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/dwgsim-0.1.12/src/contigs.c
Examining data/dwgsim-0.1.12/src/contigs.h
Examining data/dwgsim-0.1.12/src/dwgsim.c
Examining data/dwgsim-0.1.12/src/dwgsim.h
Examining data/dwgsim-0.1.12/src/dwgsim_eval.c
Examining data/dwgsim-0.1.12/src/dwgsim_eval.h
Examining data/dwgsim-0.1.12/src/dwgsim_opt.c
Examining data/dwgsim-0.1.12/src/dwgsim_opt.h
Examining data/dwgsim-0.1.12/src/mut.c
Examining data/dwgsim-0.1.12/src/mut.h
Examining data/dwgsim-0.1.12/src/mut_bed.c
Examining data/dwgsim-0.1.12/src/mut_bed.h
Examining data/dwgsim-0.1.12/src/mut_input.c
Examining data/dwgsim-0.1.12/src/mut_input.h
Examining data/dwgsim-0.1.12/src/mut_txt.c
Examining data/dwgsim-0.1.12/src/mut_txt.h
Examining data/dwgsim-0.1.12/src/mut_vcf.c
Examining data/dwgsim-0.1.12/src/mut_vcf.h
Examining data/dwgsim-0.1.12/src/regions_bed.c
Examining data/dwgsim-0.1.12/src/regions_bed.h
FINAL RESULTS:
data/dwgsim-0.1.12/src/dwgsim.c:470:17: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
while(0 < fscanf(opt->fp_fai, "%s\t%d\t%d\t%d\t%d", name, &l, &dummy_int[0], &dummy_int[1], &dummy_int[2])) {
data/dwgsim-0.1.12/src/dwgsim.c:1067:3: [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(fn_fai, argv[optind+0]); strcat(fn_fai, ".fai");
data/dwgsim-0.1.12/src/dwgsim.c:1069:3: [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(fn_tmp, argv[optind+1]); strcat(fn_tmp, ".mutations.txt");
data/dwgsim-0.1.12/src/dwgsim.c:1071:3: [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(fn_tmp, argv[optind+1]); strcat(fn_tmp, ".mutations.vcf");
data/dwgsim-0.1.12/src/dwgsim.c:1074:7: [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(fn_tmp, argv[optind+1]); strcat(fn_tmp, ".bfast.fastq");
data/dwgsim-0.1.12/src/dwgsim.c:1076:7: [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(fn_tmp, argv[optind+1]); strcat(fn_tmp, ".bwa.read1.fastq");
data/dwgsim-0.1.12/src/dwgsim.c:1078:7: [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(fn_tmp, argv[optind+1]); strcat(fn_tmp, ".bwa.read2.fastq");
data/dwgsim-0.1.12/src/dwgsim_eval.c:318:12: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
if(14 != sscanf(name, "%s %d %d %1d %1d %1d %1d %d %d %d %d %d %d %s",
data/dwgsim-0.1.12/src/dwgsim_eval.c:691:7: [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(stdout, format,
data/dwgsim-0.1.12/src/mut_bed.c:55:13: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
while(0 < fscanf(fp, "%s\t%u\t%u\t%s\t%s", name, &start, &end, bases, type)) {
data/dwgsim-0.1.12/src/mut_txt.c:54:13: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
while(0 < fscanf(fp, "%s\t%u\t%c\t%s\t%d", name, &pos, &ref, mut, &is_hap)) {
data/dwgsim-0.1.12/src/mut_vcf.c:88:21: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
if(EOF == sscanf(buffer+s, "%s\t%u\t%s\t%s\t%s", name, &pos, id, ref, alt)) {
data/dwgsim-0.1.12/src/regions_bed.c:54:13: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
while(0 < fscanf(fp, "%s\t%u\t%u", name, &start, &end)) {
data/dwgsim-0.1.12/src/dwgsim.c:163:22: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
v1 = 2.0 * drand48() - 1.0;
data/dwgsim-0.1.12/src/dwgsim.c:164:22: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
v2 = 2.0 * drand48() - 1.0;
data/dwgsim-0.1.12/src/dwgsim.c:181:10: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
if(drand48() < prob) r++;
data/dwgsim-0.1.12/src/dwgsim.c:263:17: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
else if(drand48() < e[_j]->start + e[_j]->by*i) { \
data/dwgsim-0.1.12/src/dwgsim.c:264:30: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
c = (c + (mut_t)(drand48() * 3.0 + 1)) & 3; \
data/dwgsim-0.1.12/src/dwgsim.c:313:17: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
while(drand48() < e) { // how many bases should we insert/delete
data/dwgsim-0.1.12/src/dwgsim.c:317:18: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
if(drand48() < 0.5) { // insert
data/dwgsim-0.1.12/src/dwgsim.c:362:33: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
k = (int)(drand48() * j);
data/dwgsim-0.1.12/src/dwgsim.c:384:17: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
while(drand48() < e) {
data/dwgsim-0.1.12/src/dwgsim.c:633:35: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
if(opt->rand_read < drand48()) {
data/dwgsim-0.1.12/src/dwgsim.c:645:53: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
pos = (int)((l - d + 1) * drand48());
data/dwgsim-0.1.12/src/dwgsim.c:661:53: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
pos = (int)((l - d + 1) * drand48());
data/dwgsim-0.1.12/src/dwgsim.c:683:46: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
mutseq_t *currseq = mutseq[drand48()<opt->mut_freq?0:1]; // haplotype from which the reads are generated
data/dwgsim-0.1.12/src/dwgsim.c:701:23: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
if (drand48() < 0.5) { // which strand ?
data/dwgsim-0.1.12/src/dwgsim.c:930:49: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
tmp_seq[j][i] = (int)(drand48() * 4.0) & 3;
data/dwgsim-0.1.12/src/dwgsim_eval.c:122:19: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while(0 <= (c = getopt(argc, argv, "a:d:e:g:m:n:q:s:bchimpzSP:"))) {
data/dwgsim-0.1.12/src/dwgsim_opt.c:195:15: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ((c = getopt(argc, argv, "id:s:N:C:1:2:e:E:r:F:R:X:I:c:S:n:y:BHf:z:Mm:b:v:x:P:q:Q:h")) >= 0) {
data/dwgsim-0.1.12/src/dwgsim_opt.c:370:38: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
tmp_seq[k] = (int)(drand48() * 4.0) & 3;
data/dwgsim-0.1.12/src/mut.c:292:82: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
} while (num_ins < ins_long_length_max && (num_ins < opt->indel_min || drand48() < opt->indel_extend));
data/dwgsim-0.1.12/src/mut.c:301:26: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
if (opt->is_hap || drand48() < 0.333333) { // hom-ins
data/dwgsim-0.1.12/src/mut.c:303:18: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
} else if (drand48() < 0.5) {
data/dwgsim-0.1.12/src/mut.c:314:42: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
ins = (ins << 2) | (mut_t)(drand48() * 4.0);
data/dwgsim-0.1.12/src/mut.c:348:30: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
b = ((uint8_t)(drand48() * 4.0)) << (bit_index << 1);
data/dwgsim-0.1.12/src/mut.c:606:55: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
if (deletion_length < opt->indel_min || drand48() < opt->indel_extend) {
data/dwgsim-0.1.12/src/mut.c:613:24: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
if (c < 4 && drand48() < opt->mut_rate) { // mutation
data/dwgsim-0.1.12/src/mut.c:614:19: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
if (drand48() >= opt->indel_frac) { // substitution
data/dwgsim-0.1.12/src/mut.c:615:30: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
double r = drand48();
data/dwgsim-0.1.12/src/mut.c:617:38: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
if (opt->is_hap || drand48() < 0.333333) { // hom
data/dwgsim-0.1.12/src/mut.c:620:27: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
ret[drand48()<0.5?0:1]->s[i] = SUBSTITUTE|c;
data/dwgsim-0.1.12/src/mut.c:623:23: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
if (drand48() < 0.5) { // deletion
data/dwgsim-0.1.12/src/mut.c:624:42: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
if (opt->is_hap || drand48() < 0.3333333) { // hom-del
data/dwgsim-0.1.12/src/mut.c:628:38: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
deleting = drand48()<0.5?1:2;
data/dwgsim-0.1.12/src/mut.c:657:38: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
if (opt->is_hap || drand48() < 0.333333) {
data/dwgsim-0.1.12/src/mut.c:662:35: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
which_hap = drand48()<0.5?0:1;
data/dwgsim-0.1.12/src/mut.c:671:42: [3] (random) drand48:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
double r = drand48();
data/dwgsim-0.1.12/src/dwgsim.c:250:13: [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(fn, mode)) == 0) {
data/dwgsim-0.1.12/src/dwgsim.c:426:3: [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 name[1024], *qstr;
data/dwgsim-0.1.12/src/dwgsim.c:1058:3: [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 fn_fai[1024]="\0";
data/dwgsim-0.1.12/src/dwgsim.c:1059:3: [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 fn_tmp[1024]="\0";
data/dwgsim-0.1.12/src/dwgsim.c:1067:35: [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.
strcpy(fn_fai, argv[optind+0]); strcat(fn_fai, ".fai");
data/dwgsim-0.1.12/src/dwgsim.c:1068:17: [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).
opt->fp_fai = fopen(fn_fai, "r"); // NB: depends on returning NULL;
data/dwgsim-0.1.12/src/dwgsim.c:1069:35: [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.
strcpy(fn_tmp, argv[optind+1]); strcat(fn_tmp, ".mutations.txt");
data/dwgsim-0.1.12/src/dwgsim.c:1071:35: [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.
strcpy(fn_tmp, argv[optind+1]); strcat(fn_tmp, ".mutations.vcf");
data/dwgsim-0.1.12/src/dwgsim.c:1074:39: [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.
strcpy(fn_tmp, argv[optind+1]); strcat(fn_tmp, ".bfast.fastq");
data/dwgsim-0.1.12/src/dwgsim.c:1076:39: [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.
strcpy(fn_tmp, argv[optind+1]); strcat(fn_tmp, ".bwa.read1.fastq");
data/dwgsim-0.1.12/src/dwgsim.c:1078:39: [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.
strcpy(fn_tmp, argv[optind+1]); strcat(fn_tmp, ".bwa.read2.fastq");
data/dwgsim-0.1.12/src/dwgsim_eval.c:124:28: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'a': args.a = atoi(optarg); break;
data/dwgsim-0.1.12/src/dwgsim_eval.c:127:28: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'd': args.d = atoi(optarg); break;
data/dwgsim-0.1.12/src/dwgsim_eval.c:128:28: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'g': args.g = atoi(optarg); break;
data/dwgsim-0.1.12/src/dwgsim_eval.c:131:28: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'n': args.n = atoi(optarg); break;
data/dwgsim-0.1.12/src/dwgsim_eval.c:132:28: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'q': args.q = atoi(optarg); break;
data/dwgsim-0.1.12/src/dwgsim_eval.c:136:28: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 's': args.s = atoi(optarg); break;
data/dwgsim-0.1.12/src/dwgsim_eval.c:137:28: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'e': args.e = atoi(optarg); break;
data/dwgsim-0.1.12/src/dwgsim_eval.c:286:3: [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 chr_name[1028]="\0";
data/dwgsim-0.1.12/src/dwgsim_eval.c:287:3: [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 read_num[1028]="\0";
data/dwgsim-0.1.12/src/dwgsim_eval.c:597:3: [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 format[1024]="\0";
data/dwgsim-0.1.12/src/dwgsim_eval.c:609:3: [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(format, "%.2d ");
data/dwgsim-0.1.12/src/dwgsim_eval.c:611:7: [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(format + (int)strlen(format), "%%%dd ", max);
data/dwgsim-0.1.12/src/dwgsim_eval.c:613:3: [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(format + (int)strlen(format), "%.3e %.3e %.3e %.3e %.3e %.3e\n");
data/dwgsim-0.1.12/src/dwgsim_opt.c:185:10: [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(optarg);
data/dwgsim-0.1.12/src/mut_bed.c:41:3: [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 name[1024];
data/dwgsim-0.1.12/src/mut_bed.c:43:3: [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 type[1024];
data/dwgsim-0.1.12/src/mut_bed.c:44:3: [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 bases[1024];
data/dwgsim-0.1.12/src/mut_txt.c:44:3: [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 name[1024];
data/dwgsim-0.1.12/src/mut_txt.c:46:3: [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 ref, mut[1024];
data/dwgsim-0.1.12/src/mut_vcf.c:47:3: [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 name[1024]; // 1. #CHROM
data/dwgsim-0.1.12/src/mut_vcf.c:49:3: [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 id[1024]; // 3. ID
data/dwgsim-0.1.12/src/mut_vcf.c:50:3: [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 ref[1024]; // 4. REF
data/dwgsim-0.1.12/src/mut_vcf.c:51:3: [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 alt[1025]; // 5. ALT
data/dwgsim-0.1.12/src/mut_vcf.c:55:3: [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[BUFFER_L];
data/dwgsim-0.1.12/src/regions_bed.c:41:3: [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 name[1024];
data/dwgsim-0.1.12/src/dwgsim.c:189:13: [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).
for(i=0;i<strlen(str);i++) {
data/dwgsim-0.1.12/src/dwgsim.c:526:29: [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).
if(name_len_max < strlen(name)) {
data/dwgsim-0.1.12/src/dwgsim.c:527:30: [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).
name_len_max = strlen(name);
data/dwgsim-0.1.12/src/dwgsim.c:530:38: [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).
for(i=0;i<name_len_max-strlen(name);i++) {
data/dwgsim-0.1.12/src/dwgsim_eval.c:309:11: [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).
j = strlen(name);
data/dwgsim-0.1.12/src/dwgsim_eval.c:310:13: [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).
tmp = strlen(args->P);
data/dwgsim-0.1.12/src/dwgsim_eval.c:336:15: [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).
i = strlen(name);
data/dwgsim-0.1.12/src/dwgsim_eval.c:337:17: [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).
tmp = strlen(header->target_name[j]);
data/dwgsim-0.1.12/src/dwgsim_eval.c:611:29: [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).
sprintf(format + (int)strlen(format), "%%%dd ", max);
data/dwgsim-0.1.12/src/dwgsim_eval.c:613:24: [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).
strcat(format + (int)strlen(format), "%.3e %.3e %.3e %.3e %.3e %.3e\n");
data/dwgsim-0.1.12/src/dwgsim_opt.c:151:13: [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).
for(i=0;i<strlen(str);i++) {
data/dwgsim-0.1.12/src/dwgsim_opt.c:156:8: [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).
if(i<strlen(str)-1) {
data/dwgsim-0.1.12/src/dwgsim_opt.c:169:17: [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).
int32_t len = strlen(optarg);
data/dwgsim-0.1.12/src/dwgsim_opt.c:289:41: [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(NULL != opt->fixed_quality && 1 != strlen(opt->fixed_quality)) {
data/dwgsim-0.1.12/src/dwgsim_opt.c:334:33: [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).
opt->flow_order_len = strlen((char*)opt->flow_order);
data/dwgsim-0.1.12/src/mut.c:55:23: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (!feof(fp) && fgetc(fp) != '>');
data/dwgsim-0.1.12/src/mut.c:58:28: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (!feof(fp) && (c = fgetc(fp)) != ' ' && c != '\t' && c != '\n')
data/dwgsim-0.1.12/src/mut.c:64:37: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (!feof(fp) && ((c = fgetc(fp)) == ' ' || c == '\t'));
data/dwgsim-0.1.12/src/mut.c:67:40: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (!feof(fp) && (c = fgetc(fp)) != '\n')
data/dwgsim-0.1.12/src/mut.c:72:45: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
} else if (c != '\n') while (!feof(fp) && fgetc(fp) != '\n');
data/dwgsim-0.1.12/src/mut.c:74:28: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while (!feof(fp) && (c = fgetc(fp)) != '>') {
data/dwgsim-0.1.12/src/mut.c:295:17: [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).
num_ins = strlen(bases); // ignores num_ins
data/dwgsim-0.1.12/src/mut_bed.c:76:59: [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).
else if(0 != strcmp("*", bases) && (end - start) != strlen(bases)) {
data/dwgsim-0.1.12/src/mut_vcf.c:142:19: [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).
ref_l = strlen(ref);
data/dwgsim-0.1.12/src/mut_vcf.c:143:19: [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).
alt_l = strlen(alt);
data/dwgsim-0.1.12/src/regions_bed.c:107:25: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while(EOF != (b = fgetc(fp))) {
ANALYSIS SUMMARY:
Hits = 110
Lines analyzed = 4373 in approximately 0.20 seconds (21794 lines/second)
Physical Source Lines of Code (SLOC) = 3505
Hits@level = [0] 242 [1] 26 [2] 36 [3] 35 [4] 13 [5] 0
Hits@level+ = [0+] 352 [1+] 110 [2+] 84 [3+] 48 [4+] 13 [5+] 0
Hits/KSLOC@level+ = [0+] 100.428 [1+] 31.3837 [2+] 23.9658 [3+] 13.6947 [4+] 3.70899 [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.