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/libgclib-0.11.10+ds/GAlnExtend.cpp
Examining data/libgclib-0.11.10+ds/GAlnExtend.h
Examining data/libgclib-0.11.10+ds/GArgs.cpp
Examining data/libgclib-0.11.10+ds/GArgs.h
Examining data/libgclib-0.11.10+ds/GBam.cpp
Examining data/libgclib-0.11.10+ds/GBam.h
Examining data/libgclib-0.11.10+ds/GBase.cpp
Examining data/libgclib-0.11.10+ds/GBase.h
Examining data/libgclib-0.11.10+ds/GBitVec.h
Examining data/libgclib-0.11.10+ds/GCdbYank.cpp
Examining data/libgclib-0.11.10+ds/GCdbYank.h
Examining data/libgclib-0.11.10+ds/GFaSeqGet.cpp
Examining data/libgclib-0.11.10+ds/GFaSeqGet.h
Examining data/libgclib-0.11.10+ds/GFastaFile.h
Examining data/libgclib-0.11.10+ds/GFastaIndex.cpp
Examining data/libgclib-0.11.10+ds/GFastaIndex.h
Examining data/libgclib-0.11.10+ds/GResUsage.cpp
Examining data/libgclib-0.11.10+ds/GResUsage.h
Examining data/libgclib-0.11.10+ds/GStr.cpp
Examining data/libgclib-0.11.10+ds/GStr.h
Examining data/libgclib-0.11.10+ds/GThreads.cpp
Examining data/libgclib-0.11.10+ds/GThreads.h
Examining data/libgclib-0.11.10+ds/GapAssem.cpp
Examining data/libgclib-0.11.10+ds/GapAssem.h
Examining data/libgclib-0.11.10+ds/codons.cpp
Examining data/libgclib-0.11.10+ds/codons.h
Examining data/libgclib-0.11.10+ds/gcdb.cpp
Examining data/libgclib-0.11.10+ds/gcdb.h
Examining data/libgclib-0.11.10+ds/gdimg.cpp
Examining data/libgclib-0.11.10+ds/gdimg.h
Examining data/libgclib-0.11.10+ds/gdna.cpp
Examining data/libgclib-0.11.10+ds/gdna.h
Examining data/libgclib-0.11.10+ds/gff.cpp
Examining data/libgclib-0.11.10+ds/gff.h
Examining data/libgclib-0.11.10+ds/gsocket.cpp
Examining data/libgclib-0.11.10+ds/gsocket.h
Examining data/libgclib-0.11.10+ds/gstopwatch.cpp
Examining data/libgclib-0.11.10+ds/gstopwatch.h
Examining data/libgclib-0.11.10+ds/gtest.cpp
Examining data/libgclib-0.11.10+ds/htest.cpp
Examining data/libgclib-0.11.10+ds/mdtest.cpp
Examining data/libgclib-0.11.10+ds/proc_mem.cpp
Examining data/libgclib-0.11.10+ds/proc_mem.h
FINAL RESULTS:
data/libgclib-0.11.10+ds/GAlnExtend.h:408:10: [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(f, &sa[aend]);
data/libgclib-0.11.10+ds/GAlnExtend.h:444:10: [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(f, &sb[bend]);
data/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/GFastaFile.h:52:27: [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).
GMALLOC(id, l+1);strcpy(id,cname);
data/libgclib-0.11.10+ds/GFastaFile.h:65:12: [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(descr,cdescr);
data/libgclib-0.11.10+ds/GFastaFile.h:95:15: [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(seq,cseq);
data/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/GStr.cpp:402:11: [4] (format) vsprintf:
Potential format string problem (CWE-134). Make format string constant.
int len=vsprintf(buf,fmt,arguments);
data/libgclib-0.11.10+ds/GStr.cpp:419:3: [4] (format) vsprintf:
Potential format string problem (CWE-134). Make format string constant.
vsprintf(buf,fmt,arguments);
data/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/GapAssem.cpp:1047:3: [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(f, fmtstr, " ", ' ');
data/libgclib-0.11.10+ds/GapAssem.cpp:1055:3: [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(f, fmtstr, s->name(), orientation);
data/libgclib-0.11.10+ds/gcdb.cpp:11:62: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
void *mmap(char *address, size_t length, int protection, int access,
data/libgclib-0.11.10+ds/gcdb.cpp:600:3: [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(fname, afname);
data/libgclib-0.11.10+ds/gcdb.cpp:838:3: [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(fname, afname);
data/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/GThreads.cpp:62:3: [3] (misc) InitializeCriticalSection:
Exceptions can be thrown in low-memory situations. Use
InitializeCriticalSectionAndSpinCount instead.
InitializeCriticalSection(&mWaitersCountLock);
data/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/GThreads.h:188:7: [3] (misc) InitializeCriticalSection:
Exceptions can be thrown in low-memory situations. Use
InitializeCriticalSectionAndSpinCount instead.
InitializeCriticalSection(&mHandle);
data/libgclib-0.11.10+ds/GThreads.h:211:7: [3] (misc) EnterCriticalSection:
On some versions of Windows, exceptions can be thrown in low-memory
situations. Use InitializeCriticalSectionAndSpinCount instead.
EnterCriticalSection(&mHandle);
data/libgclib-0.11.10+ds/GThreads.h:277:7: [3] (misc) InitializeCriticalSection:
Exceptions can be thrown in low-memory situations. Use
InitializeCriticalSectionAndSpinCount instead.
InitializeCriticalSection(&mHandle);
data/libgclib-0.11.10+ds/GThreads.h:303:7: [3] (misc) EnterCriticalSection:
On some versions of Windows, exceptions can be thrown in low-memory
situations. Use InitializeCriticalSectionAndSpinCount instead.
EnterCriticalSection(&mHandle);
data/libgclib-0.11.10+ds/GThreads.h:376:7: [3] (misc) InitializeCriticalSection:
Exceptions can be thrown in low-memory situations. Use
InitializeCriticalSectionAndSpinCount instead.
InitializeCriticalSection(&mHandle);
data/libgclib-0.11.10+ds/GThreads.h:416:7: [3] (misc) EnterCriticalSection:
On some versions of Windows, exceptions can be thrown in low-memory
situations. Use InitializeCriticalSectionAndSpinCount instead.
EnterCriticalSection(&mHandle);
data/libgclib-0.11.10+ds/GThreads.h:623:7: [3] (misc) EnterCriticalSection:
On some versions of Windows, exceptions can be thrown in low-memory
situations. Use InitializeCriticalSectionAndSpinCount instead.
EnterCriticalSection(&mWaitersCountLock);
data/libgclib-0.11.10+ds/GAlnExtend.cpp:9:2: [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 COLOR_buf[6]={0x1B,'[', 'n','m','m','\0'};
data/libgclib-0.11.10+ds/GAlnExtend.cpp:13:2: [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((char *)(&COLOR_buf[2]),"%dm",c+30);
data/libgclib-0.11.10+ds/GAlnExtend.cpp:19:2: [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((char *)(&COLOR_buf[2]),"%dm",c+40);
data/libgclib-0.11.10+ds/GAlnExtend.cpp:25:2: [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((char *)(&COLOR_buf[2]),"39m");
data/libgclib-0.11.10+ds/GAlnExtend.cpp:31:2: [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((char *)(&COLOR_buf[2]),"49m");
data/libgclib-0.11.10+ds/GAlnExtend.cpp:37:2: [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((char *)(&COLOR_buf[2]),"0m");
data/libgclib-0.11.10+ds/GAlnExtend.cpp:43:2: [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((char *)(&COLOR_buf[2]),"22m");
data/libgclib-0.11.10+ds/GAlnExtend.cpp:50:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char xgapcodes[4]={'S','I', 'D', 'X'};
data/libgclib-0.11.10+ds/GAlnExtend.h:381:5: [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 al[1024]; //display buffer for seq A
data/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/GBam.h:132:24: [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/libgclib-0.11.10+ds/GBam.h:151:7: [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/libgclib-0.11.10+ds/GBam.h:154:24: [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/libgclib-0.11.10+ds/GBam.h:189:26: [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/libgclib-0.11.10+ds/GBam.h:193:22: [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/libgclib-0.11.10+ds/GBam.h:194:20: [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/libgclib-0.11.10+ds/GBam.h:195:24: [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/libgclib-0.11.10+ds/GBam.h:196:2: [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/libgclib-0.11.10+ds/GBam.h:196:22: [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/libgclib-0.11.10+ds/GBam.h:197:2: [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/libgclib-0.11.10+ds/GBam.h:197:23: [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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/GBase.cpp:924:3: [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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/GCdbYank.cpp:154:14: [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* zf=fopen(p, "rb");
data/libgclib-0.11.10+ds/GCdbYank.cpp:161:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char ztag[5];
data/libgclib-0.11.10+ds/GCdbYank.cpp:204:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[4];
data/libgclib-0.11.10+ds/GCdbYank.cpp:270:11: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
return atoi(p);
data/libgclib-0.11.10+ds/GCdbYank.cpp:276:4: [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 buf[16];
data/libgclib-0.11.10+ds/GCdbYank.cpp:293:11: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
return atoi(p);
data/libgclib-0.11.10+ds/GCdbYank.cpp:351:17: [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).
fz=fopen(dbname, "rb");
data/libgclib-0.11.10+ds/GCdbYank.cpp:352:18: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
else fdb=open(dbname, O_RDONLY|O_BINARY);
data/libgclib-0.11.10+ds/GCdbYank.cpp:361:20: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
int ftmp = open(dbname, O_RDONLY|O_BINARY);
data/libgclib-0.11.10+ds/GCdbYank.cpp:416:2: [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 bytes[32]; // data buffer -- should just accomodate fastarec_pos, fastarec_length
data/libgclib-0.11.10+ds/GCdbYank.cpp:473:2: [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 bytes[64]; // data buffer -- should just accomodate fastarec_pos, fastarec_length
data/libgclib-0.11.10+ds/GCdbYank.h:19:3: [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 lbuf[GCDBZ_LBUF_LEN]; //larger buffer
data/libgclib-0.11.10+ds/GCdbYank.h: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 sbuf[GCDBZ_SBUF_LEN]; //smaller buffer
data/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/GFastaFile.h:317:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fh = fopen(filename, mode)) == NULL)
data/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/GResUsage.cpp:194:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ( (fp = fopen( "/proc/self/statm", "r" )) == NULL )
data/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/GapAssem.cpp:1042:2: [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 fmtstr[128];
data/libgclib-0.11.10+ds/GapAssem.cpp:1044:2: [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(&fmtstr[1], "%d", max);
data/libgclib-0.11.10+ds/GapAssem.cpp:1045:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat(fmtstr, "s %c ");
data/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/gcdb.cpp:169:17: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
typedef union { char irrelevant[ALIGNMENT]; double d; } aligned;
data/libgclib-0.11.10+ds/gcdb.cpp:376:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char b[4];
data/libgclib-0.11.10+ds/gcdb.cpp:381:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char b[2];
data/libgclib-0.11.10+ds/gcdb.cpp:422:11: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char b[8];
data/libgclib-0.11.10+ds/gcdb.cpp:485:18: [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 uint32_pack(char s[4],uint32 u)
data/libgclib-0.11.10+ds/gcdb.cpp:495:22: [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.
void uint32_pack_big(char s[4],uint32 u)
data/libgclib-0.11.10+ds/gcdb.cpp:508:20: [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.
void uint32_unpack(char s[4],uint32 *u)
data/libgclib-0.11.10+ds/gcdb.cpp:523:24: [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 uint32_unpack_big(char s[4],uint32 *u)
data/libgclib-0.11.10+ds/gcdb.cpp:584:9: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fd = open(afname,O_WRONLY | O_TRUNC | O_BINARY | O_CREAT, S_IREAD|S_IWRITE);
data/libgclib-0.11.10+ds/gcdb.cpp:586:9: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fd = open(afname,O_WRONLY | O_NDELAY | O_TRUNC | O_CREAT, 0664);
data/libgclib-0.11.10+ds/gcdb.cpp:648:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[8];
data/libgclib-0.11.10+ds/gcdb.cpp:698:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[8];
data/libgclib-0.11.10+ds/gcdb.cpp:832:10: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fd = open(afname, O_RDONLY|O_BINARY);
data/libgclib-0.11.10+ds/gcdb.cpp:834:10: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fd = open(afname, O_RDONLY);
data/libgclib-0.11.10+ds/gcdb.cpp:898:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[32];
data/libgclib-0.11.10+ds/gcdb.cpp:913:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[8];
data/libgclib-0.11.10+ds/gcdb.h:130:6: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char oldtag[4]; // 'CIDX' for old tag style
data/libgclib-0.11.10+ds/gcdb.h:147:6: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tag[4]; //'CDBX' for new files with LFS
data/libgclib-0.11.10+ds/gcdb.h:211:4: [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 bspace[8192];
data/libgclib-0.11.10+ds/gcdb.h:212:4: [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 fname[1024];
data/libgclib-0.11.10+ds/gcdb.h:213:4: [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 final[2048];
data/libgclib-0.11.10+ds/gcdb.h:275:3: [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 fname[1024];
data/libgclib-0.11.10+ds/gcdb.h:355:7: [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((void*)(outbuf+rd),(void*)(buf+bufpos), to_read);
data/libgclib-0.11.10+ds/gcdb.h:418:5: [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*)outbuf, (void*)(buf+bufpos), mlen);
data/libgclib-0.11.10+ds/gdimg.cpp:65:10: [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).
fout=fopen(fname, "wb");
data/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/gff.h:101:8: [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/libgclib-0.11.10+ds/gff.h:282:6: [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/libgclib-0.11.10+ds/gff.h:284:6: [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/libgclib-0.11.10+ds/gff.h:295:7: [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/libgclib-0.11.10+ds/gff.h:1282:10: [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/libgclib-0.11.10+ds/gsocket.cpp:121:12: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
return atoi(service.chars()); /* Service is port number */
data/libgclib-0.11.10+ds/gsocket.cpp:172:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[1024];
data/libgclib-0.11.10+ds/htest.cpp:118:5: [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).
f=fopen(a, "r");
data/libgclib-0.11.10+ds/htest.cpp:126:8: [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=fopen(a, "r");
data/libgclib-0.11.10+ds/GAlnExtend.cpp:14:21: [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).
fwrite(COLOR_buf,1,strlen(COLOR_buf), f);
data/libgclib-0.11.10+ds/GAlnExtend.cpp:20:21: [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).
fwrite(COLOR_buf,1,strlen(COLOR_buf),f);
data/libgclib-0.11.10+ds/GAlnExtend.cpp:26:21: [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).
fwrite(COLOR_buf,1,strlen(COLOR_buf), f);
data/libgclib-0.11.10+ds/GAlnExtend.cpp:32:21: [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).
fwrite(COLOR_buf,1,strlen(COLOR_buf), f);
data/libgclib-0.11.10+ds/GAlnExtend.cpp:38:21: [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).
fwrite(COLOR_buf,1,strlen(COLOR_buf), f);
data/libgclib-0.11.10+ds/GAlnExtend.cpp:44:21: [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).
fwrite(COLOR_buf,1,strlen(COLOR_buf), f);
data/libgclib-0.11.10+ds/GAlnExtend.cpp:558:12: [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 q_max=strlen(q_seq); //query
data/libgclib-0.11.10+ds/GAlnExtend.cpp:559:12: [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 s_max=strlen(s_seq); //subj
data/libgclib-0.11.10+ds/GAlnExtend.h:438:14: [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) color_bg(c_red,f);
data/libgclib-0.11.10+ds/GAlnExtend.h:440:14: [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) color_bg(c_blue,f);
data/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/GCdbYank.cpp:89:17: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ((c =fgetc(zf))!=EOF) {
data/libgclib-0.11.10+ds/GCdbYank.cpp:216:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int r=read(fd, &dbstat, cdbInfoSIZE );
data/libgclib-0.11.10+ds/GCdbYank.cpp:247:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
r=read(fd, dbname, dbstat.dbnamelen);
data/libgclib-0.11.10+ds/GCdbYank.cpp:258:8: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
e=fgetc(stdin);
data/libgclib-0.11.10+ds/GCdbYank.cpp:267:7: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
e=fgetc(stdin);
data/libgclib-0.11.10+ds/GCdbYank.cpp:336:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(namebuf, idxfile, nlen);
data/libgclib-0.11.10+ds/GCdbYank.cpp:417:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (cdb->read(bytes,len,pos) == -1)
data/libgclib-0.11.10+ds/GCdbYank.cpp:449:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (reclen-- && read(fdb, &c, 1)==1) {
data/libgclib-0.11.10+ds/GCdbYank.cpp:474:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (cdb->read(bytes,len,pos) == -1)
data/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/GFastaFile.h:51:12: [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).
l=strlen(cname);
data/libgclib-0.11.10+ds/GFastaFile.h:63:14: [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).
l=strlen(cdescr);
data/libgclib-0.11.10+ds/GFastaFile.h:77:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (send<0) send=strlen(cseq)-1;
data/libgclib-0.11.10+ds/GFastaFile.h:82:19: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(seq, cseq+sbeg, len);
data/libgclib-0.11.10+ds/GFastaFile.h:93:17: [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).
l=strlen(cseq);
data/libgclib-0.11.10+ds/GFastaFile.h:227:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (newlen==0) newlen=strlen(newseq);
data/libgclib-0.11.10+ds/GFastaFile.h:381:19: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = getc(fh)) != EOF && c != '>') {
data/libgclib-0.11.10+ds/GFastaFile.h:411:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int c = getc(fh);
data/libgclib-0.11.10+ds/GFastaFile.h:414:34: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (c!=EOF && c<=32) { c=getc(fh); cur_fpos++; }//skip spaces etc.
data/libgclib-0.11.10+ds/GFastaFile.h:429:18: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = getc(fh)) != EOF) {
data/libgclib-0.11.10+ds/GFastaFile.h:449:14: [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).
dt_len=strlen(trim_delim);
data/libgclib-0.11.10+ds/GFastaFile.h:505:23: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = getc(fh)) != EOF && c != '\n' && c !='\r') cur_fpos++; // skip defline
data/libgclib-0.11.10+ds/GFastaFile.h:511:23: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = getc(fh)) != EOF && c != '>') {
data/libgclib-0.11.10+ds/GFastaFile.h:526:26: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = getc(fh)) != EOF && c != '>') {
data/libgclib-0.11.10+ds/GFastaFile.h:545:26: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = getc(fh)) != EOF && c != '>') {
data/libgclib-0.11.10+ds/GFastaFile.h:586:31: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (skipacc<slen && ((c=getc(fh))!= EOF && c != '>')) {
data/libgclib-0.11.10+ds/GFastaFile.h:622:19: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = getc(fh)) != EOF && c != '>') {
data/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/gcdb.cpp:665:20: [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).
unsigned int klen=strlen(key);
data/libgclib-0.11.10+ds/gcdb.cpp:867:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int GCdbRead::read(char *buf,unsigned int len, uint32 pos) {
data/libgclib-0.11.10+ds/gcdb.cpp:883:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
r = ::read(fd,buf,len);
data/libgclib-0.11.10+ds/gcdb.cpp:903:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (GCdbRead::read(buf,n,pos) == -1) return -1;
data/libgclib-0.11.10+ds/gcdb.cpp:918:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (GCdbRead::read(buf,8,(u << 3) & 2047) == -1) return -1;
data/libgclib-0.11.10+ds/gcdb.cpp:930:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (GCdbRead::read(buf,8,kpos) == -1) return - 1;
data/libgclib-0.11.10+ds/gcdb.cpp:938:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (GCdbRead::read(buf,8,pos) == -1) return -1;
data/libgclib-0.11.10+ds/gcdb.cpp:971:14: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c=getc(file))!=EOF) {
data/libgclib-0.11.10+ds/gcdb.cpp:979:17: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ((c=getc(file))!='\n') ungetc(c,file);
data/libgclib-0.11.10+ds/gcdb.h:283:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int read(char *,unsigned int,uint32);
data/libgclib-0.11.10+ds/gcdb.h:437:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (cmplen<0) cmplen=strlen(cmpstr);
data/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/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/libgclib-0.11.10+ds/gff.h:100:20: [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/libgclib-0.11.10+ds/htest.cpp:32:12: [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 len=strlen(line);
ANALYSIS SUMMARY:
Hits = 401
Lines analyzed = 20899 in approximately 0.65 seconds (32250 lines/second)
Physical Source Lines of Code (SLOC) = 16207
Hits@level = [0] 142 [1] 148 [2] 203 [3] 11 [4] 39 [5] 0
Hits@level+ = [0+] 543 [1+] 401 [2+] 253 [3+] 50 [4+] 39 [5+] 0
Hits/KSLOC@level+ = [0+] 33.504 [1+] 24.7424 [2+] 15.6105 [3+] 3.08509 [4+] 2.40637 [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.