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/andi-0.13/libs/pfasta.c
Examining data/andi-0.13/libs/pfasta.h
Examining data/andi-0.13/opt/compat-stdlib.h
Examining data/andi-0.13/opt/compat-string.h
Examining data/andi-0.13/opt/reallocarray.c
Examining data/andi-0.13/opt/strchrnul.c
Examining data/andi-0.13/src/andi.c
Examining data/andi-0.13/src/dist_hack.h
Examining data/andi-0.13/src/esa.c
Examining data/andi-0.13/src/esa.h
Examining data/andi-0.13/src/global.h
Examining data/andi-0.13/src/io.c
Examining data/andi-0.13/src/io.h
Examining data/andi-0.13/src/model.c
Examining data/andi-0.13/src/model.h
Examining data/andi-0.13/src/process.c
Examining data/andi-0.13/src/process.h
Examining data/andi-0.13/src/sequence.c
Examining data/andi-0.13/src/sequence.h
Examining data/andi-0.13/test/test_esa.c
Examining data/andi-0.13/test/test_fasta.cxx
Examining data/andi-0.13/test/test_process.c
Examining data/andi-0.13/test/test_seq.c
FINAL RESULTS:
data/andi-0.13/libs/pfasta.c:92:9: [4] (format) snprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
(void)snprintf(errstr_buffer, PF_ERROR_STRING_LENGTH, __VA_ARGS__); \
data/andi-0.13/src/io.c:310:3: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
printf(FLAGS & F_TRUNCATE_NAMES ? "%-10.10s" : "%-10s",
data/andi-0.13/src/io.c:315:4: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
printf(use_scientific ? " %1.4e" : " %1.4f", DD(i, j));
data/andi-0.13/src/andi.c:92:11: [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.
int c = getopt_long(argc, argv, "jvht:p:m:b:l", long_options,
data/andi-0.13/test/test_fasta.cxx:27:17: [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((check = getopt(argc, argv, "s:l:L:d:r")) != -1){
data/andi-0.13/libs/pfasta.c:48:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
thread_local char errstr_buffer[PF_ERROR_STRING_LENGTH];
data/andi-0.13/libs/pfasta.c:209:3: [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(&chunk, begin + vec_offset * vec_size, vec_size);
data/andi-0.13/libs/pfasta.c:532:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ds->str + ds->count, str, length);
data/andi-0.13/src/esa.c:79:2: [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 str[CACHE_LENGTH + 1];
data/andi-0.13/src/io.c:104:40: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *file = strcmp(file_name, "-") ? fopen(file_name, "r") : stdin;
data/andi-0.13/src/io.c:200:28: [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).
strcmp(file_name, "-") ? open(file_name, O_RDONLY) : STDIN_FILENO;
data/andi-0.13/src/sequence.c:109:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(next, it->S, it->len);
data/andi-0.13/src/sequence.c:114:3: [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(next, it->S, it->len);
data/andi-0.13/src/sequence.c:186:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(rev + len + 1, s, len + 1);
data/andi-0.13/test/test_esa.c:178:2: [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 str[MAX_DEPTH+1];
data/andi-0.13/test/test_fasta.cxx:76:2: [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[line_length+1];
data/andi-0.13/libs/pfasta.c:144:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ssize_t count = read(pp->file_descriptor, pp->buffer, BUFFER_SIZE);
data/andi-0.13/src/andi.c:288:37: [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 ((FLAGS & F_TRUNCATE_NAMES) && strlen(seq->name) > 10) {
data/andi-0.13/src/dist_hack.h:78:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
#pragma omp atomic read
data/andi-0.13/src/io.c:132:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(str) == 0) {
data/andi-0.13/src/sequence.c:248:11: [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).
S->len = strlen(S->S);
ANALYSIS SUMMARY:
Hits = 21
Lines analyzed = 3987 in approximately 0.11 seconds (36120 lines/second)
Physical Source Lines of Code (SLOC) = 2366
Hits@level = [0] 10 [1] 5 [2] 11 [3] 2 [4] 3 [5] 0
Hits@level+ = [0+] 31 [1+] 21 [2+] 16 [3+] 5 [4+] 3 [5+] 0
Hits/KSLOC@level+ = [0+] 13.1023 [1+] 8.87574 [2+] 6.76247 [3+] 2.11327 [4+] 1.26796 [5+] 0
Dot directories skipped = 1 (--followdotdir overrides)
Minimum risk level = 1
Not every hit is necessarily a security vulnerability.
There may be other security vulnerabilities; review your code!
See 'Secure Programming HOWTO'
(https://dwheeler.com/secure-programs) for more information.