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/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/zutil.h
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/zutil.c
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/zlib.h
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/uncompr.c
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/trees.h
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/trees.c
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/inftrees.h
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/inftrees.c
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/inflate.h
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/inflate.c
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/inffixed.h
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/inffast.h
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/inffast.c
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/infback.c
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzwrite.c
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzread.c
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzlib.c
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzguts.h
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzclose.c
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/deflate.h
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/deflate.c
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/crc32.h
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/crc32.c
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/compress.c
Examining data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/adler32.c
Examining data/mapsembler2-2.2.4+dfsg1/minia/Utils.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/Utils.cpp
Examining data/mapsembler2-2.2.4+dfsg1/minia/ttmath/ttmathuint_x86_64.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/ttmath/ttmathuint_x86.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/ttmath/ttmathuint_noasm.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/ttmath/ttmathuint.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/ttmath/ttmathtypes.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/ttmath/ttmaththreads.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/ttmath/ttmathparser.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/ttmath/ttmathobjects.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/ttmath/ttmathmisc.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/ttmath/ttmathint.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/ttmath/ttmathbig.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/ttmath/ttmath.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/Traversal.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/Traversal.cpp
Examining data/mapsembler2-2.2.4+dfsg1/minia/Terminator.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/Terminator.cpp
Examining data/mapsembler2-2.2.4+dfsg1/minia/SortingCount.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/SortingCount.cpp
Examining data/mapsembler2-2.2.4+dfsg1/minia/Set.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/Set.cpp
Examining data/mapsembler2-2.2.4+dfsg1/minia/rvalues.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/Pool.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/Pool.cpp
Examining data/mapsembler2-2.2.4+dfsg1/minia/OAHash.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/lut.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/LinearCounter.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/LinearCounter.cpp
Examining data/mapsembler2-2.2.4+dfsg1/minia/LargeInt.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/LargeInt.cpp
Examining data/mapsembler2-2.2.4+dfsg1/minia/Kmer.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/Kmer.cpp
Examining data/mapsembler2-2.2.4+dfsg1/minia/Hash16.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/Hash16.cpp
Examining data/mapsembler2-2.2.4+dfsg1/minia/GraphOutput.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/Debloom.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/Debloom.cpp
Examining data/mapsembler2-2.2.4+dfsg1/minia/Bloom.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/Bloom.cpp
Examining data/mapsembler2-2.2.4+dfsg1/minia/Bank.h
Examining data/mapsembler2-2.2.4+dfsg1/minia/Bank.cpp
Examining data/mapsembler2-2.2.4+dfsg1/minia/OAHash.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/tools/KmerChecksum.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/tools/dbgtopology.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/tools/dbginfo.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/tools/dbgh5.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/tools/dbgcheck.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/tools/ClearCache.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/tools/bankgen.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/tools/BankDownload.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/test_mphf_hem.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/test_mphf_generic.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/test_mphf.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/ranked_bitpair_vector.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/perfutils.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/packed_vector.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/packed_edge_list.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/mphf_hem.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/mphf.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/mmap_memory_model.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/internal_memory_model.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/hypergraph_sorter_seq.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/hypergraph_sorter_scan.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/hypergraph.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/gen_synthetic_data.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/emphf_config.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/compute_mphf_seq.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/compute_mphf_scan_mmap.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/compute_mphf_scan.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/compute_mphf_hem.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/compute_mphf_generic.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/common.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/bitstream.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/bitpair_vector.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/base_hash.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/storage/TestStorage.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/misc/TestMisc.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/math/TestMath.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/designpattern/TestIterators.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/collections/TestMap.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/collections/TestIterable.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/collections/TestContainer.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/collections/TestCollection.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/collections/TestBag.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/system/TestSystem.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/main.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/kmer/TestMPHF.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/kmer/TestKmerBank.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/kmer/TestKmer.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/kmer/TestDSK.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/kmer/TestDebloom.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/CppunitCommon.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/bank/TestBank.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/benchmark/bench_bloom.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/benchmark/bench1.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageTools.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageTools.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/Storage.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/Storage.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionFile.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/Cell.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/api/ICell.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/XmlReader.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/XmlReader.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Tool.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Tool.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Tokenizer.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Tokenizer.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/TimeInfo.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Stringify.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Property.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Property.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Progress.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Progress.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Pool.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/OptionsParser.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/LibraryInfo.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Histogram.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Histogram.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Algorithm.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Vector.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/StringsRepository.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Range.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Macros.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/IProperty.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Enums.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Data.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Abundance.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/Integer.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/LargeInt.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt128.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt16.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt64.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt8.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Observer.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Observer.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/IteratorHelpers.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Command.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/api/Iterator.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/api/IObserver.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/OAHash.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/MPHF.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/IterableHelpers.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Hash16.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/EMPHF.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/ContainerSet.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/CollectionCache.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/CollectionAbstract.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagPartition.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/api/Iterable.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/api/Container.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/api/Collection.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/api/Bag.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/TimeCommon.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/ThreadMacos.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/ThreadMacos.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/ThreadLinux.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/ThreadLinux.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/SystemInfoCommon.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/System.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/System.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/MemoryCommon.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemMacos.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemLinux.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemCommon.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/api/types.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/api/ITime.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/api/IThread.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/api/ISystemInfo.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/api/ISmartPointer.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/api/IMemory.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/api/IFileSystem.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/api/Exception.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithmTemplates4.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithmTemplates3.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithmTemplates2.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithmTemplates1.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/PartitionsCommand.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/PartitionsCommand.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/Model.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/Model.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/BloomBuilder.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/BloomBuilder.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/BankKmers.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/BankKmerIterator.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/api/IModel.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/gatb_core.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/Traversal.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/Traversal.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/Terminator.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/Terminator.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/Graph.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/Graph.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/Frontline.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/Frontline.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/ContainerNode.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/api/IContainerNode.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankStrings.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankSplitter.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankSplitter.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/Banks.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankRegistery.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankRegistery.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankRandom.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankRandom.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankHelpers.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankHelpers.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankFasta.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankFasta.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankComposite.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankBinary.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankBinary.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankAlbum.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankAlbum.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/Alphabet.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/AbstractBank.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/api/Sequence.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/api/IBank.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/api/IAlphabet.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/scripts/NewProject/XXX.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/scripts/NewProject/XXX.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/scripts/NewProject/main.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/tools/ToyTool.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/tools/multithreading6.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/tools/multithreading5.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/tools/multithreading4.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/tools/multithreading3.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/tools/multithreading2.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/tools/multithreading1.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/tools/iterators5.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/tools/iterators4.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/tools/iterators3.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/tools/iterators2.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/tools/iterators1.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/storage/storage8.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/storage/storage7.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/storage/storage6.cpp
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Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/storage/storage4.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/storage/storage3.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/storage/storage2.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/storage/storage1.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/protos/MicroSNP.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/kmer/kmer8.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/kmer/kmer7.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/kmer/kmer6.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/kmer/kmer5.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/kmer/kmer4.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/kmer/kmer3.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/kmer/kmer2.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/kmer/kmer1.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn9.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn8.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn7.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn6.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn5.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn4.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn3.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn24.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn23.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn22.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn21.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn20.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn2.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn19.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn18.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn17.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn16.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn15.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn14.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn13.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn12.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn11.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn10.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn1.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank9.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank8.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank7.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank6.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank5.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank4.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank3.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank2.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank15.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank14.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank13.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank12.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank11.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank10.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank1.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/doc/doxygen/src/testspage.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/doc/doxygen/src/snippetspage.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/doc/doxygen/src/mainpage.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/doc/doxygen/src/downloadpage.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/doc/doxygen/src/designpage.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/src/mapsembler2_extremities.hpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/src/mapsembler2_extremities.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/src/main.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/IterativeExtensions.h
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/GraphOutput.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/Fragment_Bank.h
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/Fragment_Bank.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/Fragment.h
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/Fragment.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/commons.h
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/commons.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/mapsembler_extend.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/IterativeExtensions.cpp
Examining data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/GraphOutput.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/ReadMapper.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/ReadMapper.cpp
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/simplehash.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/simplehash.cpp
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_groups.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_groups.cpp
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_groups.c
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/Read_coherence_mapsembler.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/Read_coherence_mapsembler.c
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_coherence.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_coherence.cpp
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/misc_tools.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/misc_tools.cpp
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/misc_tools.c
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/list.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/list.cpp
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/list.c
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.cpp
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.c
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/interface_libchash.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/interface_libchash.cpp
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/interface_libchash.c
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/hash.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/couple.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/couple.cpp
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/couple.c
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.cpp
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.c
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/advanced_hash.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/advanced_hash.cpp
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/Loader.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/Loader.cpp
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/json.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/json.cpp
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/Fragment.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/Fragment.cpp
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/commons.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/commons.cpp
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/BooleanVector.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/BooleanVector.cpp
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/block_allocator.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/block_allocator.cpp
Examining data/mapsembler2-2.2.4+dfsg1/kissreads_graph/KissReadsGraph.cpp
Examining data/mapsembler2-2.2.4+dfsg1/kissreads/src/outputs.c
Examining data/mapsembler2-2.2.4+dfsg1/kissreads/src/list.c
Examining data/mapsembler2-2.2.4+dfsg1/kissreads/src/libchash.c
Examining data/mapsembler2-2.2.4+dfsg1/kissreads/src/kissReads.c
Examining data/mapsembler2-2.2.4+dfsg1/kissreads/src/interface_libchash.c
Examining data/mapsembler2-2.2.4+dfsg1/kissreads/src/fragment_index.c
Examining data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c
Examining data/mapsembler2-2.2.4+dfsg1/kissreads/src/couple.c
Examining data/mapsembler2-2.2.4+dfsg1/kissreads/src/commons.c
Examining data/mapsembler2-2.2.4+dfsg1/kissreads/src/coherent_algorithm.c
Examining data/mapsembler2-2.2.4+dfsg1/kissreads/include/outputs.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads/include/list.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads/include/libchash.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads/include/hash.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads/include/fragment_info.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads/include/extension_algorithm.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads/include/couple.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads/include/coherence_algorithm.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads/include/commons.h
Examining data/mapsembler2-2.2.4+dfsg1/kissreads/include/fragment_index.h
FINAL RESULTS:
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:63:29: [5] (buffer) gets:
Does not check for buffer overflows (CWE-120, CWE-20). Use fgets() instead.
int len = file->gets (buffer, sizeof(buffer));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/api/IFileSystem.hpp:89:17: [5] (buffer) gets:
Does not check for buffer overflows (CWE-120, CWE-20). Use fgets() instead.
virtual int gets (char* s, int size) = 0;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemCommon.hpp:83:9: [5] (buffer) gets:
Does not check for buffer overflows (CWE-120, CWE-20). Use fgets() instead.
int gets (char *s, int size)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Property.cpp:440:26: [5] (buffer) gets:
Does not check for buffer overflows (CWE-120, CWE-20). Use fgets() instead.
while (file->gets (buffer, sizeof(buffer) ) != 0)
data/mapsembler2-2.2.4+dfsg1/kissreads/src/commons.c:227:3: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(sequence, line); // concat the restult in the sequence
data/mapsembler2-2.2.4+dfsg1/kissreads/src/commons.c:347:4: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(sequence, line); // concat the restult in the sequence
data/mapsembler2-2.2.4+dfsg1/kissreads/src/libchash.c:155:7: [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((char *)(keyTo), (char *)(keyFrom)); \
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1941:5: [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(new_left_sequence, a->fragment->fragment_sequence);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1942:5: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(new_left_sequence, b->fragment->fragment_sequence+size_seeds-1);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/Loader.cpp:18:13: [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.
printf(value->type == JSON_OBJECT ? "{\n" : "[\n");
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/Loader.cpp:24:13: [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.
printf(value->type == JSON_OBJECT ? "}\n" : "]\n");
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/Loader.cpp:36:13: [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.
printf(value->int_value ? "true\n" : "false\n");
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/Loader.cpp:116:17: [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(sequence, value->string_value);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/Loader.cpp:278:17: [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(sequence, value->string_value);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.c:228:4: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(cur_consensus,error_corrected);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.cpp:228:4: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(cur_consensus,error_corrected);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.c:161:7: [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((char *)(keyTo), (char *)(keyFrom)); \
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.cpp:161:7: [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((char *)(keyTo), (char *)(keyFrom)); \
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/misc_tools.c:65:2: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(dest, src);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/misc_tools.c:77:2: [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(res, src);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/misc_tools.c:78:2: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(res,dest);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/misc_tools.cpp:64:2: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(dest, src);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/misc_tools.cpp:76:2: [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(res, src);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/misc_tools.cpp:77:2: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(res,dest);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/simplehash.cpp:166:5: [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(new_string,string);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/IterativeExtensions.cpp:189:9: [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(node,kmer_seq);// + starting_kmer if we ask for the de bruijn graph or for a text output
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/IterativeExtensions.cpp:190:9: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(node,right_traversal);// + right_traversal
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/IterativeExtensions.cpp:407:9: [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(node,kmer_seq);// + starting_kmer if we ask for the de bruijn graph or for a text output
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/IterativeExtensions.cpp:408:9: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(node,right_traversal);// + right_traversal
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/IterativeExtensions.cpp:721:5: [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(node,kmer_seq);// + starting_kmer if we ask for the de bruijn graph or for a text output
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/IterativeExtensions.cpp:722:5: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(node,right_traversal);// + right_traversal
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/mapsembler_extend.cpp:156:17: [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(res_prefix,optarg);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/mapsembler_extend.cpp:169:17: [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(index_file_prefix, optarg);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/mapsembler_extend.cpp:208:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(prefix,"%s_k_%d_c_%d", index_file_prefix, sizeKmer, min_coverage);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/mapsembler_extend.cpp:211:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(final_res_prefix,"%s_k_%d_c_%d_t_%d", res_prefix, sizeKmer, min_coverage, (int)extension_type);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/mapsembler_extend.cpp:248:9: [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.
if( access( (string(prefix)+string(".debloom")).c_str(), F_OK ) != -1 &&
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/mapsembler_extend.cpp:249:8: [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( (string(prefix)+string(".debloom2")).c_str(), F_OK ) != -1 &&
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/mapsembler_extend.cpp:250:8: [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( (string(prefix)+string(".false_positive_kmers")).c_str(), F_OK ) != -1 &&
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/mapsembler_extend.cpp:251:8: [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( (string(prefix)+string(".solid_kmers_binary")).c_str(), F_OK ) != -1){
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/mapsembler_extend.cpp:320:70: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
command = string("rm -f ")+string(prefix_trashable)+string("*"); system((char *)command.c_str());
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank10.cpp:113:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank11.cpp:47:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank12.cpp:78:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank13.cpp:68:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank2.cpp:34:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank4.cpp:48:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank5.cpp:40:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank6.cpp:85:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank7.cpp:56:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank8.cpp:79:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank9.cpp:77:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/kmer/kmer4.cpp:70:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/kmer/kmer5.cpp:155:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/kmer/kmer8.cpp:84:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/api/IBank.hpp:121:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class IBankFactory : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/AbstractBank.hpp:42:43: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class AbstractBank : public IBank, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:28:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:50:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = getFile (name, deleteIfExists ? "w+" : NULL);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:169:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = getFile (_name);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:207:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = getFile (_name, "a+");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:241:1: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* BankAlbum::getFile (const std::string& name, const char* mode)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankAlbum.hpp:87:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* getFile (const std::string& name, const char* mode=NULL);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankBinary.cpp:28:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankBinary.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankBinary.cpp:230:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw gatb::core::system::ExceptionErrno (STR_BANK_unable_write_file);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankBinary.cpp:253:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw gatb::core::system::ExceptionErrno (STR_BANK_unable_open_file, _filename.c_str());
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankBinary.cpp:333:58: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (binary_read_file == 0) { throw gatb::core::system::ExceptionErrno (STR_BANK_unable_open_file, _ref._filename.c_str()); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankComposite.hpp:92:51: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void insert (const Sequence& item) { throw system::Exception ("Can't insert sequence in a composite bank."); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp:31:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankConverterAlgorithm.cpp:32:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankFasta.cpp:36:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankFasta.cpp:37:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankFasta.cpp:171:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw gatb::core::system::Exception (STR_BANK_bad_file_number, _filenames.size(), getMaxNbFiles());
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankFasta.cpp:653:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw gatb::core::system::ExceptionErrno (STR_BANK_unable_open_file, fname);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankHelpers.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankHelpers.cpp:30:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankRandom.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankRandom.cpp:30:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankSplitter.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankSplitter.cpp:30:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:27:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:28:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/BranchingAlgorithm.cpp:35:19: [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.
#define DEBUG(a) printf a
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/ContainerNode.hpp:50:84: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item> class ContainerNode : public IContainerNode<Item>, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/ContainerNode.hpp:99:93: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item> class ContainerNodeCascading : public IContainerNode<Item>, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/Graph.cpp:49:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/Graph.cpp:180:18: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
else { throw system::Exception ("Graph failure because of unhandled kmer size %d", kmerSize); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/Graph.cpp:304:56: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
(props->getStr(STR_URI_OUTPUT_DIR) + "/" + system::impl::System::file().getBaseName (bank->getId()));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/Graph.cpp:2168:56: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class Cmd : public tools::dp::ICommand, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/Terminator.hpp:101:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class Terminator : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/Traversal.hpp:51:26: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class Traversal : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/gatb_core.hpp:78:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/gatb_core.hpp:79:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/BankKmers.hpp:69:55: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void insert (const bank::Sequence& item) { throw system::Exception ("Can't insert sequence to BankKmers"); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/BankKmers.hpp:72:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void flush () { throw system::Exception ("Can't flush BankKmers"); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:55:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/BloomAlgorithm.cpp:56:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.cpp:56:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/DebloomAlgorithm.cpp:57:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:31:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/MPHFAlgorithm.cpp:32:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/Model.hpp:281:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class ModelAbstract : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/Model.hpp:295:23: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception ("Type '%s' has too low precision (%d bits) for the required %d kmer size",
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/Model.hpp:515:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
default: throw system::Exception ("BAD FORMAT IN 'execute'");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/Model.hpp:751:53: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (kmerSize <= minimizerSize) { throw system::Exception ("Bad values for kmer %d and minimizer %d", kmerSize, minimizerSize); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/PartitionsCommand.hpp:39:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/PartitionsCommand.hpp:40:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/PartitionsCommand.hpp:72:51: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class PartitionsCommand : public ICommand, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:36:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/kmer/impl/SortingCountAlgorithm.cpp:37:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/api/Exception.hpp:52:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/api/Exception.hpp:84:10: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
vsnprintf (buffer, sizeof(buffer), format, args);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/api/IFileSystem.hpp:37:12: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/api/IMemory.hpp:40:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/api/ISmartPointer.hpp:34:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/api/ISmartPointer.hpp:205:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
#define LOCAL(object) gatb::core::system::LocalObject __##object (object)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/api/ISystemInfo.hpp:35:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/api/IThread.hpp:38:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/api/IThread.hpp:93:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
virtual void addException (system::Exception e) = 0;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/api/ITime.hpp:38:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp:34:45: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace gatb { namespace core { namespace system { namespace impl {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemCommon.hpp:43:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemCommon.hpp:111:15: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf (getHandle(), format, args);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp:37:45: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace gatb { namespace core { namespace system { namespace impl {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp:165:5: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
vsnprintf (buffer, sizeof(buffer), fmt, ap);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemLinux.hpp:36:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp:37:45: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace gatb { namespace core { namespace system { namespace impl {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp:123:14: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
return ::system("purge");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp:161:5: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
vsnprintf (buffer, sizeof(buffer), fmt, ap);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemMacos.hpp:36:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/MemoryCommon.hpp:40:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/System.cpp:23:45: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace gatb { namespace core { namespace system { namespace impl {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/System.cpp:56:22: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
for (std::vector<system::IThread*>::iterator it = _threads.begin(); it != _threads.end(); it++)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/System.cpp:91:22: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
for (std::vector<system::IThread*>::iterator it = _threads.begin(); it != _threads.end(); it++)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/System.hpp:47:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/System.hpp:169:49: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class ThreadGroup : public IThreadGroup, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/System.hpp:189:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void addException (system::Exception e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/System.hpp:204:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _startSynchro;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/System.hpp:208:15: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
std::list<system::Exception> _exceptions;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/System.hpp:218:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_synchro = system::impl::System::thread().newSynchronizer();
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/System.hpp:283:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp:28:45: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace gatb { namespace core { namespace system { namespace impl {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/SystemInfoCommon.hpp:39:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/ThreadLinux.cpp:33:45: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace gatb { namespace core { namespace system { namespace impl {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/ThreadLinux.cpp:44:44: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class ThreadLinux : public IThread, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/ThreadLinux.cpp:64:56: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class SynchronizerLinux : public ISynchronizer, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/ThreadLinux.hpp:34:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/ThreadMacos.cpp:33:45: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace gatb { namespace core { namespace system { namespace impl {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/ThreadMacos.cpp:44:44: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class ThreadMacos : public IThread, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/ThreadMacos.cpp:64:56: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class SynchronizerMacos : public ISynchronizer, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/ThreadMacos.hpp:34:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/TimeCommon.hpp:41:11: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
namespace system {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/TimeCommon.hpp:70:9: [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.
snprintf (buffer, sizeof(buffer), format,
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/api/Bag.hpp:49:51: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class Bag : public virtual system::ISmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/api/Container.hpp:46:56: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class Container : public virtual system::ISmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/api/Iterable.hpp:51:55: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class Iterable : public virtual system::ISmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:47:68: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item> class BagCache : public Bag<Item>, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:55:49: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
BagCache (Bag<Item>* ref, size_t cacheSize, system::ISynchronizer* synchro=0)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:60:26: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_items = (Item*) system::impl::System::memory().calloc (_nbMax, sizeof(Item));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:61:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().memset (_items, 0, _nbMax*sizeof(Item));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:70:26: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_items = (Item*) system::impl::System::memory().calloc (_nbMax, sizeof(Item));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:71:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().memset (_items, 0, _nbMax*sizeof(Item));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:84:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().free (_items);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:114:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:115:22: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void setSynchro (system::ISynchronizer* synchro) { SP_SETATTR(synchro); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:143:129: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
BagCacheSortedBuffered (Bag<Item>* ref, size_t cacheSize, Item* sharedBuffer, size_t sharedCacheSize, size_t * idxShared, system::ISynchronizer* outsynchro=0, system::ISynchronizer* synchro=0
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:143:166: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
BagCacheSortedBuffered (Bag<Item>* ref, size_t cacheSize, Item* sharedBuffer, size_t sharedCacheSize, size_t * idxShared, system::ISynchronizer* outsynchro=0, system::ISynchronizer* synchro=0
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:201:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _outsynchro;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:202:25: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void setOutSynchro (system::ISynchronizer* outsynchro) { SP_SETATTR(outsynchro); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:220:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().memcpy (_sharedBuffer + *_idxShared, this->_items, this->_idx*sizeof(Item));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:276:55: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
BagCacheSorted (Bag<Item>* ref, size_t cacheSize, system::ISynchronizer* synchro=0)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:50:67: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item> class BagFile : public Bag<Item>, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:58:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::file().remove (filename);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:61:17: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_file = system::impl::System::file().newFile (filename, "wb+");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:93:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* _file;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:100:69: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item> class BagGzFile : public Bag<Item>, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:108:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::file().remove (filename);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:146:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* _file;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:154:82: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item> class BagCountCompressedFile : public Bag<Item>, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:162:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::file().remove (filename);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:165:17: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_file = system::impl::System::file().newFile (filename, "wb+");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:277:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* _file;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagPartition.hpp:52:57: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
for (size_t i=0; i<_partitions.size(); i++) { system::impl::System::file().remove (getFilename(i)); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagPartition.hpp:82:30: [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.
char filename[128]; snprintf (filename, sizeof(filename), _uriFormat.c_str(), idx);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagPartition.hpp:95:59: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
BagCachePartition (BagFilePartition<Item>& partition, system::ISynchronizer* synchro)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagPartition.hpp:134:73: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
virtual BagCache<Item>* createBag (Bag<Item>*& b, size_t cacheSize, system::ISynchronizer* synchro)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagPartition.hpp:142:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:96:90: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item> class IBloom : public Container<Item>, public Bag<Item>, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:124:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
blooma = (unsigned char *) system::impl::System::memory().malloc (nchar*sizeof(unsigned char)); // 1 bit per elem
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:125:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().memset (blooma, 0, nchar*sizeof(unsigned char));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:140:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().free (blooma);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:372:70: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item, size_t prec=1> class BloomGroupOld : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:382:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_blooma = (Result*) system::impl::System::memory().malloc (_size*sizeof(Result));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:383:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().memset (_blooma, 0, _size*sizeof(Result));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:394:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
~BloomGroupOld () { system::impl::System::memory().free (_blooma); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:421:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "wb+");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:421:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "wb+");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:451:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "rb+");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:451:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "rb+");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:461:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_blooma = (Result*) system::impl::System::memory().malloc (_size*sizeof(Result));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:462:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().memset (_blooma, 0, _size*sizeof(Result));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:507:67: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item, size_t prec=1> class BloomGroup : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:529:39: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void memset (u_int64_t v) { system::impl::System::memory().memset (value, v, prec*sizeof(u_int64_t)); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:549:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_blooma = (Result*) system::impl::System::memory().malloc (_size*sizeof(Result));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:550:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().memset (_blooma, 0, _size*sizeof(Result));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:561:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
~BloomGroup () { system::impl::System::memory().free (_blooma); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:572:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "wb+");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:572:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "wb+");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:591:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "rb+");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:591:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "rb+");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:601:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_blooma = (Result*) system::impl::System::memory().malloc (_size*sizeof(Result));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:602:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().memset (_blooma, 0, _size*sizeof(Result));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:673:80: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item, size_t prec=1> class BloomGroupCacheCoherent : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:685:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_blooma = (Result*) system::impl::System::memory().malloc (_size*sizeof(Result));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:686:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().memset (_blooma, 0, _size*sizeof(Result));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:703:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
~BloomGroupCacheCoherent () { system::impl::System::memory().free (_blooma); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:714:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "wb+");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:714:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "wb+");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:736:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "rb+");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:736:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* file = system::impl::System::file().newFile (uri, "rb+");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:749:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_blooma = (Result*) system::impl::System::memory().malloc (_size*sizeof(Result));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:750:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().memset (_blooma, 0, _size*sizeof(Result));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:843:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
default: throw system::Exception ("bad Bloom kind %d in createBloom", kind);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/CollectionCache.hpp:49:87: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class CollectionCache : public CollectionAbstract<Item>, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/CollectionCache.hpp:54:64: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CollectionCache (Collection<Item>& ref, size_t cacheSize, system::ISynchronizer* synchro)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/CollectionCache.hpp:78:93: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class CollectionCacheSorted : public CollectionAbstract<Item>, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/CollectionCache.hpp:83:95: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CollectionCacheSorted (Collection<Item>& ref, size_t cacheSize, size_t sharedCacheSize, system::ISynchronizer* synchro, system::ISynchronizer* outsynchro, Item* sharedBuffer, size_t * idxShared) //
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/CollectionCache.hpp:83:127: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CollectionCacheSorted (Collection<Item>& ref, size_t cacheSize, size_t sharedCacheSize, system::ISynchronizer* synchro, system::ISynchronizer* outsynchro, Item* sharedBuffer, size_t * idxShared) //
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/ContainerSet.hpp:48:78: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item> class ContainerSet : public Container<Item>, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/EMPHF.hpp:55:50: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class MPHF<Key,Adaptator,Progress,true> : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/EMPHF.hpp:80:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (isBuilt==true) { throw system::Exception ("MFHP: built already done"); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Hash16.hpp:66:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IMemory& _memory;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Hash16.hpp:71:93: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Hash16 (size_t sizeMB) : datah(0), mask(0), tai(0), nb_elem(0), max_nb_elem(0), _memory(system::impl::System::memory())
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Hash16.hpp:79:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (tai_Hash16 > 32) { throw system::Exception ("Hash16: max size for this hash is 2^32, but ask for %d", tai_Hash16); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Hash16.hpp:96:121: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
Hash16 (u_int64_t nb_entries, u_int64_t * nb_created) : datah(0), mask(0), tai(0), nb_elem(0), max_nb_elem(0), _memory(system::impl::System::memory())
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Hash16.hpp:104:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (tai_Hash16 > 32) { throw system::Exception ("Hash16: max size for this hash is 2^32, but ask for %d", tai_Hash16); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/IterableHelpers.hpp:60:53: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class IterableAdaptor : public Iterable<T2>, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:62:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_file = system::impl::System::file().newFile (_filename, "rb");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:71:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_file = system::impl::System::file().newFile (filename, "rb");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:96:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_file = system::impl::System::file().newFile (it._filename, "rb");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:142:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* _file;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:275:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_file = system::impl::System::file().newFile (_filename, "rb");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:284:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_file = system::impl::System::file().newFile (filename, "rb");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:309:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_file = system::impl::System::file().newFile (it._filename, "rb");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:379:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IFile* _file;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:423:102: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class IterableFile : public tools::collections::Iterable<Item>, public virtual system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:438:39: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
int64_t getNbItems () { return system::impl::System::file().getSize(_filename) / sizeof(Item); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:449:104: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class IterableGzFile : public tools::collections::Iterable<Item>, public virtual system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:466:48: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
int64_t estimateNbItems () { return 3* (system::impl::System::file().getSize(_filename) / sizeof(Item)); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:473:117: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class IterableCountCompressedFile : public tools::collections::Iterable<Item>, public virtual system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:490:48: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
int64_t estimateNbItems () { return 2* (system::impl::System::file().getSize(_filename) / sizeof(Item)); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/MPHF.hpp:79:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class MPHF : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/MPHF.hpp:132:45: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void error () const { throw gatb::core::system::ExceptionNotImplemented(); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/MapMPHF.hpp:46:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class MapMPHF : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/OAHash.hpp:62:39: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (hash_size == 0) { throw system::Exception ("empty OAHash allocated"); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/OAHash.hpp:197:46: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (exceptionOnBadKey) { throw system::Exception ("OAHash: max rehashes reached: %lld (notify a developer)", hash_size); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:77:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class ICommand : virtual public system::ISmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:136:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class IDispatcher : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:179:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* synchro = newSynchro();
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:246:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
virtual system::ISynchronizer* newSynchro () = 0;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:249:96: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <typename Item, typename Functor> class IteratorCommand : public ICommand, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:258:61: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
IteratorCommand (Iterator<Item>* it, Functor*& fct, system::ISynchronizer& synchro, size_t groupSize)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/api/ICommand.hpp:292:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer& _synchro;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/api/IObserver.hpp:62:26: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class EventInfo : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/api/Iterator.hpp:107:47: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class Iterator : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/api/Iterator.hpp:213:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class IteratorListener : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:26:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:37:53: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class CommandStartSynchro : public ICommand, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:41:41: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CommandStartSynchro (ICommand* ref, system::ISynchronizer* synchro) : _ref(0), _synchro(synchro) { setRef(ref); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:60:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:64:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class SynchronizerNull : public system::ISynchronizer, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:64:63: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class SynchronizerNull : public system::ISynchronizer, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:104:1: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* SerialDispatcher::newSynchro ()
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:119:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (_nbUnits==0) { _nbUnits = system::impl::System::info().getNbCores(); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:134:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IThreadGroup* threadGroup = system::impl::ThreadGroup::create ();
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:134:41: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IThreadGroup* threadGroup = system::impl::ThreadGroup::create ();
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:159:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::ThreadGroup::destroy (threadGroup);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:175:1: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* Dispatcher::newSynchro ()
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:177:12: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
return system::impl::System::thread().newSynchronizer();
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:188:1: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IThread* Dispatcher::newThread (ICommand* command)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:190:12: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
return system::impl::System::thread().newThread (mainloop, command);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Command.cpp:220:12: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (system::Exception& e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Command.hpp:73:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* newSynchro ();
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Command.hpp:120:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* newSynchro ();
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/designpattern/impl/Command.hpp:123:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::IThread* newThread (ICommand* command);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/LargeInt.hpp:94:40: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
u_int64_t toInt () const { throw system::Exception ("LargeInt<%d> no support of toInt", precision); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Enums.hpp:43:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
else { throw system::Exception ("bad bank convert kind '%s'", s.c_str()); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Enums.hpp:53:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
default: throw system::Exception ("bad bank convert kind %d", kind);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Enums.hpp:67:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
else { throw system::Exception ("bad Bloom kind '%s'", s.c_str()); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Enums.hpp:78:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
default: throw system::Exception ("bad Bloom kind %d", kind);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Enums.hpp:92:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
else { throw system::Exception ("bad debloom kind '%s'", s.c_str()); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Enums.hpp:103:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
default: throw system::Exception ("bad debloom kind %d", kind);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Enums.hpp:115:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
else { throw system::Exception ("bad branching kind '%s'", s.c_str()); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Enums.hpp:124:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
default: throw system::Exception ("bad branching kind %d", kind);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Enums.hpp:136:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
else { throw system::Exception ("bad mphf kind '%s'", s.c_str()); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Enums.hpp:145:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
default: throw system::Exception ("bad mphf kind %d", kind);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/IHistogram.hpp:47:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class IHistogram : virtual public system::ISmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/IProperty.hpp:54:26: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class IProperty : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/IProperty.hpp:119:35: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class IPropertiesVisitor : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/IProperty.hpp:154:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class IProperties : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Range.hpp:46:74: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class T> class Range : public collections::Iterable<T>, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Vector.hpp:46:44: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template<typename T> class Vector : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Algorithm.cpp:26:19: [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.
#define DEBUG(a) printf a
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Algorithm.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Algorithm.cpp:30:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Algorithm.hpp:51:26: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class Algorithm : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Histogram.cpp:28:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Histogram.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Histogram.hpp:48:45: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class Histogram : public IHistogram, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Histogram.hpp:59:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_histogram = (Entry*) system::impl::System::memory().calloc (_length + 1, sizeof (Entry));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Histogram.hpp:62:34: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
_histogram_smoothed = (Entry*) system::impl::System::memory().calloc (_length + 1, sizeof (Entry));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Histogram.hpp:78:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().free (_histogram);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Histogram.hpp:79:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().free (_histogram_smoothed);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Histogram.hpp:116:49: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class HistogramNull : public IHistogram, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Histogram.hpp:141:50: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class HistogramCache : public IHistogram, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Histogram.hpp:146:38: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
HistogramCache (IHistogram* ref, system::ISynchronizer* synchro=0)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Histogram.hpp:152:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::LocalSynchronizer ls (_synchro);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Histogram.hpp:180:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/LibraryInfo.hpp:50:16: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
static system::SmartObject singleton;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/LibraryInfo.hpp:57:52: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
props->add (1, "version", "%s", system::impl::System::info().getVersion().c_str());
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/LibraryInfo.hpp:58:52: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
props->add (1, "build_date", "%s", system::impl::System::info().getBuildDate().c_str());
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/LibraryInfo.hpp:59:52: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
props->add (1, "build_system", "%s", system::impl::System::info().getBuildSystem().c_str());
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/LibraryInfo.hpp:60:52: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
props->add (1, "build_compiler", "%s", system::impl::System::info().getBuildCompiler().c_str());
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp:32:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp:33:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/OptionsParser.hpp:54:23: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class Option : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/OptionsParser.hpp:255:30: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class OptionsParser : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Pool.hpp:67:30: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
tab_pool = (cell**) system::impl::System::memory().malloc (N_POOL*sizeof(cell*) );
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Pool.hpp:72:33: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
pool_courante =(cell*) system::impl::System::memory().malloc (TAI_POOL*sizeof(cell) );
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Pool.hpp:81:43: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
for(size_t i=1;i<n_pools;i++) { system::impl::System::memory().free( tab_pool[i] ); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Pool.hpp:83:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().free(tab_pool);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Pool.hpp:104:23: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw system::Exception ("Internal memory allocator is full!");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Pool.hpp:106:37: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
pool_courante =(cell*) system::impl::System::memory().malloc(TAI_POOL*sizeof(cell) );
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Pool.hpp:132:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::memory().free( tab_pool[i] );
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:30:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:160:5: [4] (format) vsprintf:
Potential format string problem (CWE-134). Make format string constant.
vsprintf (buffer, format, args);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Progress.hpp:152:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ITime::Value heure_debut;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Progress.hpp:153:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ITime::Value heure_actuelle;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Progress.hpp:204:49: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
ProgressSynchro (dp::IteratorListener* ref, system::ISynchronizer* synchro)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Progress.hpp:220:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Progress.hpp:221:22: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void setSynchro (system::ISynchronizer* synchro) { SP_SETATTR(synchro); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Property.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Property.cpp:30:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Property.cpp:186:9: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
vsnprintf (buffer, sizeof(buffer), format, ap);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Property.cpp:916:9: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
vsnprintf (buffer, sizeof(buffer), format, ap);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp:27:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp:28:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp:42:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeInfo::TimeInfo () : _time(system::impl::System::time())
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/TimeInfo.cpp:54:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeInfo::TimeInfo (system::ITime& aTime) : _time(aTime)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/TimeInfo.hpp:71:25: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class TimeInfo : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/TimeInfo.hpp:81:15: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
TimeInfo (system::ITime& aTime);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/TimeInfo.hpp:112:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ITime& _time;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Tokenizer.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Tokenizer.cpp:30:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Tool.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Tool.cpp:30:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Tool.hpp:52:21: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class Tool : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/XmlReader.cpp:29:19: [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.
#define DEBUG(a) printf a
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/api/ICell.hpp:43:30: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class ICell : public virtual system::ISmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/Cell.hpp:43:43: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class Cell : public virtual ICell, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionFile.hpp:52:105: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class CollectionFile : public collections::impl::CollectionAbstract<Item>, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionFile.hpp:68:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void remove () { gatb::core::system::impl::System::file().remove (_name); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionFile.hpp:77:107: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class CollectionGzFile : public collections::impl::CollectionAbstract<Item>, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionFile.hpp:93:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void remove () { gatb::core::system::impl::System::file().remove (_name); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionFile.hpp:102:110: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class CollectionCountFile : public collections::impl::CollectionAbstract<Item>, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionFile.hpp:117:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
void remove () { gatb::core::system::impl::System::file().remove (_name); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:53:77: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class BagHDF5 : public collections::Bag<Item>, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:58:65: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
BagHDF5 (hid_t datasetId, hid_t typeId, u_int64_t& nbItems, system::ISynchronizer* synchro)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:77:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::LocalSynchronizer localsynchro (_synchro);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:120:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:128:87: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class IterableHDF5 : public collections::Iterable<Item>, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:133:74: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
IterableHDF5 (hid_t datasetId, hid_t typeId, u_int64_t& nbItems, system::ISynchronizer* synchro)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:169:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:180:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::LocalSynchronizer localsynchro (_synchro);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:330:105: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
template <class Item> class CollectionHDF5 : public collections::impl::CollectionAbstract<Item>, public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:335:64: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CollectionHDF5 (hid_t fileId, const std::string& filename, system::ISynchronizer* synchro)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:340:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::LocalSynchronizer localsynchro (synchro);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:231:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:254:64: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
PartitionCache (Partition<Type>& ref, size_t nbItemsCache, system::ISynchronizer* synchro=0);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:281:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:282:18: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
std::vector <system::ISynchronizer*> _synchros;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:293:92: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
PartitionCacheSorted (Partition<Type>& ref, size_t nbItemsCache, u_int32_t max_memory, system::ISynchronizer* synchro=0);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:320:5: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* _synchro;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:324:18: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
std::vector <system::ISynchronizer*> _synchros;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:325:18: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
std::vector <system::ISynchronizer*> _outsynchros;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:428:31: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
class StorageFactory : public system::SmartPointer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/Storage.hpp:453:85: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CollectionNode<Type>* createCollection (ICell* parent, const std::string& name, system::ISynchronizer* synchro);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp:84:92: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
static CollectionNode<Type>* createCollection (ICell* parent, const std::string& name, system::ISynchronizer* synchro)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp:139:92: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
static CollectionNode<Type>* createCollection (ICell* parent, const std::string& name, system::ISynchronizer* synchro)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageFile.hpp:192:92: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
static CollectionNode<Type>* createCollection (ICell* parent, const std::string& name, system::ISynchronizer* synchro)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:104:92: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
static CollectionNode<Type>* createCollection (ICell* parent, const std::string& name, system::ISynchronizer* synchro)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:123:16: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
static system::ISynchronizer* singleton()
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:130:39: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
GlobalSynchro () { synchro = system::impl::System::thread().newSynchronizer(); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:132:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::ISynchronizer* synchro;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:142:36: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
if (deleteIfExist) { system::impl::System::file().remove (getActualName()); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:145:27: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
bool exists = system::impl::System::file().doesExist(getActualName());
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/StorageHDF5.hpp:169:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system::impl::System::file().remove (getActualName());
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/benchmark/bench1.cpp:44:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/benchmark/bench1.cpp:45:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/benchmark/bench1.cpp:358:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/benchmark/bench_bloom.cpp:59:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/benchmark/bench_bloom.cpp:60:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/benchmark/bench_bloom.cpp:272:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/bank/TestBank.cpp:38:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/bank/TestBank.cpp:39:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/bank/TestBank.cpp:324:75: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CPPUNIT_ASSERT_THROW (BankFasta::Iterator it(bankKO), gatb::core::system::Exception);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/bank/TestBank.cpp:361:68: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CPPUNIT_ASSERT_THROW (BankFasta b (filenames), gatb::core::system::Exception);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/bank/TestBank.cpp:372:68: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CPPUNIT_ASSERT_THROW (BankFasta b (filenames), gatb::core::system::Exception);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:64:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:65:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/kmer/TestDSK.cpp:41:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/kmer/TestDSK.cpp:42:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/kmer/TestDebloom.cpp:38:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/kmer/TestDebloom.cpp:39:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/kmer/TestKmer.cpp:42:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/kmer/TestKmer.cpp:43:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/kmer/TestKmer.cpp:340:28: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/kmer/TestKmerBank.cpp:33:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/kmer/TestKmerBank.cpp:34:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/kmer/TestMPHF.cpp:40:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/kmer/TestMPHF.cpp:41:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/kmer/TestMPHF.cpp:269:32: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::ExceptionNotImplemented& e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/system/TestSystem.cpp:32:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/system/TestSystem.cpp:33:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/system/TestSystem.cpp:212:77: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CPPUNIT_ASSERT_THROW (p2 = mem.malloc (KBYTE+1), gatb::core::system::Exception);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/system/TestSystem.cpp:570:79: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CPPUNIT_ASSERT_THROW (TimeSystem s (ITime::UNDEFINED), gatb::core::system::Exception);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/system/TestSystem.cpp:727:25: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
throw core::system::Exception ("something wrong");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/system/TestSystem.cpp:729:22: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (core::system::Exception& e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/system/TestSystem.cpp:761:22: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (core::system::Exception& e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/collections/TestBag.cpp:44:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/collections/TestBag.cpp:45:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/collections/TestCollection.cpp:49:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/collections/TestCollection.cpp:50:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/collections/TestMap.cpp:46:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/collections/TestMap.cpp:85:62: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
CPPUNIT_ASSERT_THROW (hash.increment (badKey), core::system::Exception);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/misc/TestMisc.cpp:34:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/misc/TestMisc.cpp:35:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/storage/TestStorage.cpp:49:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/storage/TestStorage.cpp:50:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/tools/BankDownload.cpp:71:20: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
int res1 = system (ss1.str().c_str());
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/tools/BankDownload.cpp:105:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
int res2 = system (ss2.str().c_str());
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/tools/BankDownload.cpp:113:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
int res3 = system (ss3.str().c_str());
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/tools/BankDownload.cpp:156:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system (Stringify::format ("mv %s %s/", finalBankFile.c_str(), options->getStr(STR_URI_OUTPUT_DIR).c_str()).c_str());
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/tools/BankDownload.cpp:184:24: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
catch (gatb::core::system::Exception& e)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/tools/ClearCache.cpp:29:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/tools/KmerChecksum.cpp:28:29: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
using namespace gatb::core::system::impl;
data/mapsembler2-2.2.4+dfsg1/minia/Bank.cpp:520:5: [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(filename,given_filename);
data/mapsembler2-2.2.4+dfsg1/minia/Bank.cpp:760:5: [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(filename,given_filename);
data/mapsembler2-2.2.4+dfsg1/minia/Debloom.cpp:280:41: [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.
if ((NbInsertedKmers%10000)==0) fprintf (stderr,(char*)"%cInsert false positive Kmers in hash table %lld",13,NbInsertedKmers);
data/mapsembler2-2.2.4+dfsg1/minia/SortingCount.cpp:37:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(temp_dir,"%s_temp",prefix);
data/mapsembler2-2.2.4+dfsg1/minia/SortingCount.cpp:45:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(p_buf, "%s/%s", temp_dir, ep->d_name);
data/mapsembler2-2.2.4+dfsg1/minia/SortingCount.cpp:281:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system("purge");
data/mapsembler2-2.2.4+dfsg1/minia/SortingCount.cpp:283:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system("echo 3 > /proc/sys/vm/drop_caches");
data/mapsembler2-2.2.4+dfsg1/minia/SortingCount.cpp:326:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(redundant_filename[p],"%s/partition%d.redundant_kmers",temp_dir,p);
data/mapsembler2-2.2.4+dfsg1/minia/SortingCount.cpp:535:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system("purge");
data/mapsembler2-2.2.4+dfsg1/minia/SortingCount.cpp:537:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system("echo 3 > /proc/sys/vm/drop_caches");
data/mapsembler2-2.2.4+dfsg1/minia/Utils.cpp:28:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(fileName,"%s.%s",prefix,suffix);
data/mapsembler2-2.2.4+dfsg1/minia/Utils.cpp:30:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(fileName,"%s",suffix);
data/mapsembler2-2.2.4+dfsg1/minia/Utils.cpp:68:32: [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.
if ((NbRead%10000)==0) fprintf (stderr,stderr_message,13,NbRead);
data/mapsembler2-2.2.4+dfsg1/minia/Utils.cpp:92:30: [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.
if ((NbRead%10000)==0) fprintf (stderr,stderr_message,13,(long long)NbRead);
data/mapsembler2-2.2.4+dfsg1/minia/Utils.cpp:434:32: [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.
if ((NbRead%10000)==0) fprintf (stderr,(char*)"%cExtrapolating number of distinct kmers %lld",13,NbRead);
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzguts.h:78:18: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
# if !defined(vsnprintf) && !defined(NO_vsnprintf)
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzguts.h:80:18: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
# define vsnprintf _vsnprintf
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzguts.h:103:11: [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.
# define snprintf _snprintf
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzguts.h:103:20: [4] (format) _snprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
# define snprintf _snprintf
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzlib.c:216:9: [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(state->path, path);
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzlib.c:610:5: [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(state->msg, state->path);
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzlib.c:612:5: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(state->msg, msg);
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzwrite.c:346:11: [4] (format) vsprintf:
Potential format string problem (CWE-134). Make format string constant.
(void)vsprintf((char *)(state->in), format, va);
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzwrite.c:350:11: [4] (format) vsprintf:
Potential format string problem (CWE-134). Make format string constant.
len = vsprintf((char *)(state->in), format, va);
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzwrite.c:354:11: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
(void)vsnprintf((char *)(state->in), size, format, va);
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzwrite.c:357:11: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
len = vsnprintf((char *)(state->in), size, format, va);
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzwrite.c:431:5: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf((char *)(state->in), format, a1, a2, a3, a4, a5, a6, a7, a8,
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzwrite.c:436:11: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
len = sprintf((char *)(state->in), format, a1, a2, a3, a4, a5, a6, a7, a8,
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzwrite.c:441:5: [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((char *)(state->in), size, format, a1, a2, a3, a4, a5, a6, a7, a8,
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzwrite.c:445:11: [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.
len = snprintf((char *)(state->in), size, format, a1, a2, a3, a4, a5, a6,
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/zutil.h:224:39: [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 Trace(x) {if (z_verbose>=0) fprintf x ;}
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/zutil.h:225:39: [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 Tracev(x) {if (z_verbose>0) fprintf x ;}
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/zutil.h:226:40: [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 Tracevv(x) {if (z_verbose>1) fprintf x ;}
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/zutil.h:227:48: [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 Tracec(c,x) {if (z_verbose>0 && (c)) fprintf x ;}
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/zutil.h:228:49: [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 Tracecv(c,x) {if (z_verbose>1 && (c)) fprintf x ;}
data/mapsembler2-2.2.4+dfsg1/kissreads/src/kissReads.c:183:22: [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.
int temoin = getopt (argc-number_of_read_sets-1, &argv[number_of_read_sets+1], "c:d:k:O:o:u:q:m:i:fs-:j:l:t:");
data/mapsembler2-2.2.4+dfsg1/kissreads/src/kissReads.c:185:22: [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.
int temoin = getopt (argc-number_of_read_sets-1, &argv[number_of_read_sets+1], "c:d:k:O:o:u:q:m:i:fsnI-:t:");
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/KissReadsGraph.cpp:90:22: [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.
int temoin = getopt (argc-number_of_read_sets-1, &argv[number_of_read_sets+1], "hd:c:k:o:t:M");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/mapsembler_extend.cpp:129:22: [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.
int temoin = getopt (argc-number_of_read_sets-1, &argv[number_of_read_sets+1], "t:c:g:x:y:o:f:i:k:h");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankRandom.cpp:91:5: [3] (random) srand:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
srand (time(NULL));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp:100:22: [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.
if ( (dir = getenv ("TMPDIR")) != 0) { return dir; }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp:101:22: [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.
else if ( (dir = getenv ("TMP")) != 0) { return dir; }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp:102:22: [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.
else if ( (dir = getenv ("TEMPDIR")) != 0) { return dir; }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp:149:9: [3] (buffer) realpath:
This function does not protect against buffer overflows, and some
implementations can overflow internally (CWE-120/CWE-785!). Ensure that the
destination buffer is at least of size MAXPATHLEN, andto protect against
implementation problems, the input argument should also be checked to
ensure it is no larger than MAXPATHLEN.
if (realpath (file.c_str(), buf) != 0)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/SystemInfoCommon.hpp:64:54: [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.
std::string getHomeDirectory () const { return getenv("HOME") ? getenv("HOME") : "."; }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/SystemInfoCommon.hpp:64:71: [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.
std::string getHomeDirectory () const { return getenv("HOME") ? getenv("HOME") : "."; }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/benchmark/bench_bloom.cpp:80:22: [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.
#define srandomdev() srand((unsigned) time(NULL))
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/benchmark/bench_bloom.cpp:85:11: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
low = random();
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/benchmark/bench_bloom.cpp:86:12: [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.
high = random();
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/benchmark/bench_bloom.cpp:129:23: [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.
kmer_type start = random();
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/bank/TestBank.cpp:90:26: [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.
void setUp () { srand (time(NULL)); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/system/TestSystem.cpp:87:26: [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.
void setUp () { srand (time(NULL)); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/collections/TestContainer.cpp:58:26: [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.
void setUp () { srand (time(NULL)); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/collections/TestIterable.cpp:48:26: [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.
void setUp () { srand (time(NULL)); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/collections/TestMap.cpp:69:26: [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.
void setUp () { srand (time(NULL)); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/tools/misc/TestMisc.cpp:64:26: [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.
void setUp () { srand (time(NULL)); }
data/mapsembler2-2.2.4+dfsg1/kissreads/include/commons.h:52:29: [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.
__attribute__((__common__)) char comp ['t'+1];
data/mapsembler2-2.2.4+dfsg1/kissreads/include/commons.h:53:29: [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.
__attribute__((__common__)) char nuc [4];
data/mapsembler2-2.2.4+dfsg1/kissreads/src/commons.c:247:2: [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 quality[96000];
data/mapsembler2-2.2.4+dfsg1/kissreads/src/fragment_index.c:209:70: [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.
all_starters[fragment_id]->read_coherent_positions[i] = (unsigned char *) malloc (strlen(all_starters[fragment_id]->w)*sizeof(unsigned char)); test_alloc(all_starters[fragment_id]->read_coherent_positions[i]);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/fragment_index.c:211:71: [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.
all_starters[fragment_id]->sum_quality_per_position[i] = (unsigned char *) malloc (strlen(all_starters[fragment_id]->w)*sizeof(unsigned char)); test_alloc(all_starters[fragment_id]->sum_quality_per_position[i]);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/kissReads.c:193:30: [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).
min_coverage=atoi(optarg);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/kissReads.c:199:29: [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).
min_overlap=atoi(optarg);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/kissReads.c:202:33: [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).
countingOption = atoi(optarg);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/kissReads.c:207:32: [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).
coherent_out = fopen(optarg, "w");
data/mapsembler2-2.2.4+dfsg1/kissreads/src/kissReads.c:215:28: [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).
uncoherent_out = fopen(optarg, "w");
data/mapsembler2-2.2.4+dfsg1/kissreads/src/kissReads.c:222:35: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
max_substitutions=atoi(optarg);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/kissReads.c:225:29: [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).
max_threads=atoi(optarg);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/kissReads.c:228:30: [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).
index_stride=atoi(optarg);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/kissReads.c:250:38: [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).
minimal_read_overlap=atoi(optarg);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/kissReads.c:254:28: [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).
size_seeds=atoi(optarg);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/kissReads.c:272:27: [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).
sam_out = fopen(optarg, "w");
data/mapsembler2-2.2.4+dfsg1/kissreads/src/libchash.c:131:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char grgKeyTruncMask[sizeof(ulong)][sizeof(ulong)];
data/mapsembler2-2.2.4+dfsg1/kissreads/src/libchash.c:160:7: [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( (char *)(keyTo), (char *)(keyFrom), (ht)->cchKey); \
data/mapsembler2-2.2.4+dfsg1/kissreads/src/libchash.c:1404:4: [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 szMagicKey[4], *rgchKeys;
data/mapsembler2-2.2.4+dfsg1/kissreads/src/libchash.c:1450:6: [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(&bck->key, rgchKeys, ht->cchKey);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/BooleanVector.h:16:5: [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 mask [8];
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:17:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
extern char comp['t'+1]; // in commons.cpp
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:18:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
extern char nuc [4]; // in commons.cpp
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:141:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
extern char keyi2nucleotide_array ['T'+1]; // commons.cpp
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:332:2: [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 firstNodeId[10];
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:370:3: [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(firstNodeId, "n%d", firstNodeInt);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:500:10: [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).
fp = fopen(original_json, "r");
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:922:5: [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 last_kmers [2*size_seeds]; // size of this fragment: 2k-1 (so alloc 2k for \0)
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/Fragment.cpp:3:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
extern char comp['t'+1];
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/KissReadsGraph.cpp:101:30: [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).
min_coverage=atoi(optarg);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/KissReadsGraph.cpp:106:35: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
max_substitutions=atoi(optarg);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/KissReadsGraph.cpp:111:28: [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).
size_seeds=atoi(optarg);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/KissReadsGraph.cpp:278:15: [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).
res = fopen(output_file,"w");
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/Loader.cpp:296:25: [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).
node_id=atoi((value->string_value)+1); // change the string id (n4) into an int id (4)
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/Loader.cpp:301:24: [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).
source=atoi((value->string_value)+1); // change the string id (n4) into an int id (4)
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/Loader.cpp:306:24: [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).
target=atoi((value->string_value)+1); // change the string id (n4) into an int id (4)
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/ReadMapper.cpp:26:5: [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 seed [size_seeds+1];
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/commons.cpp:52:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char comp['t'+1];
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/commons.cpp:53:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char nuc [4];
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/commons.cpp:54:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char keyi2nucleotide_array ['T'+1];
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/commons.cpp:81:19: [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 (char *) memcpy (result, s, len);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/commons.cpp:194:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[1048576];
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/json.cpp:13:7: [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).
char *atoi(char *first, char *last, int *out)
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/json.cpp:190:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *fp = fopen(filename, "rb");
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/json.cpp:473:37: [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).
if (object->type == JSON_INT && atoi(first, it, &object->int_value) != it)
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/Read_coherence_mapsembler.c:191:43: [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.
#define PRINT_VOTES() {int vx,vy,start_vx;char ACTG[4]={'A','C','T','G'};printf("votes for %s\n",fragment);start_vx=0;while (votes[start_vx][1]==0 &&votes[start_vx][0]==0&&votes[start_vx][2]==0&&votes[start_vx][3]==0) start_vx++;for (vx=start_vx;vx<MAX_VOTES;vx++){int cont=0;for (vy=0;vy<4;vy++) if (votes[vx][vy]!=0) cont=1;if (cont==0)break;printf(" vote[%d] ",vx);for (vy=0;vy<4;vy++)printf("%c:%d ",ACTG[vy],votes[vx][vy]);printf("\n"); }}
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/Read_coherence_mapsembler.c:194:47: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
#define PRINT_CONSENSUS() {int vx,vy,start_vx;char ACTG[4]={'A','C','T','G'};printf("nucleotide consensus for\n%s\n",fragment);start_vx=0;while (votes[start_vx][1]==0 &&votes[start_vx][0]==0&&votes[start_vx][2]==0&&votes[start_vx][3]==0) start_vx++;int nb_subst=0;for (vx=start_vx;vx<MAX_VOTES;vx++){int cont=0;for (vy=0;vy<4;vy++) if (votes[vx][vy]!=0) cont=1;if (cont==0)break;int max=0, max_vy=0; for (vy=0;vy<4;vy++)if (votes[vx][vy]>max){max=votes[vx][vy]; max_vy=vy;} printf("%c",ACTG[max_vy]); if (ACTG[max_vy]!=fragment[vx])nb_subst++;}printf(" (%d substitutions)\n",nb_subst);}
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.c:163:21: [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.
void populate_votes(char *read, int read_len, int position_read, int position_reference, int votes[MAX_VOTES][4])
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.c:196:34: [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.
void perform_consensus_with_read(char *fragment, char *read, int position, int threshold, int votes[MAX_VOTES][4], char ** consensus , int *nb_consensuses, int * consensuses_weights, char ** consensuses_coverages)
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.c:196:50: [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.
void perform_consensus_with_read(char *fragment, char *read, int position, int threshold, int votes[MAX_VOTES][4], char ** consensus , int *nb_consensuses, int * consensuses_weights, char ** consensuses_coverages)
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.c: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.
int rudimentary_error_correction( char *ext, int votes[MAX_VOTES][4], int vote_start_pos, int threshold, char *error_corrected)
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.c:312:2: [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 ACTG[4]={'A','C','T','G'};
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.cpp:163:21: [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.
void populate_votes(char *read, int read_len, int position_read, int position_reference, int votes[MAX_VOTES][4])
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.cpp:196:34: [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.
void perform_consensus_with_read(char *fragment, char *read, int position, int threshold, int votes[MAX_VOTES][4], char ** consensus , int *nb_consensuses, int * consensuses_weights, char ** consensuses_coverages)
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.cpp:196:50: [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.
void perform_consensus_with_read(char *fragment, char *read, int position, int threshold, int votes[MAX_VOTES][4], char ** consensus , int *nb_consensuses, int * consensuses_weights, char ** consensuses_coverages)
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.cpp: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.
int rudimentary_error_correction( char *ext, int votes[MAX_VOTES][4], int vote_start_pos, int threshold, char *error_corrected)
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.cpp:312:2: [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 ACTG[4]={'A','C','T','G'};
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.h:50:34: [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.
void perform_consensus_with_read(char *fragment, char *read, int position, int threshold, int votes[MAX_VOTES][4], char ** consensus , int *nb_consensuses, int * consensuses_weights, char ** consensuses_coverages);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.h:50:50: [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.
void perform_consensus_with_read(char *fragment, char *read, int position, int threshold, int votes[MAX_VOTES][4], char ** consensus , int *nb_consensuses, int * consensuses_weights, char ** consensuses_coverages);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.h:51:21: [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.
void populate_votes(char *read, int read_len, int position_read, int position_reference, int votes[MAX_VOTES][4]);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.h:52:35: [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.
int rudimentary_error_correction( char *ext, int votes[MAX_VOTES][4], int vote_start_pos, int threshold, char *error_corrected);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.h:54:31: [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.
void maximal_consensus_prefix(char consensus[MAX_CONSENSUS][MAX_LEN_EXTENTION], int nb_consensuses);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.c:137:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char grgKeyTruncMask[sizeof(ulong)][sizeof(ulong)];
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.c:166:7: [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( (char *)(keyTo), (char *)(keyFrom), (ht)->cchKey); \
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.c:1410:4: [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 szMagicKey[4], *rgchKeys;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.c:1456:6: [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(&bck->key, rgchKeys, ht->cchKey);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.cpp:137:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char grgKeyTruncMask[sizeof(ulong)][sizeof(ulong)];
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.cpp:166:7: [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( (char *)(keyTo), (char *)(keyFrom), (ht)->cchKey); \
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.cpp:1410:4: [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 szMagicKey[4], *rgchKeys;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.cpp:1456:6: [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(&bck->key, rgchKeys, ht->cchKey);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_coherence.cpp:149:43: [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.
#define PRINT_VOTES() {int vx,vy,start_vx;char ACTG[4]={'A','C','T','G'};printf("votes for %s\n",fragment);start_vx=0;while (votes[start_vx][1]==0 &&votes[start_vx][0]==0&&votes[start_vx][2]==0&&votes[start_vx][3]==0) start_vx++;for (vx=start_vx;vx<MAX_VOTES;vx++){int cont=0;for (vy=0;vy<4;vy++) if (votes[vx][vy]!=0) cont=1;if (cont==0)break;printf(" vote[%d] ",vx);for (vy=0;vy<4;vy++)printf("%c:%d ",ACTG[vy],votes[vx][vy]);printf("\n"); }}
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_coherence.cpp:152:47: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
#define PRINT_CONSENSUS() {int vx,vy,start_vx;char ACTG[4]={'A','C','T','G'};printf("nucleotide consensus for\n%s\n",fragment);start_vx=0;while (votes[start_vx][1]==0 &&votes[start_vx][0]==0&&votes[start_vx][2]==0&&votes[start_vx][3]==0) start_vx++;int nb_subst=0;for (vx=start_vx;vx<MAX_VOTES;vx++){int cont=0;for (vy=0;vy<4;vy++) if (votes[vx][vy]!=0) cont=1;if (cont==0)break;int max=0, max_vy=0; for (vy=0;vy<4;vy++)if (votes[vx][vy]>max){max=votes[vx][vy]; max_vy=vy;} printf("%c",ACTG[max_vy]); if (ACTG[max_vy]!=fragment[vx])nb_subst++;}printf(" (%d substitutions)\n",nb_subst);}
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/simplehash.cpp:52:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
extern char keyi2nucleotide_array ['T'+1];
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/simplehash.h:50:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
extern char keyi2nucleotide_array ['T'+1];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/Fragment.cpp:3:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
extern char comp['t'+1];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/Fragment.cpp:116:30: [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 * output_res_file = fopen((char *) output_res.c_str(), erase?"w":"a");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/GraphOutput.cpp:19:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
nodes_file = fopen(json_nodes_file_name.c_str(),erase?"w":"a");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/GraphOutput.cpp:20:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
edges_file = fopen(json_edges_file_name.c_str(),erase?"w":"a");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/GraphOutput.cpp:21:21: [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).
starters_file = fopen(json_starters_file_name.c_str(),erase?"w":"a");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/GraphOutput.cpp:22:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
graph_file = fopen(json_file_name.c_str(),erase?"w":"a");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/IterativeExtensions.cpp:108:5: [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 kmer_seq[sizeKmer+1];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/IterativeExtensions.cpp:129:28: [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).
linear_seqs_file = fopen((char * )output_file.c_str(),"w");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/IterativeExtensions.cpp:336:5: [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 bin2NT[4] = {'A','C','T','G'};
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/IterativeExtensions.cpp:337:5: [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 bin2NTrev[4] = {'T','G','A','C'};
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/IterativeExtensions.cpp:338:5: [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 binrev[4] = {2,3,0,1};
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/IterativeExtensions.cpp:342:5: [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 kmer_seq[sizeKmer+1];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/IterativeExtensions.cpp:363:28: [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).
linear_seqs_file = fopen((char * )output_file.c_str(),"w");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/IterativeExtensions.cpp:586:37: [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 seq[100];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/IterativeExtensions.cpp:678:5: [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 kmer_seq[sizeKmer+1];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/commons.cpp:53:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char comp['t'+1];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/commons.cpp:54:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char nuc [4];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/commons.cpp:55:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char keyi2nucleotide_array ['T'+1];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/commons.cpp:80:19: [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 (char *) memcpy (result, s, len);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/commons.cpp:185:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[1048576];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/mapsembler_extend.cpp:109:5: [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.
strcpy(index_file_prefix,"index");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/mapsembler_extend.cpp:110:5: [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.
strcpy(res_prefix,"res_mapsembler");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/mapsembler_extend.cpp:136:32: [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).
extension_type=atoi(optarg);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/mapsembler_extend.cpp:140:30: [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).
min_coverage=atoi(optarg);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/mapsembler_extend.cpp:148:27: [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).
max_nodes=atoi(optarg);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/mapsembler_extend.cpp:152:33: [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).
max_graph_depth=atoi(optarg);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/mapsembler_extend.cpp:160:30: [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).
process_type=atoi(optarg);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/mapsembler_extend.cpp:173:26: [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).
sizeKmer=atoi(optarg);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/mapsembler_extend.cpp:210:5: [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 final_res_prefix [4096];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/src/mapsembler2_extremities.cpp:336:19: [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).
output_file = fopen(output_filename.c_str(),"w");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank12.cpp:40:22: [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* file = fopen (options->getStr(STR_URI_SEQ_IDS).c_str(), "r");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank12.cpp:43:13: [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[128];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank12.cpp:44:78: [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).
while (fgets (buffer, sizeof(buffer), file)) { indexes.insert (atoi(buffer)); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank6.cpp:35:40: [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).
size_t dataLineSize = argc >= 3 ? atoi(argv[2]) : 60;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank6.cpp:44:17: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
int m = atoi (argv[3]);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank6.cpp:50:43: [2] (integer) atol:
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).
u_int64_t nbSequences = (argc >= 5 ? atol (argv[4]) : ~0);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank7.cpp:35:17: [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).
threshold = atoi (argv[1]);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank8.cpp:58:27: [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).
if (argc >= 4 && atoi(argv[3])==1)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/bank/bank9.cpp:53:34: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
int modulo = argc >= 4 ? atoi (argv[3]) : 1;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn18.cpp:32:35: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
size_t nbCores = (argc >= 3 ? atoi (argv[2]) : 0);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/debruijn/debruijn24.cpp:36:24: [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* output = fopen (outputFile.c_str(), "w");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/kmer/kmer4.cpp:29:23: [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).
size_t kmerSize = atoi(argv[1]);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/kmer/kmer5.cpp:83:23: [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).
size_t kmerSize = atoi(argv[1]);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/kmer/kmer5.cpp:84:23: [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).
size_t mmerSize = atoi(argv[2]);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/kmer/kmer5.cpp:93:34: [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).
bool display = argc>=5 ? atoi(argv[4]) : false;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/kmer/kmer8.cpp:42:23: [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).
size_t kmerSize = atoi(argv[1]);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/kmer/kmer8.cpp:43:23: [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).
size_t mmerSize = atoi(argv[2]);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/kmer/kmer8.cpp:49:34: [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).
bool display = argc>=5 ? atoi(argv[4]) : false;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/protos/MicroSNP.cpp:17:23: [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).
FILE * snps = fopen ("snps","w");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/storage/storage6.cpp:30:20: [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).
bool display = atoi (argv[2]);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/tools/multithreading1.cpp:24:34: [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).
size_t nbCores = (argc >=2 ? atoi(argv[1]) : 0);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/tools/multithreading2.cpp:19:34: [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).
size_t nbCores = (argc >=2 ? atoi(argv[1]) : 0);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/tools/multithreading3.cpp:37:34: [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).
size_t nbCores = (argc >=2 ? atoi(argv[1]) : 0);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/tools/multithreading4.cpp:20:34: [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).
size_t nbCores = (argc >=2 ? atoi(argv[1]) : 0);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/tools/multithreading5.cpp:19:34: [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).
size_t nbCores = (argc >=2 ? atoi(argv[1]) : 0);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/tools/multithreading6.cpp:27:34: [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).
size_t nbCores = (argc >=3 ? atoi(argv[2]) : 0);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:55:9: [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[256];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:107:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* file = fopen (uri.c_str(), "r");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:110:9: [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[256];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankBinary.cpp:164:40: [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 (binary_read_file == 0) { open (true); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankBinary.cpp:189:9: [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(buffer+cpt_buffer,&readlen,sizeof(int));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankBinary.cpp:248:18: [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).
void BankBinary::open (bool write)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankBinary.cpp:250:24: [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).
binary_read_file = fopen (_filename.c_str(), write?"wb":"rb");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankBinary.cpp:330:28: [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).
binary_read_file = fopen (_ref._filename.c_str(), "rb");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankBinary.cpp:390:9: [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 (&len, _bufferData->getBuffer() + cpt_buffer, sizeof(int)); // read len
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankBinary.cpp:448:17: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy (&readlen, loop, sizeof(int));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankBinary.hpp:160:10: [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 (bool write);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankFasta.cpp:233:25: [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).
_insertHandle = fopen (_filenames[_filenames.size()-1].c_str(), "w");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankFasta.cpp:270:9: [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[4*1024];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankFasta.cpp:451:10: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy (s->string + s->length, bf->buffer + bf->buffer_start, i - bf->buffer_start);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankFasta.cpp:767:9: [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[256];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/Graph.cpp:636:37: [2] (integer) atol:
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).
_state = (Graph::StateMask) atol (getGroup().getProperty ("state").c_str());
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/debruijn/impl/Graph.cpp:637:37: [2] (integer) atol:
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).
_kmerSize = atol (getGroup().getProperty ("kmer_size").c_str());
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/api/Exception.hpp:83:10: [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.
char buffer[256];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/api/IMemory.hpp:106:19: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
virtual void* memcpy (void* dest, const void* src, size_t n) = 0;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp:66:5: [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 path[1000];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp:147:5: [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 [4*1024];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemCommon.cpp:166:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* fp = fopen (path.c_str(), "rb");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemCommon.hpp:60:42: [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).
_handle = _isStdout ? stdout : fopen (path, mode);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp:140:5: [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[4*1024];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp:161:5: [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[4*1024];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp:136:5: [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[4*1024];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp:157:5: [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[4*1024];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/MemoryCommon.hpp:106:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
void* memcpy (void* dest, const void* src, size_t n) { return ::memcpy (dest, src, n); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/MemoryCommon.hpp:106:72: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
void* memcpy (void* dest, const void* src, size_t n) { return ::memcpy (dest, src, n); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/MemoryCommon.hpp:149:12: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
void* memcpy (void* dest, const void* src, size_t n) { return _ope.memcpy (dest, src, n); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/MemoryCommon.hpp:149:76: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
void* memcpy (void* dest, const void* src, size_t n) { return _ope.memcpy (dest, src, n); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp:51:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* file = fopen ("/proc/cpuinfo", "r");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp:54:9: [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[256];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp:69:5: [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 hostname[1024];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp:160:5: [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 hostname[1024];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp:249:5: [2] (buffer) TCHAR:
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.
TCHAR infoBuf[1024];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/TimeCommon.hpp:63:9: [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[256];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagCache.hpp:220:44: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
system::impl::System::memory().memcpy (_sharedBuffer + *_idxShared, this->_items, this->_idx*sizeof(Item));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:260:9: [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(_bufferOut+_idx,&abundance, 1 ); _idx+= 1;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagFile.hpp:261:9: [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(_bufferOut+_idx,&elem, _size_item ); _idx+= _size_item;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/BagPartition.hpp:82:9: [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 filename[128]; snprintf (filename, sizeof(filename), _uriFormat.c_str(), idx);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:226:22: [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* file = fopen(filename,"wb");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:851:49: [2] (integer) atol:
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).
return createBloom<T> (kind, (u_int64_t)atol (sizeStr.c_str()), (size_t)atol (nbHashStr.c_str()));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/Bloom.hpp:851:81: [2] (integer) atol:
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).
return createBloom<T> (kind, (u_int64_t)atol (sizeStr.c_str()), (size_t)atol (nbHashStr.c_str()));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/EMPHF.hpp:134:16: [2] (integer) atol:
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).
return atol (group.getProperty("nb_keys").c_str());
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/collections/impl/IteratorFile.hpp:400:13: [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 (_buffer,_buffer + _idx,_cpt_buffer ); _idx = 0;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/LargeInt.hpp:75:16: [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 buffer[256];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/LargeInt.hpp:447:9: [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 seq[sizeKmer+1];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/LargeInt.hpp:448:9: [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 bin2NT[4] = {'A','C','T','G'};
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt128.hpp:135:9: [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 seq[65];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt128.hpp: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 bin2NT[4] = {'A','C','T','G'};
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt64.hpp:111:9: [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 seq[33];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt64.hpp:112:9: [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 bin2NT[4] = {'A','C','T','G'};
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt64.hpp:133:9: [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 seq[33];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/math/NativeInt64.hpp:134:9: [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 bin2NT[4] = {'A','C','T','G'};
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/IProperty.hpp:89:48: [2] (integer) atol:
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).
long getInt () { return atol (value.c_str()); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Vector.hpp:131:9: [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 (_buffer, buffer, _size*sizeof(char));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp:220:21: [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[128];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp:226:21: [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[128];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp:410:9: [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 [128];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp:615:17: [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[128];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/OptionsParser.cpp:655:13: [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[128];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Progress.cpp:156:5: [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[256];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Progress.hpp:120:5: [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[256];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Property.cpp:183:9: [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[256];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Property.cpp:396:5: [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[64];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Property.cpp:416:5: [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[64];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Property.cpp:438:13: [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[256];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Property.cpp:912:9: [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[4*1024];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Property.cpp:935:13: [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 (filename.c_str(), "w");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/CollectionHDF5.hpp:257:13: [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 (_data, it._data, _blockSize*sizeof(Item));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/storage/impl/Storage.cpp:133:5: [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[bufferSize]; // data buffer
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/benchmark/bench1.cpp:311:23: [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).
size_t kmerSize = atoi(argv[1]);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/benchmark/bench_bloom.cpp:241:9: [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 temp[250];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/benchmark/bench_bloom.cpp:258:9: [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(temp,"expected theoretical with %i hash",ideal_nb_hash);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/benchmark/bench_bloom.cpp:261:9: [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(temp,"expected theoretical with %lli hash",nhash);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/bank/TestBank.cpp:113:13: [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[32];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/bank/TestBank.cpp:182:13: [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[32];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/system/TestSystem.cpp:444:26: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
System::memory().memcpy (ptr2, ptr1, nb);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/system/TestSystem.cpp:481:26: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
System::memory().memcpy (ptr2, ptr1, nb);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/base_hash.hpp:15:9: [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(reinterpret_cast<char*>(&tmp), from, 8);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/common.hpp:151:20: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
m_is = fopen(filename, "rb");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/common.hpp:174:13: [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 buf[buf_size];
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/gen_synthetic_data.cpp:15:14: [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 f = fopen(filename, "w");
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/mmap_memory_model.hpp:57:22: [2] (tmpfile) mkstemp:
Potential for temporary file vulnerability in some circumstances. Some
older Unix-like systems create temp files with permission to write by all
by default, so be sure to set the umask to override this. Also, some older
Unix systems might fail to use O_EXCL when opening the file, so make sure
that O_EXCL is used by the library (CWE-377).
int fd = mkstemp(tmpl);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/tools/ClearCache.cpp:77:52: [2] (integer) atol:
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).
u_int64_t toErase = 1024 * 1024 * (argc >= 2 ? atol (argv[1]) : 0);
data/mapsembler2-2.2.4+dfsg1/minia/Bank.cpp:109:9: [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->string + s->length, bf->buffer + bf->buffer_start, i - bf->buffer_start);
data/mapsembler2-2.2.4+dfsg1/minia/Bank.cpp:371:5: [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 *fname[1] = { fname0 };
data/mapsembler2-2.2.4+dfsg1/minia/Bank.cpp:521:5: [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(write);
data/mapsembler2-2.2.4+dfsg1/minia/Bank.cpp:564:5: [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_pt + cpt_buffer_tid[tid] , element, size);
data/mapsembler2-2.2.4+dfsg1/minia/Bank.cpp:640:5: [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((unsigned char *)buffer + (cpt_buffer * sizeElement), element, sizeElement);
data/mapsembler2-2.2.4+dfsg1/minia/Bank.cpp:663:5: [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(element, (unsigned char *)buffer + (cpt_init_buffer -1 - (cpt_buffer-1)) * sizeElement, sizeElement);//ca les depile dans le meme sens que la lecture
data/mapsembler2-2.2.4+dfsg1/minia/Bank.cpp:707:18: [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).
void BinaryBank::open(bool write)
data/mapsembler2-2.2.4+dfsg1/minia/Bank.cpp:709:24: [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).
binary_read_file = fopen(filename,write?"wb":"rb");
data/mapsembler2-2.2.4+dfsg1/minia/Bank.cpp:761:5: [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(write);
data/mapsembler2-2.2.4+dfsg1/minia/Bank.cpp:792:19: [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 BinaryReads::open(bool write)
data/mapsembler2-2.2.4+dfsg1/minia/Bank.cpp:794:24: [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).
binary_read_file = fopen(filename,write?"wb":"rb");
data/mapsembler2-2.2.4+dfsg1/minia/Bank.cpp:867:5: [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+cpt_buffer,&readlen,sizeof(int));
data/mapsembler2-2.2.4+dfsg1/minia/Bank.cpp:1013:13: [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(len,buffer+cpt_buffer,sizeof(int)); // the sequence length
data/mapsembler2-2.2.4+dfsg1/minia/Bank.h:95:9: [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 filename[TAILLE_NOM];
data/mapsembler2-2.2.4+dfsg1/minia/Bank.h:116:14: [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(bool write);
data/mapsembler2-2.2.4+dfsg1/minia/Bank.h:146:5: [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 filename[TAILLE_NOM];
data/mapsembler2-2.2.4+dfsg1/minia/Bank.h:162:10: [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(bool write);
data/mapsembler2-2.2.4+dfsg1/minia/Bloom.cpp:245:14: [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_data = fopen(filename,"wb");
data/mapsembler2-2.2.4+dfsg1/minia/Bloom.cpp:255:14: [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_data = fopen(filename,"rb");
data/mapsembler2-2.2.4+dfsg1/minia/Bloom.h:37:23: [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 bit_mask[bits_per_char] = {
data/mapsembler2-2.2.4+dfsg1/minia/Bloom.h:50:23: [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 cpt_mask[cpt_per_char] = {
data/mapsembler2-2.2.4+dfsg1/minia/Debloom.cpp:20:5: [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 false_positive_kmer_char[sizeKmer+1];
data/mapsembler2-2.2.4+dfsg1/minia/Debloom.cpp:32:20: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
F_debloom_write = fopen(return_file_name("debloom2"),"wb+");
data/mapsembler2-2.2.4+dfsg1/minia/Debloom.cpp:38:37: [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_false_positive_kmers = fopen(return_file_name(false_positive_kmers_file),"wb");
data/mapsembler2-2.2.4+dfsg1/minia/Debloom.cpp:78:27: [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 * debloom_file = fopen(return_file_name("debloom"),"wb+");
data/mapsembler2-2.2.4+dfsg1/minia/Debloom.cpp:79:29: [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 * debloom_file_2 = fopen(return_file_name("debloom2"),"wb+");
data/mapsembler2-2.2.4+dfsg1/minia/Debloom.cpp:346:19: [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 *T2_file = fopen(return_file_name("t2_kmers"), "w+"); // We will read this file later, when filling T4
data/mapsembler2-2.2.4+dfsg1/minia/Kmer.cpp:152:5: [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 bin2NT[4] = {'A','C','T','G'};
data/mapsembler2-2.2.4+dfsg1/minia/Kmer.cpp:363:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char debug_kmer_buffer[1024];
data/mapsembler2-2.2.4+dfsg1/minia/Set.cpp:240:5: [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 seq[100];
data/mapsembler2-2.2.4+dfsg1/minia/Set.cpp:274:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file_data = fopen(filename,"wb");
data/mapsembler2-2.2.4+dfsg1/minia/Set.cpp:284:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file_data = fopen(filename,"rb");
data/mapsembler2-2.2.4+dfsg1/minia/SortingCount.cpp:36:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp_dir[1024];
data/mapsembler2-2.2.4+dfsg1/minia/SortingCount.cpp:42:5: [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 p_buf[512] = {0};
data/mapsembler2-2.2.4+dfsg1/minia/SortingCount.cpp:55:9: [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 current_path[1000];
data/mapsembler2-2.2.4+dfsg1/minia/SortingCount.cpp:135:5: [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 redundant_filename[nb_partitions][256];
data/mapsembler2-2.2.4+dfsg1/minia/SortingCount.cpp:291:5: [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 message[1000];
data/mapsembler2-2.2.4+dfsg1/minia/SortingCount.cpp:292:5: [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(message,"Counting kmers");
data/mapsembler2-2.2.4+dfsg1/minia/SortingCount.cpp:319:22: [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).
binread->open(false);
data/mapsembler2-2.2.4+dfsg1/minia/SortingCount.cpp:337:9: [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 message[1000];
data/mapsembler2-2.2.4+dfsg1/minia/SortingCount.cpp:338:9: [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(message,"Pass %d/%d, Step 1: partitioning",current_pass+1,nb_passes);
data/mapsembler2-2.2.4+dfsg1/minia/SortingCount.cpp:508:13: [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(message,"Pass %d/%d, Step 2: computing kmer count per partition",current_pass+1,nb_passes);
data/mapsembler2-2.2.4+dfsg1/minia/SortingCount.cpp:526:47: [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).
redundant_partitions_file[p]->open(false);
data/mapsembler2-2.2.4+dfsg1/minia/SortingCount.cpp:821:29: [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 * histo_file = fopen(return_file_name(histo_file_name),"w");
data/mapsembler2-2.2.4+dfsg1/minia/Traversal.cpp:179:5: [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 newNT[2];
data/mapsembler2-2.2.4+dfsg1/minia/Traversal.cpp:219:5: [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 newNT[2];
data/mapsembler2-2.2.4+dfsg1/minia/Traversal.cpp:277:5: [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 newNT[2];
data/mapsembler2-2.2.4+dfsg1/minia/Traversal.cpp:318:13: [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 useless_string[max_depth+1];
data/mapsembler2-2.2.4+dfsg1/minia/Traversal.cpp:397:5: [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 newNT[max_depth+1];
data/mapsembler2-2.2.4+dfsg1/minia/Traversal.cpp:455:5: [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 bin2NT[4] = {'A','C','T','G'};
data/mapsembler2-2.2.4+dfsg1/minia/Traversal.cpp:487:5: [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 bin2NT[4] = {'A','C','T','G'};
data/mapsembler2-2.2.4+dfsg1/minia/Traversal.cpp:737:5: [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 bin2NT[4] = {'A','C','T','G'};
data/mapsembler2-2.2.4+dfsg1/minia/Utils.cpp:23:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char prefix[1024];
data/mapsembler2-2.2.4+dfsg1/minia/Utils.cpp:24:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char fileName[1024];
data/mapsembler2-2.2.4+dfsg1/minia/Utils.cpp:190:23: [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).
F_kmercpt_write = fopen("kmer_count2","wb+");
data/mapsembler2-2.2.4+dfsg1/minia/Utils.cpp:228:26: [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).
F_kmercpt_read = fopen("kmer_count2","wb+");
data/mapsembler2-2.2.4+dfsg1/minia/Utils.cpp:239:24: [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 * count_file = fopen("kmer_count","wb+");
data/mapsembler2-2.2.4+dfsg1/minia/Utils.cpp:240:26: [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 * count_file_2 = fopen("kmer_count2","wb+");
data/mapsembler2-2.2.4+dfsg1/minia/Utils.h:43:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
extern char prefix[1024];
data/mapsembler2-2.2.4+dfsg1/minia/lut.h:8:16: [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 comp_NT[4] = {
data/mapsembler2-2.2.4+dfsg1/minia/lut.h:13:16: [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 revcomp_4NT[256] = {
data/mapsembler2-2.2.4+dfsg1/minia/ttmath/ttmathparser.h:1424:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[30]; // char, not wchar_t
data/mapsembler2-2.2.4+dfsg1/minia/ttmath/ttmathparser.h:1432:2: [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(buf, "%d", par);
data/mapsembler2-2.2.4+dfsg1/minia/ttmath/ttmathparser.h:1470:3: [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[30];
data/mapsembler2-2.2.4+dfsg1/minia/ttmath/ttmaththreads.h:115:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buffer, "TTMATH_LOCK_%ul", (unsigned long)GetCurrentProcessId());
data/mapsembler2-2.2.4+dfsg1/minia/ttmath/ttmaththreads.h:127:3: [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[50];
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/crc32.c:145:15: [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).
out = fopen("crc32.h", "w");
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzguts.h:39:11: [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).
# define open _open
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzlib.c:36:12: [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.
static char buf[1024];
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzlib.c:65:9: [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(buf, "unknown win32 error (%ld)", error);
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzlib.c:245:9: [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((const char *)path, oflag, 0666));
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzlib.c:296:5: [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(path, "<fd:%d>", fd); /* for debugging */
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzlib.c:611:5: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(state->msg, ": ");
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzread.c:158:9: [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(state->x.next, strm->next_in, strm->avail_in);
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzread.c:332:13: [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, state->x.next, n);
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzread.c:391:14: [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[1];
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzread.c:531:9: [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, state->x.next, n);
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzwrite.c:218:13: [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(state->in + have, buf, copy);
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzwrite.c:250:14: [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[1];
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/inflate.c:623:14: [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 hbuf[4]; /* buffer for gzip header crc calculation */
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/inflate.c:1382:14: [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[4]; /* to restore bit buffer to byte string */
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/trees.c:330:20: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *header = fopen("trees.h", "w");
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/zutil.c:17:9: [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.
z_const char * const z_errmsg[10] = {
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/zutil.h:47:16: [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.
extern z_const char * const z_errmsg[10]; /* indexed by 2-zlib_error */
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/zutil.h:107:6: [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).
fopen((name), (mode), "mbc=60", "ctx=stm", "rfm=fix", "mrs=512")
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/zutil.h:184:30: [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).
# define F_OPEN(name, mode) fopen((name), (mode))
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/zutil.h:208:21: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define zmemcpy memcpy
data/mapsembler2-2.2.4+dfsg1/kissreads/include/coherence_algorithm.h:47:80: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
char read_coherent_generic (const int pwi, const char * fragment, const char * read, const int subst_allowed);
data/mapsembler2-2.2.4+dfsg1/kissreads/include/coherence_algorithm.h:48:75: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
char read_coherent_SNP(const int pwi, const char * fragment, const char * read, const int subst_allowed);
data/mapsembler2-2.2.4+dfsg1/kissreads/include/commons.h:85:50: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int get_next_fasta_sequence (gzFile file, char * read, char * line);
data/mapsembler2-2.2.4+dfsg1/kissreads/include/commons.h:87:54: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int get_next_sequence_for_fastq (gzFile file, char * read, char * quality, char * line);
data/mapsembler2-2.2.4+dfsg1/kissreads/include/libchash.h:252:47: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
struct HashTable *HashLoad(FILE *fp, char * (*read)(FILE *, int));
data/mapsembler2-2.2.4+dfsg1/kissreads/include/libchash.h:253:51: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
struct HashTable *HashLoadKeys(FILE *fp, char * (*read)(FILE *, int));
data/mapsembler2-2.2.4+dfsg1/kissreads/src/coherent_algorithm.c:57:79: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
char read_coherent_generic(const int pwi, const char * fragment, const char * read, const int subst_allowed){
data/mapsembler2-2.2.4+dfsg1/kissreads/src/coherent_algorithm.c:92:43: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while(fragment[pos_on_fragment]!='\0' && read[pos_on_read]!='\0'){
data/mapsembler2-2.2.4+dfsg1/kissreads/src/coherent_algorithm.c:94:33: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(fragment[pos_on_fragment]!=read[pos_on_read] && fragment[pos_on_fragment]!='*' && fragment[pos_on_fragment]!='?' && fragment[pos_on_fragment]!='N'){ // one subsitution
data/mapsembler2-2.2.4+dfsg1/kissreads/src/coherent_algorithm.c:116:75: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
char read_coherent_SNP(const int pwi, const char * fragment, const char * read, const int subst_allowed){
data/mapsembler2-2.2.4+dfsg1/kissreads/src/coherent_algorithm.c:145:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int snp_pos = strlen(fragment)/2;
data/mapsembler2-2.2.4+dfsg1/kissreads/src/coherent_algorithm.c:148:43: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while(fragment[pos_on_fragment]!='\0' && read[pos_on_read]!='\0'){
data/mapsembler2-2.2.4+dfsg1/kissreads/src/coherent_algorithm.c:149:33: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(fragment[pos_on_fragment]!=read[pos_on_read] &&
data/mapsembler2-2.2.4+dfsg1/kissreads/src/commons.c:84:24: [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).
sum_memory_strdup+=strlen(s1);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/commons.c:139:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int len=strlen(s);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/commons.c:193:10: [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).
int l = strlen(raw_comment);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/commons.c:239:9: [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).
return strlen(sequence); // readlen
data/mapsembler2-2.2.4+dfsg1/kissreads/src/commons.c:274:9: [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).
return strlen(sequence); // readlen
data/mapsembler2-2.2.4+dfsg1/kissreads/src/commons.c:314:9: [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).
return strlen(sequence); // readlen
data/mapsembler2-2.2.4+dfsg1/kissreads/src/commons.c:354:9: [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).
return strlen(sequence); // readlen
data/mapsembler2-2.2.4+dfsg1/kissreads/src/commons.c:382:9: [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).
return strlen(sequence); // readlen
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:77:82: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void print_mapping(const int pos_on_fragment, const char * fragment, const char *read){
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:84:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
printf("%s\n", read);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:93:23: [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(start+length_read<strlen(the_starter->w)) stop_on_starter=start+length_read; else stop_on_starter=strlen(the_starter->w);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:93:103: [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(start+length_read<strlen(the_starter->w)) stop_on_starter=start+length_read; else stop_on_starter=strlen(the_starter->w);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:122:28: [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).
const int pos_SB = strlen(the_starter->w)-(size_seeds);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:176:44: [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(start+length_read-minimal_read_overlap<strlen(the_starter->w)) stop_on_starter=start+length_read-minimal_read_overlap; else stop_on_starter=strlen(the_starter->w);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:176:145: [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(start+length_read-minimal_read_overlap<strlen(the_starter->w)) stop_on_starter=start+length_read-minimal_read_overlap; else stop_on_starter=strlen(the_starter->w);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:206:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int stopi=strlen(the_starter->w);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:223:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int stop=strlen(the_starter->w)-minimal_read_overlap;
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:225:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int stop=strlen(the_starter->w);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:323:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
test_alloc(read);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:334:55: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read_len = get_next_sequence_for_fastq(reads_file, read, quality,line);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:336:51: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read_len = get_next_fasta_sequence(reads_file, read,line);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:356:38: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
printf("new read = %s-\n", read);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:412:49: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int maximal_pwi = strlen(starter)-minimal_read_overlap;
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:425:78: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read_coherence = read_coherent_SNP(pwi, starter, read, subst_allowed);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:427:82: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read_coherence = read_coherent_generic(pwi, starter, read, subst_allowed);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:437:74: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
print_mapping(pwi,all_starters[value->a]->w ,read); //DEB
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:439:87: [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).
feed_coherent_positions(all_starters[value->a], pwi, (int)strlen(read), qual, quality, i, read_file);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:439:94: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
feed_coherent_positions(all_starters[value->a], pwi, (int)strlen(read), qual, quality, i, read_file);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:440:139: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if( sam_out ) fprintf(sam_out,"%d %d %s\t%s\tC%d\t%d\n", value->a, value->b, all_starters[value->a]->comment, read, read_file+1, pwi);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:451:48: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
printf("%s\n", read);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:463:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
revcomp(read,read_len);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/extension_algorithm.c:494:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
free(read);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/fragment_index.c:61:13: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while((c = fgetc(f)) != EOF) if(c == '\n') lines++;
data/mapsembler2-2.2.4+dfsg1/kissreads/src/fragment_index.c:88:15: [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).
for(i=0;i<strlen(in);i++) if(in[i]>='A' && in[i]<='Z') count++;
data/mapsembler2-2.2.4+dfsg1/kissreads/src/fragment_index.c:91:15: [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).
for(i=0;i<strlen(in);i++) if(in[i]>='A' && in[i]<='Z') temp[j++]=in[i];
data/mapsembler2-2.2.4+dfsg1/kissreads/src/fragment_index.c:101:15: [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).
for(i=0;i<strlen(in);i++)
data/mapsembler2-2.2.4+dfsg1/kissreads/src/fragment_index.c:106:15: [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).
for(i=0;i<strlen(in);i++)
data/mapsembler2-2.2.4+dfsg1/kissreads/src/fragment_index.c:118:11: [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).
for(i=strlen(in)-1;i>=0;i--)
data/mapsembler2-2.2.4+dfsg1/kissreads/src/fragment_index.c:126:11: [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).
for(i=strlen(in)-1;i>=0;i--)
data/mapsembler2-2.2.4+dfsg1/kissreads/src/fragment_index.c:209:86: [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).
all_starters[fragment_id]->read_coherent_positions[i] = (unsigned char *) malloc (strlen(all_starters[fragment_id]->w)*sizeof(unsigned char)); test_alloc(all_starters[fragment_id]->read_coherent_positions[i]);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/fragment_index.c:211:87: [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).
all_starters[fragment_id]->sum_quality_per_position[i] = (unsigned char *) malloc (strlen(all_starters[fragment_id]->w)*sizeof(unsigned char)); test_alloc(all_starters[fragment_id]->sum_quality_per_position[i]);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/fragment_index.c:213:86: [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).
all_starters[fragment_id]->sum_quality_per_position[i] = (int *) malloc (strlen(all_starters[fragment_id]->w)*sizeof(int)); test_alloc(all_starters[fragment_id]->sum_quality_per_position[i]);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/fragment_index.c:216:14: [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).
for(z=0;z<strlen(all_starters[fragment_id]->w); z++) all_starters[fragment_id]->read_coherent_positions[i][z]=0;
data/mapsembler2-2.2.4+dfsg1/kissreads/src/fragment_index.c:217:14: [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).
for(z=0;z<strlen(all_starters[fragment_id]->w); z++) all_starters[fragment_id]->read_coherent_positions[i][z]=0;
data/mapsembler2-2.2.4+dfsg1/kissreads/src/fragment_index.c:218:14: [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).
for(z=0;z<strlen(all_starters[fragment_id]->w); z++) all_starters[fragment_id]->sum_quality_per_position[i][z]=0;
data/mapsembler2-2.2.4+dfsg1/kissreads/src/fragment_index.c:251:8: [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).
stop=strlen(all_starters[fragment_id]->w)-k+1;
data/mapsembler2-2.2.4+dfsg1/kissreads/src/fragment_index.c:296:8: [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).
stop=strlen(all_starters[fragment_id]->w)-k+1;
data/mapsembler2-2.2.4+dfsg1/kissreads/src/libchash.c:154:46: [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).
(keyTo) = (ulong)HTsmalloc( WORD_ROUND(strlen((char *)(keyFrom))+1) ); \
data/mapsembler2-2.2.4+dfsg1/kissreads/src/libchash.c:167:42: [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).
HTfree((char *)(key), WORD_ROUND(strlen((char *)(key))+1)); \
data/mapsembler2-2.2.4+dfsg1/kissreads/src/libchash.c:888:49: [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).
cchKeyOrig = ht->cchKey == NULL_TERMINATED ? strlen(key) : ht->cchKey;
data/mapsembler2-2.2.4+dfsg1/kissreads/src/libchash.c:1382:8: [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).
strlen(KEY_PTR(ht, bck->key))+1 : ht->cchKey), fp);
data/mapsembler2-2.2.4+dfsg1/kissreads/src/libchash.c:1510:17: [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).
WORD_ROUND(strlen((char *)item->key)+1) : ht->cchKey;
data/mapsembler2-2.2.4+dfsg1/kissreads/src/outputs.c:337:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int snp_pos = strlen(results_against_set[cycle_id]->w)/2;
data/mapsembler2-2.2.4+dfsg1/kissreads/src/outputs.c:349:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int snp_pos = strlen(results_against_set[cycle_id+1]->w)/2;
data/mapsembler2-2.2.4+dfsg1/kissreads/src/outputs.c:478:35: [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).
for (j=kmer_size-1;j<=strlen(results_against_set[cycle_id]->w)-kmer_size;j++){
data/mapsembler2-2.2.4+dfsg1/kissreads/src/outputs.c:743:35: [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).
for (j=kmer_size-1;j<=strlen(results_against_set[cycle_id]->w)-kmer_size;j++){
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:290:27: [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).
for(int j=0;j<strlen(all_nodes[i]->edges[edge_id]->to->fragment->fragment_sequence);j++)
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:358:6: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy (new_id, &line_c[start], size);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:373:22: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
if(set_line!=NULL) strncpy(set_line,firstNodeId,strlen(firstNodeId));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:373:51: [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(set_line!=NULL) strncpy(set_line,firstNodeId,strlen(firstNodeId));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:392:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for(int j=0;j<strlen(all_nodes[i]->fragment->fragment_sequence);j++){
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:396:29: [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).
avg/=(float)strlen(all_nodes[i]->fragment->fragment_sequence);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:405:42: [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).
fprintf(out,", \"length\": %lu", strlen(all_nodes[i]->fragment->fragment_sequence));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:481:15: [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).
for(int i=0;i<strlen(line);i++) {\
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:496:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ssize_t read;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:729:74: [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).
last_kmonemer= strndup(current_node->fragment->fragment_sequence+strlen(current_node->fragment->fragment_sequence)-size_seeds+1, size_seeds-1);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:754:54: [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).
first_kmonemer = strndup(target_sequence+strlen(target_sequence)-size_seeds+1, size_seeds-1);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:802:23: [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).
int size_fragment=strlen(fragment);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:839:23: [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).
int size_fragment=strlen(fragment);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:886:13: [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).
int n = strlen(current_node->fragment->fragment_sequence);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:923:13: [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).
int n = strlen(current_node->fragment->fragment_sequence);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1053:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
left_length+=strlen(left_path[i]->to->fragment->fragment_sequence)-size_seeds+1;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1064:23: [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).
right_length+=strlen(right_path[i]->to->fragment->fragment_sequence)-size_seeds+1;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1066:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int total_length = left_length+strlen(anchoring_node->fragment->fragment_sequence)+right_length;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1067:48: [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).
const int dontmap = total_length-pwi_first-strlen(mapped_fragment);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1069:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(right_path.size()) last_mapped = strlen(right_path[right_path.size()-1]->to->fragment->fragment_sequence) - dontmap;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1070:29: [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).
else last_mapped = pwi+strlen(mapped_fragment);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1076:30: [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).
const int stop = min(pwi+strlen(mapped_fragment), strlen(anchoring_node->fragment->fragment_sequence));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1076:55: [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).
const int stop = min(pwi+strlen(mapped_fragment), strlen(anchoring_node->fragment->fragment_sequence));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1083:23: [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).
for(int j=0;j<strlen(left_path[i]->to->fragment->fragment_sequence);j++)
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1113:35: [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).
for(int i=pwi_first;i<strlen(left_path[left_path.size()-1]->to->fragment->fragment_sequence);i++)
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1116:27: [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).
for(int i=0;i<strlen(left_path[left_path.size()-1]->to->fragment->fragment_sequence)-pwi_first-1;i++)
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1123:23: [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).
for(int j=0;j<strlen(right_path[i]->to->fragment->fragment_sequence);j++)
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1162:23: [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).
for(int i=strlen(right_path[right_path.size()-1]->to->fragment->fragment_sequence)-last_mapped;i<strlen(right_path[right_path.size()-1]->to->fragment->fragment_sequence);i++){
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1162:110: [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).
for(int i=strlen(right_path[right_path.size()-1]->to->fragment->fragment_sequence)-last_mapped;i<strlen(right_path[right_path.size()-1]->to->fragment->fragment_sequence);i++){
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1253:44: [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(!forward) revcomp(test_ref_sequence,strlen(test_ref_sequence)); // if the target is reverse, change the direction
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1255:44: [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(!forward) revcomp(test_ref_sequence,strlen(test_ref_sequence)); // change back the direction to retreive the original one
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1265:50: [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(starting_on_fragment - starting_on_node + strlen(current_node->fragment->fragment_sequence) >= strlen(fragment)) {
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1265:103: [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(starting_on_fragment - starting_on_node + strlen(current_node->fragment->fragment_sequence) >= strlen(fragment)) {
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1298:73: [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).
starting_on_fragment + strlen(current_node->fragment->fragment_sequence)-starting_on_node,
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1395:27: [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).
revcomp(fragment, strlen(fragment));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1398:35: [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).
strlen(fragment)-i, // ibar = strlen(fragment)-i-size_seeds; fragmentbar+ibar+sizeseeds = frgamentbar+strlen(fragment)-i-size_seeds+size_seeds = fragmentbar cqfd
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1399:35: [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).
strlen(node->fragment->fragment_sequence)-b, // we start position size-b on the reverse complement of the node
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1405:27: [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).
revcomp(fragment, strlen(fragment)); // put back the right order
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1410:58: [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).
* first_left_edge = node->get_map(false)->at(strlen(node->fragment->fragment_sequence)-b-(strlen(fragment)-i)).second;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1410:103: [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).
* first_left_edge = node->get_map(false)->at(strlen(node->fragment->fragment_sequence)-b-(strlen(fragment)-i)).second;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1935:49: [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).
revcomp(a->fragment->fragment_sequence, strlen(a->fragment->fragment_sequence));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1937:49: [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).
revcomp(b->fragment->fragment_sequence, strlen(b->fragment->fragment_sequence));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1940:62: [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).
char * new_left_sequence = (char *) malloc(sizeof(char)*(strlen(a->fragment->fragment_sequence)+strlen(b->fragment->fragment_sequence)-size_seeds+2));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1940:101: [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).
char * new_left_sequence = (char *) malloc(sizeof(char)*(strlen(a->fragment->fragment_sequence)+strlen(b->fragment->fragment_sequence)-size_seeds+2));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:1946:49: [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).
revcomp(a->fragment->fragment_sequence, strlen(a->fragment->fragment_sequence));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/DeBruijnGraph.cpp:2105:43: [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).
for(int pos = 0;remove && pos<strlen(current->fragment->fragment_sequence); pos++){
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/Fragment.cpp:23:8: [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(fragment_sequence)%2) return false;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/Fragment.cpp:24:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int size = strlen(fragment_sequence);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/Fragment.cpp:40:65: [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).
coverage[i]= (unsigned char *) malloc(sizeof(unsigned char)*strlen(fragment_sequence));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/Fragment.cpp:46:45: [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).
coverage[i]= (int *) malloc(sizeof(int)*strlen(fragment->fragment_sequence));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/Fragment.cpp:50:37: [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).
for(int i=0;i<nb;i++) for(int j=0;j<strlen(fragment_sequence);j++) coverage[i][j]=0;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/Loader.cpp:115:57: [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).
sequence = (char *) malloc(sizeof(char)*strlen(value->string_value)+1);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/Loader.cpp:277:57: [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).
sequence = (char *) malloc(sizeof(char)*strlen(value->string_value)+1);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/ReadMapper.cpp:23:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
char * read;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/ReadMapper.cpp:36:50: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while(read_bank->get_next_seq_from_file(&read,&size_read, file_id)){ // each read
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/ReadMapper.cpp:41:27: [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).
for(int i=0;i<strlen(read);i++) read[i] = toupper(read[i]);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/ReadMapper.cpp:41:34: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for(int i=0;i<strlen(read);i++) read[i] = toupper(read[i]);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/ReadMapper.cpp:41:45: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for(int i=0;i<strlen(read);i++) read[i] = toupper(read[i]);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/ReadMapper.cpp:41:63: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for(int i=0;i<strlen(read);i++) read[i] = toupper(read[i]);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/ReadMapper.cpp:117:113: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool is_mapped = graph->map_approx_a_fragment(graph->seed_table[ii].b, i, node, read, distance, &first_left_edge, &first_right_edge);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/ReadMapper.cpp:161:33: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
revcomp(read,size_read); // this was the revcomp read that was mapped.
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/ReadMapper.cpp:171:69: [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).
int current_pwi=size_seeds-1+pwis[id_best_path]-strlen(anchoring_nodes[id_best_path]->fragment->fragment_sequence);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/ReadMapper.cpp:176:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len_current=strlen(current->fragment->fragment_sequence);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/ReadMapper.cpp:189:50: [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).
current_pwi=size_seeds-1-strlen(read)-pwis[id_best_path];
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/ReadMapper.cpp:189:57: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
current_pwi=size_seeds-1-strlen(read)-pwis[id_best_path];
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/ReadMapper.cpp:196:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len_current=strlen(current->fragment->fragment_sequence);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/ReadMapper.cpp:204:132: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
graph->populate_given_paths(left_path, right_path, anchoring_nodes[id_best_path], pwis[id_best_path], file_id, read);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/ReadMapper.cpp:208:33: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
revcomp(read,size_read); // this was the revcomp read that was mapped. Put it back.
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/ReadMapper.cpp:229:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
revcomp(read,size_read); // know switch to the reverse complement for the second run
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/commons.cpp:51:15: [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).
extern size_t strlen (const char*);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/commons.cpp:71:16: [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_t len = strlen (s);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/commons.cpp:142:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int len=strlen(s);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/commons.cpp:199:12: [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).
for(i=0;i<strlen(string);i++) if(string[i]==character) pos=i;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/Read_coherence_mapsembler.c:91:20: [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).
current_read_len=strlen(key); /* needed to compute votes*/ \
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/Read_coherence_mapsembler.c:110:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
cell *read; \
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/Read_coherence_mapsembler.c:154:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (read != NULL) \
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/Read_coherence_mapsembler.c:175:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
cell *read;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/Read_coherence_mapsembler.c:179:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (read != NULL) \
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/Read_coherence_mapsembler.c:238:25: [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).
int current_read_len = strlen(current_read);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/Read_coherence_mapsembler.c:272:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len_potential_consensus = strlen(potential_consensus);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/Read_coherence_mapsembler.c:393:17: [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).
len_fragment = strlen(fragment);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.c:163:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void populate_votes(char *read, int read_len, int position_read, int position_reference, int votes[MAX_VOTES][4])
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.c:170:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (!is_ACTG(read[i])) continue;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.c:173:52: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
votes[position_reference+i-position_read][ACTG(read[i])]++;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.c:196:56: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void perform_consensus_with_read(char *fragment, char *read, int position, int threshold, int votes[MAX_VOTES][4], char ** consensus , int *nb_consensuses, int * consensuses_weights, char ** consensuses_coverages)
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.c:216:46: [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).
char * error_corrected = (char *)malloc((strlen(read)+1));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.c:216:53: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
char * error_corrected = (char *)malloc((strlen(read)+1));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.c:222:33: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
rudimentary_error_correction(read,votes,position,threshold,error_corrected);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.c:242:10: [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(consensus[i])<strlen(cur_consensus))
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.c:242:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(consensus[i])<strlen(cur_consensus))
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.c:257:61: [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).
increase_consensus_coverage(consensuses_coverages[i],strlen(consensus[i]));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.c:271:64: [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).
increase_consensus_coverage(consensuses_coverages[subsume],strlen(cur_consensus));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.c:285:70: [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).
init_consensus_coverage(consensuses_coverages[*nb_consensuses], strlen(consensus[*nb_consensuses]), max_consensus_length);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.c:309:14: [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).
int len_ext=strlen(ext);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.cpp:163:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void populate_votes(char *read, int read_len, int position_read, int position_reference, int votes[MAX_VOTES][4])
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.cpp:170:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (!is_ACTG(read[i])) continue;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.cpp:173:52: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
votes[position_reference+i-position_read][ACTG(read[i])]++;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.cpp:196:56: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void perform_consensus_with_read(char *fragment, char *read, int position, int threshold, int votes[MAX_VOTES][4], char ** consensus , int *nb_consensuses, int * consensuses_weights, char ** consensuses_coverages)
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.cpp:216:46: [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).
char * error_corrected = (char *)malloc((strlen(read)+1));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.cpp:216:53: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
char * error_corrected = (char *)malloc((strlen(read)+1));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.cpp:222:33: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
rudimentary_error_correction(read,votes,position,threshold,error_corrected);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.cpp:242:10: [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(consensus[i])<strlen(cur_consensus))
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.cpp:242:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(consensus[i])<strlen(cur_consensus))
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.cpp:257:61: [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).
increase_consensus_coverage(consensuses_coverages[i],strlen(consensus[i]));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.cpp:271:64: [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).
increase_consensus_coverage(consensuses_coverages[subsume],strlen(cur_consensus));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.cpp:285:70: [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).
init_consensus_coverage(consensuses_coverages[*nb_consensuses], strlen(consensus[*nb_consensuses]), max_consensus_length);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.cpp:309:14: [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).
int len_ext=strlen(ext);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.h:50:56: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void perform_consensus_with_read(char *fragment, char *read, int position, int threshold, int votes[MAX_VOTES][4], char ** consensus , int *nb_consensuses, int * consensuses_weights, char ** consensuses_coverages);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/consensus_common.h:51:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void populate_votes(char *read, int read_len, int position_read, int position_reference, int votes[MAX_VOTES][4]);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/couple.c:76:13: [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).
cpl->a_len=strlen(a);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/couple.cpp:77:13: [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).
cpl->a_len=strlen(a);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.c:160:46: [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).
(keyTo) = (ulong)HTsmalloc( WORD_ROUND(strlen((char *)(keyFrom))+1) ); \
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.c:173:42: [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).
HTfree((char *)(key), WORD_ROUND(strlen((char *)(key))+1)); \
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.c:894:49: [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).
cchKeyOrig = ht->cchKey == NULL_TERMINATED ? strlen(key) : ht->cchKey;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.c:1388:8: [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).
strlen(KEY_PTR(ht, bck->key))+1 : ht->cchKey), fp);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.c:1516:17: [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).
WORD_ROUND(strlen((char *)item->key)+1) : ht->cchKey;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.cpp:160:46: [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).
(keyTo) = (ulong)HTsmalloc( WORD_ROUND(strlen((char *)(keyFrom))+1) ); \
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.cpp:173:42: [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).
HTfree((char *)(key), WORD_ROUND(strlen((char *)(key))+1)); \
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.cpp:894:49: [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).
cchKeyOrig = ht->cchKey == NULL_TERMINATED ? strlen(key) : ht->cchKey;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.cpp:1388:8: [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).
strlen(KEY_PTR(ht, bck->key))+1 : ht->cchKey), fp);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.cpp:1516:17: [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).
WORD_ROUND(strlen((char *)item->key)+1) : ht->cchKey;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.h:252:47: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
struct HashTable *HashLoad(FILE *fp, char * (*read)(FILE *, int));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/libchash.h:253:51: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
struct HashTable *HashLoadKeys(FILE *fp, char * (*read)(FILE *, int));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/misc_tools.c:62:23: [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).
dest = realloc(dest, strlen(dest)+strlen(src)+1);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/misc_tools.c:62:36: [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).
dest = realloc(dest, strlen(dest)+strlen(src)+1);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/misc_tools.c:76:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
char * res = (char *) malloc (strlen(dest)+strlen(src)+1); test_alloc(res);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/misc_tools.c:76:45: [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).
char * res = (char *) malloc (strlen(dest)+strlen(src)+1); test_alloc(res);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/misc_tools.cpp:61:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
dest = (char*) realloc(dest, strlen(dest)+strlen(src)+1);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/misc_tools.cpp:61:44: [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).
dest = (char*) realloc(dest, strlen(dest)+strlen(src)+1);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/misc_tools.cpp:75:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
char * res = (char *) malloc (strlen(dest)+strlen(src)+1); test_alloc(res);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/misc_tools.cpp:75:45: [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).
char * res = (char *) malloc (strlen(dest)+strlen(src)+1); test_alloc(res);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_coherence.cpp:84:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
current_read_len=strlen(key); /* needed to compute votes*/ \
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_coherence.cpp:103:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
cell_mapsembler *read; \
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_coherence.cpp:112:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (read != NULL) \
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_coherence.cpp:133:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
cell_mapsembler *read;
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_coherence.cpp:137:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (read != NULL) \
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_coherence.cpp:196:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int current_read_len = strlen(current_read);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_coherence.cpp:230:39: [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).
int len_potential_consensus = strlen(potential_consensus);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_coherence.cpp:352:24: [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).
len_fragment = strlen(fragment);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_groups.c:65:50: [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).
(*current_group_info)->fragment_coverage=calloc(strlen(fragment),sizeof(int));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_groups.c:84:20: [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).
current_read_len=strlen(current_read);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_groups.c:165:21: [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).
current_read_len=strlen(current_read);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_groups.c:267:52: [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).
if(position_fragment+p>=0 && position_fragment+p<strlen(fragment) && current_read[p] != fragment[position_fragment+p]) printf("%c", tolower(current_read[p]));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_groups.c:278:47: [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).
for(j=0;j<space;j++) printf(" "); for (j=0;j<strlen(fragment);j++) { int coverage = group_info->fragment_coverage[j]; if (coverage>0xF) printf("+");
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_groups.c:288:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (read != NULL)
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_groups.cpp:57:58: [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).
(*current_group_info)->fragment_coverage= (int*) calloc(strlen(fragment),sizeof(int));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_groups.cpp:76:20: [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).
current_read_len=strlen(current_read);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_groups.cpp:157:21: [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).
current_read_len=strlen(current_read);
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_groups.cpp:259:60: [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(position_fragment+p>=0 && position_fragment+p<(signed)strlen(fragment) && current_read[p] != fragment[position_fragment+p]) printf("%c", tolower(current_read[p]));
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_groups.cpp:270:55: [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).
for(j=0;j<space;j++) printf(" "); for (j=0;j<(signed)strlen(fragment);j++) {int coverage = group_info->fragment_coverage[j]; if (coverage>0xF) printf("+");
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/read_groups.cpp:280:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (read != NULL)
data/mapsembler2-2.2.4+dfsg1/kissreads_graph/read_coherence_mapsembler/simplehash.cpp:165:46: [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).
char *new_string = (char *)pool_malloc(map,strlen(string)+1);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/Fragment.cpp:66:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int k=strlen(kmer_char);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/Fragment_Bank.cpp:24:21: [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).
size_t lenpre = strlen(pre),
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/Fragment_Bank.cpp:25:14: [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).
lenstr = strlen(str);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/Fragment_Bank.cpp:64:39: [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).
revcomp(sequence, strlen(sequence));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/GraphOutput.cpp:145:138: [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).
fprintf(starters_file,"\"Starter_%d\":{\"data\":{\"id\":\"S%d\", \"sequence\":\"%s\", \"length\":%ld,\n", index,index, sequence, strlen(sequence));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/GraphOutput.cpp:204:124: [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).
fprintf(nodes_file," { \"data\": { \"id\":\"n%ld\", \"sequence\":\"%s\", \"length\":%ld}}\n",index,ascii_node, strlen(ascii_node));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/IterativeExtensions.cpp:181:144: [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).
printf(" --- iteration: kmer %s%s (of length %d) depth %d nbNodes explored %lli ---\n",kmer_seq,strand?" (internally rc)":"", (int)strlen(kmer_seq), depth,nbNodes);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/IterativeExtensions.cpp:400:131: [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).
printf("iteration: kmer %s%s (of length %zu) depth %d nbNodes explored %lli\n",kmer_seq,strand?" (internally rc)":"", strlen(kmer_seq), depth,nbNodes);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/IterativeExtensions.cpp:724:26: [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).
int first_divergence=strlen(node);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/commons.cpp:52:15: [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).
extern size_t strlen (const char*);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/commons.cpp:70:16: [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_t len = strlen (s);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/commons.cpp:133:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int len=strlen(s);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extend/commons.cpp:190:12: [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).
for(i=0;i<strlen(string);i++) if(string[i]==character) pos=i;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/kmer/kmer2.cpp:20:23: [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_t kmerSize = strlen(seq);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/examples/storage/storage8.cpp:51:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read (reinterpret_cast<char*>(buffer), nbItems*sizeof(float));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:116:23: [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).
int len = strlen(buffer);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankAlbum.cpp:123:17: [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(buffer) > 0)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankFasta.cpp:83:30: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
buffered_strings_t () : read(new variable_string_t), dummy(new variable_string_t), header(new variable_string_t), quality(new variable_string_t) {}
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankFasta.cpp:86:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
delete read;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankFasta.cpp:92:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
variable_string_t *read, *dummy, *header, *quality;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankFasta.cpp:186:46: [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 (strstr (fname, "gz") == (fname + strlen (fname) - 2))
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/bank/impl/BankFasta.cpp:526:32: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
buffered_gets (bf, bs->read, NULL, true, true);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemCommon.hpp:77:40: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int get () { return (isOpen() ? fgetc (getHandle()) : 0); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemCommon.hpp:94:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
result = strlen (tmp);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemCommon.hpp:97:89: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (result > 0) { for (char c = tmp[result-1]; c !='\n' && c!=EOF; c = fgetc (getHandle())) {} }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemLinux.cpp:168:83: [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 ::setxattr (filename.c_str(), (string("user.") + key).c_str(), buffer, strlen(buffer), XATTR_CREATE);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/FileSystemMacos.cpp:164:83: [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 ::setxattr (filename.c_str(), (string("user.") + key).c_str(), buffer, strlen(buffer), 0, XATTR_CREATE);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp:72:30: [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).
result.assign (hostname, strlen(hostname));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp:163:30: [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).
result.assign (hostname, strlen(hostname));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/system/impl/SystemInfoCommon.cpp:254:33: [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).
result.assign (infoBuf, strlen(infoBuf));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/api/Data.hpp:75:60: [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).
Data (char* buffer) : encoding(ASCII) { setRef(buffer,strlen(buffer)); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Property.cpp:445:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
char* value = key + strlen (key) + 1;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/Property.cpp:551:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
reader.read ();
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/XmlReader.cpp:71:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void XmlReader::read ()
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/src/gatb/tools/misc/impl/XmlReader.hpp:181:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void read ();
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/bank/TestBank.cpp:699:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
actualTotalSize += strlen (table[i]);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/bank/TestBank.cpp:700:33: [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 (actualMaxSize < strlen(table[i])) { actualMaxSize = strlen(table[i]); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/bank/TestBank.cpp:700:70: [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 (actualMaxSize < strlen(table[i])) { actualMaxSize = strlen(table[i]); }
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/bank/TestBank.cpp:713:53: [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).
CPPUNIT_ASSERT ((*it)->getDataSize() == strlen(table[idx]) );
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:240:25: [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_t seqLen = strlen (seq);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:275:27: [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).
size_t seqLen = strlen (seq);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:524:40: [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).
CPPUNIT_ASSERT (path.rank() == strlen (seq) - kmerSize);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:722:70: [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).
CPPUNIT_ASSERT (graph.getInfo().getInt ("kmers_nb_valid") == strlen(seq) - kmerSize + 1);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:731:27: [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).
size_t kmerSize = strlen (sequences[0]);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/debruijn/TestDebruijn.cpp:783:27: [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).
size_t kmerSize = strlen (sequences[0]);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/kmer/TestDebloom.cpp:102:73: [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).
CPPUNIT_ASSERT (sortingCount.getSolidCounts()->getNbItems() == (strlen(seqs[0]) - kmerSize + 1) );
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/kmer/TestKmer.cpp:156:35: [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).
data.set ((char*)seq, strlen(seq));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/kmer/TestKmer.cpp:358:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t sequenceSize = strlen(seq);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/kmer/TestKmer.cpp:464:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
data.set ((char*)seq, strlen(seq));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/kmer/TestMPHF.cpp:111:72: [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).
CPPUNIT_ASSERT (sortingCount.getSolidKmers()->getNbItems() == (strlen(seqs[0]) - kmerSize + 1) );
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/system/TestSystem.cpp:671:13: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
usleep (rand() % 10 + 1);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/system/TestSystem.cpp:885:50: [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).
CPPUNIT_ASSERT (writer->getSize() == strlen (info));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/test/unit/src/system/TestSystem.cpp:907:47: [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).
CPPUNIT_ASSERT (reader->tell() == strlen (info));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/base_hash.hpp:121:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&m_seed), sizeof(m_seed));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/base_hash.hpp:209:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&m_seed), sizeof(m_seed));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/bitpair_vector.hpp:84:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&m_size), sizeof(m_size));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/bitpair_vector.hpp:86:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(m_bits.data()), (std::streamsize)(sizeof(m_bits[0]) * m_bits.size()));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/bitstream.hpp:50:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
uint64_t read(uint64_t l)
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/bitstream.hpp:89:47: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
return (((uint64_t(1) << l) | read(l)) - 1);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/common.hpp:38:47: [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).
std::localtime(&t), fmt, fmt + strlen(fmt));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/hypergraph_sorter_scan.hpp:66:41: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
node_t v1s = (node_t)rr.read(node_bits);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/hypergraph_sorter_scan.hpp:67:41: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
node_t v2s = (node_t)rr.read(node_bits);
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/mphf.hpp:120:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&m_n), sizeof(m_n));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/mphf.hpp:121:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&m_hash_domain),
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/mphf_hem.hpp:138:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&m_n), sizeof(m_n));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/mphf_hem.hpp:139:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&m_chunk_shift),
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/mphf_hem.hpp:145:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&chunks),
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/mphf_hem.hpp:149:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(m_offsets.data()),
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/packed_vector.hpp:73:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (read < m_k) {
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/packed_vector.hpp:74:48: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
val |= m_bits[word_pos + 1] << read;
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/packed_vector.hpp:99:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&m_size), sizeof(m_size));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/packed_vector.hpp:100:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(&m_k), sizeof(m_k));
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/packed_vector.hpp:102:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(m_bits.data()),
data/mapsembler2-2.2.4+dfsg1/mapsembler2_extremities/thirdparty/gatb-core/thirdparty/emphf/ranked_bitpair_vector.hpp:76:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.read(reinterpret_cast<char*>(m_block_ranks.data()),
data/mapsembler2-2.2.4+dfsg1/minia/Bank.cpp:178:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
buffered_gets(bf, read, NULL, true, true);
data/mapsembler2-2.2.4+dfsg1/minia/Bank.cpp:345:48: [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).
if (strstr(fname[i],"gz") == (fname[i]+strlen(fname[i])-2) ) compressed=true;
data/mapsembler2-2.2.4+dfsg1/minia/Bank.cpp:382:39: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
variable_string_t * to_free[3] = {read, dummy, header};
data/mapsembler2-2.2.4+dfsg1/minia/Bank.cpp:680:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
size_t BinaryBank::read( void *element, int size)
data/mapsembler2-2.2.4+dfsg1/minia/Bank.cpp:835:37: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void BinaryReads::write_read(char * read, int readlen)
data/mapsembler2-2.2.4+dfsg1/minia/Bank.cpp:839:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
char * pt = read;
data/mapsembler2-2.2.4+dfsg1/minia/Bank.h:69:28: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
variable_string_t *read, *dummy, *header;
data/mapsembler2-2.2.4+dfsg1/minia/Bank.h:113:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
size_t read( void *element, int size);
data/mapsembler2-2.2.4+dfsg1/minia/Bank.h:159:28: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void write_read(char * read, int readlen);
data/mapsembler2-2.2.4+dfsg1/minia/Utils.cpp:27:9: [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).
if (strlen(prefix)>0)
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzguts.h:40:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
# define read _read
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzlib.c:199:15: [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).
len = strlen((const char *)path);
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzlib.c:601:38: [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 ((state->msg = (char *)malloc(strlen(state->path) + strlen(msg) + 3)) ==
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzlib.c:601:60: [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 ((state->msg = (char *)malloc(strlen(state->path) + strlen(msg) + 3)) ==
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzlib.c:607:26: [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).
snprintf(state->msg, strlen(state->path) + strlen(msg) + 3,
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzlib.c:607:48: [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).
snprintf(state->msg, strlen(state->path) + strlen(msg) + 3,
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzread.c:30:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ret = read(state->fd, buf + *have, len - *have);
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzwrite.c:301:21: [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).
len = (unsigned)strlen(str);
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzwrite.c:355:11: [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).
len = strlen((char *)(state->in));
data/mapsembler2-2.2.4+dfsg1/thirdparty/zlib/gzwrite.c:443:11: [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).
len = strlen((char *)(state->in));
ANALYSIS SUMMARY:
Hits = 1122
Lines analyzed = 121504 in approximately 3.38 seconds (35955 lines/second)
Physical Source Lines of Code (SLOC) = 65109
Hits@level = [0] 921 [1] 315 [2] 303 [3] 21 [4] 479 [5] 4
Hits@level+ = [0+] 2043 [1+] 1122 [2+] 807 [3+] 504 [4+] 483 [5+] 4
Hits/KSLOC@level+ = [0+] 31.3782 [1+] 17.2326 [2+] 12.3946 [3+] 7.74087 [4+] 7.41833 [5+] 0.0614354
Dot directories skipped = 1 (--followdotdir overrides)
Minimum risk level = 1
Not every hit is necessarily a security vulnerability.
There may be other security vulnerabilities; review your code!
See 'Secure Programming HOWTO'
(https://dwheeler.com/secure-programs) for more information.