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/libssw-1.1/src/example.c
Examining data/libssw-1.1/src/example.cpp
Examining data/libssw-1.1/src/kseq.h
Examining data/libssw-1.1/src/ssw_cpp.cpp
Examining data/libssw-1.1/src/ssw_cpp.h
Examining data/libssw-1.1/src/ssw.c
Examining data/libssw-1.1/src/ssw.h
Examining data/libssw-1.1/src/main.c
Examining data/libssw-1.1/src/sswjni.c
Examining data/libssw-1.1/debian/include/simde/check.h
Examining data/libssw-1.1/debian/include/simde/debug-trap.h
Examining data/libssw-1.1/debian/include/simde/hedley.h
Examining data/libssw-1.1/debian/include/simde/simde-arch.h
Examining data/libssw-1.1/debian/include/simde/simde-common.h
Examining data/libssw-1.1/debian/include/simde/x86/mmx.h
Examining data/libssw-1.1/debian/include/simde/x86/sse.h
Examining data/libssw-1.1/debian/include/simde/x86/sse2.h
FINAL RESULTS:
data/libssw-1.1/debian/include/simde/check.h:60:40: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
# define simde_errorf(format, ...) (fprintf(stderr, format, __VA_ARGS__), abort())
data/libssw-1.1/debian/include/simde/hedley.h:1207:79: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
# define HEDLEY_PRINTF_FORMAT(string_idx,first_to_check) __declspec(vaformat(printf,string_idx,first_to_check))
data/libssw-1.1/src/main.c:288:14: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
case 'a': strcpy(mat_name, optarg); break;
data/libssw-1.1/src/main.c:282:14: [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 ((l = getopt(argc, argv, "m:x:o:e:a:f:pcrsh")) >= 0) {
data/libssw-1.1/debian/include/simde/hedley.h:1679:25: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
((struct { char v[sizeof(void) * 2]; } *) 1) \
data/libssw-1.1/debian/include/simde/simde-common.h:499:44: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define simde_memcpy(dest, src, n) memcpy(dest, src, n)
data/libssw-1.1/debian/include/simde/simde-common.h:513:42: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
# define simde_memcpy(dest, src, n) memcpy(dest, src, n)
data/libssw-1.1/src/example.c:108:15: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static const char ref_seq[40] = {'C', 'A', 'G', 'C', 'C', 'T', 'T', 'T', 'C', 'T', 'G', 'A', 'C', 'C', 'C', 'G', 'G', 'A', 'A', 'A', 'T',
data/libssw-1.1/src/example.c:110:15: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static const char read_seq[16] = {'C', 'T', 'G', 'A', 'G', 'C', 'C', 'G', 'G', 'T', 'A', 'A', 'A', 'T', 'C', '\0'}; // read sequence
data/libssw-1.1/src/kseq.h:123:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(str->s + str->l, ks->buf + ks->begin, i - ks->begin); \
data/libssw-1.1/src/main.c:221:2: [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 mat_name[16];
data/libssw-1.1/src/main.c:284:22: [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).
case 'm': match = atoi(optarg); break;
data/libssw-1.1/src/main.c:285:25: [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).
case 'x': mismatch = atoi(optarg); break;
data/libssw-1.1/src/main.c:286:25: [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).
case 'o': gap_open = atoi(optarg); break;
data/libssw-1.1/src/main.c:287:30: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'e': gap_extension = atoi(optarg); break;
data/libssw-1.1/src/main.c:289:23: [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).
case 'f': filter = atoi(optarg); break;
data/libssw-1.1/src/main.c:329:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *f_mat = fopen(mat_name, "r");
data/libssw-1.1/src/main.c:330:3: [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 line[128];
data/libssw-1.1/src/main.c:337:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[4], *s = str;
data/libssw-1.1/src/main.c:344:27: [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).
mata[k++] = (int8_t)atoi(str);
data/libssw-1.1/src/main.c:352:26: [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).
mata[k++] = (int8_t)atoi(str);
data/libssw-1.1/src/ssw_cpp.cpp:275:3: [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(score_matrix_, score_matrix, sizeof(int8_t) * score_matrix_size_ * score_matrix_size_);
data/libssw-1.1/src/ssw_cpp.cpp:277:3: [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(translation_matrix_, translation_matrix, sizeof(int8_t) * translation_matrix_size);
data/libssw-1.1/src/ssw_cpp.cpp:454:3: [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(score_matrix_, score_matrix, sizeof(int8_t) * score_matrix_size_ * score_matrix_size_);
data/libssw-1.1/src/ssw_cpp.cpp:456:3: [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(translation_matrix_, translation_matrix, sizeof(int8_t) * translation_matrix_size);
data/libssw-1.1/src/ssw_cpp.cpp:466:3: [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(translation_matrix_, kBaseTranslation, sizeof(int8_t) * SizeOfArray(kBaseTranslation));
data/libssw-1.1/src/sswjni.c:14:23: [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.
int charsPrinted = sprintf(currentBufferPosition, "%d%c", cigar_int_to_len(align->cigar[i]), cigar_int_to_op(align->cigar[i]));
data/libssw-1.1/src/example.c:137:57: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
for (m = 0; m < 4; ++m) mat[k++] = l == m ? match : - mismatch; /* weight_match : -weight_mismatch */
data/libssw-1.1/src/main.c:36:16: [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).
int32_t end = strlen(seq), start = 0;
data/libssw-1.1/src/main.c:60:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const kseq_t* read,
data/libssw-1.1/src/main.c:66:10: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
int32_t mismatch;
data/libssw-1.1/src/main.c:317:65: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
for (m = 0; LIKELY(m < 4); ++m) mata[k++] = l == m ? match : -mismatch; /* weight_match : -weight_mismatch */
data/libssw-1.1/src/ssw.c:71:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int32_t read; //alignment ending position on read, 0-based
data/libssw-1.1/src/ssw.c:82:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const int8_t* read;
data/libssw-1.1/src/ssw.c:565:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const int8_t* read,
data/libssw-1.1/src/ssw.c:636:39: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
temp2 = h_b[d] + mat[ref[j] * n + read[i]];
data/libssw-1.1/src/ssw.c:765:36: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
s_profile* ssw_init (const int8_t* read, const int32_t readLen, const int8_t* mat, const int32_t n, const int8_t score_size) {
data/libssw-1.1/src/ssw.c:778:30: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
p->profile_byte = qP_byte (read, mat, readLen, n, bias);
data/libssw-1.1/src/ssw.c:780:69: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (score_size == 1 || score_size == 2) p->profile_word = qP_word (read, mat, readLen, n);
data/libssw-1.1/src/ssw.c:781:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
p->read = read;
data/libssw-1.1/src/ssw.c:840:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
r->read_end1 = bests[0].read;
data/libssw-1.1/src/ssw.c:852:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read_reverse = seq_reverse(prof->read, r->read_end1);
data/libssw-1.1/src/ssw.c:863:51: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
r->read_begin1 = r->read_end1 - bests_reverse[0].read;
data/libssw-1.1/src/ssw.c:930:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const char* read,
data/libssw-1.1/src/ssw.c:947:65: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
fprintf(stderr, "ref[%d]: %c\tread[%d]: %c\n", j, *ref, j, *read);
data/libssw-1.1/src/ssw.c:948:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (*ref != *read) {
data/libssw-1.1/src/ssw.c:960:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
++ read;
data/libssw-1.1/src/ssw.h:76:36: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
s_profile* ssw_init (const int8_t* read, const int32_t readLen, const int8_t* mat, const int32_t n, const int8_t score_size);
data/libssw-1.1/src/ssw.h:151:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const char* read,
data/libssw-1.1/src/ssw_cpp.cpp:331:19: [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).
int query_len = strlen(query);
data/libssw-1.1/src/ssw_cpp.cpp:366:19: [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).
int query_len = strlen(query);
data/libssw-1.1/src/sswjni.c:38:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
jbyteArray read, jbyteArray matrix, jint matrixSize, jint score_size,
data/libssw-1.1/src/sswjni.c:46:53: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
jbyte* readPtr = (*env)->GetByteArrayElements(env, read, NULL);
data/libssw-1.1/src/sswjni.c:47:46: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
jsize readLen = (*env)->GetArrayLength(env, read);
data/libssw-1.1/src/sswjni.c:57:40: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(*env)->ReleaseByteArrayElements(env, read, readPtr, JNI_ABORT);
ANALYSIS SUMMARY:
Hits = 55
Lines analyzed = 17590 in approximately 0.47 seconds (37445 lines/second)
Physical Source Lines of Code (SLOC) = 15027
Hits@level = [0] 79 [1] 28 [2] 23 [3] 1 [4] 3 [5] 0
Hits@level+ = [0+] 134 [1+] 55 [2+] 27 [3+] 4 [4+] 3 [5+] 0
Hits/KSLOC@level+ = [0+] 8.91728 [1+] 3.66008 [2+] 1.79677 [3+] 0.266188 [4+] 0.199641 [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.