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/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/samRead.cpp
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/empdist.h
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art.h
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/readSeqFile.h
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/seqRead.h
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/seqRead.cpp
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina.cpp
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/empdist.cpp
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina_m.cpp
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/readSeqFile.cpp
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/samRead.h
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_qual_scale.cpp
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/samRead.cpp
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/read_SOLiD.cpp
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/art.h
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/readSeqFile.h
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/utility.hpp
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/readSeqFile.cpp
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/art_SOLiD_jason.cpp
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/read_SOLiD.h
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/art.cpp
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/samRead.h
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/art_SOLiD.cpp
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_454_src/samRead.cpp
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_454_src/read_profile.cpp
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_454_src/art.h
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_454_src/readSeqFile.h
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_454_src/read_profile.h
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_454_src/seqRead.h
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_454_src/seqRead.cpp
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_454_src/readSeqFile.cpp
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_454_src/art.cpp
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_454_src/samRead.h
Examining data/art-nextgen-simulation-tools-20160605+dfsg/art_454_src/art_454.cpp

FINAL RESULTS:

data/art-nextgen-simulation-tools-20160605+dfsg/art_454_src/art_454.cpp:166:5:  [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(rand_seed);
data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/art_SOLiD.cpp:216:5:  [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(rand_seed);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina.cpp:418:5:  [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 (rand_seed);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina_m.cpp:415:5:  [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 (rand_seed);
data/art-nextgen-simulation-tools-20160605+dfsg/art_454_src/art_454.cpp:93:38:  [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(i<argc) num_flow_cycles = atoi(argv[++i]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_454_src/art_454.cpp:98:21:  [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).
					    rand_seed =atoi(argv[++i]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_454_src/art_454.cpp:181:17:  [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).
	fsize_mean=abs(atoi(argv[i+3]));
data/art-nextgen-simulation-tools-20160605+dfsg/art_454_src/art_454.cpp:203:14:  [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).
	    SAMFILE.open(samfile.c_str(),ios::binary); 
data/art-nextgen-simulation-tools-20160605+dfsg/art_454_src/art_454.cpp:212:14:  [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).
	    ALNFILE.open(alnfasta.c_str(),ios::binary);
data/art-nextgen-simulation-tools-20160605+dfsg/art_454_src/art_454.cpp:279:19:  [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).
	       	ALNFILE2.open(alnfasta2.c_str(),ios::binary);
data/art-nextgen-simulation-tools-20160605+dfsg/art_454_src/readSeqFile.cpp:45:12:  [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(fileName);
data/art-nextgen-simulation-tools-20160605+dfsg/art_454_src/readSeqFile.cpp:139:12:  [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(file_name);
data/art-nextgen-simulation-tools-20160605+dfsg/art_454_src/read_profile.h:122:5:  [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 cyc_base[4];
data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/art_SOLiD.cpp:127:21:  [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).
					    rand_seed =atoi(argv[++i]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/art_SOLiD.cpp:229:21:  [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).
    int read_len  = atoi(argv[i+2]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/art_SOLiD.cpp:244:25:  [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).
	       	fsize_mean=abs(atoi(argv[i+4]));
data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/art_SOLiD.cpp:250:25:  [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).
	       	read_len_R3F5 =atoi(argv[i+3]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/art_SOLiD.cpp:255:25:  [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).
	       	fsize_mean=abs(atoi(argv[i+5]));
data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/art_SOLiD.cpp:273:25:  [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).
	       	read_len_R3F5 =atoi(argv[i+3]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/art_SOLiD.cpp:318:14:  [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).
	    SAMFILE.open(samfile.c_str(),ios::binary); 
data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/art_SOLiD_jason.cpp:99:28:  [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).
                read_len = atoi(argv[i]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/art_SOLiD_jason.cpp:135:24:  [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).
                mean = atoi(argv[i]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/readSeqFile.cpp:45:12:  [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(fileName);
data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/readSeqFile.cpp:137:12:  [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(file_name);
data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/read_SOLiD.cpp:86:5:  [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 base_type[4]={'0','1','2','3'}; //color space
data/art-nextgen-simulation-tools-20160605+dfsg/art_SOLiD_src/utility.hpp:36:2:  [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 error_color[3]; //error color 	
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina.cpp:135:15:  [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).
		max_num_n = atoi(argv[i]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina.cpp:161:14:  [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).
		read_len = atoi(argv[i]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina.cpp:170:17:  [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).
		maxNumIndel = atoi(argv[i]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina.cpp:197:15:  [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).
		read_count= atoi(argv[i]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina.cpp:205:10:  [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).
		mean = atoi(argv[i]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina.cpp:213:16:  [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).
		min_qual_s = atoi(argv[i]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina.cpp:220:16:  [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).
		max_qual_s = atoi(argv[i]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina.cpp:227:16:  [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).
		q_shift_up = atoi(argv[i]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina.cpp:231:18:  [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).
		q_shift_up_2 = atoi(argv[i]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina.cpp:260:19:  [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).
		rand_seed = abs(atoi(argv[i]));
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina.cpp:430:14:  [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).
	    SAMFILE.open(samfile.c_str(),ios::binary); 
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina.cpp:433:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		    SAMFILE_EF.open(samfile_ef.c_str(),ios::binary); 
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina.cpp:442:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	       	ALNFILE.open(alnfasta.c_str(),ios::binary);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina.cpp:662:19:  [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).
	       	ALNFILE2.open(alnfasta2.c_str(),ios::binary);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina_m.cpp:135:15:  [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).
		max_num_n = atoi(argv[i]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina_m.cpp:161:14:  [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).
		read_len = atoi(argv[i]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina_m.cpp:194:15:  [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).
		read_count= atoi(argv[i]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina_m.cpp:202:10:  [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).
		mean = atoi(argv[i]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina_m.cpp:210:16:  [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).
		min_qual_s = atoi(argv[i]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina_m.cpp:217:16:  [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).
		max_qual_s = atoi(argv[i]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina_m.cpp:224:16:  [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).
		q_shift_up = atoi(argv[i]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina_m.cpp:228:18:  [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).
		q_shift_up_2 = atoi(argv[i]);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina_m.cpp:257:19:  [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).
		rand_seed = abs(atoi(argv[i]));
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina_m.cpp:427:14:  [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).
	    SAMFILE.open(samfile.c_str(),ios::binary); 
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina_m.cpp:430:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
		    SAMFILE_EF.open(samfile_ef.c_str(),ios::binary); 
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina_m.cpp:439:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
	       	ALNFILE.open(alnfasta.c_str(),ios::binary);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/art_illumina_m.cpp:672:19:  [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).
	       	ALNFILE2.open(alnfasta2.c_str(),ios::binary);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/readSeqFile.cpp:45:12:  [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(fileName);
data/art-nextgen-simulation-tools-20160605+dfsg/art_illumina_src/readSeqFile.cpp:139:12:  [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(file_name);

ANALYSIS SUMMARY:

Hits = 55
Lines analyzed = 10418 in approximately 5.86 seconds (1778 lines/second)
Physical Source Lines of Code (SLOC) = 7952
Hits@level = [0]   0 [1]   0 [2]  51 [3]   4 [4]   0 [5]   0
Hits@level+ = [0+]  55 [1+]  55 [2+]  55 [3+]   4 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 6.9165 [1+] 6.9165 [2+] 6.9165 [3+] 0.503018 [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.