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/salmon-1.4.0+ds1/include/AlevinHash.hpp
Examining data/salmon-1.4.0+ds1/include/AlevinOpts.hpp
Examining data/salmon-1.4.0+ds1/include/AlevinTypes.hpp
Examining data/salmon-1.4.0+ds1/include/AlevinUtils.hpp
Examining data/salmon-1.4.0+ds1/include/AlignmentGroup.hpp
Examining data/salmon-1.4.0+ds1/include/AlignmentLibrary.hpp
Examining data/salmon-1.4.0+ds1/include/AlignmentModel.hpp
Examining data/salmon-1.4.0+ds1/include/AtomicMatrix.hpp
Examining data/salmon-1.4.0+ds1/include/BAMQueue.hpp
Examining data/salmon-1.4.0+ds1/include/BAMUtils.hpp
Examining data/salmon-1.4.0+ds1/include/BarcodeGroup.hpp
Examining data/salmon-1.4.0+ds1/include/BarcodeModel.hpp
Examining data/salmon-1.4.0+ds1/include/BiasParams.hpp
Examining data/salmon-1.4.0+ds1/include/BinaryLiteral.hpp
Examining data/salmon-1.4.0+ds1/include/BootstrapWriter.hpp
Examining data/salmon-1.4.0+ds1/include/ClusterForest.hpp
Examining data/salmon-1.4.0+ds1/include/CollapsedCellOptimizer.hpp
Examining data/salmon-1.4.0+ds1/include/CollapsedEMOptimizer.hpp
Examining data/salmon-1.4.0+ds1/include/CollapsedGibbsSampler.hpp
Examining data/salmon-1.4.0+ds1/include/CommonTypes.hpp
Examining data/salmon-1.4.0+ds1/include/DedupUMI.hpp
Examining data/salmon-1.4.0+ds1/include/DistributionUtils.hpp
Examining data/salmon-1.4.0+ds1/include/EMUtils.hpp
Examining data/salmon-1.4.0+ds1/include/EffectiveLengthStats.hpp
Examining data/salmon-1.4.0+ds1/include/EquivalenceClassBuilder.hpp
Examining data/salmon-1.4.0+ds1/include/FASTAParser.hpp
Examining data/salmon-1.4.0+ds1/include/FastxParser.hpp
Examining data/salmon-1.4.0+ds1/include/FastxParserThreadUtils.hpp
Examining data/salmon-1.4.0+ds1/include/FragmentLengthDistribution.hpp
Examining data/salmon-1.4.0+ds1/include/FragmentList.hpp
Examining data/salmon-1.4.0+ds1/include/FragmentStartPositionDistribution.hpp
Examining data/salmon-1.4.0+ds1/include/GCFragModel.hpp
Examining data/salmon-1.4.0+ds1/include/GZipWriter.hpp
Examining data/salmon-1.4.0+ds1/include/GenomicFeature.hpp
Examining data/salmon-1.4.0+ds1/include/Graph.hpp
Examining data/salmon-1.4.0+ds1/include/IOUtils.hpp
Examining data/salmon-1.4.0+ds1/include/IndexVersionInfo.hpp
Examining data/salmon-1.4.0+ds1/include/KmerContext.hpp
Examining data/salmon-1.4.0+ds1/include/LibraryFormat.hpp
Examining data/salmon-1.4.0+ds1/include/LibraryTypeDetector.hpp
Examining data/salmon-1.4.0+ds1/include/MappingStatistics.hpp
Examining data/salmon-1.4.0+ds1/include/MicroOpts.hpp
Examining data/salmon-1.4.0+ds1/include/MiniBatchInfo.hpp
Examining data/salmon-1.4.0+ds1/include/MultinomialSampler.hpp
Examining data/salmon-1.4.0+ds1/include/NullFragmentFilter.hpp
Examining data/salmon-1.4.0+ds1/include/OutputUnmappedFilter.hpp
Examining data/salmon-1.4.0+ds1/include/PCA.hpp
Examining data/salmon-1.4.0+ds1/include/ProgramOptionsGenerator.hpp
Examining data/salmon-1.4.0+ds1/include/ReadExperiment.hpp
Examining data/salmon-1.4.0+ds1/include/ReadKmerDist.hpp
Examining data/salmon-1.4.0+ds1/include/ReadLibrary.hpp
Examining data/salmon-1.4.0+ds1/include/ReadPair.hpp
Examining data/salmon-1.4.0+ds1/include/ReadProducer.hpp
Examining data/salmon-1.4.0+ds1/include/SBModel.hpp
Examining data/salmon-1.4.0+ds1/include/SGSmooth.hpp
Examining data/salmon-1.4.0+ds1/include/SalmonConfig.hpp
Examining data/salmon-1.4.0+ds1/include/SalmonDefaults.hpp
Examining data/salmon-1.4.0+ds1/include/SalmonExceptions.hpp
Examining data/salmon-1.4.0+ds1/include/SalmonIndex.hpp
Examining data/salmon-1.4.0+ds1/include/SalmonIndexVersionInfo.hpp
Examining data/salmon-1.4.0+ds1/include/SalmonMappingUtils.hpp
Examining data/salmon-1.4.0+ds1/include/SalmonMath.hpp
Examining data/salmon-1.4.0+ds1/include/SalmonOpts.hpp
Examining data/salmon-1.4.0+ds1/include/SalmonSpinLock.hpp
Examining data/salmon-1.4.0+ds1/include/SalmonStringUtils.hpp
Examining data/salmon-1.4.0+ds1/include/Sampler.hpp
Examining data/salmon-1.4.0+ds1/include/SequenceBiasModel.hpp
Examining data/salmon-1.4.0+ds1/include/SimplePosBias.hpp
Examining data/salmon-1.4.0+ds1/include/SingleCellProtocols.hpp
Examining data/salmon-1.4.0+ds1/include/StadenUtils.hpp
Examining data/salmon-1.4.0+ds1/include/SufficientStatisticsQueue.hpp
Examining data/salmon-1.4.0+ds1/include/TextBootstrapWriter.hpp
Examining data/salmon-1.4.0+ds1/include/Transcript.hpp
Examining data/salmon-1.4.0+ds1/include/TranscriptCluster.hpp
Examining data/salmon-1.4.0+ds1/include/TranscriptGeneMap.hpp
Examining data/salmon-1.4.0+ds1/include/TranscriptGroup.hpp
Examining data/salmon-1.4.0+ds1/include/TryableSpinLock.hpp
Examining data/salmon-1.4.0+ds1/include/UnpairedRead.hpp
Examining data/salmon-1.4.0+ds1/include/UtilityFunctions.hpp
Examining data/salmon-1.4.0+ds1/include/VersionChecker.hpp
Examining data/salmon-1.4.0+ds1/include/WhiteList.hpp
Examining data/salmon-1.4.0+ds1/include/atomicops.h
Examining data/salmon-1.4.0+ds1/include/blockingconcurrentqueue.h
Examining data/salmon-1.4.0+ds1/include/concurrentqueue.h
Examining data/salmon-1.4.0+ds1/include/core/algorithm.hpp
Examining data/salmon-1.4.0+ds1/include/core/any.hpp
Examining data/salmon-1.4.0+ds1/include/core/array.hpp
Examining data/salmon-1.4.0+ds1/include/core/deque.hpp
Examining data/salmon-1.4.0+ds1/include/core/forward_list.hpp
Examining data/salmon-1.4.0+ds1/include/core/functional.hpp
Examining data/salmon-1.4.0+ds1/include/core/internal.hpp
Examining data/salmon-1.4.0+ds1/include/core/iterator.hpp
Examining data/salmon-1.4.0+ds1/include/core/list.hpp
Examining data/salmon-1.4.0+ds1/include/core/map.hpp
Examining data/salmon-1.4.0+ds1/include/core/memory.hpp
Examining data/salmon-1.4.0+ds1/include/core/memory_resource.hpp
Examining data/salmon-1.4.0+ds1/include/core/meta.hpp
Examining data/salmon-1.4.0+ds1/include/core/numeric.hpp
Examining data/salmon-1.4.0+ds1/include/core/optional.hpp
Examining data/salmon-1.4.0+ds1/include/core/propagate_const.hpp
Examining data/salmon-1.4.0+ds1/include/core/range.hpp
Examining data/salmon-1.4.0+ds1/include/core/regex.hpp
Examining data/salmon-1.4.0+ds1/include/core/set.hpp
Examining data/salmon-1.4.0+ds1/include/core/string.hpp
Examining data/salmon-1.4.0+ds1/include/core/string_view.hpp
Examining data/salmon-1.4.0+ds1/include/core/type_traits.hpp
Examining data/salmon-1.4.0+ds1/include/core/typeinfo.hpp
Examining data/salmon-1.4.0+ds1/include/core/unordered_map.hpp
Examining data/salmon-1.4.0+ds1/include/core/unordered_set.hpp
Examining data/salmon-1.4.0+ds1/include/core/utility.hpp
Examining data/salmon-1.4.0+ds1/include/core/variant.hpp
Examining data/salmon-1.4.0+ds1/include/core/vector.hpp
Examining data/salmon-1.4.0+ds1/include/edlib.h
Examining data/salmon-1.4.0+ds1/include/ezETAProgressBar.hpp
Examining data/salmon-1.4.0+ds1/include/fastapprox.h
Examining data/salmon-1.4.0+ds1/include/format.h
Examining data/salmon-1.4.0+ds1/include/httplib.hpp
Examining data/salmon-1.4.0+ds1/include/jellyfish/int128.hpp
Examining data/salmon-1.4.0+ds1/include/jellyfish/mer_dna.hpp
Examining data/salmon-1.4.0+ds1/include/jellyfish/misc.hpp
Examining data/salmon-1.4.0+ds1/include/json.hpp
Examining data/salmon-1.4.0+ds1/include/kseq.h
Examining data/salmon-1.4.0+ds1/include/lightweightsemaphore.h
Examining data/salmon-1.4.0+ds1/include/make_unique.hpp
Examining data/salmon-1.4.0+ds1/include/nonstd/optional.hpp
Examining data/salmon-1.4.0+ds1/include/nonstd/string_view.hpp
Examining data/salmon-1.4.0+ds1/include/parallel_hashmap/meminfo.h
Examining data/salmon-1.4.0+ds1/include/parallel_hashmap/phmap.h
Examining data/salmon-1.4.0+ds1/include/parallel_hashmap/phmap_base.h
Examining data/salmon-1.4.0+ds1/include/parallel_hashmap/phmap_bits.h
Examining data/salmon-1.4.0+ds1/include/parallel_hashmap/phmap_config.h
Examining data/salmon-1.4.0+ds1/include/parallel_hashmap/phmap_fwd_decl.h
Examining data/salmon-1.4.0+ds1/include/parallel_hashmap/phmap_utils.h
Examining data/salmon-1.4.0+ds1/include/pcg_extras.hpp
Examining data/salmon-1.4.0+ds1/include/pcg_random.hpp
Examining data/salmon-1.4.0+ds1/include/peglib.h
Examining data/salmon-1.4.0+ds1/include/radicl/BasicBinWriter.hpp
Examining data/salmon-1.4.0+ds1/include/radicl/RADHeader.hpp
Examining data/salmon-1.4.0+ds1/include/readerwriterqueue.h
Examining data/salmon-1.4.0+ds1/include/spdlog/async_logger.h
Examining data/salmon-1.4.0+ds1/include/spdlog/common.h
Examining data/salmon-1.4.0+ds1/include/spdlog/details/async_log_helper.h
Examining data/salmon-1.4.0+ds1/include/spdlog/details/async_logger_impl.h
Examining data/salmon-1.4.0+ds1/include/spdlog/details/file_helper.h
Examining data/salmon-1.4.0+ds1/include/spdlog/details/log_msg.h
Examining data/salmon-1.4.0+ds1/include/spdlog/details/logger_impl.h
Examining data/salmon-1.4.0+ds1/include/spdlog/details/mpmc_bounded_q.h
Examining data/salmon-1.4.0+ds1/include/spdlog/details/null_mutex.h
Examining data/salmon-1.4.0+ds1/include/spdlog/details/os.h
Examining data/salmon-1.4.0+ds1/include/spdlog/details/pattern_formatter_impl.h
Examining data/salmon-1.4.0+ds1/include/spdlog/details/registry.h
Examining data/salmon-1.4.0+ds1/include/spdlog/details/spdlog_impl.h
Examining data/salmon-1.4.0+ds1/include/spdlog/fmt/bundled/container.h
Examining data/salmon-1.4.0+ds1/include/spdlog/fmt/bundled/format.cc
Examining data/salmon-1.4.0+ds1/include/spdlog/fmt/bundled/format.h
Examining data/salmon-1.4.0+ds1/include/spdlog/fmt/bundled/ostream.cc
Examining data/salmon-1.4.0+ds1/include/spdlog/fmt/bundled/ostream.h
Examining data/salmon-1.4.0+ds1/include/spdlog/fmt/bundled/posix.cc
Examining data/salmon-1.4.0+ds1/include/spdlog/fmt/bundled/posix.h
Examining data/salmon-1.4.0+ds1/include/spdlog/fmt/bundled/printf.cc
Examining data/salmon-1.4.0+ds1/include/spdlog/fmt/bundled/printf.h
Examining data/salmon-1.4.0+ds1/include/spdlog/fmt/bundled/string.h
Examining data/salmon-1.4.0+ds1/include/spdlog/fmt/bundled/time.h
Examining data/salmon-1.4.0+ds1/include/spdlog/fmt/fmt.h
Examining data/salmon-1.4.0+ds1/include/spdlog/fmt/ostr.h
Examining data/salmon-1.4.0+ds1/include/spdlog/formatter.h
Examining data/salmon-1.4.0+ds1/include/spdlog/logger.h
Examining data/salmon-1.4.0+ds1/include/spdlog/sinks/android_sink.h
Examining data/salmon-1.4.0+ds1/include/spdlog/sinks/ansicolor_sink.h
Examining data/salmon-1.4.0+ds1/include/spdlog/sinks/base_sink.h
Examining data/salmon-1.4.0+ds1/include/spdlog/sinks/dist_sink.h
Examining data/salmon-1.4.0+ds1/include/spdlog/sinks/file_sinks.h
Examining data/salmon-1.4.0+ds1/include/spdlog/sinks/msvc_sink.h
Examining data/salmon-1.4.0+ds1/include/spdlog/sinks/null_sink.h
Examining data/salmon-1.4.0+ds1/include/spdlog/sinks/ostream_sink.h
Examining data/salmon-1.4.0+ds1/include/spdlog/sinks/sink.h
Examining data/salmon-1.4.0+ds1/include/spdlog/sinks/stdout_sinks.h
Examining data/salmon-1.4.0+ds1/include/spdlog/sinks/syslog_sink.h
Examining data/salmon-1.4.0+ds1/include/spdlog/sinks/wincolor_sink.h
Examining data/salmon-1.4.0+ds1/include/spdlog/sinks/windebug_sink.h
Examining data/salmon-1.4.0+ds1/include/spdlog/spdlog.h
Examining data/salmon-1.4.0+ds1/include/spdlog/tweakme.h
Examining data/salmon-1.4.0+ds1/include/spline.h
Examining data/salmon-1.4.0+ds1/include/strict_fstream.hpp
Examining data/salmon-1.4.0+ds1/include/stx/any.hpp
Examining data/salmon-1.4.0+ds1/include/stx/optional.hpp
Examining data/salmon-1.4.0+ds1/include/stx/string_view.hpp
Examining data/salmon-1.4.0+ds1/include/stx/variant.hpp
Examining data/salmon-1.4.0+ds1/include/xxhash.h
Examining data/salmon-1.4.0+ds1/include/zstr.hpp
Examining data/salmon-1.4.0+ds1/include/ForgettingMassCalculator.hpp
Examining data/salmon-1.4.0+ds1/include/SalmonUtils.hpp
Examining data/salmon-1.4.0+ds1/scripts/v1_10x/wrapper.cpp
Examining data/salmon-1.4.0+ds1/src/Alevin.cpp
Examining data/salmon-1.4.0+ds1/src/AlevinHash.cpp
Examining data/salmon-1.4.0+ds1/src/AlevinUtils.cpp
Examining data/salmon-1.4.0+ds1/src/AlignmentModel.cpp
Examining data/salmon-1.4.0+ds1/src/BAMUtils.cpp
Examining data/salmon-1.4.0+ds1/src/BuildSalmonIndex.cpp
Examining data/salmon-1.4.0+ds1/src/CollapsedCellOptimizer.cpp
Examining data/salmon-1.4.0+ds1/src/CollapsedEMOptimizer.cpp
Examining data/salmon-1.4.0+ds1/src/CollapsedGibbsSampler.cpp
Examining data/salmon-1.4.0+ds1/src/DedupUMI.cpp
Examining data/salmon-1.4.0+ds1/src/DistributionUtils.cpp
Examining data/salmon-1.4.0+ds1/src/EMUtils.cpp
Examining data/salmon-1.4.0+ds1/src/EffectiveLengthStats.cpp
Examining data/salmon-1.4.0+ds1/src/FASTAParser.cpp
Examining data/salmon-1.4.0+ds1/src/FastxParser.cpp
Examining data/salmon-1.4.0+ds1/src/FragmentLengthDistribution.cpp
Examining data/salmon-1.4.0+ds1/src/FragmentList.cpp
Examining data/salmon-1.4.0+ds1/src/FragmentStartPositionDistribution.cpp
Examining data/salmon-1.4.0+ds1/src/GZipWriter.cpp
Examining data/salmon-1.4.0+ds1/src/GenomicFeature.cpp
Examining data/salmon-1.4.0+ds1/src/Graph.cpp
Examining data/salmon-1.4.0+ds1/src/LibraryFormat.cpp
Examining data/salmon-1.4.0+ds1/src/PCA.cpp
Examining data/salmon-1.4.0+ds1/src/PCAUtils.cpp
Examining data/salmon-1.4.0+ds1/src/SBModel.cpp
Examining data/salmon-1.4.0+ds1/src/SGSmooth.cpp
Examining data/salmon-1.4.0+ds1/src/SalmonAlevin.cpp
Examining data/salmon-1.4.0+ds1/src/SalmonExceptions.cpp
Examining data/salmon-1.4.0+ds1/src/SalmonQuantMerge.cpp
Examining data/salmon-1.4.0+ds1/src/SalmonQuantify.cpp
Examining data/salmon-1.4.0+ds1/src/SalmonQuantifyAlignments.cpp
Examining data/salmon-1.4.0+ds1/src/SalmonStringUtils.cpp
Examining data/salmon-1.4.0+ds1/src/SequenceBiasModel.cpp
Examining data/salmon-1.4.0+ds1/src/SimplePosBias.cpp
Examining data/salmon-1.4.0+ds1/src/SingleCellProtocols.cpp
Examining data/salmon-1.4.0+ds1/src/StadenUtils.cpp
Examining data/salmon-1.4.0+ds1/src/TestUtils.cpp
Examining data/salmon-1.4.0+ds1/src/TranscriptGroup.cpp
Examining data/salmon-1.4.0+ds1/src/VersionChecker.cpp
Examining data/salmon-1.4.0+ds1/src/WhiteList.cpp
Examining data/salmon-1.4.0+ds1/src/edlib.cpp
Examining data/salmon-1.4.0+ds1/src/jellyfish/mer_dna.cc
Examining data/salmon-1.4.0+ds1/src/xxhash.c
Examining data/salmon-1.4.0+ds1/src/ProgramOptionsGenerator.cpp
Examining data/salmon-1.4.0+ds1/src/SalmonUtils.cpp
Examining data/salmon-1.4.0+ds1/src/Salmon.cpp
Examining data/salmon-1.4.0+ds1/tests/GCSampleTests.cpp
Examining data/salmon-1.4.0+ds1/tests/KmerHistTests.cpp
Examining data/salmon-1.4.0+ds1/tests/LibraryTypeTests.cpp
Examining data/salmon-1.4.0+ds1/tests/UnitTests.cpp
Examining data/salmon-1.4.0+ds1/tests/catch.hpp
Examining data/salmon-1.4.0+ds1/tests/compile_tests/int128_numeric_limits.cpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BinWriter.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BulkChunk.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/CanonicalKmer.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/CanonicalKmerIterator.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/CommonTypes.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/Kmer.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/MemChainer.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/MemCollector.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/PairedAlignmentFormatter.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/ProgOpts.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/PuffAligner.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/PufferfishBaseIndex.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/PufferfishConfig.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/PufferfishIndex.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/PufferfishLossyIndex.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/PufferfishSparseIndex.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/PufferfishTypes.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/SAMWriter.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/SelectiveAlignmentUtils.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/SpinLock.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/Util.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/chobo/flat_map.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/chobo/memory_view.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/chobo/optional.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/chobo/small_vector.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/chobo/static_vector.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/chobo/vector.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/chobo/vector_ptr.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/chobo/vector_view.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/compact_iterator.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/compact_vector.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/const_iterator_traits.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/mio.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/parallel_iterator_traits.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/prefetch_iterator_traits.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/ksw2pp/KSW2Aligner.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/ksw2pp/kalloc.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/ksw2pp/ksw2.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/libdivide/libdivide.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/macros.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/metro/metrohash.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/metro/metrohash128.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/metro/metrohash128crc.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/metro/metrohash64.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/metro/platform.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/metro/testvector.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/rank9b.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/rank9sel.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/select.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/sparsepp/spp.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/sparsepp/spp_config.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/sparsepp/spp_dlalloc.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/sparsepp/spp_memory.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/sparsepp/spp_smartptr.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/sparsepp/spp_stdint.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/sparsepp/spp_timer.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/sparsepp/spp_traits.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/sparsepp/spp_utils.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/string_view.hpp
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/tsl/array_growth_policy.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/tsl/array_hash.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/tsl/array_map.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/tsl/array_set.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/tsl/bhopscotch_map.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/tsl/bhopscotch_set.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/tsl/hopscotch_growth_policy.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/tsl/hopscotch_hash.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/tsl/hopscotch_map.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/tsl/hopscotch_set.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/tsl/robin_growth_policy.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/tsl/robin_hash.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/tsl/robin_map.h
Examining data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/tsl/robin_set.h
Examining data/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/metro/metrohash128.cpp
Examining data/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/metro/metrohash128crc.cpp
Examining data/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/metro/metrohash64.cpp
Examining data/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/rank9b.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/examples/gtk_scheduler.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/include/async++/aligned_alloc.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/include/async++/cancel.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/include/async++/continuation_vector.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/include/async++/parallel_for.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/include/async++/parallel_invoke.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/include/async++/parallel_reduce.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/include/async++/partitioner.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/include/async++/range.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/include/async++/ref_count.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/include/async++/scheduler.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/include/async++/scheduler_fwd.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/include/async++/task.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/include/async++/task_base.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/include/async++/traits.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/include/async++/when_all_any.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/include/async++.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/src/fifo_queue.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/src/internal.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/src/scheduler.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/src/singleton.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/src/task_wait_event.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/src/threadpool_scheduler.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/src/work_steal_queue.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/Fcontrol.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/Fcontrol.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/SignalHandler.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/SignalHandler.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/StringUtil.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/Uncompress.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/Uncompress.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/ntHashIterator.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/nthash.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/nthll.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/dnachar.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/dnachar.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/junctionapi/junctionapi.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/ngramhashing/characterhash.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/ngramhashing/cyclichash.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/ngramhashing/example.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/ngramhashing/example2.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/ngramhashing/example3.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/ngramhashing/example4.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/ngramhashing/example64bits.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/ngramhashing/generalhash.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/ngramhashing/mersennetwister.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/ngramhashing/rabinkarphash.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/ngramhashing/speedtesting.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/ngramhashing/threewisehash.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/ngramhashing/unit.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/ngramhashing/ztimer.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/spooky/SpookyV2.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/spooky/SpookyV2.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/streamfastaparser.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/streamfastaparser.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/Arg.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/ArgException.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/ArgTraits.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/CmdLine.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/CmdLineInterface.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/CmdLineOutput.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/Constraint.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/DocBookOutput.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/HelpVisitor.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/IgnoreRestVisitor.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/MultiArg.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/MultiSwitchArg.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/OptionalUnlabeledTracker.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/StandardTraits.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/StdOutput.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/SwitchArg.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/UnlabeledMultiArg.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/UnlabeledValueArg.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/ValueArg.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/ValuesConstraint.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/VersionVisitor.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/Visitor.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/XorHandler.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/tclap/ZshCompletionOutput.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/assemblyedgeconstructor.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/assemblyedgeconstructor.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/bifurcationstorage.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/candidateoccurence.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/common.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/common.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/compressedstring.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/compressedstring.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/concurrentbitvector.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/concurrentbitvector.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/constructor.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/test.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/test.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/vertexrollinghash.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/const_iterator_traits.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/mio.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/parallel_iterator_traits.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/prefetch_iterator_traits.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/graphdump.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/graphdumpBinaryWriter.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/pufferize.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/naiveconstructor/naiveconstructor.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/BinWriter.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/BulkChunk.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/CLI/App.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/CLI/CLI.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/CLI/Error.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/CLI/Ini.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/CLI/Option.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/CLI/Split.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/CLI/StringTools.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/CLI/Timer.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/CLI/TypeTools.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/CLI/Validators.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/CanonicalKmer.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/CanonicalKmerIterator.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/Cedar.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/CommonTypes.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/EquivalenceClassBuilder.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/FastxParser.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/FastxParserThreadUtils.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/FatPufferGraph.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/KSW2Aligner.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/Kmer.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/KrakMap.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/MemChainer.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/MemCollector.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PairedAlignmentFormatter.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ProgOpts.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PuffAligner.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PuffMappingReader.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PufferFS.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PufferGraph.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PufferfishBaseIndex.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PufferfishBinaryGFAReader.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PufferfishConfig.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PufferfishGFAReader.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PufferfishIndex.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PufferfishLossyIndex.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PufferfishSparseIndex.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PufferfishTypes.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/RefSeqConstructor.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/SAMReader.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/SAMWriter.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ScopedTimer.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/SelectiveAlignmentUtils.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/SpinLock.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/TargetGroup.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/Taxa.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/Util.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/access.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/archives/adapters.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/archives/binary.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/archives/json.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/archives/portable_binary.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/archives/xml.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/cereal.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/helpers.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/polymorphic_impl.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/polymorphic_impl_fwd.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/static_object.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/util.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/base64.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/allocators.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/document.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/encodedstream.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/encodings.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/error/en.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/error/error.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/filereadstream.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/filewritestream.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/fwd.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/internal/biginteger.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/internal/diyfp.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/internal/dtoa.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/internal/ieee754.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/internal/itoa.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/internal/meta.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/internal/pow10.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/internal/regex.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/internal/stack.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/internal/strfunc.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/internal/strtod.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/internal/swap.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/istreamwrapper.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/memorybuffer.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/memorystream.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/msinttypes/inttypes.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/msinttypes/stdint.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/ostreamwrapper.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/pointer.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/prettywriter.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/rapidjson.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/reader.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/schema.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/stream.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/stringbuffer.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/writer.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidxml/rapidxml.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidxml/rapidxml_iterators.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidxml/rapidxml_print.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidxml/rapidxml_utils.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/macros.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/specialize.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/array.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/atomic.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/base_class.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/bitset.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/boost_variant.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/chrono.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/common.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/complex.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/concepts/pair_associative_container.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/deque.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/forward_list.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/functional.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/list.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/map.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/memory.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/optional.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/polymorphic.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/queue.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/set.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/stack.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/string.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/tuple.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/unordered_map.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/unordered_set.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/utility.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/valarray.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/variant.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/vector.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/version.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/chobo/flat_map.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/chobo/memory_view.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/chobo/optional.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/chobo/small_vector.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/chobo/static_vector.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/chobo/vector.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/chobo/vector_ptr.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/chobo/vector_view.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/clipp.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/compact_iterator.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/compact_vector.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/const_iterator_traits.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/mio.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/parallel_iterator_traits.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/prefetch_iterator_traits.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/concurrentqueue.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/algorithm.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/any.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/array.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/deque.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/forward_list.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/functional.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/internal.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/iterator.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/list.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/map.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/memory.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/memory_resource.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/meta.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/numeric.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/optional.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/propagate_const.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/range.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/regex.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/set.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/string.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/string_view.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/type_traits.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/typeinfo.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/unordered_map.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/unordered_set.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/utility.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/variant.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/vector.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/blake.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/blake2.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/blake2_provider.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/blake_provider.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/constants/blake2_constants.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/constants/blake_constants.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/constants/groestl_constants.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/constants/jh_constants.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/constants/kupyna_constants.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/constants/md5_constants.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/constants/sha1_constants.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/constants/sha2_constants.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/constants/sha3_constants.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/constants/skein_constants.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/constants/streebog_constants.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/constants/whirlpool_constants.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/groestl_provider.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/jh_provider.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/k12m14_provider.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/kmac_provider.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/kupyna_provider.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/md5_provider.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/sha1_provider.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/sha2_provider.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/sha3_provider.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/shake_provider.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/skein_provider.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/sm3_provider.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/streebog_provider.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/detail/whirlpool_provider.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/groestl.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/jh.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/k12m14.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/kmac.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/kupyna.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/md5.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/mixin/blake2_mixin.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/mixin/blake_mixin.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/mixin/cshake_mixin.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/mixin/k12m14_mixin.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/mixin/kmac_mixin.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/mixin/null_mixin.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/mixin/skein_mixin.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/sha1.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/sha2.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/sha3.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/shake.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/skein.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/sm3.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/streebog.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/algorithm/whirlpool.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/detail/absorb_data.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/detail/functions.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/detail/stream_width_fixer.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/detail/traits.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/detail/validate_hash_size.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/digestpp.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/digestpp/hasher.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/edlib.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/fs_fwd.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/fs_impl.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/fs_std.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/fs_std_fwd.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/fs_std_impl.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/jellyfish/int128.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/jellyfish/mer_dna.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/jellyfish/misc.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/kalloc.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/kseq.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ksw2pp/KSW2Aligner.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ksw2pp/kalloc.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ksw2pp/ksw2.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/libdivide/libdivide.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/macros.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/metro/metrohash.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/metro/metrohash128.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/metro/metrohash128crc.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/metro/metrohash64.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/metro/platform.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/metro/testvector.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/nonstd/string_view.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/parallel_hashmap/meminfo.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/parallel_hashmap/phmap.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/parallel_hashmap/phmap_base.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/parallel_hashmap/phmap_bits.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/parallel_hashmap/phmap_config.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/parallel_hashmap/phmap_fwd_decl.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/parallel_hashmap/phmap_utils.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/popl.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/rank9b.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/rank9sel.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/select.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/sparsepp/spp.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/sparsepp/spp_config.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/sparsepp/spp_dlalloc.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/sparsepp/spp_memory.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/sparsepp/spp_smartptr.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/sparsepp/spp_stdint.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/sparsepp/spp_timer.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/sparsepp/spp_traits.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/sparsepp/spp_utils.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/async_logger.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/common.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/details/async_log_helper.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/details/async_logger_impl.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/details/file_helper.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/details/log_msg.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/details/logger_impl.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/details/mpmc_bounded_q.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/details/null_mutex.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/details/os.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/details/pattern_formatter_impl.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/details/registry.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/details/spdlog_impl.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/fmt/bundled/container.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/fmt/bundled/format.cc
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/fmt/bundled/format.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/fmt/bundled/ostream.cc
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/fmt/bundled/ostream.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/fmt/bundled/posix.cc
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/fmt/bundled/posix.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/fmt/bundled/printf.cc
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/fmt/bundled/printf.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/fmt/bundled/string.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/fmt/bundled/time.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/fmt/fmt.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/fmt/ostr.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/formatter.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/logger.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/sinks/android_sink.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/sinks/ansicolor_sink.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/sinks/base_sink.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/sinks/dist_sink.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/sinks/file_sinks.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/sinks/msvc_sink.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/sinks/null_sink.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/sinks/ostream_sink.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/sinks/sink.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/sinks/stdout_sinks.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/sinks/syslog_sink.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/sinks/wincolor_sink.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/sinks/windebug_sink.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/spdlog.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/tweakme.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/string_view.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/tsl/array_growth_policy.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/tsl/array_hash.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/tsl/array_map.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/tsl/array_set.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/tsl/bhopscotch_map.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/tsl/bhopscotch_set.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/tsl/hopscotch_growth_policy.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/tsl/hopscotch_hash.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/tsl/hopscotch_map.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/tsl/hopscotch_set.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/tsl/robin_growth_policy.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/tsl/robin_hash.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/tsl/robin_map.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/tsl/robin_set.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/xxhash.h
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/zstr/strict_fstream.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/include/zstr/zstr.hpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/BCALMPufferizer.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/Cedar.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/EdgeDensity.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/EdgeDensityCustom.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/FastxParser.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/FixFasta.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/KrakMap.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/MemChainer.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/MemCollector.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/MyGFATester.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/MyGraphTester.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PuffAligner.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferFS.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/Pufferfish.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishAligner.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishBaseIndex.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishBinaryGFAReader.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishExamine.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishGFAReader.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishIndex.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishIndexer.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishLossyIndex.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishSparseIndex.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishStats.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishTestLookup.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishValidate.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/RefSeqConstructor.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/TargetGroup.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/Taxa.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/Util.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/cli.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/constructLineage.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/edlib.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/kalloc.c
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/ksw2pp/KSW2Aligner.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/ksw2pp/kalloc.c
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/ksw2pp/ksw2_dispatch.c
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/ksw2pp/ksw2_extd.c
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/ksw2pp/ksw2_exts2_sse.c
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/ksw2pp/ksw2_extz.c
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/ksw2pp/ksw2_gg.c
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/ksw2pp/ksw2_gg2.c
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/ksw2pp/ksw2_gg2_sse.c
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/metro/metrohash128.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/metro/metrohash128crc.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/metro/metrohash64.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/rank9b.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/rank9sel.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/rank_test.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/testing/SAMFilter.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/testing/SAMStats.cpp
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/src/xxhash.c
Examining data/salmon-1.4.0+ds1/debian/external/pufferfish/tests/compile_tests/int128_numeric_limits.cpp

FINAL RESULTS:

data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:1715:21:  [5] (race) readlink:
  This accepts filename arguments; if an attacker can move those files or
  change the link content, a race condition results. Also, it does not
  terminate with ASCII NUL. (CWE-362, CWE-20). Reconsider approach.
        auto rc = ::readlink(p.c_str(), buffer.data(), buffer.size());
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:3953:15:  [5] (race) chmod:
  This accepts filename arguments; if an attacker can move those files, a
  race condition results. (CWE-362). Use fchmod( ) instead.
        if (::chmod(p.c_str(), static_cast<mode_t>(prms)) != 0) {
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:1383:4:  [4] (format) sprintf:
  Potential format string problem (CWE-134). Make format string constant.
			sprintf(fname_old,dir.c_str(),_pid,i-2);
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:1386:4:  [4] (format) sprintf:
  Potential format string problem (CWE-134). Make format string constant.
			sprintf(fname_curr,dir.c_str(),_pid,i);
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:1389:4:  [4] (format) sprintf:
  Potential format string problem (CWE-134). Make format string constant.
			sprintf(fname_prev,dir.c_str(),_pid,i-1);
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/Uncompress.cpp:75:17:  [4] (buffer) sscanf:
  The scanf() family's %s operation, without a limit specification, permits
  buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
  different input function.
        int n = sscanf(zcat, "%s %s %s", arg0, arg1, arg2);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/Uncompress.cpp:95:17:  [4] (shell) execlp:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
                execlp(arg0, arg0, arg1, path, NULL);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/Uncompress.cpp:97:17:  [4] (shell) execlp:
  This causes a new program to execute and is difficult to use safely
  (CWE-78). try using a library call that implements the same functionality
  if available.
                execlp(arg0, arg0, arg1, arg2, path, NULL);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/compressedstring.h:241:4:  [4] (buffer) StrCpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
			StrCpy(it, 0, 0, size, Id);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/compressedstring.h:246:4:  [4] (buffer) StrCpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
			StrCpy(std::string::const_reverse_iterator(it + size), 0, 0, size, DnaChar::ReverseChar);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/compressedstring.h:253:8:  [4] (buffer) StrCpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
		void StrCpy(T src, size_t element, size_t idx, size_t size, F f)
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:1383:4:  [4] (format) sprintf:
  Potential format string problem (CWE-134). Make format string constant.
			sprintf(fname_old,dir.c_str(),_pid,i-2);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:1386:4:  [4] (format) sprintf:
  Potential format string problem (CWE-134). Make format string constant.
			sprintf(fname_curr,dir.c_str(),_pid,i);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:1389:4:  [4] (format) sprintf:
  Potential format string problem (CWE-134). Make format string constant.
			sprintf(fname_prev,dir.c_str(),_pid,i-1);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/access.hpp:240:9:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
  class access
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/access.hpp:345:15:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    ::cereal::access::construct( itsPtr, std::forward<Args>( args )... );
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/cereal.hpp:481:9:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        access::member_serialize(*self, const_cast<T &>(t));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/cereal.hpp:497:9:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        access::member_save(*self, t);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/cereal.hpp:513:24:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        self->process( access::member_save_minimal(*self, t) );
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/cereal.hpp:588:9:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        access::member_serialize(*self, const_cast<T &>(t), registerClassVersion<T>());
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/cereal.hpp:606:9:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        access::member_save(*self, t, registerClassVersion<T>());
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/cereal.hpp:624:24:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        self->process( access::member_save_minimal(*self, t, registerClassVersion<T>()) );
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/cereal.hpp:886:9:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        access::member_serialize(*self, t);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/cereal.hpp:902:9:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        access::member_load(*self, t);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/cereal.hpp:921:9:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        access::member_load_minimal(*self, t, value);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/cereal.hpp:1007:9:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        access::member_serialize(*self, t, version);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/cereal.hpp:1027:9:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        access::member_load(*self, t, version);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/cereal.hpp:1050:9:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        access::member_load_minimal(*self, t, value, version);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:194:48:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
      typename detail::Void< decltype( cereal::access::member_##name( std::declval<A&>(), std::declval<T&>() versioned ) ) >::type> : yes {}
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:203:52:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        static auto test(int) -> decltype( cereal::access::member_##name( std::declval<AA&>(), std::declval<TT&>() versioned ), yes()); \
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:286:52:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
          typename detail::Void< decltype( cereal::access::member_save( std::declval<AA&>(),                                        \
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:293:52:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
          typename detail::Void< decltype( cereal::access::member_save_non_const(                                                   \
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:307:52:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        static auto test(int) -> decltype( cereal::access::member_save( std::declval<AA&>(),                                        \
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:313:53:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        static auto test2(int) -> decltype( cereal::access::member_save_non_const(                                                  \
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:433:21:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            cereal::access::member_save_minimal( std::declval<AA const &>(),                                                                      \
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:441:21:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            cereal::access::member_save_minimal_non_const( std::declval<AA const &>(),                                                            \
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:456:52:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        static auto test(int) -> decltype( cereal::access::member_save_minimal(                \
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:463:53:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        static auto test2(int) -> decltype( cereal::access::member_save_minimal_non_const(     \
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:491:40:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        using type = decltype( cereal::access::member_save_minimal( std::declval<A const &>(),               \
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:682:19:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
          cereal::access::member_load_minimal( std::declval<A const &>(),                                                     \
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:688:21:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
            cereal::access::member_load_minimal( std::declval<A const &>(),                                                   \
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:699:52:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        static auto test(int) -> decltype( cereal::access::member_load_minimal(         \
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:709:52:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        static auto test(int) -> decltype( cereal::access::member_load_minimal(         \
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:887:32:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        std::is_same<decltype( access::load_and_construct<T>( std::declval<A&>(), std::declval< ::cereal::construct<T>&>() ) ), void>::value>
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:892:32:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        std::is_same<decltype( access::load_and_construct<T>( std::declval<A&>(), std::declval< ::cereal::construct<T>&>(), 0 ) ), void>::value>
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:1205:67:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        static auto (check)( U const & t ) -> decltype( ::cereal::access::shared_from_this(t), std::true_type() );
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:1260:64:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
      struct test<TT, typename detail::Void< decltype( cereal::access::construct<TT>() ) >::type> : yes {};
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:1264:50:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
      static auto test(int) -> decltype( cereal::access::construct<TT>(), yes());
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:1364:26:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
      { return ::cereal::access::construct<T>(); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:1373:9:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        access::load_and_construct<T>( ar, construct );
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/details/traits.hpp:1384:9:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
        access::load_and_construct<T>( ar, construct, version );
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/specialize.hpp:36:9:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
  class access;
data/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:175:33:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
inline constexpr decltype(auto) access(U &&t) noexcept
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:235:18:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<type>(lh) == impl::access<type>(rh);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:235:44:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<type>(lh) == impl::access<type>(rh);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:248:18:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<type>(lh) != impl::access<type>(rh);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:248:44:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<type>(lh) != impl::access<type>(rh);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:338:18:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<type>(lh) < impl::access<type>(rh);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:338:43:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<type>(lh) < impl::access<type>(rh);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:351:18:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<type>(lh) <= impl::access<type>(rh);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:351:44:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<type>(lh) <= impl::access<type>(rh);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:364:18:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<type>(lh) > impl::access<type>(rh);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:364:43:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<type>(lh) > impl::access<type>(rh);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:377:18:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<type>(lh) >= impl::access<type>(rh);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:377:44:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<type>(lh) >= impl::access<type>(rh);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:393:26:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
      return os << impl::access<T>(t);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:410:26:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
      return is >> impl::access<T>(t);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:498:38:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
      return static_cast<bool>(impl::access<T>(*this));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:524:11:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    impl::access<type>(*this) += value_of(t);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:531:11:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    impl::access<type>(*this) -= value_of(t);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:538:11:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    impl::access<type>(*this) *= t;
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:545:11:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    impl::access<type>(*this) /= t;
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:629:20:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return D(impl::access<type>(lh) - impl::access<type>(rh));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:629:45:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return D(impl::access<type>(lh) - impl::access<type>(rh));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:637:11:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    impl::access<type>(*this) += value_of(d);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:646:11:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    impl::access<type>(*this) -= value_of(d);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:657:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return type(impl::access<type>(lh) + value_of(d));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:667:37:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return type(value_of(d) + impl::access<type>(rh));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:677:23:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return type(impl::access<type>(lh) - value_of(d));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:754:19:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return *impl::access<type>(*this);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:1043:18:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<Type>(*this)[strong::value_of(i)];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:1055:18:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<Type>(*this)[strong::value_of(i)];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:1067:18:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<Type>(*this)[strong::value_of(i)];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:1077:18:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<Type>(*this).at(strong::value_of(i));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:1087:18:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<Type>(*this).at(strong::value_of(i));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:1097:18:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<Type>(*this).at(strong::value_of(i));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:1115:18:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<type>(*this)[strong::value_of(i)];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:1126:18:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<type>(*this)[strong::value_of(i)];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:1137:18:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<type>(*this)[strong::value_of(i)];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:1147:18:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<type>(*this).at(strong::value_of(i));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:1157:18:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<type>(*this).at(strong::value_of(i));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:1167:18:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return impl::access<type>(*this).at(strong::value_of(i));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:1219:27:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return iterator{impl::access<type>(*this).begin()};
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:1226:27:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return iterator{impl::access<type>(*this).end()};
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:1234:33:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return const_iterator{impl::access<type>(*this).begin()};
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:1242:33:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return const_iterator{impl::access<type>(*this).end()};
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:1250:33:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return const_iterator{impl::access<type>(*this).begin()};
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:1258:33:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return const_iterator{impl::access<type>(*this).end()};
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/strong_type/strong_type.hpp:1282:48:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return hash<T>::operator()(::strong::impl::access<type>(t));
data/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/src/EdgeDensityCustom.cpp:10:32:  [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 _verbose(fmt, args...) fprintf(stderr, fmt, ##args)
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/cli.cpp:193:5:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
    strcpy(algo, algos.c_str());
data/salmon-1.4.0+ds1/include/TranscriptGeneMap.hpp:70:24:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
  friend class cereal::access;
data/salmon-1.4.0+ds1/include/format.h:2434:6:  [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, BasicStringRef<Char> format, ArgList args) {
data/salmon-1.4.0+ds1/include/format.h:2447:20:  [4] (format) sprintf:
  Potential format string problem (CWE-134). Make format string constant.
inline std::string sprintf(StringRef format, ArgList args) {
data/salmon-1.4.0+ds1/include/format.h:2449:3:  [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/salmon-1.4.0+ds1/include/format.h:2462:5:  [4] (format) fprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
int fprintf(std::FILE* f, StringRef format, ArgList args);
data/salmon-1.4.0+ds1/include/format.h:2473:12:  [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(StringRef format, ArgList args) {
data/salmon-1.4.0+ds1/include/format.h:2474:10:  [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/salmon-1.4.0+ds1/include/format.h:2715:27:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
FMT_VARIADIC(std::string, sprintf, StringRef)
data/salmon-1.4.0+ds1/include/format.h:2716:19:  [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, StringRef)
data/salmon-1.4.0+ds1/include/format.h:2717:19:  [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*, StringRef)
data/salmon-1.4.0+ds1/include/httplib.hpp:77:9:  [4] (format) snprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
#define snprintf _snprintf_s
data/salmon-1.4.0+ds1/include/httplib.hpp:2913:13:  [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.
  auto sn = snprintf(buf.data(), buf.size() - 1, fmt, args...);
data/salmon-1.4.0+ds1/include/httplib.hpp:2930:11:  [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.
          snprintf(&glowable_buf[0], glowable_buf.size() - 1, fmt, args...));
data/salmon-1.4.0+ds1/include/json.hpp:1053:86:  [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 JSON_HEDLEY_PRINTF_FORMAT(string_idx,first_to_check) __declspec(vaformat(printf,string_idx,first_to_check))
data/salmon-1.4.0+ds1/include/json.hpp:5413:23:  [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.
                (std::snprintf)(cr.data(), cr.size(), "%.2hhX", static_cast<unsigned char>(element_type));
data/salmon-1.4.0+ds1/include/json.hpp:7065:15:  [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.
        (std::snprintf)(cr.data(), cr.size(), "%.2hhX", static_cast<unsigned char>(current));
data/salmon-1.4.0+ds1/include/json.hpp:8498:23:  [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.
                (std::snprintf)(cs.data(), cs.size(), "<U+%.4X>", static_cast<unsigned char>(c));
data/salmon-1.4.0+ds1/include/json.hpp:14124:43:  [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.
                                    (std::snprintf)(string_buffer.data() + bytes, 7, "\\u%04x",
data/salmon-1.4.0+ds1/include/json.hpp:14130:43:  [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.
                                    (std::snprintf)(string_buffer.data() + bytes, 13, "\\u%04x\\u%04x",
data/salmon-1.4.0+ds1/include/json.hpp:14168:35:  [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.
                            (std::snprintf)(&sn[0], sn.size(), "%.2X", byte);
data/salmon-1.4.0+ds1/include/json.hpp:14262:27:  [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.
                    (std::snprintf)(&sn[0], sn.size(), "%.2X", static_cast<std::uint8_t>(s.back()));
data/salmon-1.4.0+ds1/include/json.hpp:14463:36:  [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.
        std::ptrdiff_t len = (std::snprintf)(number_buffer.data(), number_buffer.size(), "%.*g", d, x);
data/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/src/FASTAParser.cpp:97:14:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
        std::strcpy(seqCopy, seq.c_str());
data/salmon-1.4.0+ds1/tests/GCSampleTests.cpp:31:12:  [4] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused).
      std::strcpy(txpSeqs[tn], s.c_str());
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/src/scheduler.cpp:153:24:  [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 *s = std::getenv("LIBASYNC_NUM_THREADS");
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/StringUtil.h:90:13:  [3] (random) setstate:
  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.
        iss.setstate(std::ios::failbit);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/StringUtil.h:108:13:  [3] (random) setstate:
  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.
        iss.setstate(std::ios::failbit);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/StringUtil.h:206:13:  [3] (random) setstate:
  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.
        iss.setstate(std::ios::failbit);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/StringUtil.h:221:13:  [3] (random) setstate:
  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.
        iss.setstate(std::ios::failbit);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/CLI/App.hpp:830:31:  [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.
                buffer = std::getenv(opt->envname_.c_str());
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:4260:26:  [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.
        temp_path = std::getenv(*temp_name);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/jellyfish/mer_dna.hpp:712:6:  [3] (random) setstate:
  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.
  is.setstate(std::ios::failbit);
data/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/src/cli.cpp:171:14:  [3] (buffer) getopt:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
	while ((c = getopt(argc, argv, "t:w:R:rsgz:A:B:O:E:K")) >= 0) {
data/salmon-1.4.0+ds1/include/jellyfish/mer_dna.hpp:712:6:  [3] (random) setstate:
  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.
  is.setstate(std::ios::failbit);
data/salmon-1.4.0+ds1/include/pcg_extras.hpp:191:8:  [3] (random) setstate:
  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.
    in.setstate(std::ios::failbit);
data/salmon-1.4.0+ds1/include/pcg_extras.hpp:222:8:  [3] (random) setstate:
  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.
    in.setstate(std::ios::failbit);
data/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/src/Salmon.cpp:212:43:  [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* no_version_env_ptr = std::getenv("SALMON_NO_VERSION_CHECK");
data/salmon-1.4.0+ds1/tests/catch.hpp:4594:1:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
random(T a, T b) {
data/salmon-1.4.0+ds1/tests/catch.hpp:4603:1:  [3] (random) random:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
random(T a, T b) {
data/salmon-1.4.0+ds1/tests/catch.hpp:12939:18:  [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.
            std::srand(config.rngSeed());
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:65:5:  [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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:147:10:  [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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:591:5:  [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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:605:5:  [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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:1382:4:  [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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:1385:4:  [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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:1388:4:  [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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:1402:23:  [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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/PairedAlignmentFormatter.hpp:45:3:  [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 buff1[1000];
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/PairedAlignmentFormatter.hpp:46:3:  [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 buff2[1000];
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/compact_vector.hpp:85:22:  [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_mem, rhs.m_mem, bytes());
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/compact_vector.hpp:109:18:  [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_mem, rhs.m_mem, bytes());
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/compact_vector.hpp:246:26:  [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(reinterpret_cast<void *>(&bits_per_element),
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/compact_vector.hpp:251:26:  [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(reinterpret_cast<void *>(&w_size), reinterpret_cast<void *>(const_cast<char *>(data)),
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/compact_vector.hpp:257:26:  [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(reinterpret_cast<void *>(&w_capacity),
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/mio.hpp:859:27:  [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).
    const auto handle = ::open(c_str(path),
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/select.hpp:27:16:  [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 unsigned char select_in_byte[2048] = {
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/sparsepp/spp.h:2091:21:  [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(static_cast<void *>(first), _first_group, sizeof(*first) * (std::min)(sz, old_sz));
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/include/async++/traits.h:80:9:  [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 one[1];
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/asyncplusplus/include/async++/traits.h:81:9:  [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 two[2];
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/Uncompress.cpp:74:9:  [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 arg0[16], arg1[16], arg2[16];
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/Uncompress.cpp:84:21:  [2] (race) vfork:
  On some old systems, vfork() permits race conditions, and it's very
  difficult to use correctly (CWE-362). Use fork() instead.
        pid_t pid = vfork();
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/Uncompress.cpp:126:11:  [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).
    FILE *fopen(const char *path, const char *mode)
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/Uncompress.cpp:182:9:  [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).
    int open(const char *path, int flags, mode_t mode)
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/dnachar.h:28:10:  [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.
		static char reverseTable_[CHAR_SIZE];
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/ngramhashing/mersennetwister.h:248:19:  [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* urandom = fopen("/dev/urandom", "rb");
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/spooky/SpookyV2.cpp:40:9:  [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(buf, message, length);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/spooky/SpookyV2.cpp:170:13:  [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(buf, u.p64, sc_blockSize);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/spooky/SpookyV2.cpp:178:5:  [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(buf, end, remainder);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/spooky/SpookyV2.cpp:217:9:  [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(&((uint8 *)m_data)[m_remainder], message, length);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/spooky/SpookyV2.cpp:251:9:  [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(&(((uint8 *)m_data)[m_remainder]), message, prefix);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/spooky/SpookyV2.cpp:278:13:  [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(m_data, u.p8, sc_blockSize);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/spooky/SpookyV2.cpp:286:5:  [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(m_data, end, remainder);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/streamfastaparser.h:59:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
		char buffer[TASK_SIZE + 1];
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:85:22:  [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_mem, rhs.m_mem, bytes());
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:109:18:  [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_mem, rhs.m_mem, bytes());
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:246:26:  [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(reinterpret_cast<void *>(&bits_per_element),
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:251:26:  [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(reinterpret_cast<void *>(&w_size), reinterpret_cast<void *>(const_cast<char *>(data)),
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:257:26:  [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(reinterpret_cast<void *>(&w_capacity),
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/mio.hpp:859:27:  [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).
    const auto handle = ::open(c_str(path),
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/naiveconstructor/naiveconstructor.cpp:138:11:  [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).
		tmpFile.open(tmpFileName.c_str(), tpie::access_write);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/naiveconstructor/naiveconstructor.cpp:159:11:  [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).
		tmpFile.open(tmpFileName.c_str());
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:65:5:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:147:10:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:591:5:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:605:5:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:1382:4:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:1385:4:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:1388:4:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:1402:23:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/CLI/Timer.hpp:81:13:  [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.
            char buffer[50];
data/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/include/PairedAlignmentFormatter.hpp:45:3:  [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 buff1[1000];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PairedAlignmentFormatter.hpp:46:3:  [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 buff2[1000];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PuffMappingReader.hpp:49:9:  [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 strCharBuff[len];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PuffMappingReader.hpp:50:9:  [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(&strCharBuff, chunk_.data() + currByte_, len);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PuffMappingReader.hpp:71:20:  [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).
            inFile.open(mfileName, std::ios::binary);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/archives/json.hpp:466:14:  [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( data, decoded.data(), decoded.size() );
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/archives/xml.hpp:467:14:  [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( data, decoded.data(), decoded.size() );
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/base64.hpp:52:16:  [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 char_array_3[3];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/base64.hpp:53:16:  [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 char_array_4[4];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/base64.hpp:94:16:  [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 char_array_4[4], char_array_3[3];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/allocators.h:230:22:  [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(newBuffer, originalPtr, originalSize);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/document.h:1146:20:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
            static char buffer[sizeof(GenericValue)];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/document.h:1947:9:  [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 payload[sizeof(SizeType) * 2 + 6];     // 2 x SizeType + lower 48-bit pointer
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/document.h:1949:9:  [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 payload[sizeof(SizeType) * 2 + sizeof(void*) + 6]; // 6 padding bytes
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/document.h:1951:9:  [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 payload[sizeof(SizeType) * 2 + sizeof(void*) + 2]; // 2 padding bytes
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/document.h:1984:13:  [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.
            char padding[4];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/document.h:1988:13:  [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.
            char padding2[4];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/document.h:1992:13:  [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.
            char padding[4];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/document.h:1996:13:  [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.
            char padding2[4];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/document.h:2039:18:  [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(static_cast<void*>(e), values, count * sizeof(GenericValue));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/document.h:2052:18:  [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(static_cast<void*>(m), members, count * sizeof(Member));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/document.h:2079:14:  [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(str, s, s.length * sizeof(Ch));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/internal/biginteger.h:33:14:  [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(digits_, rhs.digits_, count_ * sizeof(Type));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/internal/biginteger.h:59:18:  [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(digits_, rhs.digits_, count_ * sizeof(Type));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/internal/itoa.h:24:18:  [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 const char cDigitsLut[200] = {
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/internal/regex.h:459:9:  [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(s, &GetState(src.minIndex), count * sizeof(State));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/pointer.h:248:14:  [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(p, token.name, (token.length + 1) * sizeof(Ch));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/pointer.h:298:9:  [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 buffer[21];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/pointer.h:831:18:  [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(tokens_, rhs.tokens_, rhs.tokenCount_ * sizeof(Token));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/pointer.h:834:18:  [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(nameBuffer_, rhs.nameBuffer_, nameBufferSize * sizeof(Ch));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/pointer.h:1090:26:  [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 hexDigits[16] = { '0', '1', '2', '3', '4', '5', '6', '7', '8', '9', 'A', 'B', 'C', 'D', 'E', 'F' };
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/reader.h:297:18:  [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 const char whitespace[16] = " \n\r\t";
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/reader.h:316:18:  [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 const char whitespace[16] = " \n\r\t";
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/reader.h:349:18:  [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 const char whitespaces[4][16] = { C16(' '), C16('\n'), C16('\r'), C16('\t') };
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/reader.h:385:18:  [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 const char whitespaces[4][16] = { C16(' '), C16('\n'), C16('\r'), C16('\t') };
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/reader.h:992:22:  [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 escape[256] = {
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/reader.h:1077:22:  [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 dquote[16] = { '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"' };
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/reader.h:1078:22:  [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 bslash[16] = { '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\' };
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/reader.h:1079:22:  [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 space[16]  = { 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F };
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/reader.h:1140:22:  [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 dquote[16] = { '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"' };
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/reader.h:1141:22:  [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 bslash[16] = { '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\' };
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/reader.h:1142:22:  [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 space[16] = { 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F };
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/reader.h:1188:22:  [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 dquote[16] = { '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"' };
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/reader.h:1189:22:  [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 bslash[16] = { '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\' };
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/reader.h:1190:22:  [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 space[16] = { 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F };
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/reader.h:1807:31:  [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.
        static const unsigned char tokenMap[256] = {
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/reader.h:1830:22:  [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 G[cIterativeParsingStateCount][kTokenCount] = {
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/schema.h:467:21:  [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[256u + 24];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/schema.h:1449:9:  [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 buffer[21];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/schema.h:2224:13:  [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(documentStack_.template Push<char>(basePathSize), basePath, basePathSize);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/schema.h:2341:9:  [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(sb.Push(CurrentSchema().GetURI().GetStringLength()),
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/writer.h:313:9:  [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 buffer[11];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/writer.h:322:9:  [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 buffer[10];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/writer.h:331:9:  [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 buffer[21];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/writer.h:340:9:  [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 buffer[20];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/writer.h:368:9:  [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 buffer[25];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/writer.h:378:22:  [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 escape[256] = {
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/writer.h:597:18:  [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 const char dquote[16] = { '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"', '\"' };
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/writer.h:598:18:  [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 const char bslash[16] = { '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\', '\\' };
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/writer.h:599:18:  [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 const char space[16]  = { 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F, 0x1F };
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidxml/rapidxml.hpp:299:35:  [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 unsigned char lookup_whitespace[256];              // Whitespace table
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidxml/rapidxml.hpp:300:35:  [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 unsigned char lookup_node_name[256];               // Node name table
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidxml/rapidxml.hpp:301:35:  [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 unsigned char lookup_text[256];                    // Text table
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidxml/rapidxml.hpp:302:35:  [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 unsigned char lookup_text_pure_no_ws[256];         // Text table
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidxml/rapidxml.hpp:303:35:  [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 unsigned char lookup_text_pure_with_ws[256];       // Text table
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidxml/rapidxml.hpp:304:35:  [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 unsigned char lookup_attribute_name[256];          // Attribute name table
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidxml/rapidxml.hpp:305:35:  [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 unsigned char lookup_attribute_data_1[256];        // Attribute data table with single quote
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidxml/rapidxml.hpp:306:35:  [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 unsigned char lookup_attribute_data_1_pure[256];   // Attribute data table with single quote
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidxml/rapidxml.hpp:307:35:  [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 unsigned char lookup_attribute_data_2[256];        // Attribute data table with double quotes
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidxml/rapidxml.hpp:308:35:  [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 unsigned char lookup_attribute_data_2_pure[256];   // Attribute data table with double quotes
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidxml/rapidxml.hpp:309:35:  [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 unsigned char lookup_digits[256];                  // Digits
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidxml/rapidxml.hpp:310:35:  [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 unsigned char lookup_upcase[256];                  // To uppercase conversion table for ASCII characters
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidxml/rapidxml.hpp:649:9:  [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 m_static_memory[CEREAL_RAPIDXML_STATIC_POOL_SIZE];    // Static raw memory
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/memory.hpp:147:16:  [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( &itsState, itsPtr, sizeof(ParentType) );
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/memory.hpp:156:18:  [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( static_cast<void *>(itsPtr), &itsState, sizeof(ParentType) );
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/types/tuple.hpp:49:20:  [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 str[sizeof...(Cs) + size];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/compact_vector.hpp:85:22:  [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_mem, rhs.m_mem, bytes());
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/compact_vector.hpp:109:18:  [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_mem, rhs.m_mem, bytes());
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/compact_vector.hpp:246:26:  [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(reinterpret_cast<void *>(&bits_per_element),
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/compact_vector.hpp:251:26:  [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(reinterpret_cast<void *>(&w_size), reinterpret_cast<void *>(const_cast<char *>(data)),
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/compact_vector.hpp:257:26:  [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(reinterpret_cast<void *>(&w_capacity),
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/mio.hpp:859:27:  [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).
    const auto handle = ::open(c_str(path),
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/concurrentqueue.h:1611:45:  [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.
		MOODYCAMEL_ALIGNAS(MOODYCAMEL_ALIGNOF(T)) char elements[sizeof(T) * BLOCK_SIZE];
data/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:933:35:  [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).
    basic_filebuf<charT, traits>* open(const path& p, std::ios_base::openmode mode)
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:936:51:  [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).
        return std::basic_filebuf<charT, traits>::open(p.wstring().c_str(), mode) ? this : 0;
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:938:51:  [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).
        return std::basic_filebuf<charT, traits>::open(p.string().c_str(), mode) ? this : 0;
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:953:10:  [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 path& p, std::ios_base::openmode mode = std::ios_base::in) { std::basic_ifstream<charT, traits>::open(p.wstring().c_str(), mode); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:953:118:  [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 path& p, std::ios_base::openmode mode = std::ios_base::in) { std::basic_ifstream<charT, traits>::open(p.wstring().c_str(), mode); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:959:10:  [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 path& p, std::ios_base::openmode mode = std::ios_base::in) { std::basic_ifstream<charT, traits>::open(p.string().c_str(), mode); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:959:118:  [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 path& p, std::ios_base::openmode mode = std::ios_base::in) { std::basic_ifstream<charT, traits>::open(p.string().c_str(), mode); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:976:10:  [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 path& p, std::ios_base::openmode mode = std::ios_base::out) { std::basic_ofstream<charT, traits>::open(p.wstring().c_str(), mode); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:976:119:  [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 path& p, std::ios_base::openmode mode = std::ios_base::out) { std::basic_ofstream<charT, traits>::open(p.wstring().c_str(), mode); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:982:10:  [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 path& p, std::ios_base::openmode mode = std::ios_base::out) { std::basic_ofstream<charT, traits>::open(p.string().c_str(), mode); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:982:119:  [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 path& p, std::ios_base::openmode mode = std::ios_base::out) { std::basic_ofstream<charT, traits>::open(p.string().c_str(), mode); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:999:10:  [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 path& p, std::ios_base::openmode mode = std::ios_base::in | std::ios_base::out) { std::basic_fstream<charT, traits>::open(p.wstring().c_str(), mode); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:999:138:  [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 path& p, std::ios_base::openmode mode = std::ios_base::in | std::ios_base::out) { std::basic_fstream<charT, traits>::open(p.wstring().c_str(), mode); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:1005:10:  [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 path& p, std::ios_base::openmode mode = std::ios_base::in | std::ios_base::out) { std::basic_fstream<charT, traits>::open(p.string().c_str(), mode); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:1005:138:  [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 path& p, std::ios_base::openmode mode = std::ios_base::in | std::ios_base::out) { std::basic_fstream<charT, traits>::open(p.string().c_str(), mode); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:1541:5:  [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[512];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:3262:17:  [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 ((in = ::open(from.c_str(), O_RDONLY)) < 0) {
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:3271:18:  [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 ((out = ::open(to.c_str(), mode, static_cast<int>(sf.permissions() & perms::all))) < 0) {
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:4249:5:  [2] (buffer) wchar_t:
  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.
    wchar_t buffer[512];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/jellyfish/int128.hpp:39:3:  [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 buf[50];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/jellyfish/int128.hpp:102:3:  [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 padding[nb_padding];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/jellyfish/mer_dna.hpp:71:14:  [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.
static const char rev_codes[4] = { 'A', 'C', 'G', 'T' };
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/jellyfish/mer_dna.hpp:168:5:  [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(_data, m._data, nb_words(static_cast<const derived*>(&m)->k()) * sizeof(base_type));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/jellyfish/mer_dna.hpp:307:5:  [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(_data, rhs._data, nb_words() * sizeof(base_type));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/jellyfish/mer_dna.hpp:690:3:  [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 s[mer.k() + 1];
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/jellyfish/mer_dna.hpp:702:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[mer.k() + 1];
data/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/include/parallel_hashmap/meminfo.h:135:21:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/parallel_hashmap/meminfo.h:139:21:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/parallel_hashmap/meminfo.h:141:9:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/parallel_hashmap/phmap.h:479:10:  [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(ctrl + capacity + 1, ctrl, Group::kWidth);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/parallel_hashmap/phmap_bits.h:124:3:  [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(&t, p, sizeof t);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/parallel_hashmap/phmap_bits.h:130:3:  [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(&t, p, sizeof t);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/parallel_hashmap/phmap_bits.h:136:3:  [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(&t, p, sizeof t);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/parallel_hashmap/phmap_bits.h:140:53:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
inline void UnalignedStore16(void *p, uint16_t v) { memcpy(p, &v, sizeof v); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/parallel_hashmap/phmap_bits.h:142:53:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
inline void UnalignedStore32(void *p, uint32_t v) { memcpy(p, &v, sizeof v); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/parallel_hashmap/phmap_bits.h:144:53:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
inline void UnalignedStore64(void *p, uint64_t v) { memcpy(p, &v, sizeof v); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/select.hpp:27:16:  [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 unsigned char select_in_byte[2048] = {
data/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/include/sparsepp/spp.h:2091:21:  [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(static_cast<void *>(first), _first_group, sizeof(*first) * (std::min)(sz, old_sz));
data/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/fmt/bundled/format.cc:314:16:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
  int length = MultiByteToWideChar(
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/fmt/bundled/format.cc:319:12:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
  length = MultiByteToWideChar(
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/fmt/bundled/format.h:486:5:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/fmt/bundled/format.h:1261:9:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/fmt/bundled/format.h:1262:9:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/fmt/bundled/format.h:3050:3:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/fmt/bundled/format.h:3525:11:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/src/Cedar.cpp:87:15:  [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).
        tfile.open(refId2TaxId_filename);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/Cedar.cpp:95:15:  [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).
        tfile.open(taxonomyTree_filename);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/KrakMap.cpp:30:11:  [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).
    tfile.open(refId2TaxId_filename);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/KrakMap.cpp:42:11:  [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).
    tfile.open(taxonomyTree_filename);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishAligner.cpp:1003:25:  [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).
        gene_names_file.open(mopts->genesNamesFile);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishAligner.cpp:1021:25:  [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).
        rrna_names_file.open(mopts->rrnaFile);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishAligner.cpp:1040:21:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/src/cli.cpp:24:10:  [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[256] = {
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/cli.cpp:173:27:  [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).
		else if (c == 'w') {w = atoi(optarg); config.bandwidth = w;}
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/cli.cpp:174:28:  [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).
		else if (c == 'R') rep = atoi(optarg);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/cli.cpp:175:31:  [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).
		else if (c == 'z') {zdrop = atoi(optarg); config.dropoff = zdrop;}
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/cli.cpp:180:26:  [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).
		else if (c == 'A') a = atoi(optarg);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/cli.cpp:181:26:  [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).
		else if (c == 'B') b = atoi(optarg);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/edlib.cpp:447:5:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/src/edlib.cpp:1733:5:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/src/edlib.cpp:1734:5:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/src/edlib.cpp:1771:14:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/src/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/salmon-1.4.0+ds1/debian/external/pufferfish/src/ksw2pp/KSW2Aligner.cpp:65:10:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/src/ksw2pp/ksw2_extd2_sse.c:123:2:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/src/ksw2pp/ksw2_extf2_sse.c:40:2:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/src/ksw2pp/ksw2_exts2_sse.c:112:2:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/src/ksw2pp/ksw2_extz2_sse.c:101:2:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/include/GenomicFeature.hpp:100:14:  [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).
  gf.start = atoi(l.substr(head, tail - head).c_str());
data/salmon-1.4.0+ds1/include/GenomicFeature.hpp:104:12:  [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).
  gf.end = atoi(l.substr(head, tail - head).c_str());
data/salmon-1.4.0+ds1/include/GenomicFeature.hpp:108:14:  [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).
  gf.score = atoi(l.substr(head, tail - head).c_str());
data/salmon-1.4.0+ds1/include/OutputUnmappedFilter.hpp:33:7:  [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(&qname_[0], f->getName(), qlen_);
data/salmon-1.4.0+ds1/include/OutputUnmappedFilter.hpp:41:3:  [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 qname_[255];
data/salmon-1.4.0+ds1/include/TextBootstrapWriter.hpp:24:12:  [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).
    ofile_.open(outputPath.string());
data/salmon-1.4.0+ds1/include/concurrentqueue.h:1611:45:  [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.
		MOODYCAMEL_ALIGNAS(MOODYCAMEL_ALIGNOF(T)) char elements[sizeof(T) * BLOCK_SIZE];
data/salmon-1.4.0+ds1/include/ezETAProgressBar.hpp:129:5:  [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 pctstr[5];
data/salmon-1.4.0+ds1/include/ezETAProgressBar.hpp:130:5:  [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(pctstr, "%3d%%", (int)(100 * Pct));
data/salmon-1.4.0+ds1/include/format.h:477:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[2]; // The buffer size must be >= 2 or _ecvt_s will fail.
data/salmon-1.4.0+ds1/include/format.h:762:11:  [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.
  typedef char yes[1];
data/salmon-1.4.0+ds1/include/format.h:763:11:  [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.
  typedef char no[2];
data/salmon-1.4.0+ds1/include/format.h:1955:3:  [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/salmon-1.4.0+ds1/include/format.h:2485:11:  [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/salmon-1.4.0+ds1/include/httplib.hpp:1527:9:  [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 buf[INET_ADDRSTRLEN];
data/salmon-1.4.0+ds1/include/httplib.hpp:1825:3:  [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 buf[bufsiz];
data/salmon-1.4.0+ds1/include/httplib.hpp:1864:3:  [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 buf[CPPHTTPLIB_RECV_BUFSIZ];
data/salmon-1.4.0+ds1/include/httplib.hpp:1885:3:  [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 buf[CPPHTTPLIB_RECV_BUFSIZ];
data/salmon-1.4.0+ds1/include/httplib.hpp:1896:3:  [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 buf[CPPHTTPLIB_RECV_BUFSIZ];
data/salmon-1.4.0+ds1/include/httplib.hpp:1912:3:  [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 buf[bufsiz];
data/salmon-1.4.0+ds1/include/httplib.hpp:2122:9:  [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 hex[4];
data/salmon-1.4.0+ds1/include/httplib.hpp:2146:11:  [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.
          char buff[4];
data/salmon-1.4.0+ds1/include/httplib.hpp:5014:5:  [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 name[BUFSIZ];
data/salmon-1.4.0+ds1/include/jellyfish/int128.hpp:39:3:  [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 buf[50];
data/salmon-1.4.0+ds1/include/jellyfish/int128.hpp:102:3:  [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 padding[nb_padding];
data/salmon-1.4.0+ds1/include/jellyfish/mer_dna.hpp:71:14:  [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.
static const char rev_codes[4] = { 'A', 'C', 'G', 'T' };
data/salmon-1.4.0+ds1/include/jellyfish/mer_dna.hpp:168:5:  [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(_data, m._data, nb_words(static_cast<const derived*>(&m)->k()) * sizeof(base_type));
data/salmon-1.4.0+ds1/include/jellyfish/mer_dna.hpp:307:5:  [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(_data, rhs._data, nb_words() * sizeof(base_type));
data/salmon-1.4.0+ds1/include/jellyfish/mer_dna.hpp:690:3:  [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 s[mer.k() + 1];
data/salmon-1.4.0+ds1/include/jellyfish/mer_dna.hpp:702:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[mer.k() + 1];
data/salmon-1.4.0+ds1/include/json.hpp:1441:12:  [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.
((struct { char v[sizeof(void) * 2]; } *) 1) \
data/salmon-1.4.0+ds1/include/json.hpp:7007:14:  [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(&result, vec.data(), sizeof(NumberType));
data/salmon-1.4.0+ds1/include/json.hpp:12566:14:  [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(vec.data(), &n, sizeof(NumberType));
data/salmon-1.4.0+ds1/include/json.hpp:12597:14:  [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(&result, &x, sizeof(x));
data/salmon-1.4.0+ds1/include/json.hpp:12695:10:  [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(&target, &source, sizeof(Source));
data/salmon-1.4.0+ds1/include/kseq.h:150:7:  [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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/include/parallel_hashmap/meminfo.h:135:21:  [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/salmon-1.4.0+ds1/include/parallel_hashmap/meminfo.h:139:21:  [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/salmon-1.4.0+ds1/include/parallel_hashmap/meminfo.h:141:9:  [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/salmon-1.4.0+ds1/include/parallel_hashmap/phmap.h:479:10:  [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(ctrl + capacity + 1, ctrl, Group::kWidth);
data/salmon-1.4.0+ds1/include/parallel_hashmap/phmap_bits.h:124:3:  [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(&t, p, sizeof t);
data/salmon-1.4.0+ds1/include/parallel_hashmap/phmap_bits.h:130:3:  [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(&t, p, sizeof t);
data/salmon-1.4.0+ds1/include/parallel_hashmap/phmap_bits.h:136:3:  [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(&t, p, sizeof t);
data/salmon-1.4.0+ds1/include/parallel_hashmap/phmap_bits.h:140:53:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
inline void UnalignedStore16(void *p, uint16_t v) { memcpy(p, &v, sizeof v); }
data/salmon-1.4.0+ds1/include/parallel_hashmap/phmap_bits.h:142:53:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
inline void UnalignedStore32(void *p, uint32_t v) { memcpy(p, &v, sizeof v); }
data/salmon-1.4.0+ds1/include/parallel_hashmap/phmap_bits.h:144:53:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
inline void UnalignedStore64(void *p, uint64_t v) { memcpy(p, &v, sizeof v); }
data/salmon-1.4.0+ds1/include/pcg_extras.hpp:148:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[MAX_CHARS_128BIT];
data/salmon-1.4.0+ds1/include/peglib.h:226:3:  [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 buff[4];
data/salmon-1.4.0+ds1/include/radicl/BasicBinWriter.hpp:31:10:  [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(_bin_data.data() + offset, &v, sizeof(v));
data/salmon-1.4.0+ds1/include/readerwriterqueue.h:580:5:  [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 cachelineFiller0[MOODYCAMEL_CACHE_LINE_SIZE -
data/salmon-1.4.0+ds1/include/readerwriterqueue.h:585:5:  [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 cachelineFiller1[MOODYCAMEL_CACHE_LINE_SIZE -
data/salmon-1.4.0+ds1/include/readerwriterqueue.h:628:3:  [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
data/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/include/spdlog/fmt/bundled/format.cc:314:16:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
  int length = MultiByteToWideChar(
data/salmon-1.4.0+ds1/include/spdlog/fmt/bundled/format.cc:319:12:  [2] (buffer) MultiByteToWideChar:
  Requires maximum length in CHARACTERS, not bytes (CWE-120).
  length = MultiByteToWideChar(
data/salmon-1.4.0+ds1/include/spdlog/fmt/bundled/format.h:486:5:  [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/salmon-1.4.0+ds1/include/spdlog/fmt/bundled/format.h:1261:9:  [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/salmon-1.4.0+ds1/include/spdlog/fmt/bundled/format.h:1262:9:  [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/salmon-1.4.0+ds1/include/spdlog/fmt/bundled/format.h:3050:3:  [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/salmon-1.4.0+ds1/include/spdlog/fmt/bundled/format.h:3525:11:  [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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/include/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/salmon-1.4.0+ds1/include/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/salmon-1.4.0+ds1/include/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/salmon-1.4.0+ds1/include/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/salmon-1.4.0+ds1/include/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/salmon-1.4.0+ds1/include/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/salmon-1.4.0+ds1/include/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/salmon-1.4.0+ds1/include/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/salmon-1.4.0+ds1/include/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/salmon-1.4.0+ds1/include/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/salmon-1.4.0+ds1/include/xxhash.h:219:12:  [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 digest[4];
data/salmon-1.4.0+ds1/include/xxhash.h:264:12:  [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 digest[8];
data/salmon-1.4.0+ds1/src/Alevin.cpp:318:12:  [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).
  freqFile.open(frequencyFileName);
data/salmon-1.4.0+ds1/src/GZipWriter.cpp:900:64:  [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).
  std::unique_ptr<std::FILE, int (*)(std::FILE *)> output(std::fopen(fname.c_str(), "w"), std::fclose);
data/salmon-1.4.0+ds1/src/GZipWriter.cpp:940:24:  [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).
    bcBootNameStream_->open(bcBootNameFilename.string());
data/salmon-1.4.0+ds1/src/GZipWriter.cpp:1072:24:  [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).
    bcBootNameStream_->open(bcBootNameFilename.string());
data/salmon-1.4.0+ds1/src/GZipWriter.cpp:1207:20:  [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).
    bcNameStream_->open(bcNameFilename.string());
data/salmon-1.4.0+ds1/src/GZipWriter.cpp:1211:24:  [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).
    bcFeaturesStream_->open(bcFeaturesFilename.string());
data/salmon-1.4.0+ds1/src/GZipWriter.cpp:1289:20:  [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).
    bcNameStream_->open(bcNameFilename.string());
data/salmon-1.4.0+ds1/src/GZipWriter.cpp:1293:24:  [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).
    bcFeaturesStream_->open(bcFeaturesFilename.string());
data/salmon-1.4.0+ds1/src/GZipWriter.cpp:1339:12:  [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).
      std::fopen(fname.c_str(), "w"), std::fclose);
data/salmon-1.4.0+ds1/src/GZipWriter.cpp:1367:12:  [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).
      std::fopen(fname.c_str(), "w"), std::fclose);
data/salmon-1.4.0+ds1/src/GenomicFeature.cpp:63:14:  [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).
  gf.start = atoi(line.c_str());
data/salmon-1.4.0+ds1/src/GenomicFeature.cpp:66:12:  [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).
  gf.end = atoi(line.c_str());
data/salmon-1.4.0+ds1/src/GenomicFeature.cpp:69:14:  [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).
  gf.score = atoi(line.c_str());
data/salmon-1.4.0+ds1/src/SGSmooth.cpp:75:5:  [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[1024];
data/salmon-1.4.0+ds1/src/SGSmooth.cpp:77:5:  [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(buffer, "cannot build matrix with %d rows and %d columns\n", sizedRows, sizedCols);
data/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2789:13:  [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).
      oFile.open(oFilePath.string());
data/salmon-1.4.0+ds1/src/SalmonAlevin.cpp:2820:70:  [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).
                                                                std::fopen(distFileName.c_str(), "w"), std::fclose);
data/salmon-1.4.0+ds1/src/SalmonQuantify.cpp:2712:70:  [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).
                                                                std::fopen(distFileName.c_str(), "w"), std::fclose);
data/salmon-1.4.0+ds1/src/SalmonUtils.cpp:307:12:  [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).
      std::fopen(fname.c_str(), "w"), std::fclose);
data/salmon-1.4.0+ds1/src/SalmonUtils.cpp:359:12:  [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).
      std::fopen(fname.c_str(), "w"), std::fclose);
data/salmon-1.4.0+ds1/src/SalmonUtils.cpp:1009:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[bufferSize];
data/salmon-1.4.0+ds1/src/SalmonUtils.cpp:1370:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[80] = {0};
data/salmon-1.4.0+ds1/src/SalmonUtils.cpp:1730:21:  [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).
        sopt.qmFile.open(sopt.qmFileName);
data/salmon-1.4.0+ds1/src/WhiteList.cpp:240:26:  [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).
        predictionStream.open(predictionFileName.string());
data/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/src/xxhash.c:118:10:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
  return memcpy(dest, src, size);
data/salmon-1.4.0+ds1/src/xxhash.c:380:3:  [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(dstState, srcState, sizeof(*dstState));
data/salmon-1.4.0+ds1/src/xxhash.c:394:3:  [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(statePtr, &state, sizeof(state));
data/salmon-1.4.0+ds1/src/xxhash.c:537:3:  [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(dst, &hash, sizeof(*dst));
data/salmon-1.4.0+ds1/src/xxhash.c:771:3:  [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(dstState, srcState, sizeof(*dstState));
data/salmon-1.4.0+ds1/src/xxhash.c:785:3:  [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(statePtr, &state, sizeof(state));
data/salmon-1.4.0+ds1/src/xxhash.c:929:3:  [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(dst, &hash, sizeof(*dst));
data/salmon-1.4.0+ds1/tests/GCSampleTests.cpp:30:12:  [2] (buffer) strcpy:
  Does not check for buffer overflows when copying to destination [MS-banned]
  (CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
  easily misused). Risk is low because the source is a constant string.
      std::strcpy(names[tn], "HI\0");
data/salmon-1.4.0+ds1/tests/catch.hpp:2131:13:  [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.
            char timeStamp[timeStampSize];
data/salmon-1.4.0+ds1/tests/catch.hpp:4408:29:  [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.
        alignas(alignof(T)) char storage[sizeof(T)];
data/salmon-1.4.0+ds1/tests/catch.hpp:5900:16:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
        static char line[CATCH_CONFIG_CONSOLE_WIDTH] = {0};
data/salmon-1.4.0+ds1/tests/catch.hpp:7511:14:  [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).
        void open();
data/salmon-1.4.0+ds1/tests/catch.hpp:11336:14:  [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(&i, &f, sizeof(f));
data/salmon-1.4.0+ds1/tests/catch.hpp:11343:14:  [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(&i, &d, sizeof(d));
data/salmon-1.4.0+ds1/tests/catch.hpp:11885:9:  [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 m_buffer[L_tmpnam] = { 0 };
data/salmon-1.4.0+ds1/tests/catch.hpp:11972:13:  [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.
            char buffer[100];
data/salmon-1.4.0+ds1/tests/catch.hpp:11981:23:  [2] (tmpfile) tmpfile:
  Function tmpfile() has a security flaw on some systems (e.g., older System
  V systems) (CWE-377).
        m_file = std::tmpfile();
data/salmon-1.4.0+ds1/tests/catch.hpp:12005:9:  [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 buffer[100] = {};
data/salmon-1.4.0+ds1/tests/catch.hpp:12468:30:  [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).
                    tracker->open();
data/salmon-1.4.0+ds1/tests/catch.hpp:13268:31:  [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.
        char **utf8Argv = new char *[ argc ];
data/salmon-1.4.0+ds1/tests/catch.hpp:13427:13:  [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.
            char data[bufferSize];
data/salmon-1.4.0+ds1/tests/catch.hpp:13476:23:  [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).
                m_ofs.open( filename.c_str() );
data/salmon-1.4.0+ds1/tests/catch.hpp:14179:23:  [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).
    void TrackerBase::open() {
data/salmon-1.4.0+ds1/tests/catch.hpp:14279:13:  [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();
data/salmon-1.4.0+ds1/tests/catch.hpp:15463:9:  [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 buffer[maxDoubleSize];
data/salmon-1.4.0+ds1/tests/catch.hpp:15470:14:  [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.
        std::sprintf(buffer, "%.3f", duration);
data/salmon-1.4.0+ds1/tests/catch.hpp:16063:10:  [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() {
data/salmon-1.4.0+ds1/tests/catch.hpp:16097:12:  [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).
        tp.open();
data/salmon-1.4.0+ds1/tests/catch.hpp:16498:13:  [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.
            char timeStamp[timeStampSize];
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:789:7:  [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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:790:7:  [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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:792:7:  [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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:795:7:  [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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:797:7:  [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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:1206:7:  [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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:1207:7:  [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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:1208:7:  [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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:1209:7:  [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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:1241:7:  [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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:1248:8:  [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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/BooPHF.hpp:1249:8:  [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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/MemCollector.hpp:35:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool get_raw_hits_sketch(std::string &read,
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/MemCollector.hpp:40:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool operator()(std::string &read,
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/MemCollector.hpp:49:30:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool findChains(std::string& read,
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/PuffAligner.hpp:87:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  int32_t calculateAlignments(std::string& read, pufferfish::util::JointMems& jointHit, HitCounters& hctr, bool isMultimapping, bool verbose);
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/PuffAligner.hpp:89:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool alignRead(std::string& read, std::string& read_rc, const std::vector<pufferfish::util::MemInfo>& mems, uint64_t queryChainHash, bool perfectChain, bool isFw, size_t tid, AlnCacheMap& alnCache, HitCounters& hctr, AlignmentResult& arOut, bool verbose);
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/compact_iterator.hpp:876:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static void read(const iterator<I, BITS, W, TS, UB>& p) { prefetch_iterator_traits<W*>::template read<level>(p.get_ptr()); }
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/compact_iterator.hpp:876:100:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static void read(const iterator<I, BITS, W, TS, UB>& p) { prefetch_iterator_traits<W*>::template read<level>(p.get_ptr()); }
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/compact_iterator.hpp:885:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static void read(const const_iterator<I, BITS, W, UB>& p) { prefetch_iterator_traits<const W*>::template read<level>(p.get_ptr()); }
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/compact_iterator.hpp:885:108:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static void read(const const_iterator<I, BITS, W, UB>& p) { prefetch_iterator_traits<const W*>::template read<level>(p.get_ptr()); }
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/compact_vector.hpp:32:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        ifile.read(reinterpret_cast<char *>(&static_flag), sizeof(static_flag));
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/compact_vector.hpp:34:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        ifile.read(reinterpret_cast<char *>(&bits_per_element), sizeof(bits_per_element));
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/compact_vector.hpp:268:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    ifile.read(reinterpret_cast<char *>(&static_flag), sizeof(static_flag));
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/compact_vector.hpp:271:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    ifile.read(reinterpret_cast<char *>(&bits_per_element), sizeof(bits_per_element));
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/compact_vector.hpp:276:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    ifile.read(reinterpret_cast<char *>(&w_size), sizeof(w_size));
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/compact_vector.hpp:281:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    ifile.read(reinterpret_cast<char *>(&w_capacity), sizeof(w_capacity));
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/compact_vector.hpp:288:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    ifile.read(reinterpret_cast<char *>(m_mem), sizeof(W) * elements_to_words(m_size, bits()));
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/mio.hpp:62:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    read,
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/mio.hpp:461:47:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    typename std::enable_if<A == access_mode::read, void>::type conditional_sync();
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/mio.hpp:493:51:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
using basic_mmap_source = basic_mmap<access_mode::read, ByteT>;
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/mio.hpp:805:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            mode == access_mode::read ? GENERIC_READ : GENERIC_READ | GENERIC_WRITE,
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/mio.hpp:820:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            mode == access_mode::read ? GENERIC_READ : GENERIC_READ | GENERIC_WRITE,
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/mio.hpp:860:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            mode == access_mode::read ? O_RDONLY : O_RDWR);
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/mio.hpp:911:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            mode == access_mode::read ? PAGE_READONLY : PAGE_READWRITE,
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/mio.hpp:922:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            mode == access_mode::read ? FILE_MAP_READ : FILE_MAP_WRITE,
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/mio.hpp:935:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            mode == access_mode::read ? PROT_READ : PROT_WRITE,
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/mio.hpp:1207:43:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
typename std::enable_if<A == access_mode::read, void>::type
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/mio.hpp:1301:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    read,
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/mio.hpp:1733:65:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
using basic_shared_mmap_source = basic_shared_mmap<access_mode::read, ByteT>;
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/prefetch_iterator_traits.hpp:14:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static void read(T* ptr) { __builtin_prefetch((void*)ptr, 0, level); }
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/compact_vector/prefetch_iterator_traits.hpp:22:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static void read(const T* ptr) { __builtin_prefetch((void*)ptr, 0, level); }
data/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/include/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/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/salmon-1.4.0+ds1/debian/external/install/src/pufferfish/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));
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/StringUtil.h:147:28:  [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.
    return s.size() > n && equal(s.begin(), s.begin() + n, prefix);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/StringUtil.h:155:28:  [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.
    return s.size() > n && equal(s.end() - n, s.end(), suffix);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/ntcard/Common/StringUtil.h:163:28:  [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.
    return s.size() > n && equal(s.end() - n, s.end(),
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/junctionapi/junctionapi.h:94:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				in_.read(reinterpret_cast<char*>(&pos.pos_), sizeof(pos.pos_));
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/junctionapi/junctionapi.h:95:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				in_.read(reinterpret_cast<char*>(&pos.bifId_), sizeof(pos.bifId_));
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/streamfastaparser.cpp:100:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				stream_.read(buffer_, BUF_SIZE);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/streamfastaparser.cpp:120:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				stream_.read(buffer_, BUF_SIZE);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/streamfastaparser.h:54:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		size_t read;
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/streamfastaparser.h:64:43:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			str.insert(str.end(), buffer, buffer + read);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/streamfastaparser.h:85:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			for (task.read = 0; task.read < NewTask::TASK_SIZE && in_.get(ch); task.read++)
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/streamfastaparser.h:92:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				task.buffer[task.read] = ch;
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/streamfastaparser.h:105:74:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				std::copy(task.buffer + task.read - overlapSize_, task.buffer + task.read, std::back_inserter(overlapBuffer_));
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/common/streamfastaparser.h:109:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
					start_ += task.read;
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/compressedstring.h:36:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			in.read(reinterpret_cast<char*>(str_), sizeof(str_[0]) * CAPACITY);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/compressedstring.h:152:16:  [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.
			return std::equal(str_, str_ + CAPACITY, other.str_);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/concurrentbitvector.cpp:87:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
		if (!maskStorage.read(reinterpret_cast<char*>(filter_), nowSize * sizeof(BASIC_TYPE)))
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphconstructor/concurrentbitvector.cpp:103:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
			if (!candidateMaskFile.read(reinterpret_cast<char*>(filter_), nowSize * sizeof(BASIC_TYPE)))
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:876:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static void read(const iterator<I, BITS, W, TS, UB>& p) { prefetch_iterator_traits<W*>::template read<level>(p.get_ptr()); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:876:100:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static void read(const iterator<I, BITS, W, TS, UB>& p) { prefetch_iterator_traits<W*>::template read<level>(p.get_ptr()); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:885:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static void read(const const_iterator<I, BITS, W, UB>& p) { prefetch_iterator_traits<const W*>::template read<level>(p.get_ptr()); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_iterator.hpp:885:108:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static void read(const const_iterator<I, BITS, W, UB>& p) { prefetch_iterator_traits<const W*>::template read<level>(p.get_ptr()); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:32:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        ifile.read(reinterpret_cast<char *>(&static_flag), sizeof(static_flag));
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:34:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        ifile.read(reinterpret_cast<char *>(&bits_per_element), sizeof(bits_per_element));
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:268:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    ifile.read(reinterpret_cast<char *>(&static_flag), sizeof(static_flag));
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:271:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    ifile.read(reinterpret_cast<char *>(&bits_per_element), sizeof(bits_per_element));
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:276:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    ifile.read(reinterpret_cast<char *>(&w_size), sizeof(w_size));
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:281:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    ifile.read(reinterpret_cast<char *>(&w_capacity), sizeof(w_capacity));
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/compact_vector.hpp:288:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    ifile.read(reinterpret_cast<char *>(m_mem), sizeof(W) * elements_to_words(m_size, bits()));
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/mio.hpp:62:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    read,
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/mio.hpp:461:47:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    typename std::enable_if<A == access_mode::read, void>::type conditional_sync();
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/mio.hpp:493:51:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
using basic_mmap_source = basic_mmap<access_mode::read, ByteT>;
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/mio.hpp:805:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            mode == access_mode::read ? GENERIC_READ : GENERIC_READ | GENERIC_WRITE,
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/mio.hpp:820:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            mode == access_mode::read ? GENERIC_READ : GENERIC_READ | GENERIC_WRITE,
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/mio.hpp:860:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            mode == access_mode::read ? O_RDONLY : O_RDWR);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/mio.hpp:911:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            mode == access_mode::read ? PAGE_READONLY : PAGE_READWRITE,
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/mio.hpp:922:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            mode == access_mode::read ? FILE_MAP_READ : FILE_MAP_WRITE,
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/mio.hpp:935:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            mode == access_mode::read ? PROT_READ : PROT_WRITE,
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/mio.hpp:1207:43:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
typename std::enable_if<A == access_mode::read, void>::type
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/mio.hpp:1301:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    read,
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/mio.hpp:1733:65:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
using basic_shared_mmap_source = basic_shared_mmap<access_mode::read, ByteT>;
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/prefetch_iterator_traits.hpp:14:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static void read(T* ptr) { __builtin_prefetch((void*)ptr, 0, level); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/graphdump/compact_vector/prefetch_iterator_traits.hpp:22:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static void read(const T* ptr) { __builtin_prefetch((void*)ptr, 0, level); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/naiveconstructor/naiveconstructor.cpp:102:15:  [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.
		return std::equal(a.body + OFF, a.body + OFF + k, b.body + OFF);
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/naiveconstructor/naiveconstructor.cpp:171:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
				it = tmpFile.read();
data/salmon-1.4.0+ds1/debian/external/pufferfish/external/twopaco/naiveconstructor/naiveconstructor.cpp:184:19:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
					jt = tmpFile.read();
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:789:7:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:790:7:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:792:7:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:795:7:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:797:7:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:1206:7:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:1207:7:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:1208:7:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:1209:7:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:1241:7:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:1248:8:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/BooPHF.hpp:1249:8:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/MemCollector.hpp:35:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool get_raw_hits_sketch(std::string &read,
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/MemCollector.hpp:40:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool operator()(std::string &read,
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/MemCollector.hpp:49:30:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool findChains(std::string& read,
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PuffAligner.hpp:87:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  int32_t calculateAlignments(std::string& read, pufferfish::util::JointMems& jointHit, HitCounters& hctr, bool isMultimapping, bool verbose);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PuffAligner.hpp:89:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool alignRead(std::string& read, std::string& read_rc, const std::vector<pufferfish::util::MemInfo>& mems, uint64_t queryChainHash, bool perfectChain, bool isFw, size_t tid, AlnCacheMap& alnCache, HitCounters& hctr, AlignmentResult& arOut, bool verbose);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PuffMappingReader.hpp:80:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        inFile.read(reinterpret_cast<char *>(&isPaired), sizeof(bool));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PuffMappingReader.hpp:81:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        inFile.read(reinterpret_cast<char *>(&refCount), sizeof(size_t));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PuffMappingReader.hpp:89:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            inFile.read(reinterpret_cast<char *>(&refNameSize), sizeof(refNameSize));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PuffMappingReader.hpp:91:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            inFile.read(strChar, refNameSize);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PuffMappingReader.hpp:93:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            inFile.read(reinterpret_cast<char *>(&refLen), sizeof(refLenType));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PuffMappingReader.hpp:105:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            inFile.read(reinterpret_cast<char *>(&chunksize), sizeof(chunksize));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/PuffMappingReader.hpp:109:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            inFile.read(chunk.chunk_.data(), chunksize);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/archives/json.hpp:530:35:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
            const auto len = std::strlen( searchName );
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/archives/json.hpp:536:26:  [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).
                  ( std::strlen( currentName ) == len ) )
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/archives/xml.hpp:268:30:  [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).
        strValue.resize(std::strlen(strValue.c_str()));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/internal/strfunc.h:40:26:  [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).
    return SizeType(std::strlen(s));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/internal/strfunc.h:45:26:  [1] (buffer) wcslen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
    return SizeType(std::wcslen(s));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidjson/istreamwrapper.h:101:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            if (!stream_.read(buffer_, static_cast<std::streamsize>(bufferSize_))) {
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/cereal/external/rapidxml/rapidxml_utils.hpp:45:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            stream.read(&m_data.front(), static_cast<streamsize>(size));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/clipp.h:411:29:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
        const auto n = std::strlen(s);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/compact_iterator.hpp:876:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static void read(const iterator<I, BITS, W, TS, UB>& p) { prefetch_iterator_traits<W*>::template read<level>(p.get_ptr()); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/compact_iterator.hpp:876:100:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static void read(const iterator<I, BITS, W, TS, UB>& p) { prefetch_iterator_traits<W*>::template read<level>(p.get_ptr()); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/compact_iterator.hpp:885:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static void read(const const_iterator<I, BITS, W, UB>& p) { prefetch_iterator_traits<const W*>::template read<level>(p.get_ptr()); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/compact_iterator.hpp:885:108:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static void read(const const_iterator<I, BITS, W, UB>& p) { prefetch_iterator_traits<const W*>::template read<level>(p.get_ptr()); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/compact_vector.hpp:32:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        ifile.read(reinterpret_cast<char *>(&static_flag), sizeof(static_flag));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/compact_vector.hpp:34:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        ifile.read(reinterpret_cast<char *>(&bits_per_element), sizeof(bits_per_element));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/compact_vector.hpp:268:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    ifile.read(reinterpret_cast<char *>(&static_flag), sizeof(static_flag));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/compact_vector.hpp:271:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    ifile.read(reinterpret_cast<char *>(&bits_per_element), sizeof(bits_per_element));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/compact_vector.hpp:276:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    ifile.read(reinterpret_cast<char *>(&w_size), sizeof(w_size));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/compact_vector.hpp:281:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    ifile.read(reinterpret_cast<char *>(&w_capacity), sizeof(w_capacity));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/compact_vector.hpp:288:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    ifile.read(reinterpret_cast<char *>(m_mem), sizeof(W) * elements_to_words(m_size, bits()));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/mio.hpp:62:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    read,
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/mio.hpp:461:47:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    typename std::enable_if<A == access_mode::read, void>::type conditional_sync();
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/mio.hpp:493:51:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
using basic_mmap_source = basic_mmap<access_mode::read, ByteT>;
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/mio.hpp:805:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            mode == access_mode::read ? GENERIC_READ : GENERIC_READ | GENERIC_WRITE,
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/mio.hpp:820:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            mode == access_mode::read ? GENERIC_READ : GENERIC_READ | GENERIC_WRITE,
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/mio.hpp:860:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            mode == access_mode::read ? O_RDONLY : O_RDWR);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/mio.hpp:911:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            mode == access_mode::read ? PAGE_READONLY : PAGE_READWRITE,
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/mio.hpp:922:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            mode == access_mode::read ? FILE_MAP_READ : FILE_MAP_WRITE,
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/mio.hpp:935:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            mode == access_mode::read ? PROT_READ : PROT_WRITE,
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/mio.hpp:1207:43:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
typename std::enable_if<A == access_mode::read, void>::type
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/mio.hpp:1301:5:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    read,
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/mio.hpp:1733:65:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
using basic_shared_mmap_source = basic_shared_mmap<access_mode::read, ByteT>;
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/prefetch_iterator_traits.hpp:14:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static void read(T* ptr) { __builtin_prefetch((void*)ptr, 0, level); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/compact_vector/prefetch_iterator_traits.hpp:22:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  static void read(const T* ptr) { __builtin_prefetch((void*)ptr, 0, level); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/algorithm.hpp:273:13:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
) { return (mismatch)(first1, last1, first2, last2, equal_to<> { }); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/algorithm.hpp:282:8:  [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.
> auto mismatch (Range1&& r1, Range2&& r2, BinaryPred&& bp) -> ::std::pair<
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/algorithm.hpp:291:11:  [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.
  return (mismatch)(
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/algorithm.hpp:305:8:  [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.
> auto mismatch(Range&& rng, InputIt&& it) -> ::std::pair<
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/algorithm.hpp:312:17:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  return ::std::mismatch(
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/algorithm.hpp:326:8:  [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.
> auto mismatch(Range&& r, InputIt&& it, BinaryPredicate&& bp) -> ::std::pair<
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/algorithm.hpp:367:8:  [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.
> bool equal (Range1&& range1, Range2&& range2) {
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/algorithm.hpp:374:11:  [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.
  return (equal)(r1.begin(), r1.end(), r2.begin(), r2.end());
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/algorithm.hpp:384:8:  [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.
> bool equal (Range1&& range1, Range2&& range2, BinaryPredicate&& bp) {
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/algorithm.hpp:406:8:  [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.
> bool equal (Range&& rng, InputIt&& it) {
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/algorithm.hpp:410:17:  [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.
  return ::std::equal(
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/algorithm.hpp:424:8:  [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.
> bool equal (Range&& rng, InputIt&& it, BinaryPredicate&& bp) {
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/algorithm.hpp:2173:6:  [1] (buffer) is_permutation:
  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.
auto is_permutation (Range1&& rng1, Range2&& rng2) -> enable_if_t<
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/algorithm.hpp:2183:17:  [1] (buffer) is_permutation:
  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.
  return ::std::is_permutation(
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/algorithm.hpp:2191:6:  [1] (buffer) is_permutation:
  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.
auto is_permutation (
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/forward_list.hpp:20:27:  [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.
  f.remove_if(::std::bind(equal<>, _1, ::std::cref(value)));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/list.hpp:18:27:  [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.
  l.remove_if(::std::bind(equal<>, _1, ::std::cref(value)));
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/core/meta.hpp:64:32:  [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.
template <class, class> struct equal;
data/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:1400:46:  [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.
    return with.length() <= what.length() && equal(with.begin(), with.end(), what.begin());
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/ghc/filesystem.hpp:3277:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((br = ::read(in, buffer.data(), buffer.size())) > 0) {
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/jellyfish/mer_dna.hpp:202:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void read(std::istream& is) {
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/jellyfish/mer_dna.hpp:205:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    is.read((char*)_data, l);
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/jellyfish/mer_dna.hpp:312:8:  [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(strlen(s) < static_cast<derived*>(this)->k())
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/jellyfish/mer_dna.hpp:596:52:  [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).
  explicit mer_base_dynamic(const char* s) : super(strlen(s)), k_(strlen(s)) {
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/jellyfish/mer_dna.hpp:596:67:  [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).
  explicit mer_base_dynamic(const char* s) : super(strlen(s)), k_(strlen(s)) {
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/jellyfish/mer_dna.hpp:703:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  is.read(buffer, mer.k());
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/parallel_hashmap/meminfo.h:127:26:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/parallel_hashmap/phmap.h:3099:21:  [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.
        return std::equal(a.sets_.begin(), a.sets_.end(), b.sets_.begin());
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/popl.hpp:263:7:  [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 (strlen(value) == 0)
data/salmon-1.4.0+ds1/debian/external/pufferfish/include/popl.hpp:332:27:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
  if ((value != NULL) && (strlen(value) > 0))
data/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/fmt/bundled/format.h:2150:52:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/include/spdlog/fmt/bundled/format.h:2155:55:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/src/FixFasta.cpp:143:18:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/src/FixFasta.cpp:145:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        std::string& readStr = read.seq;
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/FixFasta.cpp:158:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        auto& readName = read.name;
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/FixFasta.cpp:212:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                        read.name);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/FixFasta.cpp:231:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                      read.name, tooLong);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/FixFasta.cpp:235:23:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                      read.name, k);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/FixFasta.cpp:242:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
          auto& recHeader = read.name;
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/FixFasta.cpp:341:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    read.name);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/MemCollector.cpp:150:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  SkipContext(std::string& read, PufferfishIndexT* pfi_in, int32_t k_in) : 
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/MemCollector.cpp:151:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    kit1(read), kit_tmp(read), pfi(pfi_in), read_len(static_cast<int32_t>(read.length())),
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/MemCollector.cpp:151:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    kit1(read), kit_tmp(read), pfi(pfi_in), read_len(static_cast<int32_t>(read.length())),
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/MemCollector.cpp:151:75:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    kit1(read), kit_tmp(read), pfi(pfi_in), read_len(static_cast<int32_t>(read.length())),
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/MemCollector.cpp:586:71:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool MemCollector<PufferfishIndexT>::get_raw_hits_sketch(std::string &read,
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/MemCollector.cpp:596:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  SkipContext<PufferfishIndexT> skip_ctx(read, pfi_, k);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/MemCollector.cpp:704:62:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool MemCollector<PufferfishIndexT>::operator()(std::string &read,
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/MemCollector.cpp:716:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  pufferfish::CanonicalKmerIterator kit1(read);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/MemCollector.cpp:719:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    std::cerr << read << "\n";
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/MemCollector.cpp:797:62:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool MemCollector<PufferfishIndexT>::findChains(std::string &read,
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/MemCollector.cpp:816:73:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    mc.findOptChain(rawHits, memClusters, maxSpliceGap, *memCollection, read.length(), 
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PuffAligner.cpp:147:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool PuffAligner::alignRead(std::string& read, std::string& read_rc, const std::vector<pufferfish::util::MemInfo> &mems, uint64_t queryChainHash, bool perfectChain,
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PuffAligner.cpp:182:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  auto readLen = read.length();
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PuffAligner.cpp:226:49:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  int32_t signedRefEndPos = signedRefStartPos + read.length();
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PuffAligner.cpp:244:59:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  const int32_t minAcceptedScore = scoreStatus_.getCutoff(read.length()); //mopts.minScoreFraction * mopts.matchScore * readLen;
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PuffAligner.cpp:339:82:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if (!isFw and read_rc.empty()) { read_rc = pufferfish::util::reverseComplement(read); }
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PuffAligner.cpp:340:43:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  nonstd::string_view readView = (isFw) ? read : read_rc;
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PuffAligner.cpp:351:59:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      auto cutoff = minAcceptedScore - mopts.matchScore * read.length();
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PuffAligner.cpp:417:63:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
          auto cutoff = minAcceptedScore - mopts.matchScore * read.length();
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PuffAligner.cpp:849:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
int32_t PuffAligner::calculateAlignments(std::string& read, pufferfish::util::JointMems& jointHit, HitCounters& hctr, bool isMultimapping, bool verbose) {
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PuffAligner.cpp:863:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    alignRead(read, read_left_rc_, oc->mems, oc->queryChainHash, oc->perfectChain, oc->isFw, tid, alnCacheLeft, hctr, ar_left, verbose);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PuffAligner.cpp:865:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      ar_left.score > threshold(read.length())  ? ar_left.score : invalidScore;
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PuffAligner.cpp:870:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      std::cerr << read.length() << " " << threshold(read.length()) << " " << ar_left.score << "\n";
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PuffAligner.cpp:870:54:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      std::cerr << read.length() << " " << threshold(read.length()) << " " << ar_left.score << "\n";
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishAligner.cpp:639:46:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            readLen = static_cast<uint32_t >(read.seq.length());
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishAligner.cpp:655:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
              memCollector(read.seq,
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishAligner.cpp:659:37:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            memCollector.findChains(read.seq,
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishAligner.cpp:695:72:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                    int32_t hitScore = puffaligner.calculateAlignments(read.seq, jointHit, hctr, isMultimapping, verbose);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishAligner.cpp:818:43:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
              writeAlignmentsToKrakenDump(read, formatter,
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishAligner.cpp:822:43:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
              writeAlignmentsToKrakenDump(read, formatter,
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishAligner.cpp:826:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
              writeAlignmentsToRADSingle(read, formatter,
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishAligner.cpp:831:47:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                writeAlignmentsToStreamSingle(read, formatter, jointAlignments, sstream, !mopts->noOrphan);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishAligner.cpp:835:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
              writeUnalignedSingleToStream(read, sstream);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:149:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            file.read(reinterpret_cast<char *>(&refIdSize), sizeof(refIdSize));
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:154:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            file.read(reinterpret_cast<char *>(&refIdLen), refIdSize);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:157:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            file.read(&(refId[0]), refIdLen);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:158:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            file.read(reinterpret_cast<char *>(&contigCntPerPath), sizeof(contigCntPerPath));
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/PufferfishBinaryGFAReader.cpp:164:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                file.read(reinterpret_cast<char *>(&contigIdAndOri), sizeof(contigIdAndOri));
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/cli.cpp:64:9:  [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).
	qlen = strlen(qseq_);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/cli.cpp:65:9:  [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).
	tlen = strlen(tseq_);
data/salmon-1.4.0+ds1/debian/external/pufferfish/src/ksw2pp/KSW2Aligner.cpp:78:49:  [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/salmon-1.4.0+ds1/debian/external/pufferfish/src/ksw2pp/KSW2Aligner.cpp:91:13:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
    int b = mismatch;
data/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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/salmon-1.4.0+ds1/debian/external/pufferfish/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));
data/salmon-1.4.0+ds1/include/AlevinUtils.hpp:81:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool extractUMI(std::string& read,
data/salmon-1.4.0+ds1/include/AlevinUtils.hpp:93:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool extractBarcode(std::string& read, std::string& read2, ProtocolT& pt, std::string& bc);
data/salmon-1.4.0+ds1/include/AlignmentGroup.hpp:32:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  std::string* read() { return read_; }
data/salmon-1.4.0+ds1/include/AlignmentModel.hpp:96:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void update(bam_seq_t* read, Transcript& ref, double p, double mass,
data/salmon-1.4.0+ds1/include/AlignmentModel.hpp:98:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  AlnModelProb logLikelihood(bam_seq_t* read, Transcript& ref,
data/salmon-1.4.0+ds1/include/UnpairedRead.hpp:28:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      : read(staden::utils::bam_init()), logProb(salmon::math::LOG_0) {}
data/salmon-1.4.0+ds1/include/UnpairedRead.hpp:31:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      : read(r), logProb(lp), libFmt(lf) {}
data/salmon-1.4.0+ds1/include/UnpairedRead.hpp:35:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    std::swap(read, other.read);
data/salmon-1.4.0+ds1/include/UnpairedRead.hpp:35:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    std::swap(read, other.read);
data/salmon-1.4.0+ds1/include/UnpairedRead.hpp:41:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    std::swap(read, other.read);
data/salmon-1.4.0+ds1/include/UnpairedRead.hpp:41:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    std::swap(read, other.read);
data/salmon-1.4.0+ds1/include/UnpairedRead.hpp:51:37:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    return new UnpairedRead(bam_dup(read), logProb, libFmt);
data/salmon-1.4.0+ds1/include/UnpairedRead.hpp:54:48:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  ~UnpairedRead() { staden::utils::bam_destroy(read); }
data/salmon-1.4.0+ds1/include/UnpairedRead.hpp:56:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inline bam_seq_t* getRead1() { return read; }
data/salmon-1.4.0+ds1/include/UnpairedRead.hpp:57:41:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inline bam_seq_t* getRead2() { return read; }
data/salmon-1.4.0+ds1/include/UnpairedRead.hpp:65:46:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inline bam_seq_t* get5PrimeRead() { return read; }
data/salmon-1.4.0+ds1/include/UnpairedRead.hpp:72:59:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    uint8_t* tp = reinterpret_cast<uint8_t*>(bam_aux_find(read, "AS"));
data/salmon-1.4.0+ds1/include/UnpairedRead.hpp:77:59:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    uint8_t* tp = reinterpret_cast<uint8_t*>(bam_aux_find(read, "AS"));
data/salmon-1.4.0+ds1/include/UnpairedRead.hpp:82:48:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inline bool fwd() const { return !bam_strand(read); }
data/salmon-1.4.0+ds1/include/UnpairedRead.hpp:85:60:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  int writeToFile(scram_fd* fp) { return scram_put_seq(fp, read); }
data/salmon-1.4.0+ds1/include/UnpairedRead.hpp:87:44:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inline char* getName() { return bam_name(read); }
data/salmon-1.4.0+ds1/include/UnpairedRead.hpp:89:57:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inline uint32_t getNameLength() { return bam_name_len(read); }
data/salmon-1.4.0+ds1/include/UnpairedRead.hpp:91:49:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inline bool isRight() const { return bam_flag(read) & BAM_FREVERSE; }
data/salmon-1.4.0+ds1/include/UnpairedRead.hpp:93:48:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inline int32_t left() const { return bam_pos(read); }
data/salmon-1.4.0+ds1/include/UnpairedRead.hpp:94:62:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inline int32_t right() const { return left() + bam_seq_len(read); }
data/salmon-1.4.0+ds1/include/UnpairedRead.hpp:101:56:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  inline int32_t transcriptID() const { return bam_ref(read); }
data/salmon-1.4.0+ds1/include/core/algorithm.hpp:273:13:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
) { return (mismatch)(first1, last1, first2, last2, equal_to<> { }); }
data/salmon-1.4.0+ds1/include/core/algorithm.hpp:282:8:  [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.
> auto mismatch (Range1&& r1, Range2&& r2, BinaryPred&& bp) -> ::std::pair<
data/salmon-1.4.0+ds1/include/core/algorithm.hpp:291:11:  [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.
  return (mismatch)(
data/salmon-1.4.0+ds1/include/core/algorithm.hpp:305:8:  [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.
> auto mismatch(Range&& rng, InputIt&& it) -> ::std::pair<
data/salmon-1.4.0+ds1/include/core/algorithm.hpp:312:17:  [1] (buffer) mismatch:
  Function does not check the second iterator for over-read conditions
  (CWE-126). This function is often discouraged by most C++ coding standards
  in favor of its safer alternatives provided since C++14. Consider using a
  form of this function that checks the second iterator before potentially
  overflowing it.
  return ::std::mismatch(
data/salmon-1.4.0+ds1/include/core/algorithm.hpp:326:8:  [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.
> auto mismatch(Range&& r, InputIt&& it, BinaryPredicate&& bp) -> ::std::pair<
data/salmon-1.4.0+ds1/include/core/algorithm.hpp:367:8:  [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.
> bool equal (Range1&& range1, Range2&& range2) {
data/salmon-1.4.0+ds1/include/core/algorithm.hpp:374:11:  [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.
  return (equal)(r1.begin(), r1.end(), r2.begin(), r2.end());
data/salmon-1.4.0+ds1/include/core/algorithm.hpp:384:8:  [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.
> bool equal (Range1&& range1, Range2&& range2, BinaryPredicate&& bp) {
data/salmon-1.4.0+ds1/include/core/algorithm.hpp:406:8:  [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.
> bool equal (Range&& rng, InputIt&& it) {
data/salmon-1.4.0+ds1/include/core/algorithm.hpp:410:17:  [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.
  return ::std::equal(
data/salmon-1.4.0+ds1/include/core/algorithm.hpp:424:8:  [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.
> bool equal (Range&& rng, InputIt&& it, BinaryPredicate&& bp) {
data/salmon-1.4.0+ds1/include/core/algorithm.hpp:2173:6:  [1] (buffer) is_permutation:
  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.
auto is_permutation (Range1&& rng1, Range2&& rng2) -> enable_if_t<
data/salmon-1.4.0+ds1/include/core/algorithm.hpp:2183:17:  [1] (buffer) is_permutation:
  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.
  return ::std::is_permutation(
data/salmon-1.4.0+ds1/include/core/algorithm.hpp:2191:6:  [1] (buffer) is_permutation:
  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.
auto is_permutation (
data/salmon-1.4.0+ds1/include/core/forward_list.hpp:20:27:  [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.
  f.remove_if(::std::bind(equal<>, _1, ::std::cref(value)));
data/salmon-1.4.0+ds1/include/core/list.hpp:18:27:  [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.
  l.remove_if(::std::bind(equal<>, _1, ::std::cref(value)));
data/salmon-1.4.0+ds1/include/core/meta.hpp:64:32:  [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.
template <class, class> struct equal;
data/salmon-1.4.0+ds1/include/httplib.hpp:356:19:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  virtual ssize_t read(char *ptr, size_t size) = 0;
data/salmon-1.4.0+ds1/include/httplib.hpp:1092:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  fs.read(&out[0], size);
data/salmon-1.4.0+ds1/include/httplib.hpp:1152:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      auto n = strm_.read(&byte, 1);
data/salmon-1.4.0+ds1/include/httplib.hpp:1294:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  ssize_t read(char *ptr, size_t size) override;
data/salmon-1.4.0+ds1/include/httplib.hpp:1313:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  ssize_t read(char *ptr, size_t size) override;
data/salmon-1.4.0+ds1/include/httplib.hpp:1332:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  ssize_t read(char *ptr, size_t size) override;
data/salmon-1.4.0+ds1/include/httplib.hpp:1869:19:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    auto n = strm.read(buf, (std::min)(read_len, CPPHTTPLIB_RECV_BUFSIZ));
data/salmon-1.4.0+ds1/include/httplib.hpp:1889:19:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    auto n = strm.read(buf, (std::min)(read_len, CPPHTTPLIB_RECV_BUFSIZ));
data/salmon-1.4.0+ds1/include/httplib.hpp:1898:19:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    auto n = strm.read(buf, CPPHTTPLIB_RECV_BUFSIZ);
data/salmon-1.4.0+ds1/include/httplib.hpp:2531:47:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      [&](const char *token) { data_length += strlen(token); },
data/salmon-1.4.0+ds1/include/httplib.hpp:2899:21:  [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 write(ptr, strlen(ptr));
data/salmon-1.4.0+ds1/include/httplib.hpp:2957:30:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
inline ssize_t SocketStream::read(char *ptr, size_t size) {
data/salmon-1.4.0+ds1/include/httplib.hpp:2993:30:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
inline ssize_t BufferStream::read(char *ptr, size_t size) {
data/salmon-1.4.0+ds1/include/httplib.hpp:4695:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
inline ssize_t SSLSocketStream::read(char *ptr, size_t size) {
data/salmon-1.4.0+ds1/include/httplib.hpp:4987:13:  [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 (strlen(name) == name_len) {
data/salmon-1.4.0+ds1/include/jellyfish/mer_dna.hpp:202:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  void read(std::istream& is) {
data/salmon-1.4.0+ds1/include/jellyfish/mer_dna.hpp:205:8:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    is.read((char*)_data, l);
data/salmon-1.4.0+ds1/include/jellyfish/mer_dna.hpp:312:8:  [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(strlen(s) < static_cast<derived*>(this)->k())
data/salmon-1.4.0+ds1/include/jellyfish/mer_dna.hpp:596:52:  [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).
  explicit mer_base_dynamic(const char* s) : super(strlen(s)), k_(strlen(s)) {
data/salmon-1.4.0+ds1/include/jellyfish/mer_dna.hpp:596:67:  [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).
  explicit mer_base_dynamic(const char* s) : super(strlen(s)), k_(strlen(s)) {
data/salmon-1.4.0+ds1/include/jellyfish/mer_dna.hpp:703:6:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  is.read(buffer, mer.k());
data/salmon-1.4.0+ds1/include/json.hpp:3935:21:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        return std::fgetc(m_file);
data/salmon-1.4.0+ds1/include/json.hpp:4242:30:  [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::strlen(reinterpret_cast<const char*>(b))) {}
data/salmon-1.4.0+ds1/include/parallel_hashmap/meminfo.h:127:26:  [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/salmon-1.4.0+ds1/include/parallel_hashmap/phmap.h:3099:21:  [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.
        return std::equal(a.sets_.begin(), a.sets_.end(), b.sets_.begin());
data/salmon-1.4.0+ds1/include/pcg_random.hpp:1195:16:  [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(std::begin(lhs.data_), std::end(lhs.data_),
data/salmon-1.4.0+ds1/include/peglib.h:2218:14:  [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 n = strlen(s);
data/salmon-1.4.0+ds1/include/peglib.h:2229:14:  [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 n = strlen(s);
data/salmon-1.4.0+ds1/include/peglib.h:2248:14:  [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 n = strlen(s);
data/salmon-1.4.0+ds1/include/peglib.h:2266:14:  [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 n = strlen(s);
data/salmon-1.4.0+ds1/include/peglib.h:3860:57:  [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).
  parser(const char *s, const Rules &rules) : parser(s, strlen(s), rules) {}
data/salmon-1.4.0+ds1/include/peglib.h:3864:37:  [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).
  parser(const char *s) : parser(s, strlen(s), Rules()) {}
data/salmon-1.4.0+ds1/include/peglib.h:3878:14:  [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 n = strlen(s);
data/salmon-1.4.0+ds1/include/peglib.h:3883:14:  [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 n = strlen(s);
data/salmon-1.4.0+ds1/include/peglib.h:3898:14:  [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 n = strlen(s);
data/salmon-1.4.0+ds1/include/peglib.h:3914:14:  [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 n = strlen(s);
data/salmon-1.4.0+ds1/include/peglib.h:3932:14:  [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 n = strlen(s);
data/salmon-1.4.0+ds1/include/peglib.h:3951:14:  [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 n = strlen(s);
data/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/include/spdlog/fmt/bundled/format.h:2150:52:  [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/salmon-1.4.0+ds1/include/spdlog/fmt/bundled/format.h:2155:55:  [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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/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/salmon-1.4.0+ds1/include/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/salmon-1.4.0+ds1/src/AlevinUtils.cpp:139:48:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool extractUMI<apt::DropSeq>(std::string& read,
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:144:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      return (read.length() >= pt.barcodeLength + pt.umiLength) ?
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:145:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        (umi.assign(read, pt.barcodeLength, pt.umiLength), true) : false;
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:148:48:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool extractUMI<apt::CITESeq>(std::string& read,
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:153:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      return (read.length() >= pt.barcodeLength + pt.umiLength) ?
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:154:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        (umi.assign(read, pt.barcodeLength, pt.umiLength), true) : false;
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:157:49:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool extractUMI<apt::Chromium>(std::string& read,
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:162:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      return (read.length() >= pt.barcodeLength + pt.umiLength) ?
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:163:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        (umi.assign(read, pt.barcodeLength, pt.umiLength), true) : false;
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:166:51:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool extractUMI<apt::ChromiumV3>(std::string& read,
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:171:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      return (read.length() >= pt.barcodeLength + pt.umiLength) ?
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:172:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        (umi.assign(read, pt.barcodeLength, pt.umiLength), true) : false;
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:175:48:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool extractUMI<apt::Gemcode>(std::string& read,
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:180:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      return (read.length() >= pt.barcodeLength + pt.umiLength) ?
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:181:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        (umi.assign(read, pt.barcodeLength, pt.umiLength), true) : false;
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:184:47:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool extractUMI<apt::Custom>(std::string& read,
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:190:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        umi.assign(read, pt.barcodeLength, pt.umiLength);
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:192:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        umi.assign(read, 0, pt.umiLength);
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:207:51:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool extractUMI<apt::QuartzSeq2>(std::string& read,
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:212:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      return (read.length() >= pt.barcodeLength + pt.umiLength) ?
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:213:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        (umi.assign(read, pt.barcodeLength, pt.umiLength), true) : false;
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:217:48:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool extractUMI<apt::CELSeq2>(std::string& read,
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:222:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      return (read.length() >= pt.umiLength) ?
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:223:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        (umi.assign(read, 0, pt.umiLength), true) : false;
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:226:47:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool extractUMI<apt::CELSeq>(std::string& read,
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:231:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      return (read.length() >= pt.umiLength) ?
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:232:21:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        (umi.assign(read, 0, pt.umiLength), true) : false;
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:236:47:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool extractUMI<apt::InDrop>(std::string& read,
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:240:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      (void)read;
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:247:52:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool extractBarcode<apt::DropSeq>(std::string& read,
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:252:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      return (read.length() >= pt.barcodeLength) ?
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:253:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        (bc.assign(read, 0, pt.barcodeLength), true) : false;
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:256:52:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool extractBarcode<apt::CITESeq>(std::string& read,
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:261:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      return (read.length() >= pt.barcodeLength) ?
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:262:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        (bc.assign(read, 0, pt.barcodeLength), true) : false;
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:265:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool extractBarcode<apt::ChromiumV3>(std::string& read,
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:270:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      return (read.length() >= pt.barcodeLength) ?
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:271:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        (bc.assign(read,0, pt.barcodeLength), true) : false;
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:274:53:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool extractBarcode<apt::Chromium>(std::string& read,
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:279:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      return (read.length() >= pt.barcodeLength) ?
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:280:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        (bc.assign(read, 0, pt.barcodeLength), true) : false;
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:283:52:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool extractBarcode<apt::Gemcode>(std::string& read,
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:288:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      return (read.length() >= pt.barcodeLength) ?
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:289:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        (bc.assign(read, 0, pt.barcodeLength), true) : false;
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:292:51:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool extractBarcode<apt::Custom>(std::string& read,
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:298:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        return (read.length() >= pt.barcodeLength) ?
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:299:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
          (bc.assign(read, 0, pt.barcodeLength), true) : false;
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:301:17:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        return (read.length() >= (pt.umiLength + pt.barcodeLength)) ?
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:302:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
          (bc.assign(read, pt.umiLength, pt.barcodeLength), true) : false;
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:315:55:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool extractBarcode<apt::QuartzSeq2>(std::string& read,
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:320:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      return (read.length() >= pt.barcodeLength) ?
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:321:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        (bc.assign(read, 0, pt.barcodeLength), true) : false;
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:324:52:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool extractBarcode<apt::CELSeq2>(std::string& read,
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:329:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      return (read.length() >= (pt.umiLength + pt.barcodeLength)) ?
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:330:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        (bc.assign(read, pt.umiLength, pt.barcodeLength), true) : false;
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:333:51:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool extractBarcode<apt::CELSeq>(std::string& read,
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:338:15:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      return (read.length() >= (pt.umiLength + pt.barcodeLength)) ?
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:339:20:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        (bc.assign(read, pt.umiLength, pt.barcodeLength), true) : false;
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:342:51:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bool extractBarcode<apt::InDrop>(std::string& read, 
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:346:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      std::string::size_type index = read.find(pt.w1);
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:350:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      bc = read.substr(0, index);
data/salmon-1.4.0+ds1/src/AlevinUtils.cpp:355:13:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      bc += read.substr(offset, offset+8);
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:43:72:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool AlignmentModel::hasIndel(UnpairedRead& hit) { return hasIndel(hit.read); }
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:45:42:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
bool AlignmentModel::hasIndel(bam_seq_t* read) {
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:46:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  uint32_t* cigar = bam_cigar(read);
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:47:37:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  uint32_t cigarLen = bam_cigar_len(read);
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:216:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bam_seq_t* read, Transcript& ref,
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:221:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  auto transcriptIdx = bam_pos(read);
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:242:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  uint32_t* cigar = bam_cigar(read);
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:243:37:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  uint32_t cigarLen = bam_cigar_len(read);
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:244:54:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  uint8_t* qseq = reinterpret_cast<uint8_t*>(bam_seq(read));
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:245:58:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  uint8_t* qualStr = reinterpret_cast<uint8_t*>(bam_qual(read));
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:246:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  int32_t readLen = bam_seq_len(read);
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:264:64:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  double invLen = static_cast<double>(readBins_) / bam_seq_len(read);
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:283:36:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                          bam_name(read));
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:308:26:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                bam_name(read), ref.RefName, transcriptLen, ref.id,
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:309:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                bam_ref(read));
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:402:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bam_seq_t* read = hit.read;
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:403:52:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  size_t readLen = static_cast<size_t>(bam_seq_len(read));
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:410:35:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  auto alnLogProb = logLikelihood(read, ref, transitionProbsLeft_);
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:430:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bam_seq_t* leftRead = hit.read;
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:435:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    bam_seq_t* read, Transcript& ref, double p, double mass,
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:440:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  auto transcriptIdx = bam_pos(read);
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:452:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  uint32_t* cigar = bam_cigar(read);
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:453:37:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  uint32_t cigarLen = bam_cigar_len(read);
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:454:54:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  uint8_t* qseq = reinterpret_cast<uint8_t*>(bam_seq(read));
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:455:58:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  uint8_t* qualStr = reinterpret_cast<uint8_t*>(bam_qual(read));
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:456:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  int32_t readLen = bam_seq_len(read);
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:488:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                            bam_name(read));
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:514:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                  bam_name(read), ref.RefName, transcriptLen, ref.id,
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:515:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                  bam_ref(read));
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:565:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    update(read, ref, p, mass, transitionProbsLeft_);
data/salmon-1.4.0+ds1/src/AlignmentModel.cpp:568:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    update(read, ref, p, mass, transitionProbsRight_);
data/salmon-1.4.0+ds1/src/FASTAParser.cpp:55:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    for (auto& read : rg) {
data/salmon-1.4.0+ds1/src/FASTAParser.cpp:56:29:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      std::string& header = read.name;
data/salmon-1.4.0+ds1/src/FASTAParser.cpp:76:28:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        std::string& seq = read.seq;
data/salmon-1.4.0+ds1/src/GZipWriter.cpp:1614:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        countMatrixStream.read(reinterpret_cast<char*>(alphasFlag.data()), flagSize * numFlags);
data/salmon-1.4.0+ds1/src/GZipWriter.cpp:1640:27:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        countMatrixStream.read(reinterpret_cast<char*>(alphasSparse.data()), elSize * numExpGenes);
data/salmon-1.4.0+ds1/src/SalmonQuantifyAlignments.cpp:698:39:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                bam_seq_t* r1 = alnp->read;
data/salmon-1.4.0+ds1/src/SalmonQuantifyAlignments.cpp:821:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
                bam_seq_t* r = alnp->read;
data/salmon-1.4.0+ds1/src/SalmonUtils.cpp:973:38:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  bool didRead = (scram_get_seq(fp, &read) >= 0);
data/salmon-1.4.0+ds1/src/SalmonUtils.cpp:977:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    isPaired = bam_flag(read) & BAM_FPAIRED;
data/salmon-1.4.0+ds1/src/SalmonUtils.cpp:982:32:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    staden::utils::bam_destroy(read);
data/salmon-1.4.0+ds1/src/SalmonUtils.cpp:988:30:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  staden::utils::bam_destroy(read);
data/salmon-1.4.0+ds1/src/SalmonUtils.cpp:1031:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  mlist.read(reinterpret_cast<char*>(&numKmers), sizeof(size_t));
data/salmon-1.4.0+ds1/src/SalmonUtils.cpp:1035:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  mlist.read(reinterpret_cast<char*>(&kmers[0]),
data/salmon-1.4.0+ds1/src/SalmonUtils.cpp:1283:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    for (auto& read : rg) {
data/salmon-1.4.0+ds1/src/SalmonUtils.cpp:1285:30:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      std::string fullHeader(read.name);
data/salmon-1.4.0+ds1/tests/catch.hpp:3680:29:  [1] (buffer) is_permutation:
  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.
                return std::is_permutation(m_target.begin(), m_target.end(), vec.begin());
data/salmon-1.4.0+ds1/tests/catch.hpp:13297:36:  [1] (buffer) getchar:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            static_cast<void>(std::getchar());
data/salmon-1.4.0+ds1/tests/catch.hpp:13302:36:  [1] (buffer) getchar:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            static_cast<void>(std::getchar());
data/salmon-1.4.0+ds1/tests/catch.hpp:13599:50:  [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.
        return s.size() >= prefix.size() && std::equal(prefix.begin(), prefix.end(), s.begin());
data/salmon-1.4.0+ds1/tests/catch.hpp:13605:50:  [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.
        return s.size() >= suffix.size() && std::equal(suffix.rbegin(), suffix.rend(), s.rbegin());
data/salmon-1.4.0+ds1/tests/catch.hpp:13693:67:  [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).
    : StringRef( rawChars, static_cast<StringRef::size_type>(std::strlen(rawChars) ) )

ANALYSIS SUMMARY:

Hits = 1286
Lines analyzed = 373799 in approximately 8.90 seconds (42023 lines/second)
Physical Source Lines of Code (SLOC) = 255606
Hits@level = [0] 108 [1] 579 [2] 514 [3]  18 [4] 173 [5]   2
Hits@level+ = [0+] 1394 [1+] 1286 [2+] 707 [3+] 193 [4+] 175 [5+]   2
Hits/KSLOC@level+ = [0+] 5.45371 [1+] 5.03118 [2+] 2.76598 [3+] 0.755068 [4+] 0.684647 [5+] 0.00782454
Dot directories skipped = 4 (--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.