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/berkeley-express-1.5.3+dfsg/src/biascorrection.cpp
Examining data/berkeley-express-1.5.3+dfsg/src/biascorrection.h
Examining data/berkeley-express-1.5.3+dfsg/src/bundles.cpp
Examining data/berkeley-express-1.5.3+dfsg/src/bundles.h
Examining data/berkeley-express-1.5.3+dfsg/src/directiondetector.cpp
Examining data/berkeley-express-1.5.3+dfsg/src/directiondetector.h
Examining data/berkeley-express-1.5.3+dfsg/src/fragments.cpp
Examining data/berkeley-express-1.5.3+dfsg/src/fragments.h
Examining data/berkeley-express-1.5.3+dfsg/src/frequencymatrix.h
Examining data/berkeley-express-1.5.3+dfsg/src/lengthdistribution.h
Examining data/berkeley-express-1.5.3+dfsg/src/library.h
Examining data/berkeley-express-1.5.3+dfsg/src/logger.h
Examining data/berkeley-express-1.5.3+dfsg/src/main.h
Examining data/berkeley-express-1.5.3+dfsg/src/mapparser.cpp
Examining data/berkeley-express-1.5.3+dfsg/src/mapparser.h
Examining data/berkeley-express-1.5.3+dfsg/src/markovmodel.cpp
Examining data/berkeley-express-1.5.3+dfsg/src/mismatchmodel.h
Examining data/berkeley-express-1.5.3+dfsg/src/robertsfilter.cpp
Examining data/berkeley-express-1.5.3+dfsg/src/robertsfilter.h
Examining data/berkeley-express-1.5.3+dfsg/src/sequence.cpp
Examining data/berkeley-express-1.5.3+dfsg/src/sequence.h
Examining data/berkeley-express-1.5.3+dfsg/src/targets.cpp
Examining data/berkeley-express-1.5.3+dfsg/src/targets.h
Examining data/berkeley-express-1.5.3+dfsg/src/threadsafety.cpp
Examining data/berkeley-express-1.5.3+dfsg/src/threadsafety.h
Examining data/berkeley-express-1.5.3+dfsg/src/lengthdistribution.cpp
Examining data/berkeley-express-1.5.3+dfsg/src/markovmodel.h
Examining data/berkeley-express-1.5.3+dfsg/src/mismatchmodel.cpp
Examining data/berkeley-express-1.5.3+dfsg/src/main.cpp

FINAL RESULTS:

data/berkeley-express-1.5.3+dfsg/src/logger.h:56:5:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
    vsnprintf(buffer, BUFF_SIZE, msg, arg);
data/berkeley-express-1.5.3+dfsg/src/logger.h:66:5:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
    vsnprintf(buffer, BUFF_SIZE, msg, arg);
data/berkeley-express-1.5.3+dfsg/src/logger.h:76:5:  [4] (format) vsnprintf:
  If format strings can be influenced by an attacker, they can be exploited,
  and note that sprintf variations do not always \0-terminate (CWE-134). Use
  a constant for the format specification.
    vsnprintf(buffer, BUFF_SIZE, msg, arg);
data/berkeley-express-1.5.3+dfsg/src/main.cpp:380:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    sprintf(buff, "%s/x_%d", output_dir.c_str(), n);
data/berkeley-express-1.5.3+dfsg/src/main.cpp:394:7:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
      sprintf(buff, "%s/params.%d.xprs", dir.c_str(), (int)l+1);
data/berkeley-express-1.5.3+dfsg/src/main.cpp:396:7:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
      sprintf(buff, "%s/params.xprs", dir.c_str());
data/berkeley-express-1.5.3+dfsg/src/main.cpp:776:3:  [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(buff, in_map_file_names.c_str());
data/berkeley-express-1.5.3+dfsg/src/main.cpp:789:7:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
      sprintf(out_map_file_name, "%s/hits.%d.prob",
data/berkeley-express-1.5.3+dfsg/src/main.cpp:793:7:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
      sprintf(out_map_file_name, "%s/hits.%d.samp",
data/berkeley-express-1.5.3+dfsg/src/main.cpp:1083:3:  [3] (random) srand:
  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.
  srand((unsigned int)time(NULL));
data/berkeley-express-1.5.3+dfsg/src/biascorrection.cpp: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 line_buff[BUFF_SIZE];
data/berkeley-express-1.5.3+dfsg/src/biascorrection.cpp:120:3:  [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 buff[200];
data/berkeley-express-1.5.3+dfsg/src/biascorrection.cpp:123:5:  [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(buff, "\t%d", i-CENTER+1);
data/berkeley-express-1.5.3+dfsg/src/lengthdistribution.cpp:72:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char line_buff[BUFF_SIZE];
data/berkeley-express-1.5.3+dfsg/src/lengthdistribution.cpp:180:3:  [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[50];
data/berkeley-express-1.5.3+dfsg/src/lengthdistribution.cpp:182:5:  [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, "%e\t",sexp(pmf(i*_bin_size)));
data/berkeley-express-1.5.3+dfsg/src/logger.h:53:5:  [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 buffer[BUFF_SIZE];
data/berkeley-express-1.5.3+dfsg/src/logger.h:63:5:  [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 buffer[BUFF_SIZE];
data/berkeley-express-1.5.3+dfsg/src/logger.h:73:5:  [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 buffer[BUFF_SIZE];
data/berkeley-express-1.5.3+dfsg/src/main.cpp:377:3:  [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 buff[500];
data/berkeley-express-1.5.3+dfsg/src/main.cpp:775:3:  [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 buff[999];
data/berkeley-express-1.5.3+dfsg/src/main.cpp:787:5:  [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 out_map_file_name[500] = "";
data/berkeley-express-1.5.3+dfsg/src/mapparser.cpp:358:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char line_buff[BUFF_SIZE];
data/berkeley-express-1.5.3+dfsg/src/mapparser.cpp:386:31:  [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).
        _targ_lengths[name] = atoi(len.c_str());
data/berkeley-express-1.5.3+dfsg/src/mapparser.cpp:404:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char line_buff[BUFF_SIZE];
data/berkeley-express-1.5.3+dfsg/src/mapparser.cpp:441:20:  [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).
        sam_flag = atoi(p);
data/berkeley-express-1.5.3+dfsg/src/mapparser.cpp:478:27:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
        r.left = (size_t)(atoi(p)-1);
data/berkeley-express-1.5.3+dfsg/src/mapparser.cpp:506:20:  [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).
        r.mate_l = atoi(p)-1;
data/berkeley-express-1.5.3+dfsg/src/mapparser.cpp:534:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char line_buff[BUFF_SIZE];
data/berkeley-express-1.5.3+dfsg/src/mismatchmodel.cpp: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 line_buff[BUFF_SIZE];
data/berkeley-express-1.5.3+dfsg/src/targets.cpp:380:12:  [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).
    infile.open(haplotype_file.c_str());
data/berkeley-express-1.5.3+dfsg/src/targets.cpp:384:7:  [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.
      char line_buff[BUFF_SIZE];
data/berkeley-express-1.5.3+dfsg/src/targets.cpp:590:22:  [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).
  FILE * expr_file = fopen((output_dir + "/results.xprs").c_str(), "w");
data/berkeley-express-1.5.3+dfsg/src/targets.cpp:594:19:  [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).
      varcov_file.open((output_dir + "/varcov.xprs").c_str());
data/berkeley-express-1.5.3+dfsg/src/targets.cpp:597:17:  [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).
      rdds_file.open((output_dir + "/rdds.xprs").c_str());
data/berkeley-express-1.5.3+dfsg/src/targets.cpp:388:13:  [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).
        if (strlen(line_buff) == 0) {

ANALYSIS SUMMARY:

Hits = 36
Lines analyzed = 8269 in approximately 0.26 seconds (31591 lines/second)
Physical Source Lines of Code (SLOC) = 4785
Hits@level = [0]   2 [1]   1 [2]  25 [3]   1 [4]   9 [5]   0
Hits@level+ = [0+]  38 [1+]  36 [2+]  35 [3+]  10 [4+]   9 [5+]   0
Hits/KSLOC@level+ = [0+] 7.94148 [1+] 7.52351 [2+] 7.31452 [3+] 2.08986 [4+] 1.88088 [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.