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/stringtie-2.1.4+ds/rlink.cpp
Examining data/stringtie-2.1.4+ds/tablemaker.h
Examining data/stringtie-2.1.4+ds/gclib/proc_mem.cpp
Examining data/stringtie-2.1.4+ds/gclib/gff.h
Examining data/stringtie-2.1.4+ds/gclib/codons.cpp
Examining data/stringtie-2.1.4+ds/gclib/GFastaIndex.cpp
Examining data/stringtie-2.1.4+ds/gclib/GBam.cpp
Examining data/stringtie-2.1.4+ds/gclib/gdna.cpp
Examining data/stringtie-2.1.4+ds/gclib/GArgs.cpp
Examining data/stringtie-2.1.4+ds/gclib/codons.h
Examining data/stringtie-2.1.4+ds/gclib/GThreads.h
Examining data/stringtie-2.1.4+ds/gclib/GStr.cpp
Examining data/stringtie-2.1.4+ds/gclib/GBase.cpp
Examining data/stringtie-2.1.4+ds/gclib/GThreads.cpp
Examining data/stringtie-2.1.4+ds/gclib/GArgs.h
Examining data/stringtie-2.1.4+ds/gclib/GFaSeqGet.cpp
Examining data/stringtie-2.1.4+ds/gclib/GFaSeqGet.h
Examining data/stringtie-2.1.4+ds/gclib/GBam.h
Examining data/stringtie-2.1.4+ds/gclib/GBase.h
Examining data/stringtie-2.1.4+ds/gclib/gff.cpp
Examining data/stringtie-2.1.4+ds/gclib/proc_mem.h
Examining data/stringtie-2.1.4+ds/gclib/gdna.h
Examining data/stringtie-2.1.4+ds/gclib/GFastaIndex.h
Examining data/stringtie-2.1.4+ds/gclib/GBitVec.h
Examining data/stringtie-2.1.4+ds/gclib/GStr.h
Examining data/stringtie-2.1.4+ds/tmerge.h
Examining data/stringtie-2.1.4+ds/rlink.h
Examining data/stringtie-2.1.4+ds/stringtie.cpp
Examining data/stringtie-2.1.4+ds/tablemaker.cpp
Examining data/stringtie-2.1.4+ds/tmerge.cpp
FINAL RESULTS:
data/stringtie-2.1.4+ds/gclib/GBase.cpp:21:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(msg,"%s(%d): ASSERT(%s) failed.\n",filename,lineno,expression);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:37:5: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format, arguments); // if a console is available
data/stringtie-2.1.4+ds/gclib/GBase.cpp:45:5: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr,format,arguments);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:61:5: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr, format , arguments); // if a console is available
data/stringtie-2.1.4+ds/gclib/GBase.cpp:69:5: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(stderr,format,arguments);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:125:3: [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(copy,str);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:197:3: [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(gpath,path);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:354:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(str,newvalue);
data/stringtie-2.1.4+ds/gclib/GBase.h:36:11: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
#ifndef popen
data/stringtie-2.1.4+ds/gclib/GBase.h:37:12: [4] (shell) popen:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
#define popen _popen
data/stringtie-2.1.4+ds/gclib/GBase.h:114:29: [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(stderr, "Error: "); fprintf(stderr, a); \
data/stringtie-2.1.4+ds/gclib/GFaSeqGet.h:243:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(s+slen, gseqname);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:40:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(data->chars, str);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:402:11: [4] (format) vsprintf:
Potential format string problem (CWE-134). Make format string constant.
int len=vsprintf(buf,fmt,arguments);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:419:3: [4] (format) vsprintf:
Potential format string problem (CWE-134). Make format string constant.
vsprintf(buf,fmt,arguments);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:774:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dest, s);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:821:12: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dest, s);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:832:11: [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(dest, s);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:870:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
::strcpy(&data->chars[idx], &my_data->chars[idx+len]);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:899:11: [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(&data->chars[idx+s.length()], &my_data->chars[idx+len]);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:932:11: [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(&data->chars[idx+s_length], &my_data->chars[idx+len]);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:956:11: [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(&data->chars[idx+s.length()], &my_data->chars[idx]);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:981:11: [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(&data->chars[idx+s_length], &my_data->chars[idx]);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1241:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(fTokenDelimiter, delimiter);
data/stringtie-2.1.4+ds/gclib/gff.cpp:1347:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(buf, id);
data/stringtie-2.1.4+ds/gclib/gff.cpp:1349:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(buf+idlen+1, ctg);
data/stringtie-2.1.4+ds/gclib/gff.cpp:1910:7: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(new_attr_name, prefix);
data/stringtie-2.1.4+ds/gclib/gff.cpp:1911:7: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(new_attr_name, attr_name);
data/stringtie-2.1.4+ds/gclib/gff.cpp:2329:5: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(fout,format,arguments);
data/stringtie-2.1.4+ds/gclib/GThreads.cpp:62:3: [3] (misc) InitializeCriticalSection:
Exceptions can be thrown in low-memory situations. Use
InitializeCriticalSectionAndSpinCount instead.
InitializeCriticalSection(&mWaitersCountLock);
data/stringtie-2.1.4+ds/gclib/GThreads.cpp:83:3: [3] (misc) EnterCriticalSection:
On some versions of Windows, exceptions can be thrown in low-memory
situations. Use InitializeCriticalSectionAndSpinCount instead.
EnterCriticalSection(&mWaitersCountLock);
data/stringtie-2.1.4+ds/gclib/GThreads.cpp:99:3: [3] (misc) EnterCriticalSection:
On some versions of Windows, exceptions can be thrown in low-memory
situations. Use InitializeCriticalSectionAndSpinCount instead.
EnterCriticalSection(&mWaitersCountLock);
data/stringtie-2.1.4+ds/gclib/GThreads.cpp:113:3: [3] (misc) EnterCriticalSection:
On some versions of Windows, exceptions can be thrown in low-memory
situations. Use InitializeCriticalSectionAndSpinCount instead.
EnterCriticalSection(&mWaitersCountLock);
data/stringtie-2.1.4+ds/gclib/GThreads.h:191:7: [3] (misc) InitializeCriticalSection:
Exceptions can be thrown in low-memory situations. Use
InitializeCriticalSectionAndSpinCount instead.
InitializeCriticalSection(&mHandle);
data/stringtie-2.1.4+ds/gclib/GThreads.h:214:7: [3] (misc) EnterCriticalSection:
On some versions of Windows, exceptions can be thrown in low-memory
situations. Use InitializeCriticalSectionAndSpinCount instead.
EnterCriticalSection(&mHandle);
data/stringtie-2.1.4+ds/gclib/GThreads.h:280:7: [3] (misc) InitializeCriticalSection:
Exceptions can be thrown in low-memory situations. Use
InitializeCriticalSectionAndSpinCount instead.
InitializeCriticalSection(&mHandle);
data/stringtie-2.1.4+ds/gclib/GThreads.h:306:7: [3] (misc) EnterCriticalSection:
On some versions of Windows, exceptions can be thrown in low-memory
situations. Use InitializeCriticalSectionAndSpinCount instead.
EnterCriticalSection(&mHandle);
data/stringtie-2.1.4+ds/gclib/GThreads.h:379:7: [3] (misc) InitializeCriticalSection:
Exceptions can be thrown in low-memory situations. Use
InitializeCriticalSectionAndSpinCount instead.
InitializeCriticalSection(&mHandle);
data/stringtie-2.1.4+ds/gclib/GThreads.h:419:7: [3] (misc) EnterCriticalSection:
On some versions of Windows, exceptions can be thrown in low-memory
situations. Use InitializeCriticalSectionAndSpinCount instead.
EnterCriticalSection(&mHandle);
data/stringtie-2.1.4+ds/gclib/GThreads.h:626:7: [3] (misc) EnterCriticalSection:
On some versions of Windows, exceptions can be thrown in low-memory
situations. Use InitializeCriticalSectionAndSpinCount instead.
EnterCriticalSection(&mWaitersCountLock);
data/stringtie-2.1.4+ds/gclib/GBam.cpp:24:3: [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((void*)b->data, (void*)odata, b->data_len);
data/stringtie-2.1.4+ds/gclib/GBam.cpp:50:4: [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(realloc_bdata(b, b->core.l_qname), qname, b->core.l_qname);
data/stringtie-2.1.4+ds/gclib/GBam.cpp:69:3: [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(realloc_bdata(b, b->core.l_qname), qname, b->core.l_qname);
data/stringtie-2.1.4+ds/gclib/GBam.cpp:108:14: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void*)(b->data+doff+b->core.n_cigar*4),(void*)after_cigar, after_cigar_len);
data/stringtie-2.1.4+ds/gclib/GBam.cpp:244:14: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(abuf, str + 5, strl - 5);
data/stringtie-2.1.4+ds/gclib/GBam.cpp:326:2: [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(cigar, p, c->n_cigar * sizeof(uint32_t));
data/stringtie-2.1.4+ds/gclib/GBam.cpp:367:38: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
uint8_t* GBamRecord::find_tag(const char tag[2]) {
data/stringtie-2.1.4+ds/gclib/GBam.cpp:371:34: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char GBamRecord::tag_char(const char tag[2]) { //retrieve tag data as single char
data/stringtie-2.1.4+ds/gclib/GBam.cpp:377:35: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char GBamRecord::tag_char1(const char tag[2]) { //just the first char from Z type tags
data/stringtie-2.1.4+ds/gclib/GBam.cpp:387:32: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
int GBamRecord::tag_int(const char tag[2]) { //get the numeric value of tag
data/stringtie-2.1.4+ds/gclib/GBam.cpp:393:36: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
float GBamRecord::tag_float(const char tag[2]) { //get the float value of tag
data/stringtie-2.1.4+ds/gclib/GBam.cpp:399:34: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char* GBamRecord::tag_str(const char tag[2]) { //return string value for a tag
data/stringtie-2.1.4+ds/gclib/GBam.h:32:4: [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 tag[2];
data/stringtie-2.1.4+ds/gclib/GBam.h:134:24: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void add_aux(const char tag[2], char atype, int len, uint8_t *data) {
data/stringtie-2.1.4+ds/gclib/GBam.h:153:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(b->data + ori_len + 3, data, len);
data/stringtie-2.1.4+ds/gclib/GBam.h:156:24: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void add_tag(const char tag[2], char atype, int len, uint8_t *data) {
data/stringtie-2.1.4+ds/gclib/GBam.h:191:26: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
uint8_t* find_tag(const char tag[2]);
data/stringtie-2.1.4+ds/gclib/GBam.h:195:22: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char* tag_str(const char tag[2]); //return tag value for tag type 'Z'
data/stringtie-2.1.4+ds/gclib/GBam.h:196:20: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
int tag_int(const char tag[2]); //return numeric value of tag (for numeric types)
data/stringtie-2.1.4+ds/gclib/GBam.h:197:24: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
float tag_float(const char tag[2]); //return float value of tag (for float types)
data/stringtie-2.1.4+ds/gclib/GBam.h:198:2: [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 tag_char(const char tag[2]); //return char value of tag (for type 'A')
data/stringtie-2.1.4+ds/gclib/GBam.h:198:22: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tag_char(const char tag[2]); //return char value of tag (for type 'A')
data/stringtie-2.1.4+ds/gclib/GBam.h:199:2: [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 tag_char1(const char tag[2]); //return char value of tag (for type 'A')
data/stringtie-2.1.4+ds/gclib/GBam.h:199:23: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tag_char1(const char tag[2]); //return char value of tag (for type 'A')
data/stringtie-2.1.4+ds/gclib/GBase.cpp:20:3: [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 msg[4096];
data/stringtie-2.1.4+ds/gclib/GBase.cpp:33:5: [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 msg[4096];
data/stringtie-2.1.4+ds/gclib/GBase.cpp:58:5: [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 msg[4096];
data/stringtie-2.1.4+ds/gclib/GBase.cpp:233:20: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (mode==NULL) f=fopen(path, "rb");
data/stringtie-2.1.4+ds/gclib/GBase.cpp:234:17: [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).
else f=fopen(path, mode);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:345:2: [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(subs, str, newlen-1);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:925:3: [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 retbuf[48];
data/stringtie-2.1.4+ds/gclib/GBase.h:438:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(fArray, a.fArray, sizeof(OBJ)* a.fCapacity);
data/stringtie-2.1.4+ds/gclib/GBase.h:453:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(fArray, a.fArray, sizeof(OBJ)*a.fCount);
data/stringtie-2.1.4+ds/gclib/GBase.h:509:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(fArray+fCount, arr, count*sizeof(OBJ));
data/stringtie-2.1.4+ds/gclib/GBase.h:516:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(fArray+fCount, arr.fArray, arr.fCount*sizeof(OBJ));
data/stringtie-2.1.4+ds/gclib/GBase.h:626:15: [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* f=fopen(fname, "rb");
data/stringtie-2.1.4+ds/gclib/GBitVec.h:141:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(fBits, RHS.fBits, Capacity * sizeof(BitWord));
data/stringtie-2.1.4+ds/gclib/GBitVec.h:412:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(fBits, RHS.fBits, RHSWords * sizeof(BitWord));
data/stringtie-2.1.4+ds/gclib/GBitVec.h:422:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(NewBits, RHS.fBits, Capacity * sizeof(BitWord));
data/stringtie-2.1.4+ds/gclib/GFaSeqGet.cpp:23:3: [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((void*)&newsq[qto], (void*)&sq[qfrom], sovl);
data/stringtie-2.1.4+ds/gclib/GFaSeqGet.cpp:31:5: [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).
fh=fopen(fn,"rb");
data/stringtie-2.1.4+ds/gclib/GFaSeqGet.cpp:45:6: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fh=fopen(faname,"rb");
data/stringtie-2.1.4+ds/gclib/GFaSeqGet.cpp:261:3: [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((void*)r,(void*)gs, clen);
data/stringtie-2.1.4+ds/gclib/GFaSeqGet.cpp:315:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void*)seqp, (void*)smem, reqrlen);
data/stringtie-2.1.4+ds/gclib/GFaSeqGet.cpp:333:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy((void*)(&seqp[sublen]), (void*)(&smem[mp]), line_len);
data/stringtie-2.1.4+ds/gclib/GFaSeqGet.cpp:348:8: [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((void*)(&seqp[sublen]), (void*)(&smem[mp]), letters_toread);
data/stringtie-2.1.4+ds/gclib/GFaSeqGet.h:175:15: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(fainame+fainamelen, ".fai");
data/stringtie-2.1.4+ds/gclib/GFaSeqGet.h:200:36: [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* fcreate=fopen(fainame, "w");
data/stringtie-2.1.4+ds/gclib/GFaSeqGet.h:208:39: [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).
if ((fcreate=fopen(fainamecwd, "w"))==NULL)
data/stringtie-2.1.4+ds/gclib/GFaSeqGet.h:247:3: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(s+slen, ".fa");
data/stringtie-2.1.4+ds/gclib/GFaSeqGet.h:250:24: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
if (!fileExists(s)) { strcpy(s+slen, "sta"); slen+=3; }
data/stringtie-2.1.4+ds/gclib/GFastaIndex.cpp:35:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* fi=fopen(fai_name,"rb");
data/stringtie-2.1.4+ds/gclib/GFastaIndex.cpp:71:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* fa=fopen(fa_name,"rb");
data/stringtie-2.1.4+ds/gclib/GFastaIndex.cpp:149:15: [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* fai=fopen(finame, "w");
data/stringtie-2.1.4+ds/gclib/GStr.cpp:92:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(data->chars, my_data->chars, my_data->length);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:167:2: [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[20];
data/stringtie-2.1.4+ds/gclib/GStr.cpp:168:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf,"%d",i);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:171:4: [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(chrs(), buf, len);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:180:2: [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[20];
data/stringtie-2.1.4+ds/gclib/GStr.cpp:181:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf,"%f",f);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:184:4: [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(chrs(), buf, len);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:232:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(my_data->chars, s, len);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:238:2: [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[20];
data/stringtie-2.1.4+ds/gclib/GStr.cpp:239:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf,"%f",f);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:242:4: [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(my_data->chars, buf, len);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:248:2: [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[20];
data/stringtie-2.1.4+ds/gclib/GStr.cpp:249:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf,"%d",i);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:252:4: [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(my_data->chars, buf, len);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:319:2: [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[20];
data/stringtie-2.1.4+ds/gclib/GStr.cpp:320:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf,"%d",i);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:325:2: [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[20];
data/stringtie-2.1.4+ds/gclib/GStr.cpp:326:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf,"%u",i);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:331:2: [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[20];
data/stringtie-2.1.4+ds/gclib/GStr.cpp:332:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf,"%ld",l);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:337:2: [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[20];
data/stringtie-2.1.4+ds/gclib/GStr.cpp:338:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf,"%lu", l);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:343:2: [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[30];
data/stringtie-2.1.4+ds/gclib/GStr.cpp:344:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buf,"%f",f);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:406:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(chrs(), buf, len);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:441:4: [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(data->chars, &my_data->chars[istart], newlen);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:460:4: [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(data->chars, & (my_data->chars[istart]), newlen);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:550:4: [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(data->chars, &my_data->chars[istart], newlen);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:568:4: [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(data->chars, &my_data->chars[istart], newlen);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:584:4: [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(&data->chars[len-length()], my_data->chars, my_data->length);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:593:4: [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(data->chars, my_data->chars, length());
data/stringtie-2.1.4+ds/gclib/GStr.cpp:606:4: [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(&data->chars[istart], my_data->chars, length());
data/stringtie-2.1.4+ds/gclib/GStr.cpp:622:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(newstring.chrs(), s1, s1_length);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:623:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(&(newstring.chrs())[s1_length], s2.chars(), s2.length());
data/stringtie-2.1.4+ds/gclib/GStr.cpp:638:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(newstring.chrs(), my_data->chars, length());
data/stringtie-2.1.4+ds/gclib/GStr.cpp:639:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(&(newstring.chrs())[length()], s.chars(), s.length());
data/stringtie-2.1.4+ds/gclib/GStr.cpp:655:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(newstring.chrs(), my_data->chars, length());
data/stringtie-2.1.4+ds/gclib/GStr.cpp:656:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(&(newstring.chrs())[length()], s, s_length);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:662:5: [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[20];
data/stringtie-2.1.4+ds/gclib/GStr.cpp:663:5: [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(buf, "%d", i);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:667:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(newstring.chrs(), my_data->chars, length());
data/stringtie-2.1.4+ds/gclib/GStr.cpp:668:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(&(newstring.chrs())[length()], buf, s_length);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:673:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[4];
data/stringtie-2.1.4+ds/gclib/GStr.cpp:674:5: [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(buf, "%c", c);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:678:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(newstring.chrs(), my_data->chars, length());
data/stringtie-2.1.4+ds/gclib/GStr.cpp:679:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(&(newstring.chrs())[length()], buf, s_length);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:684:5: [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[30];
data/stringtie-2.1.4+ds/gclib/GStr.cpp:685:5: [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(buf, "%f", f);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:689:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(newstring.chrs(), my_data->chars, length());
data/stringtie-2.1.4+ds/gclib/GStr.cpp:690:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(&(newstring.chrs())[length()], buf, s_length);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:730:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(newstring.chrs(), &my_data->chars[idx], len);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:769:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dest,s,p-s);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:816:17: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dest,s,p-s);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:825:15: [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(dest,s,p-s); //copy up rto the match
data/stringtie-2.1.4+ds/gclib/GStr.cpp:827:15: [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(dest,rto,tl); //put the replacement string
data/stringtie-2.1.4+ds/gclib/GStr.cpp:840:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(p,rto,l);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:869:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(data->chars, my_data->chars, idx);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:892:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(&chrs()[idx], s.chars(), len);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:896:15: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(data->chars, my_data->chars, idx);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:898:15: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(&data->chars[idx], s.chars(), s.length());
data/stringtie-2.1.4+ds/gclib/GStr.cpp:925:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(&chrs()[idx], s, len);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:929:15: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(data->chars, my_data->chars, idx);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:931:15: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(&data->chars[idx], s, s_length);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:954:15: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(data->chars, my_data->chars, idx);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:955:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(&data->chars[idx], s.chars(), s.length());
data/stringtie-2.1.4+ds/gclib/GStr.cpp:979:15: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(data->chars, my_data->chars, idx);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:980:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(&data->chars[idx], s, s_length);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1015:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(my_data->chars, s, len);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1023:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(my_data->chars+my_data->length, s, len);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1078:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(my_data->chars, m, len);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1087:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(my_data->chars + my_data->length, m, len);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1271:8: [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(token.chrs(), &my_data->chars[fLastTokenStart], tlen);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1306:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(token.chrs(), &my_data->chars[fLastTokenStart], tlen);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1358:11: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
::memcpy(data->chars, readbuf, numread);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1363:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&data->chars[acc_len], readbuf, numread);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1407:2: [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[24];
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1431:2: [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[24];
data/stringtie-2.1.4+ds/gclib/GStr.h:184:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char chars[1];
data/stringtie-2.1.4+ds/gclib/codons.cpp:3:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char codonTable[32768]; //32K table for fasta codon decoding
data/stringtie-2.1.4+ds/gclib/codons.h:10:2: [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 nuc[3];
data/stringtie-2.1.4+ds/gclib/gdna.cpp:16:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char v_2bit2nt[4] = {'A','C','G','T'};
data/stringtie-2.1.4+ds/gclib/gff.cpp:181:3: [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(line, l, llen+1);
data/stringtie-2.1.4+ds/gclib/gff.cpp:183:3: [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(dupline, l, llen+1);
data/stringtie-2.1.4+ds/gclib/gff.cpp:374:2: [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(line, l, llen+1);
data/stringtie-2.1.4+ds/gclib/gff.cpp:376:2: [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(dupline, l, llen+1);
data/stringtie-2.1.4+ds/gclib/gff.cpp:382:2: [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 fnamelc[128];
data/stringtie-2.1.4+ds/gclib/gff.cpp:732:6: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(track,"jigsaw");
data/stringtie-2.1.4+ds/gclib/gff.cpp:2904:2: [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 dbuf[DBUF_LEN];
data/stringtie-2.1.4+ds/gclib/gff.h:100:8: [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.
else sprintf(outs, "%.*f", precision, score);
data/stringtie-2.1.4+ds/gclib/gff.h:281:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(line, l.line, llen+1);
data/stringtie-2.1.4+ds/gclib/gff.h:283:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dupline, l.dupline, llen+1);
data/stringtie-2.1.4+ds/gclib/gff.h:294:7: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(_parents, l._parents, _parents_len);
data/stringtie-2.1.4+ds/gclib/gff.h:1280:10: [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).
fh=fopen(fname, "rb");
data/stringtie-2.1.4+ds/rlink.cpp:13997:2: [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 sbuf[20];
data/stringtie-2.1.4+ds/rlink.cpp:14102:6: [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(sbuf, "%p", junction[j]);
data/stringtie-2.1.4+ds/rlink.cpp:14118:9: [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(sbuf, "%p", junction[equal[s]]);
data/stringtie-2.1.4+ds/rlink.cpp:14128:6: [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(sbuf, "%p", ejunction[j]);
data/stringtie-2.1.4+ds/rlink.cpp:14144:9: [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(sbuf, "%p", ejunction[equal[s]]);
data/stringtie-2.1.4+ds/rlink.cpp:14184:6: [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(sbuf, "%p", rd.juncs[i-1]);
data/stringtie-2.1.4+ds/stringtie.cpp:315:12: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* f=fopen(guidegff.chars(),"r");
data/stringtie-2.1.4+ds/stringtie.cpp:383:12: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* f=fopen(ptff.chars(),"r");
data/stringtie-2.1.4+ds/stringtie.cpp:832:9: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
f_out=fopen(outfname.chars(), "w");
data/stringtie-2.1.4+ds/stringtie.cpp:844:9: [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).
g_out=fopen(genefname.chars(),"w");
data/stringtie-2.1.4+ds/stringtie.cpp:850:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* ftmp_in=fopen(tmpfname.chars(),"rt");
data/stringtie-2.1.4+ds/stringtie.cpp:930:9: [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.
static char sbuf[32];
data/stringtie-2.1.4+ds/stringtie.cpp:934:2: [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(sbuf, "%02d_%02d_%02d:%02d:%02d",t->tm_mon+1, t->tm_mday,
data/stringtie-2.1.4+ds/stringtie.cpp:1193:11: [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).
c_out=fopen(s.chars(), "w");
data/stringtie-2.1.4+ds/stringtie.cpp:1286:11: [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).
dbg_out=fopen(dbgfname.chars(), "w");
data/stringtie-2.1.4+ds/stringtie.cpp:1293:11: [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).
f_out=fopen(outfname.chars(), "w");
data/stringtie-2.1.4+ds/stringtie.cpp:1302:10: [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).
f_out=fopen(tmpfname.chars(), "w");
data/stringtie-2.1.4+ds/tablemaker.cpp:114:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* fh=fopen(fpath.chars(), "w");
data/stringtie-2.1.4+ds/tablemaker.cpp:137:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* fh=fopen(fren.chars(), "r");
data/stringtie-2.1.4+ds/tmerge.cpp:27:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* samh=fopen(samhname.chars(), "w");
data/stringtie-2.1.4+ds/tmerge.cpp:89:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* flst=fopen(this->files.First().chars(),"r");
data/stringtie-2.1.4+ds/gclib/GArgs.cpp:22:12: [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).
int fmtlen=strlen(format);
data/stringtie-2.1.4+ds/gclib/GArgs.cpp:68:13: [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 alen=strlen(p);
data/stringtie-2.1.4+ds/gclib/GBam.cpp:46:15: [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 l_qseq=strlen(qseq);
data/stringtie-2.1.4+ds/gclib/GBam.cpp:49:20: [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).
b->core.l_qname=strlen(qname)+1; //includes the \0 at the end
data/stringtie-2.1.4+ds/gclib/GBam.cpp:67:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int l_qseq=strlen(qseq);
data/stringtie-2.1.4+ds/gclib/GBam.cpp:68:19: [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).
b->core.l_qname=strlen(qname)+1; //includes the \0 at the end
data/stringtie-2.1.4+ds/gclib/GBam.cpp:143:21: [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).
if (slen<0) slen=strlen(qseq);
data/stringtie-2.1.4+ds/gclib/GBam.cpp:171:15: [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 strl=strlen(str);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:124:17: [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).
GMALLOC(copy, strlen(str)+1+xtracap);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:141:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(copy, sfrom, sto-sfrom+1);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:169:12: [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).
int blen=strlen(templ);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:181:24: [1] (access) umask:
Ensure that umask is given most restrictive possible setting (e.g., 066 or
077) (CWE-732).
mode_t process_mask = umask(0); //is this really needed?
data/stringtie-2.1.4+ds/gclib/GBase.cpp:186:5: [1] (access) umask:
Ensure that umask is given most restrictive possible setting (e.g., 066 or
077) (CWE-732).
umask(process_mask);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:189:11: [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).
int plen=strlen(path);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:198:3: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
strcat(gpath, "/");
data/stringtie-2.1.4+ds/gclib/GBase.cpp:221:4: [1] (access) umask:
Ensure that umask is given most restrictive possible setting (e.g., 066 or
077) (CWE-732).
umask(process_mask);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:227:2: [1] (access) umask:
Ensure that umask is given most restrictive possible setting (e.g., 066 or
077) (CWE-732).
umask(process_mask);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:353:15: [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).
GMALLOC(str, strlen(newvalue)+1);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:379:8: [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).
p=str+strlen(str)-1;
data/stringtie-2.1.4+ds/gclib/GBase.cpp:399:13: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c=getc(stream))!=EOF) {
data/stringtie-2.1.4+ds/gclib/GBase.cpp:402:17: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ((c=getc(stream))!='\n') ungetc(c,stream);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:428:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c=getc(stream))!=EOF) {
data/stringtie-2.1.4+ds/gclib/GBase.cpp:433:17: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ((c=getc(stream))!='\n') ungetc(c,stream);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:459:18: [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 int l=strlen(s);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:467:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len=strlen(str);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:477:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len=strlen(str);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:515:4: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
l=strlen(substr);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:516:21: [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).
char* p=(char*)str+strlen(str)-l;
data/stringtie-2.1.4+ds/gclib/GBase.cpp:532:5: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
l=strlen(substr);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:533:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
char* smax=(char*)str+strlen(str)-l;
data/stringtie-2.1.4+ds/gclib/GBase.cpp:564:8: [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).
int j=strlen(suffix)-1;
data/stringtie-2.1.4+ds/gclib/GBase.cpp:565:8: [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).
int i=strlen(s)-1;
data/stringtie-2.1.4+ds/gclib/GBase.cpp:574:8: [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).
int j=strlen(suffix)-1;
data/stringtie-2.1.4+ds/gclib/GBase.cpp:575:8: [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).
int i=strlen(s)-1;
data/stringtie-2.1.4+ds/gclib/GBase.cpp:584:8: [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).
int j=strlen(suffix)-1;
data/stringtie-2.1.4+ds/gclib/GBase.cpp:585:8: [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).
int i=strlen(s)-1;
data/stringtie-2.1.4+ds/gclib/GBase.cpp:598:8: [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).
int j=strlen(suffix)-1;
data/stringtie-2.1.4+ds/gclib/GBase.cpp:599:8: [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).
int i=strlen(s)-1;
data/stringtie-2.1.4+ds/gclib/GBase.cpp:611:21: [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).
if (slen==0) slen=strlen(str);
data/stringtie-2.1.4+ds/gclib/GBase.cpp:628:4: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
l=strlen(substr);
data/stringtie-2.1.4+ds/gclib/GFaSeqGet.cpp:77:8: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int c=getc(fh);
data/stringtie-2.1.4+ds/gclib/GFaSeqGet.cpp:83:12: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c=getc(fh))!=EOF) {
data/stringtie-2.1.4+ds/gclib/GFaSeqGet.cpp:97:12: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c=getc(fh))!=EOF) {
data/stringtie-2.1.4+ds/gclib/GFaSeqGet.cpp:111:12: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c=getc(fh))!=EOF) {
data/stringtie-2.1.4+ds/gclib/GFaSeqGet.cpp:125:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c=getc(fh))!=EOF) {
data/stringtie-2.1.4+ds/gclib/GFaSeqGet.h:167:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int fainamelen=strlen(fainame);
data/stringtie-2.1.4+ds/gclib/GFaSeqGet.h:234:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int gnl=strlen(gseqname);
data/stringtie-2.1.4+ds/gclib/GFaSeqGet.h:236:11: [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).
int slen=strlen(s);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:36:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len=strlen(str);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:169:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int len = ::strlen(buf);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:182:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int len = ::strlen(buf);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:231:21: [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).
const int len = ::strlen(s); prep_data(len);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:240:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int len = ::strlen(buf);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:250:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int len = ::strlen(buf);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:398:16: [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).
GMALLOC(buf, strlen(fmt)+1024);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:415:16: [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).
GMALLOC(buf, strlen(fmt)+1024);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:516:11: [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).
int cend=strlen(cstr)-1;
data/stringtie-2.1.4+ds/gclib/GStr.cpp:615:29: [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 int s1_length = ::strlen(s1);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:648:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int s_length = ::strlen(s);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:664:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int s_length = ::strlen(buf);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:675:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int s_length = ::strlen(buf);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:686:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int s_length = ::strlen(buf);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:754:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (length() == 0 || rfrom==NULL || strlen(rfrom)==0)
data/stringtie-2.1.4+ds/gclib/GStr.cpp:756:17: [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).
unsigned int l=strlen(rfrom);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:758:19: [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 (rto!=NULL && strlen(rto)!=l)
data/stringtie-2.1.4+ds/gclib/GStr.cpp:775:15: [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).
dest+=strlen(s);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:779:17: [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).
data->length=strlen(data->chars);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:796:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (length() == 0 || rfrom==NULL || strlen(rfrom)==0)
data/stringtie-2.1.4+ds/gclib/GStr.cpp:798:17: [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).
unsigned int l=strlen(rfrom);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:799:33: [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).
unsigned int tl= (rto==NULL)?0:strlen(rto);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:922:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int s_length = ::strlen(s);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:974:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int s_length = ::strlen(s);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1010:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
uint len=::strlen(s);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1051:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
::strncpy(my_data->chars, s, len);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1121:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(s)>(size_t)length()) return -1;
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1168:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int slen=strlen(str);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1190:23: [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).
result=substr(i+strlen(delim));
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1218:23: [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).
result=substr(i+strlen(delim));
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1240:29: [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).
GMALLOC(fTokenDelimiter,strlen(delimiter)+1);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1256:11: [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).
int dlen=strlen(fTokenDelimiter);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1313:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
size_t GStr::read(FILE* stream, const char* delimiter, size_t bufsize) {
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1335:8: [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).
dlen=strlen(delimiter);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1422:4: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, &my_data->chars[i-j], j);
data/stringtie-2.1.4+ds/gclib/GStr.cpp:1446:4: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(buf, &my_data->chars[i+1], j);
data/stringtie-2.1.4+ds/gclib/GStr.h:164:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
size_t read(FILE* stream, const char* delimiter="\n", size_t bufsize=4096);
data/stringtie-2.1.4+ds/gclib/GThreads.cpp:452:3: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
usleep((useconds_t)(mstime*1000));
data/stringtie-2.1.4+ds/gclib/codons.cpp:80:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (dnalen==0) dnalen=strlen(dnastr);
data/stringtie-2.1.4+ds/gclib/gdna.cpp:52:22: [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).
if (slen==0) slen=strlen(seq);
data/stringtie-2.1.4+ds/gclib/gdna.cpp:68:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int l=strlen(IUPAC_DEFS);
data/stringtie-2.1.4+ds/gclib/gff.cpp:105:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int attrlen=strlen(attr);
data/stringtie-2.1.4+ds/gclib/gff.cpp:179:8: [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).
llen=strlen(l);
data/stringtie-2.1.4+ds/gclib/gff.cpp:372:7: [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).
llen=strlen(l);
data/stringtie-2.1.4+ds/gclib/gff.cpp:440:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(fnamelc, ftype, 127);
data/stringtie-2.1.4+ds/gclib/gff.cpp:780:17: [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).
_parents_len=strlen(Parent)+1;
data/stringtie-2.1.4+ds/gclib/gff.cpp:1345:12: [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).
int idlen=strlen(id);
data/stringtie-2.1.4+ds/gclib/gff.cpp:1346:21: [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).
GMALLOC(buf, idlen+strlen(ctg)+2);
data/stringtie-2.1.4+ds/gclib/gff.cpp:1908:30: [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).
GMALLOC(new_attr_name, strlen(prefix)+strlen(attr_name)+1);
data/stringtie-2.1.4+ds/gclib/gff.cpp:1908:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
GMALLOC(new_attr_name, strlen(prefix)+strlen(attr_name)+1);
data/stringtie-2.1.4+ds/gclib/gff.cpp:2385:22: [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).
char* endinfo=info+strlen(info);
data/stringtie-2.1.4+ds/gclib/gff.h:99:20: [1] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source is a constant character.
if (precision<0) sprintf(outs, ".");
data/stringtie-2.1.4+ds/rlink.cpp:412:7: [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.
if(mismatch || nh>2) readlist[n]->juncs[i]->nm+=rdcount;
data/stringtie-2.1.4+ds/rlink.cpp:4096:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
mgt[s][rgno[s]][i]->read.Add(readlist[n]->pair_idx[x]);
data/stringtie-2.1.4+ds/rlink.cpp:4107:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
mt->read.Add(readlist[n]->pair_idx[x]);
data/stringtie-2.1.4+ds/rlink.cpp:5264:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
mgt[t2]->read.Add(mgt[t1]->read);
data/stringtie-2.1.4+ds/rlink.cpp:5264:32: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
mgt[t2]->read.Add(mgt[t1]->read);
data/stringtie-2.1.4+ds/rlink.cpp:5426:97: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(enableNames || (alltr.Count()==1 && mgt[alltr[0]]->transfrag->real)) for(int j=0;j<mgt[a]->read.Count();j++) {
data/stringtie-2.1.4+ds/rlink.cpp:5427:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int r=mgt[a]->read[j];
data/stringtie-2.1.4+ds/rlink.cpp:5501:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for(int j=0;j<mgt[a]->read.Count();j++) {
data/stringtie-2.1.4+ds/rlink.cpp:5502:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int r=mgt[a]->read[j];
data/stringtie-2.1.4+ds/rlink.cpp:5893:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for(int j=0;j<mgt[t]->read.Count();j++) {
data/stringtie-2.1.4+ds/rlink.cpp:5894:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int r=mgt[t]->read[j];
data/stringtie-2.1.4+ds/rlink.cpp:11728:74: [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.
if(lleftcov>1/ERROR_PERC && jd.leftsupport*mult<ERROR_PERC*lleftcov && (mismatch || lrightcov>lleftcov*(1-ERROR_PERC))) { // gave some boost (*10) to junctions here assumming not all of them are captured
data/stringtie-2.1.4+ds/rlink.cpp:11748:77: [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.
if(rrightcov>1/ERROR_PERC && jd.rightsupport*mult<rrightcov*ERROR_PERC && (mismatch || rleftcov>rrightcov*(1-ERROR_PERC))) { // gave some boost (*10) to junctions here assumming not all of them are captured
data/stringtie-2.1.4+ds/rlink.cpp:14106:17: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
GVec<int> equal;
data/stringtie-2.1.4+ds/rlink.cpp:14108:91: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
if(junction[s]->end==junction[j]->end && junction[s]->strand==junction[j]->strand) equal.Add(s);
data/stringtie-2.1.4+ds/rlink.cpp:14113:91: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
if(junction[s]->end==junction[j]->end && junction[s]->strand==junction[j]->strand) equal.Add(s);
data/stringtie-2.1.4+ds/rlink.cpp:14116:10: [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.
if(equal.Count()) { // junction j is equal to other junctions
data/stringtie-2.1.4+ds/rlink.cpp:14117:18: [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.
for(s=0;s<equal.Count();s++) {
data/stringtie-2.1.4+ds/rlink.cpp:14118:38: [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.
sprintf(sbuf, "%p", junction[equal[s]]);
data/stringtie-2.1.4+ds/rlink.cpp:14120:18: [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.
junction[equal[s]]->strand=0;
data/stringtie-2.1.4+ds/rlink.cpp:14121:18: [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.
junction[equal[s]]->guide_match=false;
data/stringtie-2.1.4+ds/rlink.cpp:14132:17: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
GVec<int> equal;
data/stringtie-2.1.4+ds/rlink.cpp:14134:99: [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.
if(ejunction[s]->start==ejunction[j]->start && ejunction[s]->strand==ejunction[j]->strand) equal.Add(s);
data/stringtie-2.1.4+ds/rlink.cpp:14139:99: [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.
if(ejunction[s]->start==ejunction[j]->start && ejunction[s]->strand==ejunction[j]->strand) equal.Add(s);
data/stringtie-2.1.4+ds/rlink.cpp:14142:10: [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.
if(equal.Count()) { // junction j is equal to other junctions
data/stringtie-2.1.4+ds/rlink.cpp:14143:18: [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.
for(s=0;s<equal.Count();s++) {
data/stringtie-2.1.4+ds/rlink.cpp:14144:39: [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.
sprintf(sbuf, "%p", ejunction[equal[s]]);
data/stringtie-2.1.4+ds/rlink.cpp:14146:19: [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.
ejunction[equal[s]]->strand=0;
data/stringtie-2.1.4+ds/rlink.cpp:14147:19: [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.
ejunction[equal[s]]->guide_match=false;
data/stringtie-2.1.4+ds/rlink.h:180:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
GVec<int> read; // all reads' indeces that are connected to this transfrag
data/stringtie-2.1.4+ds/rlink.h:184:47: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
CMTransfrag(CTransfrag *t=NULL):transfrag(t),read(),nf(0),nl(0),len(0) {}
data/stringtie-2.1.4+ds/stringtie.cpp:1564:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(tokens[2])==1) {
ANALYSIS SUMMARY:
Hits = 340
Lines analyzed = 33049 in approximately 0.93 seconds (35348 lines/second)
Physical Source Lines of Code (SLOC) = 23874
Hits@level = [0] 180 [1] 132 [2] 168 [3] 11 [4] 29 [5] 0
Hits@level+ = [0+] 520 [1+] 340 [2+] 208 [3+] 40 [4+] 29 [5+] 0
Hits/KSLOC@level+ = [0+] 21.781 [1+] 14.2414 [2+] 8.71241 [3+] 1.67546 [4+] 1.21471 [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.