always \0-terminate (CWE-134). Use a constant for the format specification. # define vsnprintf _vsnprintf data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:2144:12: [4] (buffer) StrNCpy: Does not check for buffer overflows when copying to destination [MS-banned] (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy easily misused). posix::StrNCpy(clone, str, length); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:2764:12: [4] (buffer) StrNCpy: Does not check for buffer overflows when copying to destination [MS-banned] (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy easily misused). posix::StrNCpy( data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:3017:20: [4] (format) vsnprintf: If format strings can be influenced by an attacker, they can be exploited, and note that sprintf variations do not always \0-terminate (CWE-134). Use a constant for the format specification. const int size = vsnprintf(buffer, kBufferSize, format, args); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:3021:20: [4] (format) vsnprintf: If format strings can be influenced by an attacker, they can be exploited, and note that sprintf variations do not always \0-terminate (CWE-134). Use a constant for the format specification. const int size = vsnprintf(buffer, kBufferSize, format, args); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:3938:5: [4] (format) vprintf: If format strings can be influenced by an attacker, they can be exploited (CWE-134). Use a constant for the format specification. vprintf(fmt, args); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:3957:3: [4] (format) vprintf: If format strings can be influenced by an attacker, they can be exploited (CWE-134). Use a constant for the format specification. vprintf(fmt, args); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:3964:3: [4] (format) vprintf: If format strings can be influenced by an attacker, they can be exploited (CWE-134). Use a constant for the format specification. vprintf(fmt, args); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:8605:10: [4] (format) snprintf: If format strings can be influenced by an attacker, they can be exploited, and note that sprintf variations do not always \0-terminate (CWE-134). Use a constant for the format specification. # define snprintf _snprintf data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:8605:19: [4] (format) _snprintf: If format strings can be influenced by an attacker, they can be exploited, and note that sprintf variations do not always \0-terminate (CWE-134). Use a constant for the format specification. # define snprintf _snprintf data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:8607:10: [4] (format) snprintf: If format strings can be influenced by an attacker, they can be exploited, and note that sprintf variations do not always \0-terminate (CWE-134). Use a constant for the format specification. # define snprintf _snprintf_s data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:8609:10: [4] (format) snprintf: If format strings can be influenced by an attacker, they can be exploited, and note that sprintf variations do not always \0-terminate (CWE-134). Use a constant for the format specification. # define snprintf _snprintf data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:8609:19: [4] (format) _snprintf: If format strings can be influenced by an attacker, they can be exploited, and note that sprintf variations do not always \0-terminate (CWE-134). Use a constant for the format specification. # define snprintf _snprintf data/idba-1.1.3/gtest_src/gtest/gtest.h:2671:20: [4] (buffer) StrNCpy: Does not check for buffer overflows when copying to destination [MS-banned] (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy easily misused). inline const char* StrNCpy(char* dest, const char* src, size_t n) { data/idba-1.1.3/gtest_src/gtest/gtest.h:8110:5: [4] (format) fprintf: If format strings can be influenced by an attacker, they can be exploited (CWE-134). Use a constant for the format specification. fprintf(\ data/idba-1.1.3/src/misc/utils.cpp:36:5: [4] (format) vsprintf: Potential format string problem (CWE-134). Make format string constant. vsprintf(buffer, fmt, ap); data/idba-1.1.3/src/release/parallel_blat.cpp:47:5: [4] (shell) system: This causes a new program to execute and is difficult to use safely (CWE-78). try using a library call that implements the same functionality if available. system(cmd.c_str()); data/idba-1.1.3/src/release/parallel_blat.cpp:53:5: [4] (shell) system: This causes a new program to execute and is difficult to use safely (CWE-78). try using a library call that implements the same functionality if available. system(cmd.c_str()); data/idba-1.1.3/src/release/parallel_blat.cpp:59:5: [4] (shell) system: This causes a new program to execute and is difficult to use safely (CWE-78). try using a library call that implements the same functionality if available. system(cmd.c_str()); data/idba-1.1.3/src/release/parallel_blat.cpp:96:13: [4] (shell) system: This causes a new program to execute and is difficult to use safely (CWE-78). try using a library call that implements the same functionality if available. system(cmd.c_str()); data/idba-1.1.3/src/release/sim_reads_tran.cpp:89:9: [4] (buffer) fscanf: The scanf() family's %s operation, without a limit specification, permits buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a different input function. fscanf(flist, "%s %lf", buf, &weight[i]); data/idba-1.1.3/src/release/validate_contigs_blat.cpp:131:21: [4] (buffer) sscanf: The scanf() family's %s operation, without a limit specification, permits buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a different input function. sscanf(tmp.c_str(), "%s %d", buf, &size); data/idba-1.1.3/src/release/validate_contigs_blat.cpp:388:13: [4] (buffer) fscanf: The scanf() family's %s operation, without a limit specification, permits buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a different input function. fscanf(flist, "%s %lf", buf, &coverage[i]); data/idba-1.1.3/src/tools/parallel_rna_blat.cpp:47:5: [4] (shell) system: This causes a new program to execute and is difficult to use safely (CWE-78). try using a library call that implements the same functionality if available. system(cmd.c_str()); data/idba-1.1.3/src/tools/parallel_rna_blat.cpp:53:5: [4] (shell) system: This causes a new program to execute and is difficult to use safely (CWE-78). try using a library call that implements the same functionality if available. system(cmd.c_str()); data/idba-1.1.3/src/tools/parallel_rna_blat.cpp:59:5: [4] (shell) system: This causes a new program to execute and is difficult to use safely (CWE-78). try using a library call that implements the same functionality if available. system(cmd.c_str()); data/idba-1.1.3/src/tools/parallel_rna_blat.cpp:96:13: [4] (shell) system: This causes a new program to execute and is difficult to use safely (CWE-78). try using a library call that implements the same functionality if available. system(cmd.c_str()); data/idba-1.1.3/src/tools/validate_component.cpp:69:12: [4] (buffer) fscanf: The scanf() family's %s operation, without a limit specification, permits buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a different input function. while (fscanf(ffound_list, "%s %lf", buf, &cover) != EOF) data/idba-1.1.3/src/tools/validate_component.cpp:89:9: [4] (buffer) sscanf: The scanf() family's %s operation, without a limit specification, permits buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a different input function. sscanf(tmp.c_str(), "%s", buf); data/idba-1.1.3/src/tools/validate_component.cpp:103:9: [4] (buffer) sscanf: The scanf() family's %s operation, without a limit specification, permits buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a different input function. sscanf(tmp.c_str(), "%s %d", buf, &id); data/idba-1.1.3/src/tools/validate_component.cpp:206:13: [4] (buffer) sscanf: The scanf() family's %s operation, without a limit specification, permits buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a different input function. sscanf(tmp.c_str(), "%s", buf); data/idba-1.1.3/src/tools/validate_component.cpp:297:29: [4] (buffer) sscanf: The scanf() family's %s operation, without a limit specification, permits buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a different input function. sscanf(tmp.c_str(), "%s", buf); data/idba-1.1.3/src/tools/validate_component.cpp:323:9: [4] (buffer) sscanf: The scanf() family's %s operation, without a limit specification, permits buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a different input function. sscanf(tmp.c_str(), "%s", buf); data/idba-1.1.3/src/tools/validate_contigs_mummer.cpp:233:9: [4] (buffer) sscanf: The scanf() family's %s operation, without a limit specification, permits buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a different input function. sscanf(line, "%d %d %s %d %d %s %s %s %s %lf %s %s %s", data/idba-1.1.3/src/tools/validate_rna.cpp:135:21: [4] (buffer) sscanf: The scanf() family's %s operation, without a limit specification, permits buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a different input function. sscanf(tmp.c_str(), "%s %d", buf, &size); data/idba-1.1.3/src/tools/validate_rna.cpp:396:13: [4] (buffer) fscanf: The scanf() family's %s operation, without a limit specification, permits buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a different input function. fscanf(flist, "%s %lf", buf, &coverage[i]); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:700:37: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. void ShuffleRange(internal::Random* random, int begin, int end, data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:721:39: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. inline void Shuffle(internal::Random* random, std::vector<E>* v) { data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:722:16: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. ShuffleRange(random, 0, static_cast<int>(v->size()), v); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:1172:21: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. internal::Random* random() { return &random_; } data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:3767:47: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. void TestCase::ShuffleTests(internal::Random* random) { data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:3768:11: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. Shuffle(random, &test_indices_); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:5519:7: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. random()->Reseed(random_seed_); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:5790:16: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. ShuffleRange(random(), 0, last_death_test_case_ + 1, &test_case_indices_); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:5793:16: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. ShuffleRange(random(), last_death_test_case_ + 1, data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:5798:34: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. test_cases_[i]->ShuffleTests(random()); data/idba-1.1.3/gtest_src/gtest/gtest.h:2709:27: [3] (buffer) getenv: Environment variables are untrustable input if they can be set by an attacker. They can have any content and length, and the same variable can be set more than once (CWE-807, CWE-20). Check environment variables carefully before using them. const char* const env = getenv(name); data/idba-1.1.3/gtest_src/gtest/gtest.h:2712:10: [3] (buffer) getenv: Environment variables are untrustable input if they can be set by an attacker. They can have any content and length, and the same variable can be set more than once (CWE-807, CWE-20). Check environment variables carefully before using them. return getenv(name); data/idba-1.1.3/gtest_src/gtest/gtest.h:17891:39: [3] (random) random: This function is not sufficiently random for security-related functions such as key and nonce creation (CWE-327). Use a more secure technique for acquiring random values. void ShuffleTests(internal::Random* random); data/idba-1.1.3/src/misc/options_description.cpp:69:18: [3] (buffer) getopt_long: Some older implementations do not protect against internal buffer overflows (CWE-120, CWE-20). Check implementation on installation, or limit the size of all string inputs. int ch = getopt_long(argc, argv, short_options.c_str(), long_options, &index); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:2167:7: [2] (buffer) MultiByteToWideChar: Requires maximum length in CHARACTERS, not bytes (CWE-120). MultiByteToWideChar(CP_ACP, 0, ansi, length, data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:2170:3: [2] (buffer) MultiByteToWideChar: Requires maximum length in CHARACTERS, not bytes (CWE-120). MultiByteToWideChar(CP_ACP, 0, ansi, length, data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:2658:3: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char error_text[kBufSize] = { '\0' }; data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:2826:5: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char buffer[32]; // CodePointToUtf8 requires a buffer this big. data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:3008:3: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char buffer[4096]; data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:6471:3: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char buffer[256]; data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:6890:3: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char executable_path[_MAX_PATH + 1]; // NOLINT data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:7534:3: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char cwd[GTEST_PATH_MAX_ + 1] = { '\0' }; data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:7537:3: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char cwd[GTEST_PATH_MAX_ + 1] = { '\0' }; data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:8218:3: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(buffer, regex, len); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:8296:5: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char temp_dir_path[MAX_PATH + 1] = { '\0' }; // NOLINT data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:8297:5: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char temp_file_path[MAX_PATH + 1] = { '\0' }; // NOLINT data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:8315:29: [2] (tmpfile) mkstemp: Potential for temporary file vulnerability in some circumstances. Some older Unix-like systems create temp files with permission to write by all by default, so be sure to set the umask to override this. Also, some older Unix systems might fail to use O_EXCL when opening the file, so make sure that O_EXCL is used by the library (CWE-377). const int captured_fd = mkstemp(name_template); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:8615:3: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char text[5] = ""; data/idba-1.1.3/gtest_src/gtest/gtest.h:2683:10: [2] (misc) fopen: Check when opening files - can an attacker redirect it (via symlinks), force the opening of special file type (e.g., device files), move things around to create a race condition, control its ancestors, or change its contents? (CWE-362). return fopen(path, mode); data/idba-1.1.3/gtest_src/gtest/gtest.h:3154:5: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. memcpy(str, buffer, a_length); data/idba-1.1.3/src/basic/kmer.h:32:12: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. { std::memcpy(data_, kmer.data_, sizeof(uint64_t) * kNumUint64); } data/idba-1.1.3/src/basic/kmer.h:40:12: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. { std::memcpy(data_, kmer.data_, sizeof(uint64_t) * kNumUint64); return *this; } data/idba-1.1.3/src/misc/options_description.cpp:191:35: [2] (integer) atoi: Unless checked, the resulting number can exceed the expected range (CWE-190). If source untrusted, check both minimum and maximum, even if the input had no minus sign (large numbers can roll over into negative number; consider saving to an unsigned value if that is intended). *(int *)pointer = atoi(value.c_str()); data/idba-1.1.3/src/misc/utils.cpp:30:8: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. static char buffer[kMaxLine]; data/idba-1.1.3/src/misc/utils.cpp:44:16: [2] (misc) fopen: Check when opening files - can an attacker redirect it (via symlinks), force the opening of special file type (e.g., device files), move things around to create a race condition, control its ancestors, or change its contents? (CWE-362). FILE *fp = fopen(filename.c_str(), "rb"); data/idba-1.1.3/src/misc/utils.cpp:58:16: [2] (misc) fopen: Check when opening files - can an attacker redirect it (via symlinks), force the opening of special file type (e.g., device files), move things around to create a race condition, control its ancestors, or change its contents? (CWE-362). FILE *fp = fopen(filename.c_str(), mode.c_str()); data/idba-1.1.3/src/release/parallel_blat.cpp:41:1: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char line[MaxLine]; data/idba-1.1.3/src/release/parallel_blat.cpp:42:1: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char buf[MaxLine]; data/idba-1.1.3/src/release/sim_reads_tran.cpp:48:1: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char buf[1000]; data/idba-1.1.3/src/release/sim_reads_tran.cpp:49:1: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char line[1000]; data/idba-1.1.3/src/release/validate_contigs_blat.cpp:27:1: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char line[MaxLine]; data/idba-1.1.3/src/release/validate_contigs_blat.cpp:28:1: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char buf[MaxLine]; data/idba-1.1.3/src/sequence/short_sequence.h:47:12: [2] (buffer) memcpy: Does not check for buffer overflows when copying to destination (CWE-120). Make sure destination can always hold the source data. { std::memcpy(data_, short_seq.data_, kNumBytes); return *this; } data/idba-1.1.3/src/tools/filter_blat.cpp:27:1: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char line[MaxLine]; data/idba-1.1.3/src/tools/filter_blat.cpp:28:1: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char buf[MaxLine]; data/idba-1.1.3/src/tools/parallel_rna_blat.cpp:41:1: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char line[MaxLine]; data/idba-1.1.3/src/tools/parallel_rna_blat.cpp:42:1: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char buf[MaxLine]; data/idba-1.1.3/src/tools/scaffold.cpp:361:5: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char line[MaxLine]; data/idba-1.1.3/src/tools/sort_psl.cpp:27:1: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char line[MaxLine]; data/idba-1.1.3/src/tools/sort_psl.cpp:28:1: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char buf[MaxLine]; data/idba-1.1.3/src/tools/sort_psl.cpp:67:17: [2] (misc) fopen: Check when opening files - can an attacker redirect it (via symlinks), force the opening of special file type (e.g., device files), move things around to create a race condition, control its ancestors, or change its contents? (CWE-362). FILE *fin = fopen(argv[1], "rb"); data/idba-1.1.3/src/tools/sort_psl.cpp:68:18: [2] (misc) fopen: Check when opening files - can an attacker redirect it (via symlinks), force the opening of special file type (e.g., device files), move things around to create a race condition, control its ancestors, or change its contents? (CWE-362). FILE *fout = fopen(argv[2], "wb"); data/idba-1.1.3/src/tools/validate_component.cpp:28:1: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char line[MaxLine]; data/idba-1.1.3/src/tools/validate_component.cpp:29:1: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char buf[MaxLine]; data/idba-1.1.3/src/tools/validate_contigs_mummer.cpp:33:1: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char line[MaxLine]; data/idba-1.1.3/src/tools/validate_contigs_mummer.cpp:34:1: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char buf[MaxLine]; data/idba-1.1.3/src/tools/validate_contigs_mummer.cpp:35:1: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char ref_name_buf[MaxLine]; data/idba-1.1.3/src/tools/validate_contigs_mummer.cpp:36:1: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char query_name_buf[MaxLine]; data/idba-1.1.3/src/tools/validate_reads_blat.cpp:28:1: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char line[MaxLine]; data/idba-1.1.3/src/tools/validate_reads_blat.cpp:29:1: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char buf[MaxLine]; data/idba-1.1.3/src/tools/validate_rna.cpp:27:1: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char line[MaxLine]; data/idba-1.1.3/src/tools/validate_rna.cpp:28:1: [2] (buffer) char: Statically-sized arrays can be improperly restricted, leading to potential overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use functions that limit length, or ensure that the size is larger than the maximum possible length. char buf[MaxLine]; data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:2155:47: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). NULL : CloneString(c_str, strlen(c_str)); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:2165:22: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). const int length = strlen(ansi); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:2810:34: [1] (buffer) wcslen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). num_chars = static_cast<int>(wcslen(str)); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:2975:27: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). const size_t this_len = strlen(c_str()); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:2976:29: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). const size_t suffix_len = strlen(suffix); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:2988:27: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). const size_t this_len = strlen(c_str()); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:2989:29: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). const size_t suffix_len = strlen(suffix); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:4517:32: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). segment = next_segment + strlen("]]>"); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:4746:18: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). result.reserve(strlen(str) + 1); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:5851:29: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). const size_t prefix_len = strlen(prefix); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:7952:33: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). const size_t full_regex_len = strlen(regex) + 10; data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:8206:22: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). const size_t len = strlen(regex); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:8854:29: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). PrintCharsAsStringTo(s, strlen(s), os); data/idba-1.1.3/gtest_src/gtest/gtest-all.cc:8871:33: [1] (buffer) wcslen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). PrintWideCharsAsStringTo(s, wcslen(s), os); data/idba-1.1.3/gtest_src/gtest/gtest.h:2672:10: [1] (buffer) strncpy: Easily used incorrectly; doesn't always \0-terminate or check for invalid pointers [MS-banned] (CWE-120). return strncpy(dest, src, n); data/idba-1.1.3/gtest_src/gtest/gtest.h:2694:27: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). return static_cast<int>(read(fd, buf, count)); data/idba-1.1.3/gtest_src/gtest/gtest.h:3050:33: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). ConstructNonNull(a_c_str, strlen(a_c_str)); data/idba-1.1.3/src/container/hash_table.h:651:15: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). while (is.read((char *)&value, sizeof(Value))) data/idba-1.1.3/src/graph/contig_info.cpp:15:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). is.read((char *)&contig_info.in_edges_, sizeof(BitEdges)); data/idba-1.1.3/src/graph/contig_info.cpp:16:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). is.read((char *)&contig_info.out_edges_, sizeof(BitEdges)); data/idba-1.1.3/src/graph/contig_info.cpp:17:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). is.read((char *)&contig_info.kmer_size_, sizeof(uint16_t)); data/idba-1.1.3/src/graph/contig_info.cpp:18:8: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). is.read((char *)&contig_info.kmer_count_, sizeof(uint32_t)); data/idba-1.1.3/src/graph/contig_info.cpp:21:13: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). if (!is.read((char *)&size, sizeof(int))) data/idba-1.1.3/src/graph/contig_info.cpp:26:12: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). is.read((char *)&contig_info.counts_[i], sizeof(SequenceCountUnitType)); data/idba-1.1.3/src/graph/hash_graph.h:96:82: [1] (access) umask: Ensure that umask is given most restrictive possible setting (e.g., 066 or 077) (CWE-732). int64_t InsertKmersWithPrefix(const Sequence &seq, uint64_t prefix, uint64_t umask); data/idba-1.1.3/src/misc/hash_aligner.cpp:463:13: [1] (buffer) mismatch: Function does not check the second iterator for over-read conditions (CWE-126). This function is often discouraged by most C++ coding standards in favor of its safer alternatives provided since C++14. Consider using a form of this function that checks the second iterator before potentially overflowing it. if (mismatch > max_mismatch) data/idba-1.1.3/src/misc/hash_aligner.cpp:470:36: [1] (buffer) mismatch: Function does not check the second iterator for over-read conditions (CWE-126). This function is often discouraged by most C++ coding standards in favor of its safer alternatives provided since C++14. Consider using a form of this function that checks the second iterator before potentially overflowing it. record.match_length = length - mismatch; data/idba-1.1.3/src/misc/hash_aligner.cpp:518:23: [1] (buffer) mismatch: Function does not check the second iterator for over-read conditions (CWE-126). This function is often discouraged by most C++ coding standards in favor of its safer alternatives provided since C++14. Consider using a form of this function that checks the second iterator before potentially overflowing it. ++mismatch; data/idba-1.1.3/src/misc/hash_aligner.cpp:525:23: [1] (buffer) mismatch: Function does not check the second iterator for over-read conditions (CWE-126). This function is often discouraged by most C++ coding standards in favor of its safer alternatives provided since C++14. Consider using a form of this function that checks the second iterator before potentially overflowing it. ++mismatch; data/idba-1.1.3/src/misc/hash_aligner.cpp:530:17: [1] (buffer) mismatch: Function does not check the second iterator for over-read conditions (CWE-126). This function is often discouraged by most C++ coding standards in favor of its safer alternatives provided since C++14. Consider using a form of this function that checks the second iterator before potentially overflowing it. if (mismatch > 3) data/idba-1.1.3/src/misc/hash_aligner.cpp:545:9: [1] (buffer) mismatch: Function does not check the second iterator for over-read conditions (CWE-126). This function is often discouraged by most C++ coding standards in favor of its safer alternatives provided since C++14. Consider using a form of this function that checks the second iterator before potentially overflowing it. if (mismatch >= max_mismatch) data/idba-1.1.3/src/misc/hash_aligner.cpp:561:19: [1] (buffer) mismatch: Function does not check the second iterator for over-read conditions (CWE-126). This function is often discouraged by most C++ coding standards in favor of its safer alternatives provided since C++14. Consider using a form of this function that checks the second iterator before potentially overflowing it. ++mismatch; data/idba-1.1.3/src/misc/hash_aligner.cpp:566:17: [1] (buffer) mismatch: Function does not check the second iterator for over-read conditions (CWE-126). This function is often discouraged by most C++ coding standards in favor of its safer alternatives provided since C++14. Consider using a form of this function that checks the second iterator before potentially overflowing it. if (mismatch > max_mismatch) data/idba-1.1.3/src/misc/hash_aligner.cpp:572:23: [1] (buffer) mismatch: Function does not check the second iterator for over-read conditions (CWE-126). This function is often discouraged by most C++ coding standards in favor of its safer alternatives provided since C++14. Consider using a form of this function that checks the second iterator before potentially overflowing it. --mismatch; data/idba-1.1.3/src/misc/log.cpp:120:19: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). while ((len = read(log_thread.in_fd, line, kMaxLine)) > 0) data/idba-1.1.3/src/release/sim_reads.cpp:34:30: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). int SimulateErrors(Sequence &read); data/idba-1.1.3/src/release/sim_reads_tran.cpp:34:30: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). int SimulateErrors(Sequence &read); data/idba-1.1.3/src/tools/sample_reads.cpp:34:30: [1] (buffer) read: Check buffer boundaries if used in a loop including recursive loops (CWE-120, CWE-20). int SimulateErrors(Sequence &read); data/idba-1.1.3/src/tools/validate_reads_blat.cpp:122:31: [1] (buffer) strlen: Does not handle strings that are not \0-terminated; if given one it may perform an over-read (it could cause a crash if unprotected) (CWE-126). fseek(fblat, -strlen(line), SEEK_CUR); ANALYSIS SUMMARY: Hits = 137 Lines analyzed = 52529 in approximately 1.24 seconds (42318 lines/second) Physical Source Lines of Code (SLOC) = 36571 Hits@level = [0] 92 [1] 39 [2] 48 [3] 14 [4] 36 [5] 0 Hits@level+ = [0+] 229 [1+] 137 [2+] 98 [3+] 50 [4+] 36 [5+] 0 Hits/KSLOC@level+ = [0+] 6.26179 [1+] 3.74614 [2+] 2.67972 [3+] 1.3672 [4+] 0.984387 [5+] 0 Dot directories skipped = 1 (--followdotdir overrides) Minimum risk level = 1 Not every hit is necessarily a security vulnerability. There may be other security vulnerabilities; review your code! See 'Secure Programming HOWTO' (https://dwheeler.com/secure-programs) for more information.