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/rapmap-0.15.0+dfsg/include/BooMap.hpp
Examining data/rapmap-0.15.0+dfsg/include/BooPHF.hpp
Examining data/rapmap-0.15.0+dfsg/include/Const.hpp
Examining data/rapmap-0.15.0+dfsg/include/EnumCoder.hpp
Examining data/rapmap-0.15.0+dfsg/include/FastxParser.hpp
Examining data/rapmap-0.15.0+dfsg/include/FrugalBooMap.hpp
Examining data/rapmap-0.15.0+dfsg/include/HitManager.hpp
Examining data/rapmap-0.15.0+dfsg/include/IndexHeader.hpp
Examining data/rapmap-0.15.0+dfsg/include/JFRaw.hpp
Examining data/rapmap-0.15.0+dfsg/include/Kmer.hpp
Examining data/rapmap-0.15.0+dfsg/include/PairAlignmentFormatter.hpp
Examining data/rapmap-0.15.0+dfsg/include/PairSequenceParser.hpp
Examining data/rapmap-0.15.0+dfsg/include/RapMapConfig.hpp
Examining data/rapmap-0.15.0+dfsg/include/RapMapFileSystem.hpp
Examining data/rapmap-0.15.0+dfsg/include/RapMapIndex.hpp
Examining data/rapmap-0.15.0+dfsg/include/RapMapSAIndex.hpp
Examining data/rapmap-0.15.0+dfsg/include/RapMapUtils.hpp
Examining data/rapmap-0.15.0+dfsg/include/SACollector.hpp
Examining data/rapmap-0.15.0+dfsg/include/SASearcher.hpp
Examining data/rapmap-0.15.0+dfsg/include/ScopedTimer.hpp
Examining data/rapmap-0.15.0+dfsg/include/SelectiveAlignmentUtils.hpp
Examining data/rapmap-0.15.0+dfsg/include/SingleAlignmentFormatter.hpp
Examining data/rapmap-0.15.0+dfsg/include/SparseHashSerializer.hpp
Examining data/rapmap-0.15.0+dfsg/include/SpinLock.hpp
Examining data/rapmap-0.15.0+dfsg/include/Type.hpp
Examining data/rapmap-0.15.0+dfsg/include/Util.hpp
Examining data/rapmap-0.15.0+dfsg/include/bar.h
Examining data/rapmap-0.15.0+dfsg/include/bit_array.h
Examining data/rapmap-0.15.0+dfsg/include/bit_macros.h
Examining data/rapmap-0.15.0+dfsg/include/btree/btree.h
Examining data/rapmap-0.15.0+dfsg/include/btree/btree_container.h
Examining data/rapmap-0.15.0+dfsg/include/btree/btree_map.h
Examining data/rapmap-0.15.0+dfsg/include/chobo/small_vector.hpp
Examining data/rapmap-0.15.0+dfsg/include/concurrentqueue.h
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/blake.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/blake2.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/blake2_provider.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/blake_provider.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/constants/blake2_constants.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/constants/blake_constants.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/constants/groestl_constants.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/constants/jh_constants.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/constants/kupyna_constants.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/constants/md5_constants.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/constants/sha1_constants.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/constants/sha2_constants.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/constants/sha3_constants.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/constants/skein_constants.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/constants/streebog_constants.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/constants/whirlpool_constants.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/groestl_provider.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/jh_provider.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/k12m14_provider.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/kmac_provider.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/kupyna_provider.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/md5_provider.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha1_provider.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha2_provider.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha3_provider.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/shake_provider.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/skein_provider.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sm3_provider.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/streebog_provider.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/whirlpool_provider.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/groestl.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/jh.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/k12m14.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/kmac.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/kupyna.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/md5.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/mixin/blake2_mixin.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/mixin/blake_mixin.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/mixin/cshake_mixin.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/mixin/k12m14_mixin.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/mixin/kmac_mixin.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/mixin/null_mixin.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/mixin/skein_mixin.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/sha1.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/sha2.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/sha3.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/shake.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/skein.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/sm3.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/streebog.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/whirlpool.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/detail/absorb_data.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/detail/functions.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/detail/stream_width_fixer.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/detail/traits.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/detail/validate_hash_size.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/digestpp.hpp
Examining data/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp
Examining data/rapmap-0.15.0+dfsg/include/edlib.h
Examining data/rapmap-0.15.0+dfsg/include/kseq.h
Examining data/rapmap-0.15.0+dfsg/include/ksw2pp/KSW2Aligner.hpp
Examining data/rapmap-0.15.0+dfsg/include/ksw2pp/kalloc.h
Examining data/rapmap-0.15.0+dfsg/include/ksw2pp/ksw2.h
Examining data/rapmap-0.15.0+dfsg/include/macros.h
Examining data/rapmap-0.15.0+dfsg/include/metro/metrohash.h
Examining data/rapmap-0.15.0+dfsg/include/metro/metrohash128.h
Examining data/rapmap-0.15.0+dfsg/include/metro/metrohash128crc.h
Examining data/rapmap-0.15.0+dfsg/include/metro/metrohash64.h
Examining data/rapmap-0.15.0+dfsg/include/metro/platform.h
Examining data/rapmap-0.15.0+dfsg/include/metro/testvector.h
Examining data/rapmap-0.15.0+dfsg/include/nonstd/optional.hpp
Examining data/rapmap-0.15.0+dfsg/include/nonstd/string_view.hpp
Examining data/rapmap-0.15.0+dfsg/include/picosha2.h
Examining data/rapmap-0.15.0+dfsg/include/rank9b.h
Examining data/rapmap-0.15.0+dfsg/include/sparsepp/spp.h
Examining data/rapmap-0.15.0+dfsg/include/sparsepp/spp_config.h
Examining data/rapmap-0.15.0+dfsg/include/sparsepp/spp_dlalloc.h
Examining data/rapmap-0.15.0+dfsg/include/sparsepp/spp_memory.h
Examining data/rapmap-0.15.0+dfsg/include/sparsepp/spp_smartptr.h
Examining data/rapmap-0.15.0+dfsg/include/sparsepp/spp_stdint.h
Examining data/rapmap-0.15.0+dfsg/include/sparsepp/spp_timer.h
Examining data/rapmap-0.15.0+dfsg/include/sparsepp/spp_traits.h
Examining data/rapmap-0.15.0+dfsg/include/sparsepp/spp_utils.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/async_logger.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/common.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/details/async_logger_impl.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/details/file_helper.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/details/log_msg.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/details/logger_impl.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/details/mpmc_bounded_q.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/details/null_mutex.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/details/os.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/details/pattern_formatter_impl.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/details/registry.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/details/spdlog_impl.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/details/async_log_helper.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/container.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/format.cc
Examining data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/format.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/ostream.cc
Examining data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/ostream.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/posix.cc
Examining data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/posix.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.cc
Examining data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/string.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/time.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/fmt/fmt.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/fmt/ostr.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/formatter.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/logger.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/sinks/android_sink.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/sinks/ansicolor_sink.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/sinks/base_sink.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/sinks/dist_sink.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/sinks/file_sinks.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/sinks/msvc_sink.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/sinks/null_sink.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/sinks/ostream_sink.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/sinks/sink.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/sinks/stdout_sinks.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/sinks/syslog_sink.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/sinks/wincolor_sink.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/sinks/windebug_sink.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/spdlog.h
Examining data/rapmap-0.15.0+dfsg/include/spdlog/tweakme.h
Examining data/rapmap-0.15.0+dfsg/include/stringpiece.h
Examining data/rapmap-0.15.0+dfsg/include/tsl/array_growth_policy.h
Examining data/rapmap-0.15.0+dfsg/include/tsl/array_hash.h
Examining data/rapmap-0.15.0+dfsg/include/tsl/array_map.h
Examining data/rapmap-0.15.0+dfsg/include/tsl/array_set.h
Examining data/rapmap-0.15.0+dfsg/include/tsl/bhopscotch_map.h
Examining data/rapmap-0.15.0+dfsg/include/tsl/bhopscotch_set.h
Examining data/rapmap-0.15.0+dfsg/include/tsl/hopscotch_growth_policy.h
Examining data/rapmap-0.15.0+dfsg/include/tsl/hopscotch_hash.h
Examining data/rapmap-0.15.0+dfsg/include/tsl/hopscotch_map.h
Examining data/rapmap-0.15.0+dfsg/include/tsl/hopscotch_set.h
Examining data/rapmap-0.15.0+dfsg/include/tsl/robin_growth_policy.h
Examining data/rapmap-0.15.0+dfsg/include/tsl/robin_hash.h
Examining data/rapmap-0.15.0+dfsg/include/tsl/robin_map.h
Examining data/rapmap-0.15.0+dfsg/include/tsl/robin_set.h
Examining data/rapmap-0.15.0+dfsg/include/xxhash.h
Examining data/rapmap-0.15.0+dfsg/include/zstr/strict_fstream.hpp
Examining data/rapmap-0.15.0+dfsg/include/zstr/zstr.hpp
Examining data/rapmap-0.15.0+dfsg/include/FastxParserThreadUtils.hpp
Examining data/rapmap-0.15.0+dfsg/src/EnumCoder.cpp
Examining data/rapmap-0.15.0+dfsg/src/EnumCoderTest.cpp
Examining data/rapmap-0.15.0+dfsg/src/FastxParser.cpp
Examining data/rapmap-0.15.0+dfsg/src/HitManager.cpp
Examining data/rapmap-0.15.0+dfsg/src/RapMap.cpp
Examining data/rapmap-0.15.0+dfsg/src/RapMapFileSystem.cpp
Examining data/rapmap-0.15.0+dfsg/src/RapMapIndex.cpp
Examining data/rapmap-0.15.0+dfsg/src/RapMapIndexer.cpp
Examining data/rapmap-0.15.0+dfsg/src/RapMapMapper.cpp
Examining data/rapmap-0.15.0+dfsg/src/RapMapSAIndex.cpp
Examining data/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp
Examining data/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp
Examining data/rapmap-0.15.0+dfsg/src/RapMapUtils.cpp
Examining data/rapmap-0.15.0+dfsg/src/UtilTest.cpp
Examining data/rapmap-0.15.0+dfsg/src/bit_array.c
Examining data/rapmap-0.15.0+dfsg/src/edlib.cpp
Examining data/rapmap-0.15.0+dfsg/src/ksw2pp/KSW2Aligner.cpp
Examining data/rapmap-0.15.0+dfsg/src/ksw2pp/kalloc.c
Examining data/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_dispatch.c
Examining data/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extd.c
Examining data/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extd2_sse.c
Examining data/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extf2_sse.c
Examining data/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_exts2_sse.c
Examining data/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extz.c
Examining data/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extz2_sse.c
Examining data/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_gg.c
Examining data/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_gg2.c
Examining data/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_gg2_sse.c
Examining data/rapmap-0.15.0+dfsg/src/metro/metrohash128.cpp
Examining data/rapmap-0.15.0+dfsg/src/metro/metrohash128crc.cpp
Examining data/rapmap-0.15.0+dfsg/src/metro/metrohash64.cpp
Examining data/rapmap-0.15.0+dfsg/src/rank9b.cpp
Examining data/rapmap-0.15.0+dfsg/src/stringpiece.cc
Examining data/rapmap-0.15.0+dfsg/src/xxhash.c
FINAL RESULTS:
data/rapmap-0.15.0+dfsg/include/spdlog/details/logger_impl.h:70:14: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
fmt::printf(log_msg.raw, fmt, args...);
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/format.cc:93:23: [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 FMT_SNPRINTF snprintf
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/format.cc:108:23: [4] (buffer) swprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
# define FMT_SWPRINTF swprintf
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.cc:16:6: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
void printf(BasicWriter<Char> &w, BasicCStringRef<Char> format, ArgList args);
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.cc:18:14: [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.
FMT_FUNC int fprintf(std::FILE *f, CStringRef format, ArgList args) {
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.cc:20:3: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
printf(w, format, args);
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.h:522:13: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
inline void printf(Writer &w, CStringRef format, ArgList args) {
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.h:525:20: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
FMT_VARIADIC(void, printf, Writer &, CStringRef)
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.h:527:13: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
inline void printf(WWriter &w, WCStringRef format, ArgList args) {
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.h:530:20: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
FMT_VARIADIC(void, printf, WWriter &, WCStringRef)
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.h:541:20: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
inline std::string sprintf(CStringRef format, ArgList args) {
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.h:543:3: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
printf(w, format, args);
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.h:546:27: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
FMT_VARIADIC(std::string, sprintf, CStringRef)
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.h:548:21: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
inline std::wstring sprintf(WCStringRef format, ArgList args) {
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.h:550:3: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
printf(w, format, args);
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.h:553:30: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
FMT_VARIADIC_W(std::wstring, sprintf, WCStringRef)
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.h:564:13: [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.
FMT_API int fprintf(std::FILE *f, CStringRef format, ArgList args);
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.h:565:19: [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.
FMT_VARIADIC(int, fprintf, std::FILE *, CStringRef)
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.h:576:12: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
inline int printf(CStringRef format, ArgList args) {
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.h:577:10: [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.
return fprintf(stdout, format, args);
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.h:579:19: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
FMT_VARIADIC(int, printf, CStringRef)
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.h:590:12: [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.
inline int fprintf(std::ostream &os, CStringRef format_str, ArgList args) {
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.h:592:3: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
printf(w, format_str, args);
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/printf.h:596:19: [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.
FMT_VARIADIC(int, fprintf, std::ostream &, CStringRef)
data/rapmap-0.15.0+dfsg/include/tsl/robin_growth_policy.h:59:63: [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.
# define TSL_THROW_OR_TERMINATE(ex, msg) do { std::fprintf(stderr, msg); std::terminate(); } while(0)
data/rapmap-0.15.0+dfsg/src/bit_array.c:249:32: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
#define DEBUG_PRINT(msg,...) printf("[%s:%i] "msg, __FILE__, __LINE__, ##__VA_ARGS__);
data/rapmap-0.15.0+dfsg/include/spdlog/details/os.h:461:30: [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 *env_p = std::getenv("TERM");
data/rapmap-0.15.0+dfsg/src/EnumCoderTest.cpp:39:17: [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(EnumCoder, random){
data/rapmap-0.15.0+dfsg/src/bit_array.c:211:5: [3] (random) srand:
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.
srand((((time.tv_sec ^ getpid()) * 1000001) + time.tv_usec));
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:61:5: [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(_buffer,cr._buffer,_buffsize*sizeof(basetype) );
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:143:10: [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).
_is = fopen(filename, "rb");
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:587:5: [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(_bitArray, r._bitArray, _nchar*sizeof(uint64_t) );
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:601:5: [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(_bitArray, r._bitArray, _nchar*sizeof(uint64_t) );
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1377:4: [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 fname_old[1000];
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1378:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(fname_old,"temp_p%i_level_%i",_pid,i-2);
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1380:4: [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 fname_curr[1000];
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1381:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(fname_curr,"temp_p%i_level_%i",_pid,i);
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1383:4: [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 fname_prev[1000];
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1384:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(fname_prev,"temp_p%i_level_%i",_pid,i-1);
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1397:23: [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).
_currlevelFile = fopen(fname_curr,"w");
data/rapmap-0.15.0+dfsg/include/Kmer.hpp:53:18: [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 constexpr char complements[256] = {
data/rapmap-0.15.0+dfsg/include/Kmer.hpp:101:18: [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 constexpr char revCodes[4] = {'A', 'C', 'G', 'T'};
data/rapmap-0.15.0+dfsg/include/PairAlignmentFormatter.hpp:44:5: [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 buff1[1000];
data/rapmap-0.15.0+dfsg/include/PairAlignmentFormatter.hpp:45:5: [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 buff2[1000];
data/rapmap-0.15.0+dfsg/include/SingleAlignmentFormatter.hpp:39:5: [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 buff[1000];
data/rapmap-0.15.0+dfsg/include/btree/btree.h:152:3: [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 dummy[2];
data/rapmap-0.15.0+dfsg/include/concurrentqueue.h:1597:4: [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 elements[sizeof(T) * BLOCK_SIZE];
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/blake2_provider.hpp:76:3: [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(&H[0], blake2s_constants<void>::IV, 32);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/blake2_provider.hpp:82:3: [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(&H[0], blake2b_constants<void>::IV, 64);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/blake2_provider.hpp:88:3: [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(&H[0], blake2s_constants<void>::IV, 32);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/blake2_provider.hpp:98:3: [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(&H[0], blake2b_constants<void>::IV, 64);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/blake2_provider.hpp:179:3: [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(&s[0], salt, salt_len);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/blake2_provider.hpp:187:3: [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(&p[0], personalization, personalization_len);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/blake2_provider.hpp:202:4: [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(&m[0], H.data(), N / 8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/blake2_provider.hpp:207:4: [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(hash, reinterpret_cast<unsigned char*>(H.data()) + pos, to_copy);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/blake2_provider.hpp:222:4: [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(hash + processed, H.data(), pos);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/blake2_provider.hpp:235:4: [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(hash, H.data(), hash_size() / 8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/blake2_provider.hpp:259:12: [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.
unsigned char key[N / 4];
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/blake2_provider.hpp:260:3: [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(key, k.data(), k.length());
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/blake2_provider.hpp:285:4: [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(v, H.data(), sizeof(T) * 8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/blake_provider.hpp:94:4: [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(v, H.data(), sizeof(T) * 8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/blake_provider.hpp:254:3: [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(&m[block_bytes() - 8], &mlen, sizeof(uint64_t));
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/blake_provider.hpp:260:4: [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(hash, u.H512.data(), hash_size()/8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/blake_provider.hpp:266:4: [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(hash, u.H256.data(), hash_size()/8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/constants/md5_constants.hpp:18:24: [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.
const static unsigned char S[64];
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/groestl_provider.hpp:149:3: [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(&m[limit - 8], &mlen, 64 / 8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/jh_provider.hpp:122:12: [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.
unsigned char msg[64];
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/jh_provider.hpp:146:3: [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(&m[0] + (64 - 8), &mlen, 64 / 8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/jh_provider.hpp:149:3: [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(hash, reinterpret_cast<unsigned char*>(H.data()) + 128 - hash_size() / 8, hash_size() / 8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/k12m14_provider.hpp:58:13: [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.
unsigned char buf[B / 4];
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/k12m14_provider.hpp:98:14: [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.
unsigned char buf[B / 4];
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/kmac_provider.hpp:22:12: [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.
unsigned char buf[32];
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/kmac_provider.hpp:90:13: [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.
unsigned char buf[32];
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/kupyna_provider.hpp:145:3: [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(&m[limit - 12], &total, sizeof(uint64_t));
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/kupyna_provider.hpp:151:3: [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(hash, reinterpret_cast<const unsigned char*>(h.data()) + limit - hash_size() / 8, hash_size() / 8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/md5_provider.hpp:89:3: [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(&m[0] + (64 - 8), &total, 64 / 8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/md5_provider.hpp:91:3: [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(hash, H.data(), 16);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha1_provider.hpp:80:3: [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(&m[0] + (64 - 8), &mlen, 64 / 8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha1_provider.hpp:84:3: [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(hash, H.data(), 160/8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha2_provider.hpp:158:12: [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.
unsigned char buf[512 / 8];
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha2_provider.hpp:184:3: [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(&m[N / 4 - 8], &mlen, 64 / 8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha2_provider.hpp:188:3: [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(hash, &H[0], hs/8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sha3_provider.hpp:158:3: [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(hash, A.data(), hash_size() / 8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/shake_provider.hpp:89:13: [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.
unsigned char buf[1024];
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/shake_provider.hpp:139:4: [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(hash, reinterpret_cast<unsigned char*>(A.data()) + pos, to_copy);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/shake_provider.hpp:148:4: [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(hash + processed, A.data(), pos);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/skein_provider.hpp:228:3: [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(&m[8], &size64, 8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/skein_provider.hpp:257:4: [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(&hbk[0], H.data(), N / 8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/skein_provider.hpp:264:4: [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(hash, reinterpret_cast<unsigned char*>(H.data()) + pos, to_copy);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/skein_provider.hpp:273:4: [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(&m[0], &total, 8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/skein_provider.hpp:274:4: [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(&H[0], hbk.data(), N / 8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/skein_provider.hpp:276:4: [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(hash + processed, H.data(), pos);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/skein_provider.hpp:320:4: [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(keys, H.data(), sizeof(uint64_t) * N / 64);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/skein_provider.hpp:321:4: [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(tweaks, tweak.data(), sizeof(uint64_t) * 2);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sm3_provider.hpp:93:3: [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(&m[64 - 8], &mlen, 64 / 8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/sm3_provider.hpp:97:3: [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(hash, H.data(), 32);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/streebog_provider.hpp:37:12: [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.
unsigned char ch[64];
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/streebog_provider.hpp:38:3: [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(ch, block, 64);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/streebog_provider.hpp:65:3: [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(tmp, K, 64);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/streebog_provider.hpp:79:3: [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(hN, h, 64);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/streebog_provider.hpp:140:3: [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(&m[0], &total, sizeof(total));
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/streebog_provider.hpp:145:3: [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(hash, &h[8 - hash_size()/64], hash_size() / 8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/whirlpool_provider.hpp:75:3: [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(&m[64 - 8], &mlen, 64 / 8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/whirlpool_provider.hpp:77:3: [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(hash, h.data(), hash_size() / 8);
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/whirlpool_provider.hpp:112:5: [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(K, L, sizeof(L));
data/rapmap-0.15.0+dfsg/include/digestpp/algorithm/detail/whirlpool_provider.hpp:123:5: [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(state, L, sizeof(L));
data/rapmap-0.15.0+dfsg/include/digestpp/detail/absorb_data.hpp:21:3: [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(m + pos, data, bs - pos);
data/rapmap-0.15.0+dfsg/include/digestpp/detail/absorb_data.hpp:37:2: [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(m + pos, data, len);
data/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp:135:12: [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.
unsigned char buffer[tmp_buffer_size];
data/rapmap-0.15.0+dfsg/include/kseq.h:129:4: [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->s + str->l, ks->buf + ks->begin, i - ks->begin); \
data/rapmap-0.15.0+dfsg/include/nonstd/optional.hpp:581:31: [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.
typedef struct { unsigned char data[ sizeof(value_type) ]; } aligned_storage_t;
data/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1388:13: [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(static_cast<void *>(_group + i), _group + i-1, sizeof(*_group));
data/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1492:13: [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(static_cast<void *>(_group + i), _group + i + 1, sizeof(*_group));
data/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:2090:17: [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(static_cast<void *>(first), _first_group, sizeof(*first) * (std::min)(sz, old_sz));
data/rapmap-0.15.0+dfsg/include/sparsepp/spp_dlalloc.h:548:31: [2] (misc) open:
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).
dev_zero_fd = open("/dev/zero", O_RDWR);
data/rapmap-0.15.0+dfsg/include/sparsepp/spp_dlalloc.h:1648:22: [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.
unsigned char buf[sizeof(size_t)];
data/rapmap-0.15.0+dfsg/include/sparsepp/spp_dlalloc.h:1650:23: [2] (misc) open:
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).
if ((fd = open("/dev/urandom", O_RDONLY)) >= 0 &&
data/rapmap-0.15.0+dfsg/include/sparsepp/spp_dlalloc.h:3817:21: [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(mem, oldmem, (oc < bytes) ? oc : bytes);
data/rapmap-0.15.0+dfsg/include/sparsepp/spp_memory.h:130:21: [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).
i = atoi(line);
data/rapmap-0.15.0+dfsg/include/sparsepp/spp_memory.h:134:21: [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).
auto file = fopen("/proc/self/status", "r");
data/rapmap-0.15.0+dfsg/include/sparsepp/spp_memory.h:136:9: [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[128];
data/rapmap-0.15.0+dfsg/include/spdlog/details/file_helper.h:47:10: [2] (misc) open:
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).
void open(const filename_t& fname, bool truncate = false)
data/rapmap-0.15.0+dfsg/include/spdlog/details/file_helper.h:68:9: [2] (misc) open:
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).
open(_filename, truncate);
data/rapmap-0.15.0+dfsg/include/spdlog/details/logger_impl.h:350:5: [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 date_buf[100];
data/rapmap-0.15.0+dfsg/include/spdlog/details/mpmc_bounded_q.h:160:13: [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.
typedef char cacheline_pad_t[cacheline_size];
data/rapmap-0.15.0+dfsg/include/spdlog/details/os.h:180:11: [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).
*fp = fopen((filename.c_str()), mode.c_str());
data/rapmap-0.15.0+dfsg/include/spdlog/details/os.h:398:36: [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.
inline std::string errno_to_string(char buf[256], int res)
data/rapmap-0.15.0+dfsg/include/spdlog/details/os.h:413:5: [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 buf[256];
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/format.cc:314:16: [2] (buffer) MultiByteToWideChar:
Requires maximum length in CHARACTERS, not bytes (CWE-120).
int length = MultiByteToWideChar(
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/format.cc:319:12: [2] (buffer) MultiByteToWideChar:
Requires maximum length in CHARACTERS, not bytes (CWE-120).
length = MultiByteToWideChar(
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/format.h:484:5: [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[2]; // The buffer size must be >= 2 or _ecvt_s will fail.
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/format.h:1259:9: [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.
typedef char Yes[1];
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/format.h:1260:9: [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.
typedef char No[2];
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/format.h:3048:3: [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 prefix[4] = "";
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/format.h:3523:11: [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.
mutable char buffer_[BUFFER_SIZE];
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/posix.cc:76:35: [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).
FMT_RETRY_VAL(file_, FMT_SYSTEM(fopen(filename.c_str(), mode.c_str())), 0);
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/posix.cc:106:33: [2] (misc) open:
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).
FMT_RETRY(fd_, FMT_POSIX_CALL(open(path.c_str(), oflag, mode)));
data/rapmap-0.15.0+dfsg/include/spdlog/sinks/file_sinks.h:34:22: [2] (misc) open:
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_helper.open(filename, truncate);
data/rapmap-0.15.0+dfsg/include/spdlog/sinks/file_sinks.h:76:22: [2] (misc) open:
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_helper.open(calc_filename(_base_filename, 0));
data/rapmap-0.15.0+dfsg/include/spdlog/sinks/file_sinks.h:207:22: [2] (misc) open:
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_helper.open(FileNameCalc::calc_filename(_base_filename));
data/rapmap-0.15.0+dfsg/include/spdlog/sinks/file_sinks.h:216:26: [2] (misc) open:
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_helper.open(FileNameCalc::calc_filename(_base_filename));
data/rapmap-0.15.0+dfsg/include/tsl/array_hash.h:266:18: [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(m_position + size_as_char_t<key_size_type>() + key_size() + KEY_EXTRA_SIZE,
data/rapmap-0.15.0+dfsg/include/tsl/array_hash.h:328:14: [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(m_buffer, other.m_buffer, other_buffer_size);
data/rapmap-0.15.0+dfsg/include/tsl/array_hash.h:482:14: [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(m_buffer, &end_of_bucket, sizeof(end_of_bucket));
data/rapmap-0.15.0+dfsg/include/tsl/array_hash.h:546:14: [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(buffer_append_pos, &key_size, sizeof(key_size));
data/rapmap-0.15.0+dfsg/include/tsl/array_hash.h:549:14: [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(buffer_append_pos, key, key_size * sizeof(CharT));
data/rapmap-0.15.0+dfsg/include/tsl/array_hash.h:553:14: [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(buffer_append_pos, &zero, KEY_EXTRA_SIZE * sizeof(CharT));
data/rapmap-0.15.0+dfsg/include/tsl/array_hash.h:557:14: [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(buffer_append_pos, &end_of_bucket, sizeof(end_of_bucket));
data/rapmap-0.15.0+dfsg/include/tsl/array_hash.h:564:14: [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(buffer_append_pos, &key_size, sizeof(key_size));
data/rapmap-0.15.0+dfsg/include/tsl/array_hash.h:567:14: [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(buffer_append_pos, key, key_size * sizeof(CharT));
data/rapmap-0.15.0+dfsg/include/tsl/array_hash.h:571:14: [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(buffer_append_pos, &zero, KEY_EXTRA_SIZE * sizeof(CharT));
data/rapmap-0.15.0+dfsg/include/tsl/array_hash.h:574:14: [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(buffer_append_pos, &value, sizeof(value));
data/rapmap-0.15.0+dfsg/include/tsl/array_hash.h:578:14: [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(buffer_append_pos, &end_of_bucket, sizeof(end_of_bucket));
data/rapmap-0.15.0+dfsg/include/xxhash.h:203:27: [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.
typedef struct { unsigned char digest[4]; } XXH32_canonical_t;
data/rapmap-0.15.0+dfsg/include/xxhash.h:238:27: [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.
typedef struct { unsigned char digest[8]; } XXH64_canonical_t;
data/rapmap-0.15.0+dfsg/include/zstr/strict_fstream.hpp:75:22: [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 const char * mode_name_v[n_modes] =
data/rapmap-0.15.0+dfsg/include/zstr/strict_fstream.hpp:148:9: [2] (misc) open:
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).
open(filename, mode);
data/rapmap-0.15.0+dfsg/include/zstr/strict_fstream.hpp:150:10: [2] (misc) open:
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).
void open(const std::string& filename, std::ios_base::openmode mode = std::ios_base::in)
data/rapmap-0.15.0+dfsg/include/zstr/strict_fstream.hpp:155:24: [2] (misc) open:
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).
std::ifstream::open(filename, mode);
data/rapmap-0.15.0+dfsg/include/zstr/strict_fstream.hpp:168:9: [2] (misc) open:
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).
open(filename, mode);
data/rapmap-0.15.0+dfsg/include/zstr/strict_fstream.hpp:170:10: [2] (misc) open:
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).
void open(const std::string& filename, std::ios_base::openmode mode = std::ios_base::out)
data/rapmap-0.15.0+dfsg/include/zstr/strict_fstream.hpp:175:24: [2] (misc) open:
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).
std::ofstream::open(filename, mode);
data/rapmap-0.15.0+dfsg/include/zstr/strict_fstream.hpp:187:9: [2] (misc) open:
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).
open(filename, mode);
data/rapmap-0.15.0+dfsg/include/zstr/strict_fstream.hpp:189:10: [2] (misc) open:
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).
void open(const std::string& filename, std::ios_base::openmode mode = std::ios_base::in)
data/rapmap-0.15.0+dfsg/include/zstr/strict_fstream.hpp:194:23: [2] (misc) open:
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).
std::fstream::open(filename, mode);
data/rapmap-0.15.0+dfsg/src/RapMapMapper.cpp:1034:14: [2] (misc) open:
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).
outFile.open(outname.getValue());
data/rapmap-0.15.0+dfsg/src/RapMapSAIndex.cpp:153:20: [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* rsFile = fopen(rsFileName.c_str(), "r");
data/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:760:18: [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* rsFile = fopen(rsFileName.c_str(), "w");
data/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:823:15: [2] (misc) open:
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).
outFile.open(mopts->outname);
data/rapmap-0.15.0+dfsg/src/bit_array.c:233:47: [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 inline char* _word_to_str(word_t word, char str[WORD_SIZE+1])
data/rapmap-0.15.0+dfsg/src/bit_array.c:236:47: [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 inline char* _word_to_str(word_t word, char str[WORD_SIZE+1])
data/rapmap-0.15.0+dfsg/src/bit_array.c:1498:3: [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(cpy->words, bitarr->words, bitarr->num_of_words * sizeof(word_t));
data/rapmap-0.15.0+dfsg/src/bit_array.c:3113:3: [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(seed32, &seed, sizeof(uint32_t)*2);
data/rapmap-0.15.0+dfsg/src/edlib.cpp:458:5: [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(cigar_, &(*cigar)[0], cigar->size() * sizeof(char));
data/rapmap-0.15.0+dfsg/src/edlib.cpp:1744:5: [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(*alignment, ulAlignment, ulAlignmentLength);
data/rapmap-0.15.0+dfsg/src/edlib.cpp:1745:5: [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(*alignment + ulAlignmentLength, lrAlignment, lrAlignmentLength);
data/rapmap-0.15.0+dfsg/src/edlib.cpp:1782:14: [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.
unsigned char letterIdx[256]; //!< letterIdx[c] is index of letter c in alphabet
data/rapmap-0.15.0+dfsg/src/ksw2pp/KSW2Aligner.cpp:61:10: [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.
unsigned char seq_nt4_table_loc[256] = {
data/rapmap-0.15.0+dfsg/src/ksw2pp/kalloc.c:142:2: [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(q, ap, (*p - 1) * sizeof(size_t));
data/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extd2_sse.c:121:2: [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(sf, target, tlen);
data/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extf2_sse.c:38:2: [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(sf, target, tlen);
data/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_exts2_sse.c:110:2: [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(sf, target, tlen);
data/rapmap-0.15.0+dfsg/src/ksw2pp/ksw2_extz2_sse.c:99:2: [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(sf, target, tlen);
data/rapmap-0.15.0+dfsg/src/metro/metrohash128.cpp:75:9: [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(input.b + (bytes % 32), ptr, static_cast<size_t>(fill));
data/rapmap-0.15.0+dfsg/src/metro/metrohash128.cpp:102:9: [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(input.b, ptr, end - ptr);
data/rapmap-0.15.0+dfsg/src/metro/metrohash128.cpp:162:5: [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(hash, state.v, 16);
data/rapmap-0.15.0+dfsg/src/metro/metrohash128.cpp:235:5: [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(hash, v, 16);
data/rapmap-0.15.0+dfsg/src/metro/metrohash128.cpp:342:5: [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(out, v, 16);
data/rapmap-0.15.0+dfsg/src/metro/metrohash128.cpp:420:5: [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(out, v, 16);
data/rapmap-0.15.0+dfsg/src/metro/metrohash128crc.cpp:105:5: [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(out, v, 16);
data/rapmap-0.15.0+dfsg/src/metro/metrohash128crc.cpp:181:5: [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(out, v, 16);
data/rapmap-0.15.0+dfsg/src/metro/metrohash64.cpp:70:9: [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(input.b + (bytes % 32), ptr, static_cast<size_t>(fill));
data/rapmap-0.15.0+dfsg/src/metro/metrohash64.cpp:97:9: [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(input.b, ptr, end - ptr);
data/rapmap-0.15.0+dfsg/src/metro/metrohash64.cpp:159:5: [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(hash, state.v, 8);
data/rapmap-0.15.0+dfsg/src/metro/metrohash64.cpp:231:5: [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(hash, &h, 8);
data/rapmap-0.15.0+dfsg/src/metro/metrohash64.cpp:338:5: [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(out, &hash, 8);
data/rapmap-0.15.0+dfsg/src/metro/metrohash64.cpp:415:5: [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(out, &hash, 8);
data/rapmap-0.15.0+dfsg/src/stringpiece.cc:37:3: [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(buf, ptr_ + pos, ret);
data/rapmap-0.15.0+dfsg/src/xxhash.c:106:76: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
static void* XXH_memcpy(void* dest, const void* src, size_t size) { return memcpy(dest,src,size); }
data/rapmap-0.15.0+dfsg/src/xxhash.c:362:5: [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(dstState, srcState, sizeof(*dstState));
data/rapmap-0.15.0+dfsg/src/xxhash.c:373:5: [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(statePtr, &state, sizeof(state));
data/rapmap-0.15.0+dfsg/src/xxhash.c:507:5: [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(dst, &hash, sizeof(*dst));
data/rapmap-0.15.0+dfsg/src/xxhash.c:732:5: [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(dstState, srcState, sizeof(*dstState));
data/rapmap-0.15.0+dfsg/src/xxhash.c:743:5: [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(statePtr, &state, sizeof(state));
data/rapmap-0.15.0+dfsg/src/xxhash.c:880:5: [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(dst, &hash, sizeof(*dst));
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:785:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&_size), sizeof(_size));
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:786:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&_nchar), sizeof(_nchar));
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:788:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char *>(_bitArray), (std::streamsize)(sizeof(uint64_t) * _nchar));
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:791:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char *>(&sizer), sizeof(size_t));
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:793:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(_ranks.data()), (std::streamsize)(sizeof(_ranks[0]) * _ranks.size()));
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1202:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&_gamma), sizeof(_gamma));
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1203:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&_nb_levels), sizeof(_nb_levels));
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1204:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&_lastbitsetrank), sizeof(_lastbitsetrank));
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1205:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&_nelem), sizeof(_nelem));
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1237:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char *>(&final_hash_size), sizeof(size_t));
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1244:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char *>(&key), sizeof(elem_t));
data/rapmap-0.15.0+dfsg/include/BooPHF.hpp:1245:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char *>(&value), sizeof(uint64_t));
data/rapmap-0.15.0+dfsg/include/SACollector.hpp:108:32: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool operator()(std::string& read,
data/rapmap-0.15.0+dfsg/include/SACollector.hpp:117:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
auto readLen = read.length();
data/rapmap-0.15.0+dfsg/include/SACollector.hpp:121:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
auto readStartIt = read.begin();
data/rapmap-0.15.0+dfsg/include/SACollector.hpp:122:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
auto readEndIt = read.end();
data/rapmap-0.15.0+dfsg/include/SACollector.hpp:124:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
auto rb = read.begin();
data/rapmap-0.15.0+dfsg/include/SACollector.hpp:177:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
invalidPos = read.find_first_of("nN", pos);
data/rapmap-0.15.0+dfsg/include/SACollector.hpp:179:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
rb = read.begin() + invalidPos + 1;
data/rapmap-0.15.0+dfsg/include/SACollector.hpp:187:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
mer = rapmap::utils::my_mer(read.c_str() + pos);
data/rapmap-0.15.0+dfsg/include/SACollector.hpp:250:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read, // the read
data/rapmap-0.15.0+dfsg/include/SACollector.hpp:259:34: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
rapmap::utils::reverseRead(read, rcBuffer_);
data/rapmap-0.15.0+dfsg/include/SACollector.hpp:274:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read, // the read
data/rapmap-0.15.0+dfsg/include/SACollector.hpp:275:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.begin(), // where to start the search
data/rapmap-0.15.0+dfsg/include/SACollector.hpp:446:58: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
SASearcher<RapMapIndexT>& saSearcher, std::string& read,
data/rapmap-0.15.0+dfsg/include/SACollector.hpp:460:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
auto readLen = read.length();
data/rapmap-0.15.0+dfsg/include/SACollector.hpp:461:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
auto readStartIt = read.begin();
data/rapmap-0.15.0+dfsg/include/SACollector.hpp:462:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
auto readEndIt = read.end();
data/rapmap-0.15.0+dfsg/include/SACollector.hpp:502:32: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
validMer = mer.fromChars(read.c_str() + pos);
data/rapmap-0.15.0+dfsg/include/SACollector.hpp:510:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
invalidPos = read.find_first_of("Nn", pos);
data/rapmap-0.15.0+dfsg/include/SACollector.hpp:515:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
rb = read.begin() + invalidPos + 1;
data/rapmap-0.15.0+dfsg/include/SACollector.hpp:606:44: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool validNucs = mer.fromChars(read.c_str() + kmerPos);
data/rapmap-0.15.0+dfsg/include/digestpp/hasher.hpp:137:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (istr.read(reinterpret_cast<T*>(buffer), sizeof(buffer)))
data/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:201:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
return fp->read(reinterpret_cast<char*>(data),
data/rapmap-0.15.0+dfsg/include/sparsepp/spp.h:1662:22: [1] (buffer) equal:
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.
std::equal(_group, _group + _num_items(), x._group));
data/rapmap-0.15.0+dfsg/include/sparsepp/spp_dlalloc.h:1651:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(fd, buf, sizeof(buf)) == sizeof(buf))
data/rapmap-0.15.0+dfsg/include/sparsepp/spp_memory.h:122:26: [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).
auto i = strlen(line);
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/format.cc:146:33: [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).
if (message == buffer_ && strlen(buffer_) == buffer_size_ - 1)
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/format.cc:160:29: [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).
return result == 0 && strlen(buffer_) == buffer_size_ - 1 ?
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/format.h:2148:52: [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).
Arg::StringValue<char> str = { str_value, std::strlen(str_value) };
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/format.h:2153:55: [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).
Arg::StringValue<char> str = {value, value ? std::strlen(value) : 0};
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/posix.cc:156:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::size_t fmt::File::read(void *buffer, std::size_t count) {
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/posix.cc:158:36: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
FMT_RETRY(result, FMT_POSIX_CALL(read(fd_, buffer, convert_rwcount(count))));
data/rapmap-0.15.0+dfsg/include/spdlog/fmt/bundled/posix.h:276:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
FMT_API std::size_t read(void *buffer, std::size_t count);
data/rapmap-0.15.0+dfsg/include/stringpiece.h:39:63: [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).
: ptr_(str), length_((str == NULL) ? 0 : static_cast<int>(strlen(str))) { }
data/rapmap-0.15.0+dfsg/include/stringpiece.h:58:34: [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).
length_ = static_cast<int>(strlen(str));
data/rapmap-0.15.0+dfsg/include/tsl/array_map.h:183:39: [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).
return m_ht.emplace(key, std::strlen(key), value);
data/rapmap-0.15.0+dfsg/include/tsl/array_map.h:202:39: [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).
return m_ht.emplace(key, std::strlen(key), std::move(value));
data/rapmap-0.15.0+dfsg/include/tsl/array_map.h:255:48: [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).
return m_ht.insert_or_assign(key, std::strlen(key), std::forward<M>(obj));
data/rapmap-0.15.0+dfsg/include/tsl/array_map.h:278:39: [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).
return m_ht.emplace(key, std::strlen(key), std::forward<Args>(args)...);
data/rapmap-0.15.0+dfsg/include/tsl/array_map.h:323:37: [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).
return m_ht.erase(key, std::strlen(key));
data/rapmap-0.15.0+dfsg/include/tsl/array_map.h:354:37: [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).
return m_ht.erase(key, std::strlen(key), precalculated_hash);
data/rapmap-0.15.0+dfsg/include/tsl/array_map.h:393:34: [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).
return m_ht.at(key, std::strlen(key));
data/rapmap-0.15.0+dfsg/include/tsl/array_map.h:397:34: [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).
return m_ht.at(key, std::strlen(key));
data/rapmap-0.15.0+dfsg/include/tsl/array_map.h:437:34: [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).
return m_ht.at(key, std::strlen(key), precalculated_hash);
data/rapmap-0.15.0+dfsg/include/tsl/array_map.h:444:34: [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).
return m_ht.at(key, std::strlen(key), precalculated_hash);
data/rapmap-0.15.0+dfsg/include/tsl/array_map.h:481:77: [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).
T& operator[](const CharT* key) { return m_ht.access_operator(key, std::strlen(key)); }
data/rapmap-0.15.0+dfsg/include/tsl/array_map.h:493:37: [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).
return m_ht.count(key, std::strlen(key));
data/rapmap-0.15.0+dfsg/include/tsl/array_map.h:518:37: [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).
return m_ht.count(key, std::strlen(key), precalculated_hash);
data/rapmap-0.15.0+dfsg/include/tsl/array_map.h:548:36: [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).
return m_ht.find(key, std::strlen(key));
data/rapmap-0.15.0+dfsg/include/tsl/array_map.h:552:36: [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).
return m_ht.find(key, std::strlen(key));
data/rapmap-0.15.0+dfsg/include/tsl/array_map.h:592:36: [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).
return m_ht.find(key, std::strlen(key), precalculated_hash);
data/rapmap-0.15.0+dfsg/include/tsl/array_map.h:599:36: [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).
return m_ht.find(key, std::strlen(key), precalculated_hash);
data/rapmap-0.15.0+dfsg/include/tsl/array_map.h:643:43: [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).
return m_ht.equal_range(key, std::strlen(key));
data/rapmap-0.15.0+dfsg/include/tsl/array_map.h:647:43: [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).
return m_ht.equal_range(key, std::strlen(key));
data/rapmap-0.15.0+dfsg/include/tsl/array_map.h:687:43: [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).
return m_ht.equal_range(key, std::strlen(key), precalculated_hash);
data/rapmap-0.15.0+dfsg/include/tsl/array_map.h:694:43: [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).
return m_ht.equal_range(key, std::strlen(key), precalculated_hash);
data/rapmap-0.15.0+dfsg/include/tsl/array_set.h:172:39: [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).
return m_ht.emplace(key, std::strlen(key));
data/rapmap-0.15.0+dfsg/include/tsl/array_set.h:229:39: [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).
return m_ht.emplace(key, std::strlen(key));
data/rapmap-0.15.0+dfsg/include/tsl/array_set.h:257:37: [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).
return m_ht.erase(key, std::strlen(key));
data/rapmap-0.15.0+dfsg/include/tsl/array_set.h:282:37: [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).
return m_ht.erase(key, std::strlen(key), precalculated_hash);
data/rapmap-0.15.0+dfsg/include/tsl/array_set.h:312:75: [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).
size_type count(const CharT* key) const { return m_ht.count(key, std::strlen(key)); }
data/rapmap-0.15.0+dfsg/include/tsl/array_set.h:331:37: [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).
return m_ht.count(key, std::strlen(key), precalculated_hash);
data/rapmap-0.15.0+dfsg/include/tsl/array_set.h:361:36: [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).
return m_ht.find(key, std::strlen(key));
data/rapmap-0.15.0+dfsg/include/tsl/array_set.h:365:36: [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).
return m_ht.find(key, std::strlen(key));
data/rapmap-0.15.0+dfsg/include/tsl/array_set.h:405:36: [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).
return m_ht.find(key, std::strlen(key), precalculated_hash);
data/rapmap-0.15.0+dfsg/include/tsl/array_set.h:412:36: [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).
return m_ht.find(key, std::strlen(key), precalculated_hash);
data/rapmap-0.15.0+dfsg/include/tsl/array_set.h:456:43: [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).
return m_ht.equal_range(key, std::strlen(key));
data/rapmap-0.15.0+dfsg/include/tsl/array_set.h:460:43: [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).
return m_ht.equal_range(key, std::strlen(key));
data/rapmap-0.15.0+dfsg/include/tsl/array_set.h:500:43: [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).
return m_ht.equal_range(key, std::strlen(key), precalculated_hash);
data/rapmap-0.15.0+dfsg/include/tsl/array_set.h:507:43: [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).
return m_ht.equal_range(key, std::strlen(key), precalculated_hash);
data/rapmap-0.15.0+dfsg/include/tsl/bhopscotch_map.h:135:50: [1] (buffer) equal:
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.
m_ht(bucket_count, hash, equal, alloc, ht::DEFAULT_MAX_LOAD_FACTOR, comp)
data/rapmap-0.15.0+dfsg/include/tsl/bhopscotch_map.h:158:92: [1] (buffer) equal:
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.
const Allocator& alloc = Allocator()) : bhopscotch_map(bucket_count, hash, equal, alloc)
data/rapmap-0.15.0+dfsg/include/tsl/bhopscotch_map.h:183:82: [1] (buffer) equal:
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.
bhopscotch_map(init.begin(), init.end(), bucket_count, hash, equal, alloc)
data/rapmap-0.15.0+dfsg/include/tsl/bhopscotch_set.h:118:50: [1] (buffer) equal:
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.
m_ht(bucket_count, hash, equal, alloc, ht::DEFAULT_MAX_LOAD_FACTOR, comp)
data/rapmap-0.15.0+dfsg/include/tsl/bhopscotch_set.h:141:92: [1] (buffer) equal:
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.
const Allocator& alloc = Allocator()) : bhopscotch_set(bucket_count, hash, equal, alloc)
data/rapmap-0.15.0+dfsg/include/tsl/bhopscotch_set.h:166:82: [1] (buffer) equal:
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.
bhopscotch_set(init.begin(), init.end(), bucket_count, hash, equal, alloc)
data/rapmap-0.15.0+dfsg/include/tsl/hopscotch_hash.h:603:35: [1] (buffer) equal:
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.
const KeyEqual& equal,
data/rapmap-0.15.0+dfsg/include/tsl/hopscotch_hash.h:606:54: [1] (buffer) equal:
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.
KeyEqual(equal),
data/rapmap-0.15.0+dfsg/include/tsl/hopscotch_hash.h:640:35: [1] (buffer) equal:
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.
const KeyEqual& equal,
data/rapmap-0.15.0+dfsg/include/tsl/hopscotch_hash.h:644:68: [1] (buffer) equal:
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.
KeyEqual(equal),
data/rapmap-0.15.0+dfsg/include/tsl/hopscotch_map.h:146:50: [1] (buffer) equal:
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.
m_ht(bucket_count, hash, equal, alloc, ht::DEFAULT_MAX_LOAD_FACTOR)
data/rapmap-0.15.0+dfsg/include/tsl/hopscotch_map.h:169:91: [1] (buffer) equal:
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.
const Allocator& alloc = Allocator()) : hopscotch_map(bucket_count, hash, equal, alloc)
data/rapmap-0.15.0+dfsg/include/tsl/hopscotch_map.h:194:81: [1] (buffer) equal:
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.
hopscotch_map(init.begin(), init.end(), bucket_count, hash, equal, alloc)
data/rapmap-0.15.0+dfsg/include/tsl/hopscotch_set.h:130:50: [1] (buffer) equal:
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.
m_ht(bucket_count, hash, equal, alloc, ht::DEFAULT_MAX_LOAD_FACTOR)
data/rapmap-0.15.0+dfsg/include/tsl/hopscotch_set.h:153:91: [1] (buffer) equal:
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.
const Allocator& alloc = Allocator()) : hopscotch_set(bucket_count, hash, equal, alloc)
data/rapmap-0.15.0+dfsg/include/tsl/hopscotch_set.h:178:81: [1] (buffer) equal:
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.
hopscotch_set(init.begin(), init.end(), bucket_count, hash, equal, alloc)
data/rapmap-0.15.0+dfsg/include/tsl/robin_hash.h:487:32: [1] (buffer) equal:
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.
const KeyEqual& equal,
data/rapmap-0.15.0+dfsg/include/tsl/robin_hash.h:490:49: [1] (buffer) equal:
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.
KeyEqual(equal),
data/rapmap-0.15.0+dfsg/include/tsl/robin_map.h:143:42: [1] (buffer) equal:
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.
m_ht(bucket_count, hash, equal, alloc, ht::DEFAULT_MAX_LOAD_FACTOR)
data/rapmap-0.15.0+dfsg/include/tsl/robin_map.h:166:84: [1] (buffer) equal:
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.
const Allocator& alloc = Allocator()): robin_map(bucket_count, hash, equal, alloc)
data/rapmap-0.15.0+dfsg/include/tsl/robin_map.h:191:67: [1] (buffer) equal:
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.
robin_map(init.begin(), init.end(), bucket_count, hash, equal, alloc)
data/rapmap-0.15.0+dfsg/include/tsl/robin_set.h:127:46: [1] (buffer) equal:
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.
m_ht(bucket_count, hash, equal, alloc, ht::DEFAULT_MAX_LOAD_FACTOR)
data/rapmap-0.15.0+dfsg/include/tsl/robin_set.h:150:84: [1] (buffer) equal:
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.
const Allocator& alloc = Allocator()): robin_set(bucket_count, hash, equal, alloc)
data/rapmap-0.15.0+dfsg/include/tsl/robin_set.h:175:67: [1] (buffer) equal:
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.
robin_set(init.begin(), init.end(), bucket_count, hash, equal, alloc)
data/rapmap-0.15.0+dfsg/include/zstr/strict_fstream.hpp:39:29: [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).
std::string tmp(p, std::strlen(p));
data/rapmap-0.15.0+dfsg/src/RapMapIndex.cpp:68:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bis.read(rawHashMem.get(), sizeInBytes);
data/rapmap-0.15.0+dfsg/src/RapMapIndexer.cpp:227:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (auto& read : rg) { // for each sequence
data/rapmap-0.15.0+dfsg/src/RapMapIndexer.cpp:228:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::string& readStr = read.seq;
data/rapmap-0.15.0+dfsg/src/RapMapIndexer.cpp:247:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
auto& recHeader = read.name;
data/rapmap-0.15.0+dfsg/src/RapMapIndexer.cpp:290:42: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
transcriptSeqs.push_back(read.seq);
data/rapmap-0.15.0+dfsg/src/RapMapMapper.cpp:757:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (auto& read : rg) {
data/rapmap-0.15.0+dfsg/src/RapMapMapper.cpp:758:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
readLen = read.seq.length();
data/rapmap-0.15.0+dfsg/src/RapMapMapper.cpp:761:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
hitCollector(read.seq, hits, MateStatus::SINGLE_END);
data/rapmap-0.15.0+dfsg/src/RapMapMapper.cpp:771:56: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
rapmap::utils::writeAlignmentsToStream(read, formatter,
data/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:535:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (auto& read : rg) { // for each sequence
data/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:536:32: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::string& readStr = read.seq;
data/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:547:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
auto& readName = read.name;
data/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:607:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.name);
data/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:626:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.name, tooLong);
data/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:630:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.name, k);
data/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:636:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
auto& recHeader = read.name;
data/rapmap-0.15.0+dfsg/src/RapMapSAIndexer.cpp:704:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.name);
data/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:227:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for (auto& read : rg) {
data/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:228:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.seq.length();
data/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:232:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
hitCollector(read.seq, saSearcher, hcInfo);
data/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:247:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
auto* r1 = read.seq.data();
data/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:248:46: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
auto l1 = static_cast<int32_t>(read.seq.length());
data/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:255:42: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int32_t maxReadScore = a * read.seq.length();
data/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:268:46: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
rapmap::utils::reverseRead(read.seq, rc1);
data/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:321:56: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
rapmap::utils::writeAlignmentsToStream(read, formatter,
data/rapmap-0.15.0+dfsg/src/RapMapSAMapper.cpp:324:61: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
rapmap::utils::writeUnalignedSingleToStream(read, sstream);
data/rapmap-0.15.0+dfsg/src/bit_array.c:1166:41: [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).
bit_array_from_substr(bitarr, 0, str, strlen(str), "1", "0", 1);
data/rapmap-0.15.0+dfsg/src/ksw2pp/KSW2Aligner.cpp:74:49: [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.
KSW2Aligner::KSW2Aligner(int8_t match, int8_t mismatch) {
data/rapmap-0.15.0+dfsg/src/ksw2pp/KSW2Aligner.cpp:82:11: [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.
int b = mismatch;
data/rapmap-0.15.0+dfsg/src/metro/metrohash128.cpp:245:29: [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).
MetroHash128::Hash(key, strlen(MetroHash128::test_string), hash, 0);
data/rapmap-0.15.0+dfsg/src/metro/metrohash128.cpp:248:29: [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).
MetroHash128::Hash(key, strlen(MetroHash128::test_string), hash, 1);
data/rapmap-0.15.0+dfsg/src/metro/metrohash128.cpp:255:80: [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).
metro.Update(reinterpret_cast<const uint8_t *>(MetroHash128::test_string), strlen(MetroHash128::test_string));
data/rapmap-0.15.0+dfsg/src/metro/metrohash128.cpp:260:80: [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).
metro.Update(reinterpret_cast<const uint8_t *>(MetroHash128::test_string), strlen(MetroHash128::test_string));
data/rapmap-0.15.0+dfsg/src/metro/metrohash64.cpp:241:28: [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).
MetroHash64::Hash(key, strlen(MetroHash64::test_string), hash, 0);
data/rapmap-0.15.0+dfsg/src/metro/metrohash64.cpp:244:28: [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).
MetroHash64::Hash(key, strlen(MetroHash64::test_string), hash, 1);
data/rapmap-0.15.0+dfsg/src/metro/metrohash64.cpp:251:79: [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).
metro.Update(reinterpret_cast<const uint8_t *>(MetroHash64::test_string), strlen(MetroHash64::test_string));
data/rapmap-0.15.0+dfsg/src/metro/metrohash64.cpp:256:79: [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).
metro.Update(reinterpret_cast<const uint8_t *>(MetroHash64::test_string), strlen(MetroHash64::test_string));
ANALYSIS SUMMARY:
Hits = 348
Lines analyzed = 79188 in approximately 1.96 seconds (40473 lines/second)
Physical Source Lines of Code (SLOC) = 53500
Hits@level = [0] 36 [1] 143 [2] 176 [3] 3 [4] 26 [5] 0
Hits@level+ = [0+] 384 [1+] 348 [2+] 205 [3+] 29 [4+] 26 [5+] 0
Hits/KSLOC@level+ = [0+] 7.17757 [1+] 6.50467 [2+] 3.83178 [3+] 0.542056 [4+] 0.485981 [5+] 0
Dot directories skipped = 3 (--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.