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/trinculo-0.96+dfsg/src/chisq_cdf.h
Examining data/trinculo-0.96+dfsg/src/EstCovMat.h
Examining data/trinculo-0.96+dfsg/src/GenORs.h
Examining data/trinculo-0.96+dfsg/src/MultinomNewton.h
Examining data/trinculo-0.96+dfsg/src/PropOddsNewton.h
Examining data/trinculo-0.96+dfsg/src/readBed.h
Examining data/trinculo-0.96+dfsg/src/readCovar.h
Examining data/trinculo-0.96+dfsg/src/readDosage.h
Examining data/trinculo-0.96+dfsg/src/readPhenos.h
Examining data/trinculo-0.96+dfsg/src/readPriors.h
Examining data/trinculo-0.96+dfsg/src/sims.cpp
Examining data/trinculo-0.96+dfsg/src/trinculo.cpp
Examining data/trinculo-0.96+dfsg/src/trinculo.h
Examining data/trinculo-0.96+dfsg/src/inputparser.h

FINAL RESULTS:

data/trinculo-0.96+dfsg/src/sims.cpp:19:2:  [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(t1.tv_usec * t1.tv_sec);
data/trinculo-0.96+dfsg/src/inputparser.h:236:17:  [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).
      precision=atoi(*argv); 
data/trinculo-0.96+dfsg/src/inputparser.h:278:15:  [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).
      fititer=atoi(*argv);
data/trinculo-0.96+dfsg/src/inputparser.h:370:15:  [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).
      threads=atoi(*argv);
data/trinculo-0.96+dfsg/src/readBed.h:118:7:  [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).
  fam.open((string(inprefix) + ".fam").c_str());
data/trinculo-0.96+dfsg/src/readBed.h:156:7:  [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).
  bim.open((string(inprefix) + ".bim").c_str());
data/trinculo-0.96+dfsg/src/readBed.h:194:7:  [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).
  bed.open((string(inprefix) + ".bed").c_str(), ios::in|ios::binary|ios::ate);
data/trinculo-0.96+dfsg/src/readBed.h:264:7:  [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).
  fam.open((string(inprefix) + ".fam").c_str());
data/trinculo-0.96+dfsg/src/readBed.h:273:7:  [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).
  bim.open((string(inprefix) + ".bim").c_str());
data/trinculo-0.96+dfsg/src/readBed.h:287:7:  [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).
  bed.open((string(inprefix) + ".bed").c_str(), ios::out|ios::binary);
data/trinculo-0.96+dfsg/src/readCovar.h:52:11:  [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).
  covfile.open(infile.c_str());
data/trinculo-0.96+dfsg/src/readDosage.h:56:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  dosage.open(infile.c_str());
data/trinculo-0.96+dfsg/src/readPhenos.h:45:13:  [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).
  phenofile.open(infile.c_str());
data/trinculo-0.96+dfsg/src/readPriors.h:45:13:  [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).
  priorfile.open(infile.c_str());
data/trinculo-0.96+dfsg/src/sims.cpp:44:11:  [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).
    input.open(argv[1]);
data/trinculo-0.96+dfsg/src/sims.cpp:56:45:  [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).
			if (splitline[0] == "Npheno:") {Npheno = atoi(splitline[1].c_str()); continue;}
data/trinculo-0.96+dfsg/src/sims.cpp:57:52:  [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).
      	  	if (splitline[0] == "Ncovar:") {Ncovar = atoi(splitline[1].c_str()); continue;}
data/trinculo-0.96+dfsg/src/sims.cpp:58:48:  [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).
      	  	if (splitline[0] == "Nvar:") {Nvar = atoi(splitline[1].c_str()); continue;}
data/trinculo-0.96+dfsg/src/sims.cpp:70:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		input.open(covFile.c_str());
data/trinculo-0.96+dfsg/src/sims.cpp:100:18:  [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).
				Ncounts[j] = atoi(conflines[i][1 + j].c_str());
data/trinculo-0.96+dfsg/src/sims.cpp:343:15:  [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).
    covarFILE.open((string(argv[2]) + ".covar").c_str());
data/trinculo-0.96+dfsg/src/sims.cpp:344:15:  [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).
    phenoFILE.open((string(argv[2]) + ".pheno").c_str());
data/trinculo-0.96+dfsg/src/trinculo.cpp:54:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char       buf[80];
data/trinculo-0.96+dfsg/src/trinculo.cpp:206:11:  [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).
  outfile.open((opts->outprefix + ".assoc.ordinal").c_str());
data/trinculo-0.96+dfsg/src/trinculo.cpp:322:11:  [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).
  outfile.open((opts->outprefix + ".assoc.multinom").c_str());
data/trinculo-0.96+dfsg/src/trinculo.cpp:323:37:  [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).
  if (opts->modelSelect) selectfile.open((opts->outprefix + ".select.multinom").c_str());
data/trinculo-0.96+dfsg/src/trinculo.cpp:324:33:  [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).
  if (opts->outputErrs) errfile.open((opts->outprefix + ".err.multinom").c_str());
data/trinculo-0.96+dfsg/src/trinculo.cpp:325:31:  [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).
  if (opts->PhenoPs) pvalfile.open((opts->outprefix + ".phenops.multinom").c_str());
data/trinculo-0.96+dfsg/src/trinculo.cpp:327:16:  [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).
	  fullerrfile.open((opts->outprefix + ".fullmd.errs").c_str());
data/trinculo-0.96+dfsg/src/trinculo.cpp:328:16:  [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).
	  fullparfile.open((opts->outprefix + ".fullmd.pars").c_str());
data/trinculo-0.96+dfsg/src/trinculo.cpp:331:11:  [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).
  	sefile.open((opts->outprefix + ".ses.multinom").c_str());
data/trinculo-0.96+dfsg/src/trinculo.cpp:572:11:  [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).
  logfile.open((opts.outprefix + ".log").c_str());
data/trinculo-0.96+dfsg/src/trinculo.cpp:600:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    file.open(opts.conditionfile.c_str());
data/trinculo-0.96+dfsg/src/trinculo.cpp:656:13:  [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).
		  outfile.open((opts.outprefix + ".prior").c_str());
data/trinculo-0.96+dfsg/src/readBed.h:200:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      bed.read (bedblock, size);

ANALYSIS SUMMARY:

Hits = 35
Lines analyzed = 3908 in approximately 0.14 seconds (28787 lines/second)
Physical Source Lines of Code (SLOC) = 2930
Hits@level = [0]   0 [1]   1 [2]  33 [3]   1 [4]   0 [5]   0
Hits@level+ = [0+]  35 [1+]  35 [2+]  34 [3+]   1 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 11.9454 [1+] 11.9454 [2+] 11.6041 [3+] 0.341297 [4+]   0 [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.