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/wham-align-0.1.5/hash.h
Examining data/wham-align-0.1.5/main.cpp
Examining data/wham-align-0.1.5/unittest.cpp
Examining data/wham-align-0.1.5/builder.cpp
Examining data/wham-align-0.1.5/short.h
Examining data/wham-align-0.1.5/model.h
Examining data/wham-align-0.1.5/edit_distance.cpp
Examining data/wham-align-0.1.5/error.h
Examining data/wham-align-0.1.5/writer.cpp
Examining data/wham-align-0.1.5/short.cpp
Examining data/wham-align-0.1.5/aligner.h
Examining data/wham-align-0.1.5/hitset.cpp
Examining data/wham-align-0.1.5/aligner.cpp
Examining data/wham-align-0.1.5/hash.cpp
Examining data/wham-align-0.1.5/perfcounters.h
Examining data/wham-align-0.1.5/util.h
Examining data/wham-align-0.1.5/embedhash.cpp
Examining data/wham-align-0.1.5/sequence.cpp
Examining data/wham-align-0.1.5/edit_distance.h
Examining data/wham-align-0.1.5/model.cpp
Examining data/wham-align-0.1.5/embedhash.h
Examining data/wham-align-0.1.5/error.cpp
Examining data/wham-align-0.1.5/lib.h
Examining data/wham-align-0.1.5/sorter.cpp
Examining data/wham-align-0.1.5/rdtsc.h
Examining data/wham-align-0.1.5/writer.h
Examining data/wham-align-0.1.5/bitread.h
Examining data/wham-align-0.1.5/hitset.h
Examining data/wham-align-0.1.5/interval.h
Examining data/wham-align-0.1.5/sequence.h
Examining data/wham-align-0.1.5/interval.cpp
Examining data/wham-align-0.1.5/pair.h
Examining data/wham-align-0.1.5/perfcounters.cpp

FINAL RESULTS:

data/wham-align-0.1.5/aligner.cpp:1809:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    sprintf(fname, "%s.p%d", filename, i * step);
data/wham-align-0.1.5/aligner.cpp:1859:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    sprintf(command, "rm -f %s.p%d", filename, i * step);
data/wham-align-0.1.5/aligner.cpp:1860:5:  [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.
    system(command);
data/wham-align-0.1.5/aligner.cpp:1918:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    sprintf(fname, "%s.m1.p%d", filename, i * step);
data/wham-align-0.1.5/aligner.cpp:1928:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    sprintf(fname, "%s.m2.p%d", filename, i * step);
data/wham-align-0.1.5/aligner.cpp:2001:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    sprintf(command, "rm -f %s.m1.p%d", filename, i * step);
data/wham-align-0.1.5/aligner.cpp:2002:5:  [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.
    system(command);
data/wham-align-0.1.5/aligner.cpp:2003:5:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    sprintf(command, "rm -f %s.m2.p%d", filename, i * step);
data/wham-align-0.1.5/aligner.cpp:2004:5:  [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.
    system(command);
data/wham-align-0.1.5/aligner.cpp:2040:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
  sprintf(fname, "%s.head.whm", path);
data/wham-align-0.1.5/aligner.cpp:2120:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
  sprintf(fname, "%s.head.whm", path);
data/wham-align-0.1.5/aligner.cpp:2215:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
  sprintf(fname, "%s.head.whm", path);
data/wham-align-0.1.5/aligner.cpp:2283:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
  sprintf(fname, "%s.head.whm", path);
data/wham-align-0.1.5/builder.cpp:60:40:  [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).
    tok[i] = new char[strlen(pch) + 1];strcpy(tok[i], pch);
data/wham-align-0.1.5/builder.cpp:80:5:  [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(str, argv[i]);
data/wham-align-0.1.5/builder.cpp:217:9:  [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(basepath, argv[i]);
data/wham-align-0.1.5/edit_distance.cpp:296:5:  [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(line, tmp);
data/wham-align-0.1.5/edit_distance.cpp:304:7:  [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(line, tmp);
data/wham-align-0.1.5/edit_distance.cpp:308:7:  [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(line, tmp);
data/wham-align-0.1.5/error.cpp:37:5:  [4] (format) vprintf:
  If format strings can be influenced by an attacker, they can be exploited
  (CWE-134). Use a constant for the format specification.
    vprintf(format, args);
data/wham-align-0.1.5/hash.cpp:1781:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
  sprintf(fname, "%s.i%d.whm", path, indexID);
data/wham-align-0.1.5/hash.cpp:1853:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
  sprintf(fname, "%s.i%d.whm", path, index);
data/wham-align-0.1.5/interval.cpp:289:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
  sprintf(fname, "%s.interval.whm", path);
data/wham-align-0.1.5/interval.cpp:341:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
  sprintf(fname, "%s.interval.whm", path);
data/wham-align-0.1.5/main.cpp:119:40:  [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).
    tok[i] = new char[strlen(pch) + 1];strcpy(tok[i], pch);
data/wham-align-0.1.5/main.cpp:253:5:  [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(str, argv[i]);
data/wham-align-0.1.5/main.cpp:273:3:  [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.
  system(command.c_str());
data/wham-align-0.1.5/main.cpp:278:5:  [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.
    system(command.c_str());
data/wham-align-0.1.5/main.cpp:465:9:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
        sprintf(infos[i].outputpath, "%s.t%d", outputpath, i);
data/wham-align-0.1.5/main.cpp:578:7:  [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(alignFileName, argv[++i]);
data/wham-align-0.1.5/main.cpp:581:7:  [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(unalignFileName, argv[++i]);
data/wham-align-0.1.5/main.cpp:642:9:  [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(basepath, argv[i]);
data/wham-align-0.1.5/main.cpp:644:9:  [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(outputpath, argv[i]);
data/wham-align-0.1.5/main.cpp:713:7:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
      sprintf(alFileName1, "%s_1", alignFileName);
data/wham-align-0.1.5/main.cpp:714:7:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
      sprintf(alFileName2, "%s_2", alignFileName);
data/wham-align-0.1.5/main.cpp:720:7:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
      sprintf(unFileName1, "%s_1", unalignFileName);
data/wham-align-0.1.5/main.cpp:721:7:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
      sprintf(unFileName2, "%s_2", unalignFileName);
data/wham-align-0.1.5/sequence.cpp:723:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
  sprintf(fname, "%s.sequence.whm", path);
data/wham-align-0.1.5/sequence.cpp:788:3:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
  sprintf(fname, "%s.sequence.whm", path);
data/wham-align-0.1.5/short.cpp:100:5:  [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(fnames[i], files[i]);
data/wham-align-0.1.5/short.cpp:112:5:  [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(alFileName, alignFileName);
data/wham-align-0.1.5/short.cpp:123:5:  [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(unFileName, unalignFileName);
data/wham-align-0.1.5/short.cpp:503:7:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
      sprintf(partitions[i]->alFileName, "%s.t%d", alFileName, i);
data/wham-align-0.1.5/short.cpp:510:7:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
      sprintf(partitions[i]->unFileName, "%s.t%d", unFileName, i);
data/wham-align-0.1.5/short.h:167:5:  [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(str1, str2);
data/wham-align-0.1.5/sorter.cpp:49:3:  [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(basepath, argv[1]);
data/wham-align-0.1.5/sorter.cpp:50:3:  [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(newpath, argv[2]);
data/wham-align-0.1.5/builder.cpp:165:3:  [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/wham-align-0.1.5/main.cpp:544:3:  [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/wham-align-0.1.5/perfcounters.cpp:54:17:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  if ((event0 = getenv("EVENT0")) == NULL) {
data/wham-align-0.1.5/perfcounters.cpp:58:17:  [3] (buffer) getenv:
  Environment variables are untrustable input if they can be set by an
  attacker. They can have any content and length, and the same variable can
  be set more than once (CWE-807, CWE-20). Check environment variables
  carefully before using them.
  if ((event1 = getenv("EVENT1")) == NULL) {
data/wham-align-0.1.5/sorter.cpp:47:3:  [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/wham-align-0.1.5/aligner.cpp:1646:3:  [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 mateFilename[256];
data/wham-align-0.1.5/aligner.cpp:1779:3:  [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 fname[MAX_LENGTH_PATH];
data/wham-align-0.1.5/aligner.cpp:1857:3:  [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 command[MAX_LENGTH_PATH];
data/wham-align-0.1.5/aligner.cpp:1879:3:  [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 fname[MAX_LENGTH_PATH];
data/wham-align-0.1.5/aligner.cpp:1999:3:  [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 command[MAX_LENGTH_PATH];
data/wham-align-0.1.5/aligner.cpp:2031:3:  [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 fname[MAX_LENGTH_PATH];
data/wham-align-0.1.5/aligner.cpp:2041:10:  [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).
  file = fopen(fname, "wb");
data/wham-align-0.1.5/aligner.cpp:2111:3:  [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 fname[256];
data/wham-align-0.1.5/aligner.cpp:2121:10:  [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).
  file = fopen(fname, "rb");
data/wham-align-0.1.5/aligner.cpp:2209:3:  [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 fname[256];
data/wham-align-0.1.5/aligner.cpp:2216:10:  [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).
  file = fopen(fname, "wb");
data/wham-align-0.1.5/aligner.cpp:2277:3:  [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 fname[256];
data/wham-align-0.1.5/aligner.cpp:2284:10:  [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).
  file = fopen(fname, "rb");
data/wham-align-0.1.5/builder.cpp:56:13:  [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.
  tok = new char *[num];
data/wham-align-0.1.5/builder.cpp:109:12:  [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(str);
data/wham-align-0.1.5/builder.cpp:121:17:  [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).
  return base * atoi(str);
data/wham-align-0.1.5/builder.cpp:163:3:  [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 basepath[128] = "";
data/wham-align-0.1.5/edit_distance.cpp:290:3:  [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[100] = "";
data/wham-align-0.1.5/edit_distance.cpp:294:5:  [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 tmp[4] = "";
data/wham-align-0.1.5/edit_distance.cpp:295:5:  [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(tmp, "%c ", seq_1[j]);
data/wham-align-0.1.5/edit_distance.cpp:301:5:  [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 tmp[4] = "";
data/wham-align-0.1.5/edit_distance.cpp:303:7:  [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(tmp, "%c ", seq_2[i - 1]);
data/wham-align-0.1.5/edit_distance.cpp:307:7:  [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(tmp, "%c ", traceback[i][j]);
data/wham-align-0.1.5/edit_distance.cpp:358:13:  [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).
  int prm = atoi(argv[3]);
data/wham-align-0.1.5/edit_distance.cpp:363:3:  [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 query_align[MAX],db_align[MAX];
data/wham-align-0.1.5/hash.cpp:1122:3:  [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 str[128];
data/wham-align-0.1.5/hash.cpp:1145:3:  [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 keystr[128];
data/wham-align-0.1.5/hash.cpp:1397:63:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            counters = new EntryCounter[numEntryCounter * 10];memcpy
data/wham-align-0.1.5/hash.cpp:1485:5:  [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(&overflowPool[offset], pool, sizeof(uint32) * nhit);
data/wham-align-0.1.5/hash.cpp:1580:52:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            tmp = new EntryCounter[numCounter * 2];memcpy
data/wham-align-0.1.5/hash.cpp:1733:52:  [2] (buffer) memcpy:
  Does not check for buffer overflows when copying to destination (CWE-120).
  Make sure destination can always hold the source data.
            tmp = new EntryCounter[numCounter * 2];memcpy
data/wham-align-0.1.5/hash.cpp:1775:3:  [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 fname[256];
data/wham-align-0.1.5/hash.cpp:1782:10:  [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).
  file = fopen(fname, "wb");
data/wham-align-0.1.5/hash.cpp:1847:3:  [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 fname[256];
data/wham-align-0.1.5/hash.cpp:1854:10:  [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).
  file = fopen(fname, "rb");
data/wham-align-0.1.5/hash.h:264:3:  [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 seq1[256];
data/wham-align-0.1.5/hash.h:265:3:  [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 seq2[256];
data/wham-align-0.1.5/hash.h:266:3:  [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 align1[256];
data/wham-align-0.1.5/hash.h:267:3:  [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 align2[256];
data/wham-align-0.1.5/hash.h:354:5:  [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(keyPartitions, partitions, sizeof(int) * nPartition);
data/wham-align-0.1.5/hitset.h:73:3:  [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 str[256];
data/wham-align-0.1.5/interval.cpp:283:3:  [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 fname[256];
data/wham-align-0.1.5/interval.cpp:290:10:  [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).
  file = fopen(fname, "wb");
data/wham-align-0.1.5/interval.cpp:335:3:  [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 fname[256];
data/wham-align-0.1.5/interval.cpp:342:10:  [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).
  file = fopen(fname, "rb");
data/wham-align-0.1.5/main.cpp:51:1:  [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 outputpath[MAX_LENGTH_PATH] = "";
data/wham-align-0.1.5/main.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 outputpath[MAX_LENGTH_PATH];
data/wham-align-0.1.5/main.cpp:115:13:  [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.
  tok = new char *[num];
data/wham-align-0.1.5/main.cpp:153:12:  [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(str);
data/wham-align-0.1.5/main.cpp:165:17:  [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).
  return base * atoi(str);
data/wham-align-0.1.5/main.cpp:265:3:  [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 buf[10];
data/wham-align-0.1.5/main.cpp:269:5:  [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(buf, ".t%d ", i);
data/wham-align-0.1.5/main.cpp:276:5:  [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(buf, ".t%d", i);
data/wham-align-0.1.5/main.cpp:533:3:  [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 basepath[256] = "";
data/wham-align-0.1.5/main.cpp:555:16:  [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).
      maxlen = atoi(argv[++i]);
data/wham-align-0.1.5/main.cpp:557:11:  [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).
      k = atoi(argv[++i]);
data/wham-align-0.1.5/main.cpp:559:11:  [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).
      m = atoi(argv[++i]);
data/wham-align-0.1.5/main.cpp:563:17:  [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).
      maxqual = atoi(argv[++i]);
data/wham-align-0.1.5/main.cpp:565:16:  [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).
      maxerr = atoi(argv[++i]);
data/wham-align-0.1.5/main.cpp:567:16:  [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).
      maxgap = atoi(argv[++i]);
data/wham-align-0.1.5/main.cpp:571:17:  [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).
      nThread = atoi(argv[++i]);
data/wham-align-0.1.5/main.cpp:575:17:  [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).
      maxMate = atoi(argv[++i]);
data/wham-align-0.1.5/main.cpp:611:16:  [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).
      minins = atoi(argv[++i]);
data/wham-align-0.1.5/main.cpp:613:16:  [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).
      maxins = atoi(argv[++i]);
data/wham-align-0.1.5/main.cpp:780:3:  [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(info.pairStrand, pairStrand, 4 * sizeof(bool));
data/wham-align-0.1.5/model.cpp:161:10:  [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).
  file = fopen("/proc/meminfo", "r");
data/wham-align-0.1.5/pair.h:344:5:  [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 keyStr[129], targetStr[129];
data/wham-align-0.1.5/pair.h:604:5:  [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 x[130];
data/wham-align-0.1.5/pair.h:605:5:  [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 y[130];
data/wham-align-0.1.5/pair.h:687:5:  [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[130], query[130];
data/wham-align-0.1.5/pair.h:758:5:  [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[130], query[130];
data/wham-align-0.1.5/sequence.cpp:37:7:  [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 code2Gene[8] = { 'A', 'C', 'G', 'T', 'N', 'N', 'N', 'N' };
data/wham-align-0.1.5/sequence.cpp:140:10:  [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).
  file = fopen(fname, "rb");
data/wham-align-0.1.5/sequence.cpp:307:18:  [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.
  seqNames = new char *[nSeq];
data/wham-align-0.1.5/sequence.cpp:326:12:  [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 = fopen(fname[i], "rb");
data/wham-align-0.1.5/sequence.cpp:526:20:  [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 * outfile = fopen(path, "w");
data/wham-align-0.1.5/sequence.cpp:536:12:  [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 = fopen(fname[i], "rb");
data/wham-align-0.1.5/sequence.cpp:548:9:  [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 str[256];
data/wham-align-0.1.5/sequence.cpp:717:3:  [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 fname[MAX_LENGTH_PATH];
data/wham-align-0.1.5/sequence.cpp:724:10:  [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).
  file = fopen(fname, "wb");
data/wham-align-0.1.5/sequence.cpp:782:3:  [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 fname[256];
data/wham-align-0.1.5/sequence.cpp:789:10:  [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).
  file = fopen(fname, "rb");
data/wham-align-0.1.5/short.cpp:34:3:  [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(this, read, sizeof(ShortRead));
data/wham-align-0.1.5/short.cpp:93:16:  [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.
  fnames = new char *[numFile];
data/wham-align-0.1.5/short.cpp:114:14:  [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).
    alfile = fopen(alignFileName, "w");
data/wham-align-0.1.5/short.cpp:125:14:  [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).
    unfile = fopen(unalignFileName, "w");
data/wham-align-0.1.5/short.cpp:192:3:  [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 str[256];
data/wham-align-0.1.5/short.cpp:204:12:  [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 = fopen(fnames[i], "r");
data/wham-align-0.1.5/short.cpp:312:3:  [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 str[256];
data/wham-align-0.1.5/short.cpp:335:12:  [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 = fopen(fnames[k], "r");
data/wham-align-0.1.5/short.cpp:504:31:  [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).
      partitions[i]->alfile = fopen(partitions[i]->alFileName, "w");
data/wham-align-0.1.5/short.cpp:511:31:  [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).
      partitions[i]->unfile = fopen(partitions[i]->unFileName, "w");
data/wham-align-0.1.5/short.cpp:522:3:  [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 readstr[256];
data/wham-align-0.1.5/short.h:59:3:  [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 alFileName[256];
data/wham-align-0.1.5/short.h:60:3:  [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 unFileName[256];
data/wham-align-0.1.5/short.h:65:3:  [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 code2Base[8];
data/wham-align-0.1.5/sorter.cpp: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 basepath[256] = "";
data/wham-align-0.1.5/sorter.cpp:45:3:  [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 newpath[256] = "";
data/wham-align-0.1.5/unittest.cpp:29:3:  [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 str[1024], str1[256];
data/wham-align-0.1.5/unittest.cpp:30:3:  [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 * fname[1];
data/wham-align-0.1.5/unittest.cpp:36:3:  [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(fname[1], "./tmp_test.fa");
data/wham-align-0.1.5/unittest.cpp:40:17:  [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).
  FILE * file = fopen(fname[1], "w");
data/wham-align-0.1.5/unittest.cpp:82:3:  [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 str1[256], str2[256];
data/wham-align-0.1.5/unittest.cpp:134:3:  [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 str1[256], str2[256];
data/wham-align-0.1.5/writer.cpp:30:7:  [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 code2Gene[8] = { 'A', 'C', 'G', 'T', 'N', 'N', 'N', 'N' };
data/wham-align-0.1.5/writer.cpp:35:3:  [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 qseq[128], rseq[128];
data/wham-align-0.1.5/writer.cpp:36:3:  [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 field[128];
data/wham-align-0.1.5/writer.cpp:96:9:  [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, "%2d:%c>%c,", i, reference[j], query[i]);
data/wham-align-0.1.5/writer.cpp:100:9:  [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, "%2d:_>%c,", i, query[i]);
data/wham-align-0.1.5/writer.cpp:105:9:  [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, "%2d:%c>_,", i, reference[j]);
data/wham-align-0.1.5/writer.cpp:122:9:  [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, "%2d:%c>%c,", len - 1 - i, reference[j], query[i]);
data/wham-align-0.1.5/writer.cpp:126:9:  [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, "%2d:_>%c,", len - 1 - i, query[i]);
data/wham-align-0.1.5/writer.cpp:131:9:  [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, "%2d:%c>_,", len - 1 - i, reference[j]);
data/wham-align-0.1.5/writer.cpp:225:3:  [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 shortread[128];
data/wham-align-0.1.5/writer.cpp:279:3:  [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 qseq[128], rseq[128], tag[128];
data/wham-align-0.1.5/writer.cpp:280:3:  [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 cigar[128];
data/wham-align-0.1.5/writer.cpp:281:3:  [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 shortread[256];
data/wham-align-0.1.5/writer.cpp:333:3:  [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 queryStr[128];
data/wham-align-0.1.5/writer.cpp:357:3:  [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 mdstr[256];
data/wham-align-0.1.5/writer.cpp:375:5:  [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(str, "%dM", (int) strlen(query));
data/wham-align-0.1.5/writer.cpp:392:9:  [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, "%dM", j - lastErrPos);
data/wham-align-0.1.5/writer.cpp:393:7:  [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(str, "1I");
data/wham-align-0.1.5/writer.cpp:400:9:  [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, "%dM", j - lastErrPos);
data/wham-align-0.1.5/writer.cpp:401:7:  [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(str, "1D");
data/wham-align-0.1.5/writer.cpp:413:5:  [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(str, "%dM", j - lastErrPos);
data/wham-align-0.1.5/writer.cpp:424:5:  [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(str, "%d", (int) strlen(query));
data/wham-align-0.1.5/writer.cpp:437:7:  [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(str, "%d", j - lastErrPos);
data/wham-align-0.1.5/writer.cpp:449:7:  [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(str, "%d", j - lastErrPos);
data/wham-align-0.1.5/writer.cpp:464:3:  [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, "%d", j - lastErrPos);
data/wham-align-0.1.5/writer.cpp:513:3:  [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 queryStr1[128], queryStr2[128], rcQualStr1[128], rcQualStr2[128];
data/wham-align-0.1.5/writer.cpp:514:3:  [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 refStr1[128], refStr2[128];
data/wham-align-0.1.5/writer.cpp:515:3:  [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 cigar1[16], cigar2[16];
data/wham-align-0.1.5/writer.cpp:671:3:  [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 queryStr1[128], queryStr2[128];
data/wham-align-0.1.5/writer.h:51:12:  [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 = fopen(fname, "w");
data/wham-align-0.1.5/writer.h:204:12:  [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 = fopen(fname, "r");
data/wham-align-0.1.5/aligner.cpp:1099:42:  [1] (buffer) getchar:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    HASH_DEBUG(printf("\n")); HASH_DEBUG(getchar());
data/wham-align-0.1.5/aligner.cpp:1213:48:  [1] (buffer) getchar:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
          HASH_DEBUG(printf("\n")); HASH_DEBUG(getchar());
data/wham-align-0.1.5/aligner.cpp:1399:40:  [1] (buffer) getchar:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  HASH_DEBUG(printf("\n")); HASH_DEBUG(getchar());
data/wham-align-0.1.5/aligner.cpp:1524:43:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      writer = new SimpleWriter(sequence, read, filename);
data/wham-align-0.1.5/aligner.cpp:1527:40:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      writer = new SamWriter(sequence, read, filename);
data/wham-align-0.1.5/aligner.cpp:2034:7:  [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(path) > 240)
data/wham-align-0.1.5/aligner.cpp:2114:7:  [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(path) > 240)
data/wham-align-0.1.5/aligner.cpp:2212:7:  [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(path) > 240)
data/wham-align-0.1.5/aligner.cpp:2259:7:  [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(path) > 240)
data/wham-align-0.1.5/aligner.cpp:2280:7:  [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(path) > 240)
data/wham-align-0.1.5/aligner.cpp:2356:7:  [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(path) > 240)
data/wham-align-0.1.5/builder.cpp:60:23:  [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).
    tok[i] = new char[strlen(pch) + 1];strcpy(tok[i], pch);
data/wham-align-0.1.5/builder.cpp:73:12:  [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).
    len += strlen(argv[i]) + 1;
data/wham-align-0.1.5/builder.cpp:79:7:  [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(str, " ");
data/wham-align-0.1.5/edit_distance.cpp:360:15:  [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).
  int q_len = strlen(query);
data/wham-align-0.1.5/edit_distance.cpp:361:16:  [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 db_len = strlen(db);
data/wham-align-0.1.5/hash.cpp:1247:29:  [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).
        for (int j = 0; j < strlen(set[i].str); j++)
data/wham-align-0.1.5/hash.cpp:1254:27:  [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 (int j = 0; j < strlen(set[i].str); j++)
data/wham-align-0.1.5/hash.cpp:1778:7:  [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(path) > 240)
data/wham-align-0.1.5/hash.cpp:1850:7:  [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(path) > 240)
data/wham-align-0.1.5/interval.cpp:286:7:  [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(path) > 240)
data/wham-align-0.1.5/interval.cpp:338:7:  [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(path) > 240)
data/wham-align-0.1.5/main.cpp:91:9:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    c = fgetc(file);
data/wham-align-0.1.5/main.cpp:119:23:  [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).
    tok[i] = new char[strlen(pch) + 1];strcpy(tok[i], pch);
data/wham-align-0.1.5/main.cpp:246:12:  [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).
    len += strlen(argv[i]) + 1;
data/wham-align-0.1.5/main.cpp:252:7:  [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(str, " ");
data/wham-align-0.1.5/pair.h:674:7:  [1] (buffer) getchar:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      getchar();
data/wham-align-0.1.5/sequence.cpp:62:9:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    c = fgetc(file);
data/wham-align-0.1.5/sequence.cpp:80:14:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    str[i] = fgetc(file);
data/wham-align-0.1.5/sequence.cpp:100:9:  [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).
  end = strlen(src) - 1;
data/wham-align-0.1.5/sequence.cpp:101:16:  [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 (int i = strlen(src) - 1; i >= 0; i--) {
data/wham-align-0.1.5/sequence.cpp:117:3:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
  strncpy(dest, &src[start], end - start + 1);
data/wham-align-0.1.5/sequence.cpp:151:15:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  while ((c = fgetc(file)) != EOF) {
data/wham-align-0.1.5/sequence.cpp:332:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(file)) != EOF) {
data/wham-align-0.1.5/sequence.cpp:542:17:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    while ((c = fgetc(file)) != EOF) {
data/wham-align-0.1.5/sequence.cpp:554:20:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
          str[j] = fgetc(file);
data/wham-align-0.1.5/sequence.cpp:720:7:  [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(path) > 240)
data/wham-align-0.1.5/sequence.cpp:785:7:  [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(path) > 240)
data/wham-align-0.1.5/short.cpp:33:34:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
ShortRead::ShortRead(ShortRead * read) {
data/wham-align-0.1.5/short.cpp:34:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  memcpy(this, read, sizeof(ShortRead));
data/wham-align-0.1.5/short.cpp:53:9:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    c = fgetc(file);
data/wham-align-0.1.5/short.cpp:97:9:  [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(files[i]) >= 256)
data/wham-align-0.1.5/short.cpp:353:11:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
          strncpy(&quals[curRead * lenQual], str, length);
data/wham-align-0.1.5/short.h:68:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  ShortRead(ShortRead * read);
data/wham-align-0.1.5/short.h:156:14:  [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).
      return strlen(str) + 1;
data/wham-align-0.1.5/writer.cpp:86:9:  [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).
  len = strlen(query);
data/wham-align-0.1.5/writer.cpp:142:7:  [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).
  str[strlen(str) - 1] = '\0';
data/wham-align-0.1.5/writer.cpp:375:31:  [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(str, "%dM", (int) strlen(query));
data/wham-align-0.1.5/writer.cpp:382:26:  [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, j = 0; i < strlen(query); i++, j++) {
data/wham-align-0.1.5/writer.cpp:394:14:  [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).
      str += strlen(str);
data/wham-align-0.1.5/writer.cpp:402:14:  [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).
      str += strlen(str);
data/wham-align-0.1.5/writer.cpp:424:30:  [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).
    sprintf(str, "%d", (int) strlen(query));
data/wham-align-0.1.5/writer.cpp:431:26:  [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, j = 0; i < strlen(query); i++, j++) {
data/wham-align-0.1.5/writer.cpp:438:14:  [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).
      str += strlen(str);
data/wham-align-0.1.5/writer.cpp:450:14:  [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).
      str += strlen(str);
data/wham-align-0.1.5/writer.cpp:606:7:  [1] (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 character.
      strcpy(cigar1, "*");
data/wham-align-0.1.5/writer.cpp:611:7:  [1] (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 character.
      strcpy(cigar2, "*");
data/wham-align-0.1.5/writer.cpp:701:13:  [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).
  int len = strlen(str1);

ANALYSIS SUMMARY:

Hits = 245
Lines analyzed = 13265 in approximately 0.34 seconds (38804 lines/second)
Physical Source Lines of Code (SLOC) = 8769
Hits@level = [0] 203 [1]  58 [2] 135 [3]   5 [4]  47 [5]   0
Hits@level+ = [0+] 448 [1+] 245 [2+] 187 [3+]  52 [4+]  47 [5+]   0
Hits/KSLOC@level+ = [0+] 51.0891 [1+] 27.9393 [2+] 21.3251 [3+] 5.92998 [4+] 5.35979 [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.