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/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c
Examining data/augustus-3.3.3+dfsg/auxprogs/bam2hints/bam2hints.cc
Examining data/augustus-3.3.3+dfsg/auxprogs/bam2wig/bam2wig.c
Examining data/augustus-3.3.3+dfsg/auxprogs/checkTargetSortedness/checkTargetSortedness.c
Examining data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/compileSpliceCands.c
Examining data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/list.c
Examining data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/list.h
Examining data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/bamtools/bamtools_sort.h
Examining data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/bamtools/bamtools_tool.h
Examining data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/filterBam.cc
Examining data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/functions/MatePairs.cc
Examining data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/functions/PairednessCoverage.cc
Examining data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/functions/SingleAlignment.cc
Examining data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/functions/getReferenceLength.cc
Examining data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/functions/getReferenceName.cc
Examining data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/functions/initOptions.cc
Examining data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/functions/printCigarOperations.cc
Examining data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/functions/printElapsedTime.cc
Examining data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/functions/sumDandIOperations.cc
Examining data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/functions/sumMandIOperations.cc
Examining data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/headers/filterBam.h
Examining data/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/gene.cc
Examining data/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/genome.cc
Examining data/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/main.cc
Examining data/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/sqliteDB.cc
Examining data/augustus-3.3.3+dfsg/auxprogs/joingenes/jg_ios.cpp
Examining data/augustus-3.3.3+dfsg/auxprogs/joingenes/jg_ios.h
Examining data/augustus-3.3.3+dfsg/auxprogs/joingenes/jg_transcript.cpp
Examining data/augustus-3.3.3+dfsg/auxprogs/joingenes/jg_transcript.h
Examining data/augustus-3.3.3+dfsg/auxprogs/joingenes/joingenes.cpp
Examining data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/Compute_UTRs.cpp
Examining data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/Compute_UTRs.hpp
Examining data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/Coord_Transform.cpp
Examining data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/Coord_Transform.hpp
Examining data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/Error.hpp
Examining data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/Genomic_Data.cpp
Examining data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/Genomic_Data.hpp
Examining data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/Global.hpp
Examining data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/Splice_Sites.cpp
Examining data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/Splice_Sites.hpp
Examining data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/Supporting_Methods.cpp
Examining data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/Supporting_Methods.hpp
Examining data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/Test.cpp
Examining data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/Test.hpp
Examining data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/UTRs.cpp
Examining data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/UTRs.hpp
Examining data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/flex_vec.hpp
Examining data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/main.cpp
Examining data/augustus-3.3.3+dfsg/include/table_structure.h
Examining data/augustus-3.3.3+dfsg/src/alignment.cc
Examining data/augustus-3.3.3+dfsg/src/augustus.cc
Examining data/augustus-3.3.3+dfsg/src/baumwelch.cc
Examining data/augustus-3.3.3+dfsg/src/codonMSA.cc
Examining data/augustus-3.3.3+dfsg/src/commontrain.cc
Examining data/augustus-3.3.3+dfsg/src/compgenepred.cc
Examining data/augustus-3.3.3+dfsg/src/consensus.cc
Examining data/augustus-3.3.3+dfsg/src/consensusFinder.cc
Examining data/augustus-3.3.3+dfsg/src/contTimeMC.cc
Examining data/augustus-3.3.3+dfsg/src/contentmodel.cc
Examining data/augustus-3.3.3+dfsg/src/curve2hints.cc
Examining data/augustus-3.3.3+dfsg/src/dummy.cc
Examining data/augustus-3.3.3+dfsg/src/espoca.cc
Examining data/augustus-3.3.3+dfsg/src/etraining.cc
Examining data/augustus-3.3.3+dfsg/src/evaluate.cc
Examining data/augustus-3.3.3+dfsg/src/evaluation.cc
Examining data/augustus-3.3.3+dfsg/src/exon_seg.cc
Examining data/augustus-3.3.3+dfsg/src/exoncand.cc
Examining data/augustus-3.3.3+dfsg/src/exonmodel.cc
Examining data/augustus-3.3.3+dfsg/src/exontrain.cc
Examining data/augustus-3.3.3+dfsg/src/extrinsicinfo.cc
Examining data/augustus-3.3.3+dfsg/src/fastBlockSearch.cc
Examining data/augustus-3.3.3+dfsg/src/fasta.cc
Examining data/augustus-3.3.3+dfsg/src/genbank.cc
Examining data/augustus-3.3.3+dfsg/src/gene.cc
Examining data/augustus-3.3.3+dfsg/src/geneMSA.cc
Examining data/augustus-3.3.3+dfsg/src/geneticcode.cc
Examining data/augustus-3.3.3+dfsg/src/genomicMSA.cc
Examining data/augustus-3.3.3+dfsg/src/getSeq.cc
Examining data/augustus-3.3.3+dfsg/src/googletest/include/gtest/gtest-death-test.h
Examining data/augustus-3.3.3+dfsg/src/googletest/include/gtest/gtest-matchers.h
Examining data/augustus-3.3.3+dfsg/src/googletest/include/gtest/gtest-message.h
Examining data/augustus-3.3.3+dfsg/src/googletest/include/gtest/gtest-param-test.h
Examining data/augustus-3.3.3+dfsg/src/googletest/include/gtest/gtest-printers.h
Examining data/augustus-3.3.3+dfsg/src/googletest/include/gtest/gtest-spi.h
Examining data/augustus-3.3.3+dfsg/src/googletest/include/gtest/gtest-test-part.h
Examining data/augustus-3.3.3+dfsg/src/googletest/include/gtest/gtest-typed-test.h
Examining data/augustus-3.3.3+dfsg/src/googletest/include/gtest/gtest.h
Examining data/augustus-3.3.3+dfsg/src/googletest/include/gtest/gtest_pred_impl.h
Examining data/augustus-3.3.3+dfsg/src/googletest/include/gtest/gtest_prod.h
Examining data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/custom/gtest-port.h
Examining data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/custom/gtest-printers.h
Examining data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/custom/gtest.h
Examining data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/gtest-death-test-internal.h
Examining data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/gtest-filepath.h
Examining data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/gtest-internal.h
Examining data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/gtest-param-util.h
Examining data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/gtest-port-arch.h
Examining data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/gtest-port.h
Examining data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/gtest-string.h
Examining data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/gtest-type-util.h
Examining data/augustus-3.3.3+dfsg/src/googletest/src/gtest-all.cc
Examining data/augustus-3.3.3+dfsg/src/googletest/src/gtest-death-test.cc
Examining data/augustus-3.3.3+dfsg/src/googletest/src/gtest-filepath.cc
Examining data/augustus-3.3.3+dfsg/src/googletest/src/gtest-internal-inl.h
Examining data/augustus-3.3.3+dfsg/src/googletest/src/gtest-matchers.cc
Examining data/augustus-3.3.3+dfsg/src/googletest/src/gtest-port.cc
Examining data/augustus-3.3.3+dfsg/src/googletest/src/gtest-printers.cc
Examining data/augustus-3.3.3+dfsg/src/googletest/src/gtest-test-part.cc
Examining data/augustus-3.3.3+dfsg/src/googletest/src/gtest-typed-test.cc
Examining data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc
Examining data/augustus-3.3.3+dfsg/src/googletest/src/gtest_main.cc
Examining data/augustus-3.3.3+dfsg/src/graph.cc
Examining data/augustus-3.3.3+dfsg/src/hints.cc
Examining data/augustus-3.3.3+dfsg/src/igenicmodel.cc
Examining data/augustus-3.3.3+dfsg/src/igenictrain.cc
Examining data/augustus-3.3.3+dfsg/src/intronmodel.cc
Examining data/augustus-3.3.3+dfsg/src/introntrain.cc
Examining data/augustus-3.3.3+dfsg/src/lldouble.cc
Examining data/augustus-3.3.3+dfsg/src/load2db.cc
Examining data/augustus-3.3.3+dfsg/src/load2sqlitedb.cc
Examining data/augustus-3.3.3+dfsg/src/logdoubletest.cc
Examining data/augustus-3.3.3+dfsg/src/mea.cc
Examining data/augustus-3.3.3+dfsg/src/meaPath.cc
Examining data/augustus-3.3.3+dfsg/src/merkmal.cc
Examining data/augustus-3.3.3+dfsg/src/motif.cc
Examining data/augustus-3.3.3+dfsg/src/namgene.cc
Examining data/augustus-3.3.3+dfsg/src/ncmodel.cc
Examining data/augustus-3.3.3+dfsg/src/orthoexon.cc
Examining data/augustus-3.3.3+dfsg/src/orthogene.cc
Examining data/augustus-3.3.3+dfsg/src/orthograph.cc
Examining data/augustus-3.3.3+dfsg/src/parser/parse.cc
Examining data/augustus-3.3.3+dfsg/src/parser/parser.h
Examining data/augustus-3.3.3+dfsg/src/parser/parserbase.h
Examining data/augustus-3.3.3+dfsg/src/phylotree.cc
Examining data/augustus-3.3.3+dfsg/src/pp_fastBlockSearcher.cc
Examining data/augustus-3.3.3+dfsg/src/pp_hitseq.cc
Examining data/augustus-3.3.3+dfsg/src/pp_prepare_align.cc
Examining data/augustus-3.3.3+dfsg/src/pp_profile.cc
Examining data/augustus-3.3.3+dfsg/src/pp_scoring.cc
Examining data/augustus-3.3.3+dfsg/src/projectio.cc
Examining data/augustus-3.3.3+dfsg/src/randseqaccess.cc
Examining data/augustus-3.3.3+dfsg/src/scanner/lex.cc
Examining data/augustus-3.3.3+dfsg/src/scanner/scanner.h
Examining data/augustus-3.3.3+dfsg/src/scanner/scannerbase.h
Examining data/augustus-3.3.3+dfsg/src/speciesgraph.cc
Examining data/augustus-3.3.3+dfsg/src/sqliteDB.cc
Examining data/augustus-3.3.3+dfsg/src/statemodel.cc
Examining data/augustus-3.3.3+dfsg/src/train_logReg_param.cc
Examining data/augustus-3.3.3+dfsg/src/types.cc
Examining data/augustus-3.3.3+dfsg/src/unittests/fasta_unittest.cc
Examining data/augustus-3.3.3+dfsg/src/unittests/lldouble_unittest.cc
Examining data/augustus-3.3.3+dfsg/src/utrmodel.cc
Examining data/augustus-3.3.3+dfsg/src/utrtrain.cc
Examining data/augustus-3.3.3+dfsg/src/vitmatrix.cc
Examining data/augustus-3.3.3+dfsg/src/properties.cc
FINAL RESULTS:
data/augustus-3.3.3+dfsg/src/properties.cc:707:13: [5] (race) readlink:
This accepts filename arguments; if an attacker can move those files or
change the link content, a race condition results. Also, it does not
terminate with ASCII NUL. (CWE-362, CWE-20). Reconsider approach.
if ((pos = readlink( "/proc/self/exe", path, allocated - 1 )) != -1)
data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/compileSpliceCands.c:552:6: [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(oldname,tmpData->name);
data/augustus-3.3.3+dfsg/src/etraining.cc:355:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(newSeqName, "%s.p%d", multiannoseq->seqname, pieceIndex);
data/augustus-3.3.3+dfsg/src/etraining.cc:357:4: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(newSeqName, multiannoseq->seqname);
data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/gtest-death-test-internal.h:200:5: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
fprintf(\
data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/gtest-port.h:2114:20: [4] (buffer) StrNCpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
inline const char* StrNCpy(char* dest, const char* src, size_t n) {
data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/gtest-port.h:2184:26: [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 GTEST_SNPRINTF_ _snprintf
data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/gtest-port.h:2186:26: [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 GTEST_SNPRINTF_ snprintf
data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:125:10: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
# define vsnprintf _vsnprintf
data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:3033:5: [4] (format) vprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vprintf(fmt, args);
data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:3054:3: [4] (format) vprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vprintf(fmt, args);
data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:3061:3: [4] (format) vprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vprintf(fmt, args);
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:234:14: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt (argc, argv, "t:sf:")) != -1)
data/augustus-3.3.3+dfsg/auxprogs/bam2hints/bam2hints.cc:460:16: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while((opt = getopt_long(argc, argv, "i:o:p:g:m:M:q:xe:s:InrC:STv:c:t:G:b:h", long_options, &option_index)) != -1)
data/augustus-3.3.3+dfsg/auxprogs/bam2wig/bam2wig.c:77:14: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((n = getopt(argc, argv, "r:t:")) >= 0)
data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/compileSpliceCands.c:435:14: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt (argc, argv, "f:g:c:t:m:i:d")) != -1)
data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/functions/initOptions.cc:215:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
opt = getopt_long(argc, argv, optString, longOpts, &longIndex);
data/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/main.cc:68:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "g:s:a:t:o:e:n:dium:c:h", long_options, &option_index)) != -1) {
data/augustus-3.3.3+dfsg/auxprogs/joingenes/joingenes.cpp:204:9: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
opt = getopt_long(argc, argv, optString, longOpts, &longIndex);
data/augustus-3.3.3+dfsg/auxprogs/joingenes/joingenes.cpp:275:11: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
opt = getopt_long(argc, argv, optString, longOpts, &longIndex);
data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/main.cpp:70:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ( (opt = getopt_long(argc, argv, "S:C:I:R:W:o:w:r:l:v:n:c:p:i:m:s:zfh", long_options, &option_index)) != -1) {
data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/main.cpp:96:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ( (opt = getopt_long(argc, argv, "S:C:I:R:W:o:w:r:l:v:n:c:p:i:m:s:zfh", long_options, &option_index)) != -1) {
data/augustus-3.3.3+dfsg/src/consensusFinder.cc:54:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long (argc, argv, ":thl:p:d:m:s:n:e:c:",longOpts, &longIndex)) != -1){
data/augustus-3.3.3+dfsg/src/curve2hints.cc:45:15: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long (argc, argv, ":rhi:o:c:s:z",longOpts, &longIndex)) != -1){
data/augustus-3.3.3+dfsg/src/espoca.cc:66:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "s:a:t:rb:h", long_options, &option_index)) != -1) {
data/augustus-3.3.3+dfsg/src/exon_seg.cc:11:10: [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.
#include<getopt.h>
data/augustus-3.3.3+dfsg/src/getSeq.cc:49:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "c:s:f:q:a:b:rh", long_options, &option_index)) != -1) {
data/augustus-3.3.3+dfsg/src/googletest/include/gtest/gtest.h:992:39: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
void ShuffleTests(internal::Random* random);
data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/gtest-port.h:2153:27: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
const char* const env = getenv(name);
data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/gtest-port.h:2156:10: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
return getenv(name);
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-internal-inl.h:309:37: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
void ShuffleRange(internal::Random* random, int begin, int end,
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-internal-inl.h:330:39: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
inline void Shuffle(internal::Random* random, std::vector<E>* v) {
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-internal-inl.h:331:16: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
ShuffleRange(random, 0, static_cast<int>(v->size()), v);
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-internal-inl.h:812:21: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
internal::Random* random() { return &random_; }
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-port.cc:345:5: [3] (misc) InitializeCriticalSection:
Exceptions can be thrown in low-memory situations. Use
InitializeCriticalSectionAndSpinCount instead.
::InitializeCriticalSection(critical_section_);
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-port.cc:360:5: [3] (misc) EnterCriticalSection:
On some versions of Windows, exceptions can be thrown in low-memory
situations. Use InitializeCriticalSectionAndSpinCount instead.
::EnterCriticalSection(critical_section_);
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-port.cc:433:11: [3] (misc) InitializeCriticalSection:
Exceptions can be thrown in low-memory situations. Use
InitializeCriticalSectionAndSpinCount instead.
::InitializeCriticalSection(critical_section_);
data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:2830:48: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
void TestSuite::ShuffleTests(internal::Random* random) {
data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:2831:11: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
Shuffle(random, &test_indices_);
data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:5221:7: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
random()->Reseed(random_seed_);
data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:5566:16: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
ShuffleRange(random(), 0, last_death_test_suite_ + 1, &test_suite_indices_);
data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:5569:16: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
ShuffleRange(random(), last_death_test_suite_ + 1,
data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:5574:30: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
test_suite->ShuffleTests(random());
data/augustus-3.3.3+dfsg/src/load2db.cc:70:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "s:d:hc:", long_options, &option_index)) != -1) {
data/augustus-3.3.3+dfsg/src/load2sqlitedb.cc:56:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt_long(argc, argv, "s:d:hc:imr", long_options, &option_index)) != -1) {
data/augustus-3.3.3+dfsg/src/load2sqlitedb.cc:120:28: [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.
fastafile.replace(0,1,getenv("HOME"));
data/augustus-3.3.3+dfsg/src/motif.cc:447:5: [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(1);
data/augustus-3.3.3+dfsg/src/pp_prepare_align.cc:52:26: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
const char* envval = getenv(envname);
data/augustus-3.3.3+dfsg/src/pp_prepare_align.cc:63:26: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
const char* envval = getenv(envname);
data/augustus-3.3.3+dfsg/src/properties.cc:407:14: [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.
char *dir = getenv(CFGPATH_KEY); // second priority: environment variable
data/augustus-3.3.3+dfsg/src/train_logReg_param.cc:349:3: [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/augustus-3.3.3+dfsg/src/train_logReg_param.cc:385:3: [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/augustus-3.3.3+dfsg/src/types.cc:481:23: [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.
filename.replace(0,1,getenv("HOME"));
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:160:2: [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 buffer [FILEBUFFER];
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:163:2: [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 line [ 1024 ];
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:166:3: [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 firstline [TOKEN_SIZE];
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:174:9: [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 name[TOKEN_SIZE];
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:177:2: [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 oldname[TOKEN_SIZE];
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:264:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
handle = fopen ( filename, "r" );
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:295:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
chromosomeLength=atoi(tokens[14]);
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:331:23: [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).
chromosomeLength=atoi(tokens[14]);
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:342:19: [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).
blockCounts = atoi(tokens[17])+1;
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:368:15: [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).
for (j = atoi(startTokens[i]); j < atoi(startTokens[i])+atoi(sizeTokens[i]); j++)
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:368:41: [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).
for (j = atoi(startTokens[i]); j < atoi(startTokens[i])+atoi(sizeTokens[i]); j++)
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:368:62: [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).
for (j = atoi(startTokens[i]); j < atoi(startTokens[i])+atoi(sizeTokens[i]); j++)
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:435:22: [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).
chromosomeLength=atoi(tokens[4]);
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:467:17: [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).
contigStart=atoi(tokens[3]);
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:468:15: [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).
contigEnd=atoi(tokens[4]);
data/augustus-3.3.3+dfsg/auxprogs/bam2hints/bam2hints.cc:467:31: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'p': Pri = atoi(optarg); break;
data/augustus-3.3.3+dfsg/auxprogs/bam2hints/bam2hints.cc:468:31: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'g': MaxGapLen = atoi(optarg); break;
data/augustus-3.3.3+dfsg/auxprogs/bam2hints/bam2hints.cc:469:31: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'm': MinIntLen = atoi(optarg); break;
data/augustus-3.3.3+dfsg/auxprogs/bam2hints/bam2hints.cc:470:31: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'M': MaxIntLen = atoi(optarg); break;
data/augustus-3.3.3+dfsg/auxprogs/bam2hints/bam2hints.cc:471:32: [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).
case 'b': MinEndBlockLen = atoi(optarg); break;
data/augustus-3.3.3+dfsg/auxprogs/bam2hints/bam2hints.cc:472:31: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'q': MaxQGapLen = atoi(optarg); break;
data/augustus-3.3.3+dfsg/auxprogs/bam2hints/bam2hints.cc:473:31: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'e': EpCutoff = atoi(optarg); break;
data/augustus-3.3.3+dfsg/auxprogs/bam2hints/bam2hints.cc:479:31: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'C': MaxCov = atoi(optarg); break;
data/augustus-3.3.3+dfsg/auxprogs/bam2hints/bam2hints.cc:485:31: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'G': MaxGeneLen = atoi(optarg); break;
data/augustus-3.3.3+dfsg/auxprogs/bam2hints/bam2hints.cc:596:15: [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).
FILE* GFF = fopen(OutFileName, "w");
data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/compileSpliceCands.c:192:9: [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[LINEBUFFER];
data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/compileSpliceCands.c:219:18: [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).
genome_handle = fopen ( fn, "r" );
data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/compileSpliceCands.c:293:14: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
d->startPos=atoi(tokens[3]);
data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/compileSpliceCands.c:294:12: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
d->endPos=atoi(tokens[4]);
data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/compileSpliceCands.c:393:2: [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 buffer[FILEBUFFER];
data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/compileSpliceCands.c:395:2: [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 line[LINEBUFFER];
data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/compileSpliceCands.c:398:9: [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 oldname[LINEBUFFER];
data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/compileSpliceCands.c:445:17: [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).
checkWidth = atoi(optarg);
data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/compileSpliceCands.c:448:24: [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).
maxSpliceSiteDiff = atoi(optarg);
data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/compileSpliceCands.c:454:22: [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).
maxIntronLength = atoi(optarg);
data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/compileSpliceCands.c:499:15: [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).
gff_handle = fopen ( gff_filename, "r" );
data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/list.h:8:4: [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 name[LINELENGTH];
data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/filterBam.cc:460:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
bedFile.open(pairBedFile);
data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/filterBam.cc:1406:18: [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).
geneFile.open(commonGeneFile);
data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/filterBam.cc:1659:16: [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).
geneFile.open(commonGeneFile);
data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/functions/initOptions.cc:193:52: [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).
case 'f' : globalOptions.insertLimit = atoi(optarg); break;
data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/functions/initOptions.cc:194:53: [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).
case 'g' : globalOptions.maxIntronLen = atoi(optarg); break;
data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/functions/initOptions.cc:195:54: [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).
case 'i' : globalOptions.maxSortesTest = atoi(optarg); break;
data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/functions/initOptions.cc:196:40: [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).
case 'j' : globalOptions.minCover = atoi(optarg); break;
data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/functions/initOptions.cc:197:37: [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).
case 'k' : globalOptions.minId = atoi(optarg); break;
data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/functions/initOptions.cc:198:53: [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).
case 'l' : globalOptions.minIntronLen = atoi(optarg); break;
data/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/genome.cc:65:20: [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 int start = atol(tokens[3].c_str());
data/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/genome.cc:66:18: [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 int end = atol(tokens[4].c_str());
data/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/genome.cc:98:14: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
mult = atoi(spos);
data/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/genome.cc:180:24: [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).
gene->setTLstart(atol(tokens[3].c_str()));
data/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/genome.cc:183:22: [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).
gene->setTLend(atol(tokens[3].c_str()));
data/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/genome.cc:186:24: [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 int start = atol(tokens[3].c_str());
data/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/genome.cc:187:22: [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 int end = atol(tokens[4].c_str());
data/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/genome.cc:256:8: [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).
of.open(filename.c_str());
data/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/genome.cc:287:23: [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 int start = atol(tokens[1].c_str()) + 1;
data/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/genome.cc:354:8: [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).
of.open(filename.c_str());
data/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/genome.cc:747:8: [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).
of.open(outfile.c_str());
data/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/main.cc:90:13: [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).
maxCpus = atoi(optarg);
data/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/main.cc:332:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[256];
data/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/sqliteDB.cc:20:16: [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 SQLiteDB::open(OpenMode mode){
data/augustus-3.3.3+dfsg/auxprogs/joingenes/jg_ios.cpp:23:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[256];
data/augustus-3.3.3+dfsg/auxprogs/joingenes/jg_ios.cpp:59:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buff[1024];
data/augustus-3.3.3+dfsg/auxprogs/joingenes/jg_ios.cpp:60:3: [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 copybuff[1024];
data/augustus-3.3.3+dfsg/auxprogs/joingenes/jg_ios.cpp:110:14: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
exon.from = atoi(temp);
data/augustus-3.3.3+dfsg/auxprogs/joingenes/jg_ios.cpp:115:12: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
exon.to = atoi(temp);
data/augustus-3.3.3+dfsg/auxprogs/joingenes/jg_ios.cpp:147:2: [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 attribute[300];
data/augustus-3.3.3+dfsg/auxprogs/joingenes/jg_ios.cpp:257:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
pred_range.first = atoi(temp);
data/augustus-3.3.3+dfsg/auxprogs/joingenes/jg_ios.cpp:259:22: [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).
pred_range.second = atoi(temp);
data/augustus-3.3.3+dfsg/auxprogs/joingenes/jg_ios.cpp:374:11: [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).
outfile.open(outFileName, ios::out | ios::app);
data/augustus-3.3.3+dfsg/auxprogs/joingenes/jg_ios.cpp:644:11: [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).
outfile.open(outFileName, ios::out | ios::app);
data/augustus-3.3.3+dfsg/auxprogs/joingenes/jg_transcript.cpp:1118:11: [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).
outfile.open(filename, ios::out | ios::app);
data/augustus-3.3.3+dfsg/auxprogs/joingenes/joingenes.cpp:127:26: [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).
priorities.push_back(atoi(temp_inside));
data/augustus-3.3.3+dfsg/auxprogs/joingenes/joingenes.cpp:130:28: [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).
priorities.push_back(atoi(temp_inside));
data/augustus-3.3.3+dfsg/auxprogs/joingenes/joingenes.cpp:133:26: [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).
priorities.push_back(atoi(priority_string));
data/augustus-3.3.3+dfsg/auxprogs/joingenes/joingenes.cpp:145:25: [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).
supprList.push_back(atoi(temp_inside));
data/augustus-3.3.3+dfsg/auxprogs/joingenes/joingenes.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).
supprList.push_back(atoi(temp_inside));
data/augustus-3.3.3+dfsg/auxprogs/joingenes/joingenes.cpp:151:25: [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).
supprList.push_back(atoi(suppString));
data/augustus-3.3.3+dfsg/auxprogs/joingenes/joingenes.cpp:229:34: [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).
properties.errordistance = atoi(optarg);
data/augustus-3.3.3+dfsg/auxprogs/joingenes/joingenes.cpp:388:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
outfile.open(properties.outFileName, ios::out); // delete content of file filename
data/augustus-3.3.3+dfsg/auxprogs/joingenes/joingenes.cpp:393:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
outfile.open(filenameEqual, ios::out);
data/augustus-3.3.3+dfsg/auxprogs/joingenes/joingenes.cpp:395:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
outfile.open(filenameStop1, ios::out);
data/augustus-3.3.3+dfsg/auxprogs/joingenes/joingenes.cpp:397:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
outfile.open(filenameStop2, ios::out);
data/augustus-3.3.3+dfsg/auxprogs/joingenes/joingenes.cpp:399:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
outfile.open(filenameUne1, ios::out);
data/augustus-3.3.3+dfsg/auxprogs/joingenes/joingenes.cpp:401:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
outfile.open(filenameUne2, ios::out);
data/augustus-3.3.3+dfsg/auxprogs/joingenes/joingenes.cpp:404:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
outfile.open("cExtra1.gtf", ios::out);
data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/main.cpp:117:29: [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).
smoothing_window_size = atoi(optarg);
data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/main.cpp:120:19: [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).
read_length = atoi(optarg);
data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/main.cpp:123:13: [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).
limit = atoi(optarg);
data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/main.cpp:126:24: [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).
drop_window_size = atoi(optarg);
data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/main.cpp:129:18: [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_length = atoi(optarg);
data/augustus-3.3.3+dfsg/auxprogs/utrrnaseq/src/main.cpp:132:23: [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).
min_average_cov = atoi(optarg);
data/augustus-3.3.3+dfsg/src/augustus.cc:493:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
outputfile.open(outputfilename.c_str());
data/augustus-3.3.3+dfsg/src/augustus.cc:503:12: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
errorfile.open(errorfilename.c_str());
data/augustus-3.3.3+dfsg/src/codonMSA.cc:108:17: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
Alignmentfile.open(filename.c_str(), ifstream::in);
data/augustus-3.3.3+dfsg/src/compgenepred.cc:340:16: [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).
codonAli.open(outdir + "orthoexons_codonAlignment.maf");
data/augustus-3.3.3+dfsg/src/consensusFinder.cc:58:17: [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).
pattern_size = atoi(optarg);
data/augustus-3.3.3+dfsg/src/consensusFinder.cc:64:10: [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).
start = atoi(optarg);
data/augustus-3.3.3+dfsg/src/consensusFinder.cc:67:8: [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).
end = atoi(optarg);
data/augustus-3.3.3+dfsg/src/consensusFinder.cc:73:25: [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).
max_allowed_mismatch = atoi(optarg);
data/augustus-3.3.3+dfsg/src/consensusFinder.cc:76:18: [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).
no_iterations = atoi(optarg);
data/augustus-3.3.3+dfsg/src/contTimeMC.cc:192:14: [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).
blosumfile.open(filename.c_str(), ifstream::in);
data/augustus-3.3.3+dfsg/src/contentmodel.cc:77:5: [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 nucs[4]={'a', 'c', 'g' ,'t'};
data/augustus-3.3.3+dfsg/src/curve2hints.cc:64:11: [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).
c_thresh=atoi(optarg);
data/augustus-3.3.3+dfsg/src/curve2hints.cc:67:12: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
chunksize=atoi(optarg);
data/augustus-3.3.3+dfsg/src/etraining.cc:163:9: [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 statestring[256];
data/augustus-3.3.3+dfsg/src/etraining.cc:164:9: [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( statestring, "/EHMMTraining/state%02d", i );
data/augustus-3.3.3+dfsg/src/exon_seg.cc:224:12: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
start=atoi(fileline.substr(0,find1).c_str());
data/augustus-3.3.3+dfsg/src/exon_seg.cc:226:10: [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).
end=atoi(fileline.substr(0,find1).c_str());
data/augustus-3.3.3+dfsg/src/exon_seg.cc:506:9: [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).
span=atoi(temp_string.substr(5,found-5).c_str());
data/augustus-3.3.3+dfsg/src/exon_seg.cc:516:9: [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).
step=atoi(temp_string.substr(5,found-5).c_str());
data/augustus-3.3.3+dfsg/src/exon_seg.cc:530:10: [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).
start=atoi(temp_string.substr(6,found-6).c_str());
data/augustus-3.3.3+dfsg/src/exon_seg.cc:588:8: [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).
pos=atoi(fileline.substr(0,found+1).c_str());
data/augustus-3.3.3+dfsg/src/exon_seg.cc:589:8: [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).
val=atoi(fileline.substr(found).c_str());
data/augustus-3.3.3+dfsg/src/exon_seg.cc:594:8: [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).
val=atoi(fileline.c_str());
data/augustus-3.3.3+dfsg/src/exonmodel.cc:419:11: [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).
istrm.open(filename.c_str(), ifstream::in);
data/augustus-3.3.3+dfsg/src/exonmodel.cc:478:2: [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 zusString[6];
data/augustus-3.3.3+dfsg/src/exonmodel.cc:479:2: [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(zusString, "[%d]", parIndex);
data/augustus-3.3.3+dfsg/src/exonmodel.cc:607:9: [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).
istrm.open(filename.c_str(), ifstream::in);
data/augustus-3.3.3+dfsg/src/exonmodel.cc:666:5: [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 zusString[6];
data/augustus-3.3.3+dfsg/src/exonmodel.cc:671:7: [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(zusString, "[%d]", idx+1);
data/augustus-3.3.3+dfsg/src/extrinsicinfo.cc:2041:8: [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).
datei.open(filename.c_str());
data/augustus-3.3.3+dfsg/src/extrinsicinfo.cc:2044:12: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
datei.open(altfname.c_str());
data/augustus-3.3.3+dfsg/src/extrinsicinfo.cc:2123:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[256];
data/augustus-3.3.3+dfsg/src/extrinsicinfo.cc:2250:8: [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).
datei.open(filename);
data/augustus-3.3.3+dfsg/src/fasta.cc:52:2: [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(name, "unnamed-%d", unnamedcount);
data/augustus-3.3.3+dfsg/src/fasta.cc:103:2: [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(name, "unnamed-%d", unnamedcount);
data/augustus-3.3.3+dfsg/src/fasta.cc:172:9: [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(name, "unnamed-%d", unnamedcount);
data/augustus-3.3.3+dfsg/src/genbank.cc:352:4: [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 buffer [140];
data/augustus-3.3.3+dfsg/src/genbank.cc:353:4: [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, "Sequence was longer than the expected %d bp. Please compare the line 'source 1..X' with the actual sequence length.", pos.seqlength);
data/augustus-3.3.3+dfsg/src/genbank.cc:375:3: [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 tmp[GBMAXLINELEN] = { '\0' }; // need more than 4200 chars for human muscle gene TTN
data/augustus-3.3.3+dfsg/src/genbank.cc:420:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[GBMAXLINELEN];
data/augustus-3.3.3+dfsg/src/genbank.cc:530:9: [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).
ifstrm.open(fname.c_str());
data/augustus-3.3.3+dfsg/src/genbank.cc:647:5: [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[GBMAXLINELEN];
data/augustus-3.3.3+dfsg/src/genbank.cc:677:5: [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[GBMAXLINELEN];
data/augustus-3.3.3+dfsg/src/geneticcode.cc:389:5: [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 bases[5] = "acgt"; // 0->a, 1->c, 2->g, 3->t
data/augustus-3.3.3+dfsg/src/genomicMSA.cc:77:19: [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).
Alignmentfile.open(alignFilename.c_str(), ifstream::in);
data/augustus-3.3.3+dfsg/src/genomicMSA.cc:823:15: [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 start = atoi(s.substr(pos1+1, pos2-pos1-1).c_str());
data/augustus-3.3.3+dfsg/src/genomicMSA.cc:824:14: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
int stop = atoi(s.substr(pos2+1).c_str());
data/augustus-3.3.3+dfsg/src/getSeq.cc:65:25: [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).
start = atoi(optarg);
data/augustus-3.3.3+dfsg/src/getSeq.cc:68:23: [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).
end = atoi(optarg);
data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/gtest-port.h:2126:10: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
return fopen(path, mode);
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-death-test.cc:347:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[256];
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-death-test.cc:770:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char executable_path[_MAX_PATH + 1]; // NOLINT
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-death-test.cc:1302:22: [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).
const int cwd_fd = open(".", O_RDONLY);
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-filepath.cc:101:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char cwd[GTEST_PATH_MAX_ + 1] = { '\0' };
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-filepath.cc:104:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char cwd[GTEST_PATH_MAX_ + 1] = { '\0' };
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-port.cc:222:18: [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).
const int fd = open("/proc/self/as", O_RDONLY);
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-port.cc:1001:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buffer, regex, len);
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-port.cc:1075:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp_dir_path[MAX_PATH + 1] = { '\0' }; // NOLINT
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-port.cc:1076:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp_file_path[MAX_PATH + 1] = { '\0' }; // NOLINT
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-port.cc:1113:29: [2] (tmpfile) mkstemp:
Potential for temporary file vulnerability in some circumstances. Some
older Unix-like systems create temp files with permission to write by all
by default, so be sure to set the umask to override this. Also, some older
Unix systems might fail to use O_EXCL when opening the file, so make sure
that O_EXCL is used by the library (CWE-377).
const int captured_fd = mkstemp(name_template);
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-printers.cc:65:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char text[5] = "";
data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:887:7: [2] (buffer) MultiByteToWideChar:
Requires maximum length in CHARACTERS, not bytes (CWE-120).
MultiByteToWideChar(CP_ACP, 0, ansi, length, nullptr, 0);
data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:889:3: [2] (buffer) MultiByteToWideChar:
Requires maximum length in CHARACTERS, not bytes (CWE-120).
MultiByteToWideChar(CP_ACP, 0, ansi, length,
data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:1698:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char error_text[kBufSize] = { '\0' };
data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:1782:3: [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 str[5]; // Big enough for the largest valid code point.
data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:4390:5: [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 tmp[1024];
data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:4396:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[1024];
data/augustus-3.3.3+dfsg/src/graph.cc:951:10: [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).
file.open((filename).c_str());
data/augustus-3.3.3+dfsg/src/graph.cc:1053:10: [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).
file.open((filename).c_str());
data/augustus-3.3.3+dfsg/src/graph.cc:1223:5: [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 joinedCodon[4] = "";
data/augustus-3.3.3+dfsg/src/hints.cc:76:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buff[1024];
data/augustus-3.3.3+dfsg/src/hints.cc:77:5: [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 copybuff[1024];
data/augustus-3.3.3+dfsg/src/hints.cc:105:22: [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).
feature.start = atoi(temp);
data/augustus-3.3.3+dfsg/src/hints.cc:110:20: [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).
feature.end = atoi(temp);
data/augustus-3.3.3+dfsg/src/hints.cc:184:25: [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).
feature.priority = atoi(spos);
data/augustus-3.3.3+dfsg/src/hints.cc:195:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
feature.mult = atoi(spos);
data/augustus-3.3.3+dfsg/src/igenicmodel.cc:96:2: [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 zusString[6];
data/augustus-3.3.3+dfsg/src/igenicmodel.cc:97:2: [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(zusString, "[%d]", parIndex);
data/augustus-3.3.3+dfsg/src/igenicmodel.cc:157:2: [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 zusString[6];
data/augustus-3.3.3+dfsg/src/igenicmodel.cc:162:4: [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(zusString, "[%d]", idx+1);
data/augustus-3.3.3+dfsg/src/igenictrain.cc:106:2: [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 buff[100000];
data/augustus-3.3.3+dfsg/src/intronmodel.cc:249:2: [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 zusString[6];
data/augustus-3.3.3+dfsg/src/intronmodel.cc:250:2: [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(zusString, "[%d]", parIndex);
data/augustus-3.3.3+dfsg/src/intronmodel.cc:369:2: [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 zusString[16];
data/augustus-3.3.3+dfsg/src/intronmodel.cc:380:4: [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(zusString, "[%d]", idx+1);
data/augustus-3.3.3+dfsg/src/introntrain.cc:184:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buff[400];
data/augustus-3.3.3+dfsg/src/load2db.cc:82:18: [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).
chunksize = atoi(optarg);
data/augustus-3.3.3+dfsg/src/load2db.cc:140:9: [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).
ifstrm.open(filename.c_str());
data/augustus-3.3.3+dfsg/src/load2sqlitedb.cc:68:18: [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).
chunksize = atoi(optarg);
data/augustus-3.3.3+dfsg/src/load2sqlitedb.cc:157:9: [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).
ifstrm.open(fastafile.c_str());
data/augustus-3.3.3+dfsg/src/merkmal.cc:601:6: [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(suffix, "%d", round);
data/augustus-3.3.3+dfsg/src/motif.cc:421:5: [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 bases[5] = "acgt"; // 0->a, 1->c, 2->g, 3->t
data/augustus-3.3.3+dfsg/src/namgene.cc:632:6: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (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[38];
data/augustus-3.3.3+dfsg/src/namgene.cc:633:6: [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, "%.30s.g%d", seqname, geneid);
data/augustus-3.3.3+dfsg/src/namgene.cc:850:7: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (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 gr[16];
data/augustus-3.3.3+dfsg/src/namgene.cc:851:7: [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(gr, "s%d-", (i+1));
data/augustus-3.3.3+dfsg/src/namgene.cc:1325:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
istrm.open(fname.c_str());
data/augustus-3.3.3+dfsg/src/namgene.cc:1334:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
istrm.open(fname.c_str());
data/augustus-3.3.3+dfsg/src/namgene.cc:1402:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
istrm.open(fname.c_str());
data/augustus-3.3.3+dfsg/src/namgene.cc:1410:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
istrm.open(fname.c_str());
data/augustus-3.3.3+dfsg/src/parser/parse.cc:696:53: [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).
Treenode *temp = new Treenode(pspecies->at(atoi(d_scanner.matched().c_str())-1));
data/augustus-3.3.3+dfsg/src/phylotree.cc:68:8: [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).
fb.open(filename.c_str(),ios::in);
data/augustus-3.3.3+dfsg/src/phylotree.cc:110:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[256];
data/augustus-3.3.3+dfsg/src/phylotree.cc:202:7: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
file.open(filename.c_str());
data/augustus-3.3.3+dfsg/src/phylotree.cc:232:22: [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).
tuple.push_back(atoi((labelpattern.substr(i,1)).c_str()));
data/augustus-3.3.3+dfsg/src/pp_prepare_align.cc:66:6: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
i = atoi(envval);
data/augustus-3.3.3+dfsg/src/properties.cc:311:10: [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).
strm.open( filename.c_str() );
data/augustus-3.3.3+dfsg/src/properties.cc:322:11: [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).
strm.open(filename.c_str());
data/augustus-3.3.3+dfsg/src/properties.cc:726:5: [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[16384];
data/augustus-3.3.3+dfsg/src/randseqaccess.cc:54:5: [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[1024];
data/augustus-3.3.3+dfsg/src/randseqaccess.cc:65:15: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
datei.open(filename.c_str());
data/augustus-3.3.3+dfsg/src/randseqaccess.cc:147:15: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
datei.open(filename);
data/augustus-3.3.3+dfsg/src/randseqaccess.cc:360:2: [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 buf[256];
data/augustus-3.3.3+dfsg/src/randseqaccess.cc:392:19: [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 MysqlAccess::open(){
data/augustus-3.3.3+dfsg/src/speciesgraph.cc:749:10: [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).
file.open((filename).c_str());
data/augustus-3.3.3+dfsg/src/sqliteDB.cc:16:16: [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 SQLiteDB::open(OpenMode mode){
data/augustus-3.3.3+dfsg/src/train_logReg_param.cc:323:15: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
paramfile.open(Properties::getProperty("param_outfile"));
data/augustus-3.3.3+dfsg/src/train_logReg_param.cc:325:15: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
paramfile.open(Constant::configPath + "/cgp/log_reg_parameters_trained.cfg");
data/augustus-3.3.3+dfsg/src/train_logReg_param.cc:545:13: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
trainfile.open(filename, ifstream::in);
data/augustus-3.3.3+dfsg/src/train_logReg_param.cc:631:11: [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).
reffile.open(Constant::referenceFile, ifstream::in);
data/augustus-3.3.3+dfsg/src/types.cc:488:3: [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 dnamap[5] = "acgt"; // 0->a, 1->c, 2->g, 3->t
data/augustus-3.3.3+dfsg/src/utrmodel.cc:444:5: [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 zusString[6];
data/augustus-3.3.3+dfsg/src/utrmodel.cc:445:5: [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(zusString, "[%d]", parIndex);
data/augustus-3.3.3+dfsg/src/utrmodel.cc:605:5: [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 zusString[16]; // more than necessary, but avoids a compiler warning
data/augustus-3.3.3+dfsg/src/utrmodel.cc:609:7: [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(zusString, "[%d]", idx+1);
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:138:22: [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).
for (i=0;i < strlen(input); i++)
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:298:4: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(oldname,tokens[13],TOKEN_SIZE-1);
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:310:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name,tokens[13],TOKEN_SIZE -1);
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:327:6: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(completedChromosomes[completedChromosomeCount-1],oldname,TOKEN_SIZE-1);
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:334:6: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(oldname,name,TOKEN_SIZE-1);
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:426:4: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(oldname,tokens[1],TOKEN_SIZE -1);
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:434:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name,tokens[1],TOKEN_SIZE-1);
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:454:6: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(completedChromosomes[completedChromosomeCount-1],oldname,TOKEN_SIZE-1);
data/augustus-3.3.3+dfsg/auxprogs/aln2wig/aln2wig.c:460:6: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(oldname,name,TOKEN_SIZE-1);
data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/compileSpliceCands.c:212:21: [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).
checkstring=calloc(strlen(chromosomename)+2,1);
data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/compileSpliceCands.c:216:2: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
strncat(checkstring,chromosomename,strlen(chromosomename));
data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/compileSpliceCands.c:216:37: [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).
strncat(checkstring,chromosomename,strlen(chromosomename));
data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/compileSpliceCands.c:246:16: [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).
line_length=strlen(line);
data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/compileSpliceCands.c:292:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(d->name,tokens[0],LINEBUFFER);
data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/compileSpliceCands.c:518:22: [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).
chromosomeLength=strlen(actualChromosome);
data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/compileSpliceCands.c:519:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(oldname,tmpData->name,LINEBUFFER);
data/augustus-3.3.3+dfsg/auxprogs/compileSpliceCands/compileSpliceCands.c:551:23: [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).
chromosomeLength=strlen(actualChromosome);
data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/filterBam.cc:234:19: [1] (buffer) strlen:
Does not handle 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 ((unsigned)strlen(pairBedFile) > 0 && line%10000000 == 0)
data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/filterBam.cc:458:16: [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).
if ((unsigned)strlen(pairBedFile) > 0)
data/augustus-3.3.3+dfsg/auxprogs/filterBam/src/filterBam.cc:1428:8: [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(pairBedFile)>0)
data/augustus-3.3.3+dfsg/auxprogs/homGeneMapping/src/sqliteDB.cc:105:43: [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).
if(sqlite3_bind_text(stmt, idx, text, strlen(text), NULL) != SQLITE_OK){
data/augustus-3.3.3+dfsg/auxprogs/joingenes/jg_ios.cpp:79:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(copybuff, buff, 1014);
data/augustus-3.3.3+dfsg/auxprogs/joingenes/jg_ios.cpp:148:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(attribute, temp, 300);
data/augustus-3.3.3+dfsg/auxprogs/joingenes/jg_ios.cpp:251:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(copybuff, buff, 1014);
data/augustus-3.3.3+dfsg/auxprogs/joingenes/jg_transcript.cpp:101:21: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
list<Transcript*> equal;
data/augustus-3.3.3+dfsg/auxprogs/joingenes/jg_transcript.cpp:138:7: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
equal.push_back(*it);
data/augustus-3.3.3+dfsg/auxprogs/joingenes/jg_transcript.cpp:151:15: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
saveOverlap(equal, filenameEqual, properties);
data/augustus-3.3.3+dfsg/src/augustus.cc:392:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
<< strlen(curseq->sequence) << ", name = "
data/augustus-3.3.3+dfsg/src/baumwelch.cc:160:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(td->seq + curpos, curSeq->sequence + exon->begin, cplength);
data/augustus-3.3.3+dfsg/src/baumwelch.cc:391:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(seq, td->seq, td->seqLen);
data/augustus-3.3.3+dfsg/src/baumwelch.cc:454:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (i != s2i_dummy.read(in))
data/augustus-3.3.3+dfsg/src/contTimeMC.cc:321:13: [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(e1)/3; // number of nucleotide triples
data/augustus-3.3.3+dfsg/src/contTimeMC.cc:337:23: [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 (!e1 || !e2 || strlen(e1) != strlen(e2) || strlen(e1)%3 != 0)
data/augustus-3.3.3+dfsg/src/contTimeMC.cc:337:37: [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).
if (!e1 || !e2 || strlen(e1) != strlen(e2) || strlen(e1)%3 != 0)
data/augustus-3.3.3+dfsg/src/contTimeMC.cc:337:51: [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 (!e1 || !e2 || strlen(e1) != strlen(e2) || strlen(e1)%3 != 0)
data/augustus-3.3.3+dfsg/src/contTimeMC.cc:352:13: [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(e1)/3; // number of nucleotide triples
data/augustus-3.3.3+dfsg/src/etraining.cc:353:30: [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).
char *newSeqName = new char[strlen(multiannoseq->sequence)+7];
data/augustus-3.3.3+dfsg/src/exoncand.cc:155:13: [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(dna);
data/augustus-3.3.3+dfsg/src/exonmodel.cc:498:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2i.read(istrm);
data/augustus-3.3.3+dfsg/src/exonmodel.cc:512:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
transInitMotif->read(istrm);
data/augustus-3.3.3+dfsg/src/exonmodel.cc:523:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
etMotif[0]->read(istrm);
data/augustus-3.3.3+dfsg/src/exonmodel.cc:526:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
etMotif[1]->read(istrm);
data/augustus-3.3.3+dfsg/src/exonmodel.cc:529:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
etMotif[2]->read(istrm);
data/augustus-3.3.3+dfsg/src/exonmodel.cc:551:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2i_e.read(istrm);
data/augustus-3.3.3+dfsg/src/exonmodel.cc:571:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2i_e.read(istrm);
data/augustus-3.3.3+dfsg/src/exonmodel.cc:586:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2i_e.read(istrm);
data/augustus-3.3.3+dfsg/src/exonmodel.cc:690:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2i.read(istrm);
data/augustus-3.3.3+dfsg/src/exonmodel.cc:703:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
GCtransInitMotif[idx].read(istrm);
data/augustus-3.3.3+dfsg/src/exonmodel.cc:711:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
GCtransInitBinProbs[idx].read(istrm);
data/augustus-3.3.3+dfsg/src/exonmodel.cc:717:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
GCetMotif[idx][0]->read(istrm);
data/augustus-3.3.3+dfsg/src/exonmodel.cc:719:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
GCetMotif[idx][1]->read(istrm);
data/augustus-3.3.3+dfsg/src/exonmodel.cc:721:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
GCetMotif[idx][2]->read(istrm);
data/augustus-3.3.3+dfsg/src/exonmodel.cc:744:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2i_e.read(istrm);
data/augustus-3.3.3+dfsg/src/exonmodel.cc:766:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2i_e.read(istrm);
data/augustus-3.3.3+dfsg/src/exonmodel.cc:781:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2i_e.read(istrm);
data/augustus-3.3.3+dfsg/src/extrinsicinfo.cc:474:15: [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).
int len = strlen(seq->sequence);
data/augustus-3.3.3+dfsg/src/extrinsicinfo.cc:599:15: [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).
int len = strlen(seq->sequence);
data/augustus-3.3.3+dfsg/src/extrinsicinfo.cc:2108:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
typeInfo[type].read(datei, esource(skey));
data/augustus-3.3.3+dfsg/src/extrinsicinfo.cc:2131:21: [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).
while (i< (int) strlen(buf)){
data/augustus-3.3.3+dfsg/src/extrinsicinfo.cc:2132:38: [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).
while(!isalpha(buf[i]) && i < (int) strlen(buf)){
data/augustus-3.3.3+dfsg/src/extrinsicinfo.cc:2135:16: [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).
if (i < (int) strlen(buf)){
data/augustus-3.3.3+dfsg/src/extrinsicinfo.cc:2152:21: [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).
while (i< (int) strlen(buf)){
data/augustus-3.3.3+dfsg/src/extrinsicinfo.cc:2153:38: [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).
while(!isalpha(buf[i]) && i < (int) strlen(buf)){
data/augustus-3.3.3+dfsg/src/extrinsicinfo.cc:2156:16: [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).
if (i < (int) strlen(buf)){
data/augustus-3.3.3+dfsg/src/fasta.cc:48:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name, line.c_str()+1, endpos);
data/augustus-3.3.3+dfsg/src/fasta.cc:99:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name, line.c_str()+1, endpos);
data/augustus-3.3.3+dfsg/src/fasta.cc:168:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(name, line.c_str()+1, endpos);
data/augustus-3.3.3+dfsg/src/genbank.cc:63:48: [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).
annoseq->bc.addSequence(annoseq->sequence, strlen(annoseq->sequence) );
data/augustus-3.3.3+dfsg/src/genbank.cc:69:11: [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).
idtmp += strlen("LOCUS");
data/augustus-3.3.3+dfsg/src/genbank.cc:672:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
sin.read( pos.buffer, pos.length );
data/augustus-3.3.3+dfsg/src/genbank.cc:682:61: [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).
if ((!sin.eof() && (sin.rdstate() & ios_base::failbit)) || strlen(buf) >= GBMAXLINELEN-2){
data/augustus-3.3.3+dfsg/src/gene.cc:1407:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(exonseq + curpos, annoseq->sequence - (noOffset? 0 : annoseq->offset) + exon->begin, cplength);
data/augustus-3.3.3+dfsg/src/gene.cc:1425:12: [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).
while (strlen(codingSeq)>3){
data/augustus-3.3.3+dfsg/src/geneticcode.cc:318:18: [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).
unsigned n = strlen(dna);
data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/gtest-port.h:2115:10: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
return strncpy(dest, src, n);
data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/gtest-port.h:2137:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
return static_cast<int>(read(fd, buf, count));
data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/gtest-type-util.h:66:20: [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).
if (s.compare(0, strlen(prefix), prefix) == 0) {
data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/gtest-type-util.h:67:47: [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::string::size_type end = s.find("::", strlen(prefix));
data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/gtest-type-util.h:70:15: [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).
s.erase(strlen("std"), end - strlen("std"));
data/augustus-3.3.3+dfsg/src/googletest/include/gtest/internal/gtest-type-util.h:70:36: [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).
s.erase(strlen("std"), end - strlen("std"));
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-death-test.cc:923:38: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
status_zx = stderr_socket_.read(
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-port.cc:739:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const size_t full_regex_len = strlen(regex) + 10;
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-port.cc:989:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const size_t len = strlen(regex);
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-printers.cc:333:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
PrintCharsAsStringTo(s, strlen(s), os);
data/augustus-3.3.3+dfsg/src/googletest/src/gtest-printers.cc:350:29: [1] (buffer) wcslen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
PrintCharsAsStringTo(s, wcslen(s), os);
data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:885:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int length = strlen(ansi);
data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:1843:34: [1] (buffer) wcslen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
num_chars = static_cast<int>(wcslen(str));
data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:3705:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
segment = next_segment + strlen("]]>");
data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:4294:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
result.reserve(strlen(str) + 1);
data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:5627:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const size_t prefix_len = strlen(prefix);
data/augustus-3.3.3+dfsg/src/googletest/src/gtest.cc:6052:21: [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).
else if (temp_dir[strlen(temp_dir) - 1] == '\\')
data/augustus-3.3.3+dfsg/src/graph.cc:1227:6: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
strncat(joinedCodon, sequence + end1, 1);
data/augustus-3.3.3+dfsg/src/graph.cc:1228:6: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
strncat(joinedCodon, sequence + begin2, 2);
data/augustus-3.3.3+dfsg/src/graph.cc:1231:6: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
strncat(joinedCodon, sequence + end1 - 1, 2);
data/augustus-3.3.3+dfsg/src/graph.cc:1232:6: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
strncat(joinedCodon, sequence + begin2, 1);
data/augustus-3.3.3+dfsg/src/hints.cc:82:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(copybuff, buff, 1014);
data/augustus-3.3.3+dfsg/src/igenicmodel.cc:111:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2i.read(istrm);
data/augustus-3.3.3+dfsg/src/igenicmodel.cc:130:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2i.read(istrm);
data/augustus-3.3.3+dfsg/src/igenicmodel.cc:180:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2i.read(istrm);
data/augustus-3.3.3+dfsg/src/igenicmodel.cc:209:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2i.read(istrm);
data/augustus-3.3.3+dfsg/src/igenictrain.cc:93:30: [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).
if (igenic_end > (int) strlen(sequence)-1)
data/augustus-3.3.3+dfsg/src/igenictrain.cc:94:23: [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).
igenic_end = (int) strlen(sequence)-1;
data/augustus-3.3.3+dfsg/src/igenictrain.cc:111:51: [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).
cout << "reading in sequence of length " << strlen(buff) << endl;
data/augustus-3.3.3+dfsg/src/igenictrain.cc:112:40: [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).
processSequence(buff + k, buff + strlen(buff)-1);
data/augustus-3.3.3+dfsg/src/intronmodel.cc:196:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2i_a.read(istrm);
data/augustus-3.3.3+dfsg/src/intronmodel.cc:207:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
assBinProbs.read(istrm);
data/augustus-3.3.3+dfsg/src/intronmodel.cc:217:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int dummy_pn = s2i_d.read(istrm);
data/augustus-3.3.3+dfsg/src/intronmodel.cc:231:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
dssBinProbs.read(istrm);
data/augustus-3.3.3+dfsg/src/intronmodel.cc:271:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2i.read(istrm);
data/augustus-3.3.3+dfsg/src/intronmodel.cc:280:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
assMotif->read(istrm);
data/augustus-3.3.3+dfsg/src/intronmodel.cc:314:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2i_a.read(istrm);
data/augustus-3.3.3+dfsg/src/intronmodel.cc:325:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
assBinProbs.read(istrm);
data/augustus-3.3.3+dfsg/src/intronmodel.cc:335:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int dummy_pn = s2i_d.read(istrm);
data/augustus-3.3.3+dfsg/src/intronmodel.cc:349:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
dssBinProbs.read(istrm);
data/augustus-3.3.3+dfsg/src/intronmodel.cc:400:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2i.read(istrm);
data/augustus-3.3.3+dfsg/src/intronmodel.cc:407:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
GCassMotif[idx].read(istrm);
data/augustus-3.3.3+dfsg/src/intronmodel.cc:1137:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(astr, sequence + base + ass_upwindow_size, Constant::ass_start);
data/augustus-3.3.3+dfsg/src/intronmodel.cc:1138:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(astr + Constant::ass_start, sequence + asspos + ASS_MIDDLE, Constant::ass_end);
data/augustus-3.3.3+dfsg/src/intronmodel.cc:1211:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(astr, sequence + base, Constant::dss_start);
data/augustus-3.3.3+dfsg/src/intronmodel.cc:1212:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(astr + Constant::dss_start, sequence + dsspos + DSS_MIDDLE, Constant::dss_end);
data/augustus-3.3.3+dfsg/src/introntrain.cc:240:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy( astr, dna + pos - ASS_MIDDLE - Constant::ass_start, Constant::ass_start );
data/augustus-3.3.3+dfsg/src/introntrain.cc:241:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy( astr + Constant::ass_start, dna + pos, Constant::ass_end );
data/augustus-3.3.3+dfsg/src/introntrain.cc:276:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy( dstr, dna + pos - Constant::dss_start + 1, Constant::dss_start );
data/augustus-3.3.3+dfsg/src/introntrain.cc:277:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy( dstr + Constant::dss_start, dna + pos + 3, Constant::dss_end );
data/augustus-3.3.3+dfsg/src/introntrain.cc:373:22: [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).
sequence + strlen(sequence) - 1 );
data/augustus-3.3.3+dfsg/src/lldouble.cc:276:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void LLDouble::read( istream& in ){
data/augustus-3.3.3+dfsg/src/merkmal.cc:186:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void BinnedMMGroup::read(ifstream &in){
data/augustus-3.3.3+dfsg/src/motif.cc:41:8: [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).
len = strlen(sequence);
data/augustus-3.3.3+dfsg/src/motif.cc:388:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void Motif::read(ifstream &in){
data/augustus-3.3.3+dfsg/src/motif.cc:545:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
n = strlen(dna);
data/augustus-3.3.3+dfsg/src/namgene.cc:177:16: [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).
int dnalen = strlen( dna );
data/augustus-3.3.3+dfsg/src/namgene.cc:537:16: [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).
int seqlen = strlen(dna);
data/augustus-3.3.3+dfsg/src/namgene.cc:686:13: [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(dna);
data/augustus-3.3.3+dfsg/src/namgene.cc:973:17: [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).
int restlen = strlen(dna+beginPos);
data/augustus-3.3.3+dfsg/src/namgene.cc:1007:36: [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).
groupGaps->push_back(Feature(1, strlen(dna)-1, irpartF, bothstrands, -1, "groups"));
data/augustus-3.3.3+dfsg/src/namgene.cc:1267:13: [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).
countEnd = strlen( dna ) + 100;
data/augustus-3.3.3+dfsg/src/properties.cc:738:8: [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).
pos = strlen(path);
data/augustus-3.3.3+dfsg/src/randseqaccess.cc:797:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ifstrm.read(seq,n);
data/augustus-3.3.3+dfsg/src/sqliteDB.cc:226:43: [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).
if(sqlite3_bind_text(stmt, idx, text, strlen(text), NULL) != SQLITE_OK){
data/augustus-3.3.3+dfsg/src/types.cc:448:27: [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).
endhaystack = haystack + strlen(haystack)-1;
data/augustus-3.3.3+dfsg/src/utrmodel.cc:438:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2ib.read(istrm);
data/augustus-3.3.3+dfsg/src/utrmodel.cc:459:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2i.read(istrm);
data/augustus-3.3.3+dfsg/src/utrmodel.cc:472:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2i.read(istrm);
data/augustus-3.3.3+dfsg/src/utrmodel.cc:485:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2i.read(istrm);
data/augustus-3.3.3+dfsg/src/utrmodel.cc:499:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2iup.read(istrm);
data/augustus-3.3.3+dfsg/src/utrmodel.cc:508:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
tssMotif->read(istrm);
data/augustus-3.3.3+dfsg/src/utrmodel.cc:513:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
tssMotifTATA->read(istrm);
data/augustus-3.3.3+dfsg/src/utrmodel.cc:518:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
tataMotif->read(istrm);
data/augustus-3.3.3+dfsg/src/utrmodel.cc:523:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ttsMotif->read(istrm);
data/augustus-3.3.3+dfsg/src/utrmodel.cc:597:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2ib.read(istrm);
data/augustus-3.3.3+dfsg/src/utrmodel.cc:626:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2i.read(istrm);
data/augustus-3.3.3+dfsg/src/utrmodel.cc:639:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2i.read(istrm);
data/augustus-3.3.3+dfsg/src/utrmodel.cc:652:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2i.read(istrm);
data/augustus-3.3.3+dfsg/src/utrmodel.cc:666:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int pn = s2iup.read(istrm);
data/augustus-3.3.3+dfsg/src/utrmodel.cc:673:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
GCtssMotif[idx].read(istrm);
data/augustus-3.3.3+dfsg/src/utrmodel.cc:675:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
GCtssMotifTATA[idx].read(istrm);
data/augustus-3.3.3+dfsg/src/utrmodel.cc:677:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
GCtataMotif[idx].read(istrm);
data/augustus-3.3.3+dfsg/src/utrmodel.cc:679:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
GCttsMotif[idx].read(istrm);
data/augustus-3.3.3+dfsg/src/utrtrain.cc:186:12: [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).
dnalen = strlen(annoseq->sequence);
ANALYSIS SUMMARY:
Hits = 428
Lines analyzed = 89733 in approximately 2.82 seconds (31834 lines/second)
Physical Source Lines of Code (SLOC) = 62447
Hits@level = [0] 136 [1] 159 [2] 216 [3] 41 [4] 11 [5] 1
Hits@level+ = [0+] 564 [1+] 428 [2+] 269 [3+] 53 [4+] 12 [5+] 1
Hits/KSLOC@level+ = [0+] 9.03166 [1+] 6.85381 [2+] 4.30765 [3+] 0.84872 [4+] 0.192163 [5+] 0.0160136
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.