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/srf-0.1+dfsg/src/SRF_util.cc
Examining data/srf-0.1+dfsg/src/SRF_ReadSet.cc
Examining data/srf-0.1+dfsg/src/SRF_Container.cc
Examining data/srf-0.1+dfsg/src/SRF_File.cc
Examining data/srf-0.1+dfsg/src/SRF_Read.cc
Examining data/srf-0.1+dfsg/src/SRF_Ztr.cc
Examining data/srf-0.1+dfsg/test/testRead.cc
Examining data/srf-0.1+dfsg/test/testWrite.cc
Examining data/srf-0.1+dfsg/test/testWriteFastaq.cc
Examining data/srf-0.1+dfsg/test/testWriteSFF.cc
Examining data/srf-0.1+dfsg/srf_config.h

FINAL RESULTS:

data/srf-0.1+dfsg/src/SRF_util.cc:71:5:  [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( strPtr, str );
data/srf-0.1+dfsg/src/SRF_Container.cc:47:5:  [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/srf-0.1+dfsg/src/SRF_File.cc:27:14:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        file.open(filename, std::ios::in|std::ios::binary );
data/srf-0.1+dfsg/src/SRF_File.cc:31:14:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        file.open(filename, std::ios::out|std::ios::binary );
data/srf-0.1+dfsg/src/SRF_File.cc:35:14:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        file.open(filename, std::ios::in|std::ios::out|std::ios::binary );
data/srf-0.1+dfsg/src/SRF_ReadSet.cc:72:2:  [2] (buffer) char:
  Statically-sized arrays can be improperly restricted, leading to potential
  overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
  functions that limit length, or ensure that the size is larger than the
  maximum possible length.
	char cstr[sizeZtrHeaderBlob];
data/srf-0.1+dfsg/src/SRF_Ztr.cc:234:9:  [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(&ztr->chunk[ztr->nchunks-1], chunk, sizeof(*chunk));
data/srf-0.1+dfsg/src/SRF_util.cc:183:12:  [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 char line[1024];
data/srf-0.1+dfsg/src/SRF_util.cc:207:5:  [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 line[MAX_CYCLES*20 +1];
data/srf-0.1+dfsg/src/SRF_util.cc:239:5:  [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 line[MAX_CYCLES*30 +1];
data/srf-0.1+dfsg/test/testWrite.cc:38:12:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    infile.open (argv[1], ifstream::in);
data/srf-0.1+dfsg/test/testWriteFastaq.cc:56:16:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    fastaInput.open(argv[1], std::ios::in );
data/srf-0.1+dfsg/src/SRF_Container.cc:48:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    file.read(tmp, 4);
data/srf-0.1+dfsg/src/SRF_Container.cc:57:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    file.read( reinterpret_cast<char *>(&sizeContainerHeader), 4 );
data/srf-0.1+dfsg/src/SRF_Container.cc:67:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    file.read ( &containerType, 1);
data/srf-0.1+dfsg/src/SRF_Container.cc:151:28:  [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).
    sizeContainerHeader += strlen( formatVersionStr );
data/srf-0.1+dfsg/src/SRF_Container.cc:156:28:  [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).
    sizeContainerHeader += strlen( baseCallerStr );
data/srf-0.1+dfsg/src/SRF_Container.cc:159:28:  [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).
    sizeContainerHeader += strlen( baseCallerVersionStr );
data/srf-0.1+dfsg/src/SRF_Read.cc:56:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    file.read ( &headerType, 1);
data/srf-0.1+dfsg/src/SRF_Read.cc:65:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    file.read( reinterpret_cast<char *>(&blockSize), 4 );
data/srf-0.1+dfsg/src/SRF_Read.cc:68:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    file.read ( &readFlags, 1);
data/srf-0.1+dfsg/src/SRF_Read.cc:80:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    file.read( reinterpret_cast<char *>(blob), sizeZtrBlob );
data/srf-0.1+dfsg/src/SRF_Read.cc:124:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	read_deallocate(read);
data/srf-0.1+dfsg/src/SRF_Read.cc:138:29:  [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).
    blockSize = 1 + 4 + 1 + strlen( shortIdStr ) + sizeZtr;
data/srf-0.1+dfsg/src/SRF_ReadSet.cc:46:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    file.read ( &headerType, 1);
data/srf-0.1+dfsg/src/SRF_ReadSet.cc:54:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    file.read( reinterpret_cast<char *>(&blockSize), 4 );
data/srf-0.1+dfsg/src/SRF_ReadSet.cc:57:10:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    file.read ( &subBlockType, 1);
data/srf-0.1+dfsg/src/SRF_ReadSet.cc:73:14:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        file.read( cstr,  sizeZtrHeaderBlob);
data/srf-0.1+dfsg/src/SRF_ReadSet.cc:92:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        delete read;
data/srf-0.1+dfsg/src/SRF_ReadSet.cc:95:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    return read;
data/srf-0.1+dfsg/src/SRF_ReadSet.cc:158:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        SRF_Read read( &(*stringListIterator), &(*ztrVecIterator) );
data/srf-0.1+dfsg/src/SRF_ReadSet.cc:159:9:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        read.write( file );
data/srf-0.1+dfsg/src/SRF_Ztr.cc:40:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    ztrStr.read( reinterpret_cast<char *>(h), sizeof(*h) );
data/srf-0.1+dfsg/src/SRF_Ztr.cc:69:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    ztrStr.read( reinterpret_cast<char *>(&bei4), 4 );
data/srf-0.1+dfsg/src/SRF_Ztr.cc:80:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    ztrStr.read( reinterpret_cast<char *>(&bei4), 4 );
data/srf-0.1+dfsg/src/SRF_Ztr.cc:93:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        ztrStr.read( reinterpret_cast<char *>(chunk->mdata), chunk->mdlength );
data/srf-0.1+dfsg/src/SRF_Ztr.cc:109:12:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    ztrStr.read( reinterpret_cast<char *>(&bei4), 4 );
data/srf-0.1+dfsg/src/SRF_Ztr.cc:227:16:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        ztrStr.read( reinterpret_cast<char *>(chunk->data), chunk->dlength );
data/srf-0.1+dfsg/src/SRF_util.cc:57:11:  [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).
    len = strlen( str );
data/srf-0.1+dfsg/src/SRF_util.cc:82:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    input.read (&lenStr, 1);
data/srf-0.1+dfsg/src/SRF_util.cc:91:11:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
    input.read( str, len );
data/srf-0.1+dfsg/src/SRF_util.cc:283:21:  [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).
    size_t nbases = strlen(seq), i;
data/srf-0.1+dfsg/test/testWrite.cc:61:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        ztr = SRF_output_ztr( read );
data/srf-0.1+dfsg/test/testWrite.cc:69:18:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
	read_deallocate(read);
data/srf-0.1+dfsg/test/testWriteFastaq.cc:110:35:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
            ztr = SRF_output_ztr( read );
data/srf-0.1+dfsg/test/testWriteSFF.cc:72:31:  [1] (buffer) read:
  Check buffer boundaries if used in a loop including recursive loops
  (CWE-120, CWE-20).
        ztr = SRF_output_ztr( read );

ANALYSIS SUMMARY:

Hits = 46
Lines analyzed = 1758 in approximately 0.05 seconds (36307 lines/second)
Physical Source Lines of Code (SLOC) = 1046
Hits@level = [0]   3 [1]  34 [2]  11 [3]   0 [4]   1 [5]   0
Hits@level+ = [0+]  49 [1+]  46 [2+]  12 [3+]   1 [4+]   1 [5+]   0
Hits/KSLOC@level+ = [0+] 46.8451 [1+] 43.9771 [2+] 11.4723 [3+] 0.956023 [4+] 0.956023 [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.