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/skewer-0.2.2/src/common.h
Examining data/skewer-0.2.2/src/fastq.cpp
Examining data/skewer-0.2.2/src/fastq.h
Examining data/skewer-0.2.2/src/main.cpp
Examining data/skewer-0.2.2/src/matrix.cpp
Examining data/skewer-0.2.2/src/matrix.h
Examining data/skewer-0.2.2/src/parameter.cpp
Examining data/skewer-0.2.2/src/parameter.h
FINAL RESULTS:
data/skewer-0.2.2/src/fastq.cpp:166:4: [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(tmp, fileName);
data/skewer-0.2.2/src/fastq.cpp:170:4: [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(tmp, fileName);
data/skewer-0.2.2/src/fastq.cpp:173:11: [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.
cf.fp = popen(tmp, mode);
data/skewer-0.2.2/src/fastq.cpp:180:4: [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(tmp, fileName);
data/skewer-0.2.2/src/fastq.cpp:184:4: [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(tmp, fileName);
data/skewer-0.2.2/src/fastq.cpp:187:11: [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.
cf.fp = popen(tmp, mode);
data/skewer-0.2.2/src/parameter.cpp:76:13: [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.
int iRet = vfprintf(stream, format, arglist);
data/skewer-0.2.2/src/parameter.cpp:94:13: [4] (format) vsprintf:
Potential format string problem (CWE-134). Make format string constant.
int iRet = vsprintf(str, format, arglist);
data/skewer-0.2.2/src/parameter.cpp:605:5: [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(input[nFileCnt], argv[i]);
data/skewer-0.2.2/src/parameter.cpp:620:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(errMsg, "No such an option --%s", str);
data/skewer-0.2.2/src/parameter.cpp:759:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(errMsg, "unknown format '%s', please select either 'sanger' or 'solexa'", argv[i]);
data/skewer-0.2.2/src/parameter.cpp:776:6: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(errMsg, "invalid parameter '--cut %s'", argv[i]);
data/skewer-0.2.2/src/parameter.cpp:785:6: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(errMsg, "invalid parameter: \"--cut %s\", the combined length should be in the range of (0, 24]", argv[i]);
data/skewer-0.2.2/src/parameter.cpp:842:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(errMsg, "Invalid argument of -%c: %s", chr, argv[i]);
data/skewer-0.2.2/src/parameter.cpp:920:6: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(errMsg, "Can not read adapter sequences from FASTA file \"%s\"", x_str.c_str());
data/skewer-0.2.2/src/parameter.cpp:922:6: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(errMsg, "\"%s\" is not a valid FASTA file", x_str.c_str());
data/skewer-0.2.2/src/parameter.cpp:947:6: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(errMsg, "Can not read adapter sequences from FASTA file \"%s\"", y_str.c_str());
data/skewer-0.2.2/src/parameter.cpp:949:6: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(errMsg, "\"%s\" is not a valid FASTA file", y_str.c_str());
data/skewer-0.2.2/src/parameter.cpp:979:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(errMsg, "Can not read adapter sequences from FASTA file \"%s\"", j_str.c_str());
data/skewer-0.2.2/src/parameter.cpp:1043:6: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(errMsg, "Can not open matrix file \"%s\" for reading", m_str.c_str());
data/skewer-0.2.2/src/parameter.cpp:1046:6: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(errMsg, "File format of matrix file \"%s\" is invalid", m_str.c_str());
data/skewer-0.2.2/src/parameter.cpp:1051:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(errMsg, "Number of rows in \"%s\" differs from the number of adapter sequences specified by -x", m_str.c_str());
data/skewer-0.2.2/src/parameter.cpp:1056:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(errMsg, "Number of columns in \"%s\" differs from the number of adapter sequences specified by -%c",
data/skewer-0.2.2/src/parameter.cpp:1122:3: [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(trimmed, basename);
data/skewer-0.2.2/src/parameter.cpp:1126:7: [4] (shell) system:
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.
if(system(command.c_str()) != 0){
data/skewer-0.2.2/src/parameter.cpp:1127:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(errMsg, "Can not create directory \"%s\"", basename);
data/skewer-0.2.2/src/parameter.cpp:1134:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(trimmed + (end - basename) + 1, "%s", pDecorate);
data/skewer-0.2.2/src/parameter.cpp:1135:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(end+1, "un%s", pDecorate);
data/skewer-0.2.2/src/parameter.cpp:1139:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(trimmed, "%s", pDecorate);
data/skewer-0.2.2/src/parameter.cpp:1140:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(basename, "un%s", pDecorate);
data/skewer-0.2.2/src/parameter.cpp:1151:27: [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(trimmed, "-"); strcat(trimmed, pDecorate);
data/skewer-0.2.2/src/parameter.cpp:1152:30: [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(basename, "-un"); strcat(basename, pDecorate);
data/skewer-0.2.2/src/parameter.cpp:1158:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(trimmed, "%s", pDecorate);
data/skewer-0.2.2/src/parameter.cpp:1159:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(basename, "un%s", pDecorate);
data/skewer-0.2.2/src/parameter.cpp:1169:4: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(basename, trimmed);
data/skewer-0.2.2/src/parameter.cpp:1174:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(end, "-%s", pDecorate);
data/skewer-0.2.2/src/parameter.cpp:1175:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(basename + (end - trimmed), "-un%s", pDecorate);
data/skewer-0.2.2/src/parameter.cpp:1178:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(logfile, "%s.log", trimmed);
data/skewer-0.2.2/src/fastq.cpp:33:7: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
const char * FASTQ_FORMAT_NAME[FASTQ_FORMAT_CNT] = {
data/skewer-0.2.2/src/fastq.cpp:156:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
cf.fp = fopen(fileName, "r");
data/skewer-0.2.2/src/fastq.cpp:165:4: [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(tmp, "gzip --rsyncable > '");
data/skewer-0.2.2/src/fastq.cpp:169:4: [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(tmp, "gunzip -c '");
data/skewer-0.2.2/src/fastq.cpp:179:4: [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(tmp, "zip -q '");
data/skewer-0.2.2/src/fastq.cpp:181:4: [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(tmp, "' -");
data/skewer-0.2.2/src/fastq.cpp:183:4: [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(tmp, "unzip -p '");
data/skewer-0.2.2/src/fastq.cpp:191:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
cf.fp = fopen(fileName, mode);
data/skewer-0.2.2/src/fastq.cpp:208:14: [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 * fp = fopen(fileName, "rb");
data/skewer-0.2.2/src/fastq.cpp:217:13: [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 buffer[4];
data/skewer-0.2.2/src/fastq.h:131:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
extern const char * FASTQ_FORMAT_NAME[FASTQ_FORMAT_CNT];
data/skewer-0.2.2/src/main.cpp:51:8: [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.
const char * TAG_NAME[8] = { "NORMAL", "BLURRY", "BADQUAL", "EMPTY", "SHORT", "CONTAMINANT", "UNDETERMINED", "LONG" };
data/skewer-0.2.2/src/main.cpp:423:5: [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(pNewHist, pHist, allocLen * sizeof(long));
data/skewer-0.2.2/src/main.cpp:443:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[100];
data/skewer-0.2.2/src/main.cpp:445:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buffer, "%ld", sum);
data/skewer-0.2.2/src/main.cpp:466:3: [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 bar[101];
data/skewer-0.2.2/src/main.cpp:495:10: [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 result[26];
data/skewer-0.2.2/src/main.cpp:501:3: [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(result, "%.3s %.3s%3d %.2d:%.2d:%.2d %d",
data/skewer-0.2.2/src/main.cpp:528:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[100];
data/skewer-0.2.2/src/main.cpp:530:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buffer, "%ld", sum);
data/skewer-0.2.2/src/main.cpp:841:49: [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.
cMatrix::AddAdapter(cMatrix::firstAdapters, (char *)(*pAdapters)[i].c_str(), (*pAdapters)[i].length(), trimMode);
data/skewer-0.2.2/src/main.cpp:846:50: [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.
cMatrix::AddAdapter(cMatrix::secondAdapters,(char *)(*pAdapters)[i].c_str(), (*pAdapters)[i].length(), trimMode);
data/skewer-0.2.2/src/main.cpp:854:53: [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.
cMatrix::AddAdapter(cMatrix::junctionAdapters,(char *)(*pAdapters)[i].c_str(), (*pAdapters)[i].length(), TRIM_ANY);
data/skewer-0.2.2/src/main.cpp:1099:2: [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 barcodeSeq[25];
data/skewer-0.2.2/src/main.cpp:1100:2: [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 barcodeQua[25];
data/skewer-0.2.2/src/main.cpp:1825:2: [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 barcodeSeq[25];
data/skewer-0.2.2/src/main.cpp:1826:2: [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 barcodeQua[25];
data/skewer-0.2.2/src/main.cpp:2587:2: [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 errMsg[256];
data/skewer-0.2.2/src/main.cpp:2626:10: [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).
hLog = fopen(para.logfile, "w");
data/skewer-0.2.2/src/matrix.cpp:88:1: [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 character[CD_CNT] = {
data/skewer-0.2.2/src/matrix.cpp:526:2: [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 sequence[MAX_ADAPTER_LEN+1];
data/skewer-0.2.2/src/matrix.h:88:2: [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 sequence[MAX_ADAPTER_LEN+1]; // for debug only
data/skewer-0.2.2/src/matrix.h:89:2: [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 barcode[MAX_ADAPTER_LEN+1];
data/skewer-0.2.2/src/matrix.h:90:2: [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 primer[MAX_ADAPTER_LEN+1];
data/skewer-0.2.2/src/parameter.cpp:93:3: [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(str, "\33[%d;3%dm", bBold, colorCode);
data/skewer-0.2.2/src/parameter.cpp:96:3: [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(str, "\33[0m");
data/skewer-0.2.2/src/parameter.cpp:193:14: [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 * fp = fopen(fileName, "r");
data/skewer-0.2.2/src/parameter.cpp:242:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
bval = (atoi(pch) > 0);
data/skewer-0.2.2/src/parameter.cpp:264:14: [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 * fp = fopen(fileName, "r");
data/skewer-0.2.2/src/parameter.cpp:591:2: [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 basename[MAX_PATH+1+100];
data/skewer-0.2.2/src/parameter.cpp:592:2: [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 trimmed[MAX_PATH+1+100];
data/skewer-0.2.2/src/parameter.cpp:631:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(errMsg, "No such an option -%c", chr);
data/skewer-0.2.2/src/parameter.cpp:637:5: [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(errMsg, "-%c needs an argument", chr);
data/skewer-0.2.2/src/parameter.cpp:714:17: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
minEndQual = atoi(argv[i]);
data/skewer-0.2.2/src/parameter.cpp:721:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
minAverageQual = atoi(argv[i]);
data/skewer-0.2.2/src/parameter.cpp:728:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
minLen = atoi(argv[i]);
data/skewer-0.2.2/src/parameter.cpp:736:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
maxLen = atoi(argv[i]);
data/skewer-0.2.2/src/parameter.cpp:780:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
iCutF = atoi(fnum);
data/skewer-0.2.2/src/parameter.cpp:781:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
iCutR = atoi(rnum);
data/skewer-0.2.2/src/parameter.cpp:802:57: [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).
minK = (strcasecmp(argv[i], "inf") == 0) ? INT_MAX : atoi(argv[i]);
data/skewer-0.2.2/src/parameter.cpp:811:15: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
nThreads = atoi(argv[i]);
data/skewer-0.2.2/src/parameter.cpp:850:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(errMsg, "--qiime option should only be used with --cut option\n");
data/skewer-0.2.2/src/parameter.cpp:859:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(errMsg, "No input file specified");
data/skewer-0.2.2/src/parameter.cpp:865:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(errMsg, "STDIN can not be specified with other input files");
data/skewer-0.2.2/src/parameter.cpp:871:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(errMsg, "STDOUT can not be specified for output paired files");
data/skewer-0.2.2/src/parameter.cpp:875:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(errMsg, "STDOUT can not be used for demultiplexing (-b)" );
data/skewer-0.2.2/src/parameter.cpp:879:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(errMsg, "STDOUT can not be used with -o");
data/skewer-0.2.2/src/parameter.cpp:883:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(errMsg, "STDOUT can not be used for compressing (-z)");
data/skewer-0.2.2/src/parameter.cpp:891:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(errMsg, "-k should be set to \"inf\" in amplicon mode\n");
data/skewer-0.2.2/src/parameter.cpp:899:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(errMsg, "-c option should only be used in amplicon mode\n");
data/skewer-0.2.2/src/parameter.cpp:1003:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(errMsg, "-M should not be specified for single-end reads\n");
data/skewer-0.2.2/src/parameter.cpp:1006:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[MAX_PATH];
data/skewer-0.2.2/src/parameter.cpp:1010:5: [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(buffer, "%02dx", (i+1));
data/skewer-0.2.2/src/parameter.cpp:1016:5: [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(buffer, "%c", char('A' + i));
data/skewer-0.2.2/src/parameter.cpp:1023:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buffer, "%02d", (j+1));
data/skewer-0.2.2/src/parameter.cpp:1062:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[MAX_PATH];
data/skewer-0.2.2/src/parameter.cpp:1066:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buffer, "%02dx", (i+1));
data/skewer-0.2.2/src/parameter.cpp:1072:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buffer, "%c", char('A' + i));
data/skewer-0.2.2/src/parameter.cpp:1079:5: [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(buffer, "%02d", (j+1));
data/skewer-0.2.2/src/parameter.cpp:1152:5: [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(basename, "-un"); strcat(basename, pDecorate);
data/skewer-0.2.2/src/parameter.cpp:1182:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[MAX_PATH];
data/skewer-0.2.2/src/parameter.cpp:1223:6: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(buffer, "-%02d", (i+1));
data/skewer-0.2.2/src/parameter.h:57:2: [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 arr[2][MAX_PATH+1];
data/skewer-0.2.2/src/parameter.h:77:2: [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 * input[2];
data/skewer-0.2.2/src/parameter.h:99:2: [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 logfile[MAX_PATH+1+100];
data/skewer-0.2.2/src/fastq.cpp:86:8: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
tag = fgetc(in);
data/skewer-0.2.2/src/fastq.cpp:93:12: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
char c = fgetc(in);
data/skewer-0.2.2/src/fastq.cpp:102:8: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c = fgetc(in);
data/skewer-0.2.2/src/fastq.cpp:163:28: [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).
char *tmp=(char *)malloc(strlen(fileName)+100);
data/skewer-0.2.2/src/fastq.cpp:167:4: [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(tmp, "'");
data/skewer-0.2.2/src/fastq.cpp:171:4: [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(tmp, "'");
data/skewer-0.2.2/src/fastq.cpp:177:28: [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).
char *tmp=(char *)malloc(strlen(fileName)+100);
data/skewer-0.2.2/src/fastq.cpp:185:4: [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(tmp, "'");
data/skewer-0.2.2/src/fastq.cpp:211:15: [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).
size_t len = strlen(fileName);
data/skewer-0.2.2/src/main.cpp:446:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int width = int(strlen(buffer));
data/skewer-0.2.2/src/main.cpp:531:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int width = int(strlen(buffer));
data/skewer-0.2.2/src/main.cpp:909:4: [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(1);
data/skewer-0.2.2/src/main.cpp:918:5: [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(1);
data/skewer-0.2.2/src/main.cpp:1127:4: [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(1);
data/skewer-0.2.2/src/main.cpp:1136:5: [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(1);
data/skewer-0.2.2/src/main.cpp:1338:4: [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(1);
data/skewer-0.2.2/src/main.cpp:1347:5: [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(1);
data/skewer-0.2.2/src/main.cpp:1588:4: [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(1);
data/skewer-0.2.2/src/main.cpp:1597:5: [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(1);
data/skewer-0.2.2/src/main.cpp:1854:4: [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(1);
data/skewer-0.2.2/src/main.cpp:1863:5: [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(1);
data/skewer-0.2.2/src/main.cpp:2124:4: [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(1);
data/skewer-0.2.2/src/main.cpp:2133:5: [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(1);
data/skewer-0.2.2/src/matrix.cpp:297:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool cAdapter::align(char * read, size_t rLen, uchar * qual, size_t qLen, cElementSet &result, int bc, bool bBestAlign)
data/skewer-0.2.2/src/matrix.cpp:337:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
mbits = matchBits[codeMap[uchar(read[jj])]];
data/skewer-0.2.2/src/matrix.cpp:659:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
INDEX cMatrix::findAdapter(char * read, size_t rLen, uchar * qual, size_t qLen)
data/skewer-0.2.2/src/matrix.cpp:671:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(pAdapter->align(read, rLen, qual, qLen, result, i)){
data/skewer-0.2.2/src/matrix.cpp:681:36: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
INDEX cMatrix::findAdapter2(char * read, size_t rLen, uchar * qual, size_t qLen)
data/skewer-0.2.2/src/matrix.cpp:694:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(pAdapter->align(read, rLen, qual, qLen, result, i)){
data/skewer-0.2.2/src/matrix.cpp:704:39: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
INDEX cMatrix::findJuncAdapter(char * read, size_t rLen, uchar * qual, size_t qLen)
data/skewer-0.2.2/src/matrix.cpp:716:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(pAdapter->align(read, rLen, qual, qLen, result, i)){
data/skewer-0.2.2/src/matrix.cpp:726:40: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool cMatrix::findAdapterWithPE(char * read, char * read2, size_t rLen, size_t rLen2, uchar * qual, uchar * qual2, size_t qLen, size_t qLen2, INDEX &index, INDEX &index2)
data/skewer-0.2.2/src/matrix.cpp:738:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
pAdapter->align(read, rLen, qual, qLen, result, i, false);
data/skewer-0.2.2/src/matrix.cpp:857:41: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int cMatrix::findAdaptersInARead(char * read, size_t rLen, uchar * qual, size_t qLen, INDEX &index)
data/skewer-0.2.2/src/matrix.cpp:872:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(pAdapter->align(read, nLen, qual, qLen, result, i)){
data/skewer-0.2.2/src/matrix.cpp:884:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(pAdapter->align(read, nLen, qual, qLen, result, i)){
data/skewer-0.2.2/src/matrix.cpp:901:49: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int cMatrix::findAdaptersBidirectionally(char * read, size_t rLen, uchar * qual, size_t qLen,
data/skewer-0.2.2/src/matrix.cpp:917:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(pAdapter->align(read, nLen, qual, qLen, result, i)){
data/skewer-0.2.2/src/matrix.cpp:959:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(pAdapter->align(read, nLen, qual, qLen, result, i)){
data/skewer-0.2.2/src/matrix.cpp:1059:31: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
INDEX cMatrix::mergePE(char * read, char * read2, size_t rLen, uchar * qual, uchar * qual2, size_t qLen, size_t startPos, size_t jLen)
data/skewer-0.2.2/src/matrix.cpp:1074:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(adapter.align(read, rLen, NULL, 0, result, -1)){
data/skewer-0.2.2/src/matrix.cpp:1117:38: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool cMatrix::combinePairSeqs(char * read, char * read2, int len, int len2, uchar * qual, uchar * qual2, int qLen, int qLen2)
data/skewer-0.2.2/src/matrix.cpp:1141:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
code = codeMap[uchar(read[i])];
data/skewer-0.2.2/src/matrix.cpp:1146:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read[i] = character[code2];
data/skewer-0.2.2/src/matrix.h:105:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool align(char * read, size_t rLen, uchar * qual, size_t qLen, cElementSet &result, int bc, bool bBestAlign=true);
data/skewer-0.2.2/src/matrix.h:166:34: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
static INDEX findAdapter(char * read, size_t rLen, uchar * qual, size_t qLen);
data/skewer-0.2.2/src/matrix.h:167:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
static INDEX findAdapter2(char * read, size_t rLen, uchar * qual, size_t qLen);
data/skewer-0.2.2/src/matrix.h:168:38: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
static INDEX findJuncAdapter(char * read, size_t rLen, uchar * qual, size_t qLen);
data/skewer-0.2.2/src/matrix.h:170:39: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
static bool findAdapterWithPE(char * read, char * read2, size_t rLen, size_t rLen2, uchar * qual, uchar * qual2, size_t qLen, size_t qLen2, INDEX &index, INDEX & index2);
data/skewer-0.2.2/src/matrix.h:171:48: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
static int findAdaptersBidirectionally(char * read, size_t rLen, uchar * qual, size_t qLen,
data/skewer-0.2.2/src/matrix.h:173:40: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
static int findAdaptersInARead(char * read, size_t rLen, uchar * qual, size_t qLen, INDEX &index);
data/skewer-0.2.2/src/matrix.h:176:30: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
static INDEX mergePE(char * read, char * read2, size_t rLen, uchar * qual, uchar * qual2, size_t qLen, size_t startPos, size_t jLen);
data/skewer-0.2.2/src/matrix.h:177:37: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
static bool combinePairSeqs(char * read, char * read2, int len, int len2, uchar * qual, uchar * qual2, int qLen, int qLen2);
data/skewer-0.2.2/src/parameter.cpp:1151:5: [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(trimmed, "-"); strcat(trimmed, pDecorate);
ANALYSIS SUMMARY:
Hits = 167
Lines analyzed = 6027 in approximately 0.21 seconds (28192 lines/second)
Physical Source Lines of Code (SLOC) = 5384
Hits@level = [0] 206 [1] 54 [2] 75 [3] 0 [4] 38 [5] 0
Hits@level+ = [0+] 373 [1+] 167 [2+] 113 [3+] 38 [4+] 38 [5+] 0
Hits/KSLOC@level+ = [0+] 69.2793 [1+] 31.0178 [2+] 20.9881 [3+] 7.05795 [4+] 7.05795 [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.