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/libseqlib-1.1.2+dfsg/SeqLib/BWAWrapper.h
Examining data/libseqlib-1.1.2+dfsg/SeqLib/BamReader.h
Examining data/libseqlib-1.1.2+dfsg/SeqLib/BamWriter.h
Examining data/libseqlib-1.1.2+dfsg/SeqLib/FastqReader.h
Examining data/libseqlib-1.1.2+dfsg/SeqLib/GenomicRegion.h
Examining data/libseqlib-1.1.2+dfsg/SeqLib/GenomicRegionCollection.cpp
Examining data/libseqlib-1.1.2+dfsg/SeqLib/GenomicRegionCollection.h
Examining data/libseqlib-1.1.2+dfsg/SeqLib/IntervalTree.h
Examining data/libseqlib-1.1.2+dfsg/SeqLib/ReadFilter.h
Examining data/libseqlib-1.1.2+dfsg/SeqLib/SeqLibCommon.h
Examining data/libseqlib-1.1.2+dfsg/SeqLib/SeqLibUtils.h
Examining data/libseqlib-1.1.2+dfsg/SeqLib/SeqPlot.h
Examining data/libseqlib-1.1.2+dfsg/SeqLib/UnalignedSequence.h
Examining data/libseqlib-1.1.2+dfsg/SeqLib/aho_corasick.hpp
Examining data/libseqlib-1.1.2+dfsg/SeqLib/BFC.h
Examining data/libseqlib-1.1.2+dfsg/SeqLib/BamRecord.h
Examining data/libseqlib-1.1.2+dfsg/SeqLib/BamHeader.h
Examining data/libseqlib-1.1.2+dfsg/SeqLib/RefGenome.h
Examining data/libseqlib-1.1.2+dfsg/SeqLib/FermiAssembler.h
Examining data/libseqlib-1.1.2+dfsg/SeqLib/BamWalker.h
Examining data/libseqlib-1.1.2+dfsg/benchmark/benchmark.cpp
Examining data/libseqlib-1.1.2+dfsg/seq_test/seq_test.cpp
Examining data/libseqlib-1.1.2+dfsg/src/BWAWrapper.cpp
Examining data/libseqlib-1.1.2+dfsg/src/BamHeader.cpp
Examining data/libseqlib-1.1.2+dfsg/src/BamWriter.cpp
Examining data/libseqlib-1.1.2+dfsg/src/FastqReader.cpp
Examining data/libseqlib-1.1.2+dfsg/src/GenomicRegion.cpp
Examining data/libseqlib-1.1.2+dfsg/src/RefGenome.cpp
Examining data/libseqlib-1.1.2+dfsg/src/SeqPlot.cpp
Examining data/libseqlib-1.1.2+dfsg/src/non_api/BamStats.cpp
Examining data/libseqlib-1.1.2+dfsg/src/non_api/BamStats.h
Examining data/libseqlib-1.1.2+dfsg/src/non_api/Fractions.cpp
Examining data/libseqlib-1.1.2+dfsg/src/non_api/Fractions.h
Examining data/libseqlib-1.1.2+dfsg/src/non_api/Histogram.cpp
Examining data/libseqlib-1.1.2+dfsg/src/non_api/Histogram.h
Examining data/libseqlib-1.1.2+dfsg/src/non_api/STCoverage.cpp
Examining data/libseqlib-1.1.2+dfsg/src/non_api/STCoverage.h
Examining data/libseqlib-1.1.2+dfsg/src/non_api/snowtools.cpp
Examining data/libseqlib-1.1.2+dfsg/src/seqtools/seqtools.cpp
Examining data/libseqlib-1.1.2+dfsg/src/BFC.cpp
Examining data/libseqlib-1.1.2+dfsg/src/FermiAssembler.cpp
Examining data/libseqlib-1.1.2+dfsg/src/ReadFilter.cpp
Examining data/libseqlib-1.1.2+dfsg/src/BamRecord.cpp
Examining data/libseqlib-1.1.2+dfsg/src/BamReader.cpp

FINAL RESULTS:

data/libseqlib-1.1.2+dfsg/SeqLib/BamWalker.h:47:10:  [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).
  strcat(strcpy(fn_list, fn_ref), ".fai");
data/libseqlib-1.1.2+dfsg/SeqLib/BamWalker.h:48:7:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
  if (access(fn_list, R_OK) == -1) { // fn_list is unreadable
data/libseqlib-1.1.2+dfsg/SeqLib/SeqLibUtils.h:58:13:  [4] (race) access:
  This usually indicates a security flaw. If an attacker can change anything
  along the path between the call to access() and the file's actual use
  (e.g., by moving files), the attacker can exploit the race condition
  (CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
  and try to open the file directly.
    return (access (name.c_str(), R_OK) == 0); 
data/libseqlib-1.1.2+dfsg/src/BWAWrapper.cpp:85:2:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
	sprintf(buffer, "@SQ\tSN:%s\tLN:%d\n", bns->anns[i].name, bns->anns[i].len);
data/libseqlib-1.1.2+dfsg/src/BWAWrapper.cpp:91:39:  [4] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf.
    if (hdr_line) { char buffer[200]; sprintf(buffer, "%s\n", hdr_line); out.append(buffer); } //err_printf("%s\n", hdr_line);
data/libseqlib-1.1.2+dfsg/src/BWAWrapper.cpp:465:23:  [3] (random) lrand48:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
      if (c >= 4) c = lrand48()&3;
data/libseqlib-1.1.2+dfsg/src/seqtools/seqtools.cpp:333:21:  [3] (buffer) getopt_long:
  Some older implementations do not protect against internal buffer overflows
  (CWE-120, CWE-20). Check implementation on installation, or limit the size
  of all string inputs.
  for (char c; (c = getopt_long(argc, argv, shortopts, longopts, NULL)) != -1;) {
data/libseqlib-1.1.2+dfsg/SeqLib/BamRecord.h:25:14:  [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.
static const char BASES[16] = {' ', 'A', 'C', ' ',
data/libseqlib-1.1.2+dfsg/SeqLib/BamWalker.h:47:3:  [2] (buffer) strcat:
  Does not check for buffer overflows when concatenating to destination
  [MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
  snprintf (warning: strncat is easily misused). Risk is low because the
  source is a constant string.
  strcat(strcpy(fn_list, fn_ref), ".fai");
data/libseqlib-1.1.2+dfsg/SeqLib/GenomicRegionCollection.cpp:137:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buffer[GZBUFFER];
data/libseqlib-1.1.2+dfsg/SeqLib/GenomicRegionCollection.cpp:194:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buffer[GZBUFFER];
data/libseqlib-1.1.2+dfsg/SeqLib/SeqLibCommon.h:20:16:  [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.
  static const char RCOMPLEMENT_TABLE[128] = {' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',' ',
data/libseqlib-1.1.2+dfsg/SeqLib/SeqLibUtils.h:95:5:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
    char buffer[100];
data/libseqlib-1.1.2+dfsg/SeqLib/SeqLibUtils.h:96:5:  [2] (buffer) sprintf:
  Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
  vsnprintf. Risk is low because the source has a constant maximum length.
    sprintf (buffer, "CPU: %4dm%02ds Wall: %4dm%02ds", 
data/libseqlib-1.1.2+dfsg/benchmark/benchmark.cpp:154:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  if (!open(bamFileIn, bam.c_str(), seqan::OPEN_RDONLY))
data/libseqlib-1.1.2+dfsg/benchmark/benchmark.cpp:177:8:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  if (!open(baiIndex, bami.c_str()))
data/libseqlib-1.1.2+dfsg/seq_test/seq_test.cpp:874:6:  [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).
  os.open(OREF);
data/libseqlib-1.1.2+dfsg/src/BWAWrapper.cpp:82:7:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
      char buffer[max_s + 30];
data/libseqlib-1.1.2+dfsg/src/BWAWrapper.cpp:91:21:  [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.
    if (hdr_line) { char buffer[200]; sprintf(buffer, "%s\n", hdr_line); out.append(buffer); } //err_printf("%s\n", hdr_line);
data/libseqlib-1.1.2+dfsg/src/BWAWrapper.cpp:327:7:  [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(b.b->data, name.c_str(), name.length() + 1);
data/libseqlib-1.1.2+dfsg/src/BWAWrapper.cpp:331:7:  [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(b.b->data + b.b->core.l_qname, (uint8_t*)a.cigar, a.n_cigar<<2);
data/libseqlib-1.1.2+dfsg/src/BWAWrapper.cpp:505:5:  [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(name->s, v[k].Name.c_str(), v[k].Name.length()+1);
data/libseqlib-1.1.2+dfsg/src/BWAWrapper.cpp:513:5:  [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(t->s, v[k].Seq.c_str(), v[k].Seq.length());
data/libseqlib-1.1.2+dfsg/src/BWAWrapper.cpp:599:5:  [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(ann->anno, "(null)\0");
data/libseqlib-1.1.2+dfsg/src/BamRecord.cpp:100:5:  [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(oldd, b->data, b->l_data);
data/libseqlib-1.1.2+dfsg/src/BamRecord.cpp:107:5:  [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(b->data, oldd, b->core.l_qname); 
data/libseqlib-1.1.2+dfsg/src/BamRecord.cpp:110:5:  [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(b->data + b->core.l_qname, new_cig, c.size()<<2);
data/libseqlib-1.1.2+dfsg/src/BamRecord.cpp:113:5:  [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(b->data + b->core.l_qname + (b->core.n_cigar<<2), oldd + old_seqaux_spot, old_seqaux_len);
data/libseqlib-1.1.2+dfsg/src/BamRecord.cpp:153:5:  [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(b->data, name.c_str(), name.length() + 1);
data/libseqlib-1.1.2+dfsg/src/BamRecord.cpp:232:5:  [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(oldd, b->data, b->l_data);
data/libseqlib-1.1.2+dfsg/src/BamRecord.cpp:239:5:  [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(b->data, oldd, b->core.l_qname + (b->core.n_cigar<<2));
data/libseqlib-1.1.2+dfsg/src/BamRecord.cpp:273:5:  [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(t, oldd + old_aux_spot, old_aux_len);
data/libseqlib-1.1.2+dfsg/src/BamRecord.cpp:287:5:  [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(nonq, b->data + b->core.l_qname, nonq_len);
data/libseqlib-1.1.2+dfsg/src/BamRecord.cpp:294:5:  [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(b->data, (uint8_t*)n.c_str(), n.length() + 1); // +1 for \0
data/libseqlib-1.1.2+dfsg/src/BamRecord.cpp:301:5:  [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(b->data + b->core.l_qname, nonq, nonq_len);
data/libseqlib-1.1.2+dfsg/src/BamRecord.cpp:323:5:  [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(bam_get_qual(b), q, n.length()); // dont copy /0 terminator
data/libseqlib-1.1.2+dfsg/src/BamRecord.cpp:526:16:  [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).
	out.push_back(atoi(line.c_str())); 
data/libseqlib-1.1.2+dfsg/src/BamRecord.cpp:528:21:  [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).
      out.push_back(atoi(tmp.c_str())); 
data/libseqlib-1.1.2+dfsg/src/BamRecord.cpp:592:5:  [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(b->data, name.c_str(), name.length() + 1);
data/libseqlib-1.1.2+dfsg/src/BamRecord.cpp:667:35:  [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).
      add(CigarField(ops[i], std::atoi(lens[i].c_str())));
data/libseqlib-1.1.2+dfsg/src/GenomicRegion.cpp:253:17:  [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).
    pos1 = std::atoi(tpos1.c_str());
data/libseqlib-1.1.2+dfsg/src/GenomicRegion.cpp:254:17:  [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).
    pos2 = std::atoi(tpos2.c_str());
data/libseqlib-1.1.2+dfsg/src/GenomicRegion.cpp:267:13:  [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).
	chr = std::atoi(SeqLib::scrubString(tchr, "chr").c_str());
data/libseqlib-1.1.2+dfsg/src/non_api/snowtools.cpp:50:18:  [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* inFile = fopen(script.c_str(), "rb");
data/libseqlib-1.1.2+dfsg/src/non_api/snowtools.cpp:58:3:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
  char buffer[1024];
data/libseqlib-1.1.2+dfsg/SeqLib/BamWalker.h:46:27:  [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).
  fn_list = (char*)calloc(strlen(fn_ref) + 5, 1);
data/libseqlib-1.1.2+dfsg/SeqLib/GenomicRegionCollection.cpp:139:22:  [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 bytes_read = strlen(buffer);
data/libseqlib-1.1.2+dfsg/SeqLib/GenomicRegionCollection.cpp:196:22:  [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 bytes_read = strlen(buffer);
data/libseqlib-1.1.2+dfsg/src/BFC.cpp:58:9:  [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(qual) && seq && qual) 
data/libseqlib-1.1.2+dfsg/src/BFC.cpp:59:11:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      if (strlen(seq) != strlen(qual))
data/libseqlib-1.1.2+dfsg/src/BFC.cpp:59:26:  [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).
      if (strlen(seq) != strlen(qual))
data/libseqlib-1.1.2+dfsg/src/BFC.cpp:61:10:  [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(seq))
data/libseqlib-1.1.2+dfsg/src/BFC.cpp:70:9:  [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(qual)) {
data/libseqlib-1.1.2+dfsg/src/BFC.cpp:74:16:  [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).
    s->l_seq = strlen(seq);
data/libseqlib-1.1.2+dfsg/src/BWAWrapper.cpp:79:24:  [1] (buffer) strlen:
  Does not handle strings that are not \0-terminated; if given one it may
  perform an over-read (it could cause a crash if unprotected) (CWE-126).
      max_s = std::max(strlen(bns->anns[i].name), max_s);
data/libseqlib-1.1.2+dfsg/src/BWAWrapper.cpp:597:5:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
    strncpy(ann->name, name.c_str(), name.length()+1);
data/libseqlib-1.1.2+dfsg/src/FermiAssembler.cpp:167:25:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      UnalignedSequence read;
data/libseqlib-1.1.2+dfsg/src/FermiAssembler.cpp:169:2:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	read.Seq = (std::string(s->seq));
data/libseqlib-1.1.2+dfsg/src/FermiAssembler.cpp:170:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      read.Name = m_names[i];
data/libseqlib-1.1.2+dfsg/src/FermiAssembler.cpp:171:19:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
      r.push_back(read);
data/libseqlib-1.1.2+dfsg/src/GenomicRegion.cpp:139:5:  [1] (buffer) strncpy:
  Easily used incorrectly; doesn't always \0-terminate or check for invalid
  pointers [MS-banned] (CWE-120).
    strncpy(tmp, reg.c_str(), q - reg.c_str());
data/libseqlib-1.1.2+dfsg/src/ReadFilter.cpp:12:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
#define DEBUGIV(msg, read)				\
data/libseqlib-1.1.2+dfsg/src/ReadFilter.cpp:13:7:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if (read.Qname() == QNAME && (read.AlignmentFlag() == QFLAG || QFLAG == -1)) { std::cerr << (msg) << " read " << r << std::endl; }
data/libseqlib-1.1.2+dfsg/src/ReadFilter.cpp:13:33:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
  if (read.Qname() == QNAME && (read.AlignmentFlag() == QFLAG || QFLAG == -1)) { std::cerr << (msg) << " read " << r << std::endl; }
data/libseqlib-1.1.2+dfsg/src/ReadFilter.cpp:15:22:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
#define DEBUGIV(msg, read)
data/libseqlib-1.1.2+dfsg/src/non_api/snowtools.cpp:63:15:  [1] (buffer) fgetc:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    char ch = fgetc(inFile);

ANALYSIS SUMMARY:

Hits = 66
Lines analyzed = 12400 in approximately 0.33 seconds (37070 lines/second)
Physical Source Lines of Code (SLOC) = 7170
Hits@level = [0]  13 [1]  21 [2]  38 [3]   2 [4]   5 [5]   0
Hits@level+ = [0+]  79 [1+]  66 [2+]  45 [3+]   7 [4+]   5 [5+]   0
Hits/KSLOC@level+ = [0+] 11.0181 [1+] 9.20502 [2+] 6.27615 [3+] 0.97629 [4+] 0.69735 [5+]   0
Dot directories skipped = 2 (--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.