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/libvcflib-1.0.1+dfsg/multichoose/multichoose.h
Examining data/libvcflib-1.0.1+dfsg/multichoose/multipermute.cpp
Examining data/libvcflib-1.0.1+dfsg/multichoose/multichoose.c
Examining data/libvcflib-1.0.1+dfsg/multichoose/multipermute.h
Examining data/libvcflib-1.0.1+dfsg/multichoose/multichoose.cpp
Examining data/libvcflib-1.0.1+dfsg/test/tests/mainTest.cpp
Examining data/libvcflib-1.0.1+dfsg/test/tests/variantFileTests.h
Examining data/libvcflib-1.0.1+dfsg/test/tests/variantTests.h
Examining data/libvcflib-1.0.1+dfsg/filevercmp/filevercmp.c
Examining data/libvcflib-1.0.1+dfsg/filevercmp/main.c
Examining data/libvcflib-1.0.1+dfsg/filevercmp/filevercmp.h
Examining data/libvcflib-1.0.1+dfsg/intervaltree/catch.hpp
Examining data/libvcflib-1.0.1+dfsg/intervaltree/IntervalTree.h
Examining data/libvcflib-1.0.1+dfsg/intervaltree/interval_tree_test.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfremap.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfannotate.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfleftalign.cpp
Examining data/libvcflib-1.0.1+dfsg/src/segmentIhs.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfgeno2haplo.cpp
Examining data/libvcflib-1.0.1+dfsg/src/wcFst.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfafpath.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfsamplenames.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfrandom.cpp
Examining data/libvcflib-1.0.1+dfsg/src/pdflib.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfannotategenotypes.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfremovesamples.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfunphase.cpp
Examining data/libvcflib-1.0.1+dfsg/src/normalize-iHS.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcffilter.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfcreatemulti.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfstats.cpp
Examining data/libvcflib-1.0.1+dfsg/src/veclib_types.h
Examining data/libvcflib-1.0.1+dfsg/src/split.cpp
Examining data/libvcflib-1.0.1+dfsg/src/bFst.cpp
Examining data/libvcflib-1.0.1+dfsg/src/meltEHH.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfevenregions.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfnull2ref.cpp
Examining data/libvcflib-1.0.1+dfsg/src/hapLrt.cpp
Examining data/libvcflib-1.0.1+dfsg/src/segmentFst.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcflength.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vec128int.h
Examining data/libvcflib-1.0.1+dfsg/src/vcfgenotypecompare.cpp
Examining data/libvcflib-1.0.1+dfsg/src/genotypeSummary.cpp
Examining data/libvcflib-1.0.1+dfsg/src/var.hpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfgenosummarize.cpp
Examining data/libvcflib-1.0.1+dfsg/src/cdflib.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfaltcount.cpp
Examining data/libvcflib-1.0.1+dfsg/src/abba-baba.cpp
Examining data/libvcflib-1.0.1+dfsg/src/splitUniqStarts.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfgeno2alleles.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfgenotypes.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfld.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfhetcount.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfprimers.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfsom.cpp
Examining data/libvcflib-1.0.1+dfsg/src/pFst.cpp
Examining data/libvcflib-1.0.1+dfsg/src/Variant.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfgenosamplenames.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfkeepsamples.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcf2dag.cpp
Examining data/libvcflib-1.0.1+dfsg/src/rnglib.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfToHap.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfparsealts.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfnumalt.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfglxgt.cpp
Examining data/libvcflib-1.0.1+dfsg/src/smoother.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfaddinfo.cpp
Examining data/libvcflib-1.0.1+dfsg/src/join.h
Examining data/libvcflib-1.0.1+dfsg/src/vcfinfo2qual.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfindex.cpp
Examining data/libvcflib-1.0.1+dfsg/src/var.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfhethomratio.cpp
Examining data/libvcflib-1.0.1+dfsg/src/xpEHH.cpp
Examining data/libvcflib-1.0.1+dfsg/src/cdflib.hpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfremoveaberrantgenotypes.cpp
Examining data/libvcflib-1.0.1+dfsg/src/gl-XPEHH.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfcommonsamples.cpp
Examining data/libvcflib-1.0.1+dfsg/src/dumpContigsFromHeader.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfallelicprimitives.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfsitesummarize.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfecho.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfuniqalleles.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfintersect.cpp
Examining data/libvcflib-1.0.1+dfsg/src/sequenceDiversity.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfbreakmulti.cpp
Examining data/libvcflib-1.0.1+dfsg/src/permuteRegions.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfuniq.cpp
Examining data/libvcflib-1.0.1+dfsg/src/mt19937ar.h
Examining data/libvcflib-1.0.1+dfsg/src/vcfclassify.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfcheck.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfglbound.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfrandomsample.cpp
Examining data/libvcflib-1.0.1+dfsg/src/rnglib.hpp
Examining data/libvcflib-1.0.1+dfsg/src/vcf2tsv.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfdistance.cpp
Examining data/libvcflib-1.0.1+dfsg/src/iHS.cpp
Examining data/libvcflib-1.0.1+dfsg/src/BedReader.h
Examining data/libvcflib-1.0.1+dfsg/src/popStats.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfsamplestats.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfinfosummarize.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfkeepgeno.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfcountalleles.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfroc.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcf2fasta.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfcat.cpp
Examining data/libvcflib-1.0.1+dfsg/src/permuteSmooth.cpp
Examining data/libvcflib-1.0.1+dfsg/src/plotHaps.cpp
Examining data/libvcflib-1.0.1+dfsg/src/convert.h
Examining data/libvcflib-1.0.1+dfsg/src/pdflib.hpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfflatten.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcffixup.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfcombine.cpp
Examining data/libvcflib-1.0.1+dfsg/src/pVst.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfqual2info.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfstreamsort.cpp
Examining data/libvcflib-1.0.1+dfsg/src/gpatInfo.hpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfnormalizesvs.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfsamplediff.cpp
Examining data/libvcflib-1.0.1+dfsg/src/split.h
Examining data/libvcflib-1.0.1+dfsg/src/permuteGPATsmoother.cpp
Examining data/libvcflib-1.0.1+dfsg/src/permuteGPAT++.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfcleancomplex.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfkeepinfo.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfsample2info.cpp
Examining data/libvcflib-1.0.1+dfsg/src/vcfoverlay.cpp
Examining data/libvcflib-1.0.1+dfsg/src/Variant.h
Examining data/libvcflib-1.0.1+dfsg/src/vcfentropy.cpp

FINAL RESULTS:

data/libvcflib-1.0.1+dfsg/intervaltree/catch.hpp:7567:18:  [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.
            std::srand( config.rngSeed() );
data/libvcflib-1.0.1+dfsg/intervaltree/interval_tree_test.cpp:135:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand((unsigned)time(NULL));
data/libvcflib-1.0.1+dfsg/src/abba-baba.cpp:190:9:  [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.
	iarg = getopt_long(argc, argv, "r:d:t:f:y:hv", longopts, &index);
data/libvcflib-1.0.1+dfsg/src/abba-baba.cpp:259:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(time(0)); //initialize random number generator
data/libvcflib-1.0.1+dfsg/src/bFst.cpp:345:3:  [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)time(NULL));
data/libvcflib-1.0.1+dfsg/src/bFst.cpp:380:9:  [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.
	iarg = getopt_long(argc, argv, "d:t:b:f:hv", longopts, &index);
data/libvcflib-1.0.1+dfsg/src/genotypeSummary.cpp:80:3:  [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)time(NULL));
data/libvcflib-1.0.1+dfsg/src/genotypeSummary.cpp:126:9:  [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.
	iarg = getopt_long(argc, argv, "y:r:d:t:b:f:chvsa", longopts, &index);
data/libvcflib-1.0.1+dfsg/src/gl-XPEHH.cpp:419:3:  [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)time(NULL));
data/libvcflib-1.0.1+dfsg/src/gl-XPEHH.cpp:468:9:  [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.
	iarg = getopt_long(argc, argv, "p:m:r:d:t:b:f:hv", longopts, &findex);
data/libvcflib-1.0.1+dfsg/src/hapLrt.cpp:313:3:  [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)time(NULL));
data/libvcflib-1.0.1+dfsg/src/hapLrt.cpp:359:9:  [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.
	iarg = getopt_long(argc, argv, "y:r:t:b:f:hv", longopts, &findex);
data/libvcflib-1.0.1+dfsg/src/iHS.cpp:433:9:  [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.
	iarg = getopt_long(argc, argv, "a:x:g:y:r:d:t:b:f:hv", longopts, &findex);
data/libvcflib-1.0.1+dfsg/src/meltEHH.cpp:410:9:  [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.
	iarg = getopt_long(argc, argv, "a:x:g:y:r:d:t:b:f:p:hv", longopts, &findex);
data/libvcflib-1.0.1+dfsg/src/normalize-iHS.cpp:99:11:  [3] (buffer) getopt:
  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.
    opt = getopt(argc, argv, optString);
data/libvcflib-1.0.1+dfsg/src/normalize-iHS.cpp:125:8:  [3] (buffer) getopt:
  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.
	opt = getopt( argc, argv, optString ); 
data/libvcflib-1.0.1+dfsg/src/pFst.cpp:130:9:  [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.
	iarg = getopt_long(argc, argv, "r:d:t:b:f:y:chv", longopts, &index);
data/libvcflib-1.0.1+dfsg/src/pVst.cpp:268:8:  [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.
  std::srand ( unsigned ( std::time(0) ) );
data/libvcflib-1.0.1+dfsg/src/pVst.cpp:321:9:  [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.
	iarg = getopt_long(argc, argv, "n:r:d:t:b:f:y:x:hv", longopts, &index);
data/libvcflib-1.0.1+dfsg/src/permuteGPAT++.cpp:71:11:  [3] (buffer) getopt:
  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.
    opt = getopt(argc, argv, optString);
data/libvcflib-1.0.1+dfsg/src/permuteGPAT++.cpp:97:13:  [3] (buffer) getopt:
  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.
      opt = getopt( argc, argv, optString ); 
data/libvcflib-1.0.1+dfsg/src/permuteGPAT++.cpp:181:2:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
 srand (time(NULL));
data/libvcflib-1.0.1+dfsg/src/permuteGPATsmoother.cpp:72:11:  [3] (buffer) getopt:
  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.
    opt = getopt(argc, argv, optString);
data/libvcflib-1.0.1+dfsg/src/permuteGPATsmoother.cpp:98:13:  [3] (buffer) getopt:
  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.
      opt = getopt( argc, argv, optString ); 
data/libvcflib-1.0.1+dfsg/src/permuteGPATsmoother.cpp:182:2:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
 srand (time(NULL));
data/libvcflib-1.0.1+dfsg/src/permuteRegions.cpp:137:9:  [3] (buffer) getopt:
  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.
  opt = getopt(argc, argv, optString);
data/libvcflib-1.0.1+dfsg/src/permuteRegions.cpp:194:11:  [3] (buffer) getopt:
  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.
    opt = getopt( argc, argv, optString ); 
data/libvcflib-1.0.1+dfsg/src/permuteRegions.cpp:287:1:  [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 (time(NULL));
data/libvcflib-1.0.1+dfsg/src/permuteSmooth.cpp:139:9:  [3] (buffer) getopt:
  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.
  opt = getopt(argc, argv, optString);
data/libvcflib-1.0.1+dfsg/src/permuteSmooth.cpp:197:11:  [3] (buffer) getopt:
  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.
    opt = getopt( argc, argv, optString );
data/libvcflib-1.0.1+dfsg/src/permuteSmooth.cpp:302:1:  [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 (time(NULL));
data/libvcflib-1.0.1+dfsg/src/plotHaps.cpp:169:3:  [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)time(NULL));
data/libvcflib-1.0.1+dfsg/src/plotHaps.cpp:216:9:  [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.
	iarg = getopt_long(argc, argv, "y:r:t:f:hv", longopts, &findex);
data/libvcflib-1.0.1+dfsg/src/popStats.cpp:77:3:  [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)time(NULL));
data/libvcflib-1.0.1+dfsg/src/popStats.cpp:115:9:  [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.
	iarg = getopt_long(argc, argv, "y:r:d:t:b:f:chv", longopts, &index);
data/libvcflib-1.0.1+dfsg/src/segmentFst.cpp:94:11:  [3] (buffer) getopt:
  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.
    opt = getopt(argc, argv, optString);
data/libvcflib-1.0.1+dfsg/src/segmentFst.cpp:120:8:  [3] (buffer) getopt:
  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.
	opt = getopt( argc, argv, optString );
data/libvcflib-1.0.1+dfsg/src/segmentIhs.cpp:94:11:  [3] (buffer) getopt:
  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.
    opt = getopt(argc, argv, optString);
data/libvcflib-1.0.1+dfsg/src/segmentIhs.cpp:120:8:  [3] (buffer) getopt:
  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.
	opt = getopt( argc, argv, optString ); 
data/libvcflib-1.0.1+dfsg/src/sequenceDiversity.cpp:166:3:  [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)time(NULL));
data/libvcflib-1.0.1+dfsg/src/sequenceDiversity.cpp:230:9:  [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.
	iarg = getopt_long(argc, argv, "a:w:y:r:t:b:f:edhv", longopts, &findex);
data/libvcflib-1.0.1+dfsg/src/smoother.cpp:233:12:  [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.
    iarg = getopt_long(argc, argv, "f:w:s:o:vht", longopts, &index);
data/libvcflib-1.0.1+dfsg/src/splitUniqStarts.cpp:81:9:  [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.
	iarg = getopt_long(argc, argv, "p:f:r:vh", longopts, &index);
data/libvcflib-1.0.1+dfsg/src/vcf2dag.cpp:49:13:  [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.
        c = getopt_long (argc, argv, "hr:",
data/libvcflib-1.0.1+dfsg/src/vcf2fasta.cpp:221:13:  [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.
        c = getopt_long (argc, argv, "hmf:p:P:n:",
data/libvcflib-1.0.1+dfsg/src/vcf2tsv.cpp:113:13:  [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.
        c = getopt_long (argc, argv, "hn:g",
data/libvcflib-1.0.1+dfsg/src/vcfToHap.cpp:217:9:  [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.
	iarg = getopt_long(argc, argv, "a:x:g:y:r:d:t:b:f:hv", longopts, &findex);
data/libvcflib-1.0.1+dfsg/src/vcfallelicprimitives.cpp:69:13:  [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.
        c = getopt_long (argc, argv, "hmkgt:L:",
data/libvcflib-1.0.1+dfsg/src/vcfannotate.cpp:48:13:  [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.
        c = getopt_long (argc, argv, "hb:k:d:",
data/libvcflib-1.0.1+dfsg/src/vcfbreakmulti.cpp:43:13:  [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.
        c = getopt_long (argc, argv, "h",
data/libvcflib-1.0.1+dfsg/src/vcfcheck.cpp:52:13:  [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.
        c = getopt_long (argc, argv, "hvxkf:",
data/libvcflib-1.0.1+dfsg/src/vcfcombine.cpp:47:13:  [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.
        c = getopt_long (argc, argv, "vhr:",
data/libvcflib-1.0.1+dfsg/src/vcfcreatemulti.cpp:112:13:  [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.
        c = getopt_long (argc, argv, "h",
data/libvcflib-1.0.1+dfsg/src/vcfentropy.cpp:48:13:  [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.
        c = getopt_long (argc, argv, "hf:w:",
data/libvcflib-1.0.1+dfsg/src/vcfevenregions.cpp:73:13:  [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.
        c = getopt_long (argc, argv, "hf:n:o:l:s:p:",
data/libvcflib-1.0.1+dfsg/src/vcffilter.cpp:116:13:  [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.
        c = getopt_long (argc, argv, "hvAsof:g:kt:F:r:a:",
data/libvcflib-1.0.1+dfsg/src/vcfgeno2haplo.cpp:70:13:  [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.
        c = getopt_long (argc, argv, "hvow:r:",
data/libvcflib-1.0.1+dfsg/src/vcfglbound.cpp:41:13:  [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.
        c = getopt_long (argc, argv, "hxb:",
data/libvcflib-1.0.1+dfsg/src/vcfglxgt.cpp:38:13:  [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.
        c = getopt_long (argc, argv, "hn",
data/libvcflib-1.0.1+dfsg/src/vcfinfosummarize.cpp:73:13:  [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.
        c = getopt_long (argc, argv, "hamnxfv:i:",
data/libvcflib-1.0.1+dfsg/src/vcfintersect.cpp:100:13:  [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.
        c = getopt_long (argc, argv, "hvcSlmob:i:u:w:r:t:V:M:T:R:",
data/libvcflib-1.0.1+dfsg/src/vcfld.cpp:141:3:  [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)time(NULL));
data/libvcflib-1.0.1+dfsg/src/vcfld.cpp:202:9:  [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.
	iarg = getopt_long(argc, argv, "w:y:r:t:b:f:edhv", longopts, &findex);
data/libvcflib-1.0.1+dfsg/src/vcfleftalign.cpp:506:13:  [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.
        c = getopt_long (argc, argv, "hw:r:",
data/libvcflib-1.0.1+dfsg/src/vcfnormalizesvs.cpp:37:13:  [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.
        c = getopt_long (argc, argv, "sr:i:h",
data/libvcflib-1.0.1+dfsg/src/vcfoverlay.cpp:36:11:  [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.
      c = getopt_long (argc, argv, "hv",
data/libvcflib-1.0.1+dfsg/src/vcfprimers.cpp:55:13:  [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.
        c = getopt_long (argc, argv, "hf:l:",
data/libvcflib-1.0.1+dfsg/src/vcfrandom.cpp:34:5:  [3] (random) srand:
  This function is not sufficiently random for security-related functions
  such as key and nonce creation (CWE-327). Use a more secure technique for
  acquiring random values.
    srand(time(NULL));
data/libvcflib-1.0.1+dfsg/src/vcfrandomsample.cpp:51:13:  [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.
        c = getopt_long (argc, argv, "hqr:s:p:",
data/libvcflib-1.0.1+dfsg/src/vcfrandomsample.cpp:104:17:  [3] (random) random:
  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.
        fstream random;
data/libvcflib-1.0.1+dfsg/src/vcfrandomsample.cpp:106:13:  [3] (random) random:
  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.
            random.open("/dev/urandom", fstream::in);
data/libvcflib-1.0.1+dfsg/src/vcfrandomsample.cpp:108:13:  [3] (random) random:
  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.
            random.open("/dev/random", fstream::in);
data/libvcflib-1.0.1+dfsg/src/vcfrandomsample.cpp:110:9:  [3] (random) random:
  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.
        random.get((char*) &seed, sizeof(int));
data/libvcflib-1.0.1+dfsg/src/vcfrandomsample.cpp:111:9:  [3] (random) random:
  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.
        random.close();
data/libvcflib-1.0.1+dfsg/src/vcfremap.cpp:81:13:  [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.
        c = getopt_long (argc, argv, "hza:w:r:m:x:o:e:s:R:",
data/libvcflib-1.0.1+dfsg/src/vcfroc.cpp:143:13:  [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.
        c = getopt_long (argc, argv, "hcw:r:t:",
data/libvcflib-1.0.1+dfsg/src/vcfsample2info.cpp:69:13:  [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.
        c = getopt_long (argc, argv, "hamnxf:i:",
data/libvcflib-1.0.1+dfsg/src/vcfsamplediff.cpp:70:13:  [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.
        c = getopt_long (argc, argv, "hs",
data/libvcflib-1.0.1+dfsg/src/vcfsamplestats.cpp:51:13:  [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.
        c = getopt_long (argc, argv, "h",
data/libvcflib-1.0.1+dfsg/src/vcfsom.cpp:262:13:  [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.
        c = getopt_long (argc, argv, "hpdi:x:y:a:s:f:c:T:F:",
data/libvcflib-1.0.1+dfsg/src/vcfstats.cpp:116:13:  [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.
        c = getopt_long (argc, argv, "hlatr:m:x:o:e:",
data/libvcflib-1.0.1+dfsg/src/vcfstreamsort.cpp:49:13:  [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.
        c = getopt_long (argc, argv, "haw:",
data/libvcflib-1.0.1+dfsg/src/wcFst.cpp:76:3:  [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)time(NULL));
data/libvcflib-1.0.1+dfsg/src/wcFst.cpp:122:9:  [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.
	iarg = getopt_long(argc, argv, "y:r:d:t:b:f:chv", longopts, &index);
data/libvcflib-1.0.1+dfsg/src/xpEHH.cpp:198:3:  [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)time(NULL));
data/libvcflib-1.0.1+dfsg/src/xpEHH.cpp:247:9:  [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.
	iarg = getopt_long(argc, argv, "y:r:t:b:f:hv", longopts, &findex);
data/libvcflib-1.0.1+dfsg/intervaltree/catch.hpp:1563:23:  [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.
    struct TrueType { char sizer[1]; };
data/libvcflib-1.0.1+dfsg/intervaltree/catch.hpp:1564:24:  [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.
    struct FalseType { char sizer[2]; };
data/libvcflib-1.0.1+dfsg/intervaltree/catch.hpp:2736:9:  [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 storage[sizeof(T)];
data/libvcflib-1.0.1+dfsg/intervaltree/catch.hpp:5388:14:  [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).
        void open() {
data/libvcflib-1.0.1+dfsg/intervaltree/catch.hpp:5465:26:  [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).
                section->open();
data/libvcflib-1.0.1+dfsg/intervaltree/catch.hpp:5498:26:  [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).
                tracker->open();
data/libvcflib-1.0.1+dfsg/intervaltree/catch.hpp:6558:9:  [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 data[bufferSize];
data/libvcflib-1.0.1+dfsg/intervaltree/catch.hpp:6595:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        m_ofs.open( filename.c_str() );
data/libvcflib-1.0.1+dfsg/intervaltree/catch.hpp:7735:21:  [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.
                    char asChar[sizeof (int)];
data/libvcflib-1.0.1+dfsg/intervaltree/catch.hpp:8494:16:  [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 char line[CATCH_CONFIG_CONSOLE_WIDTH] = {0};
data/libvcflib-1.0.1+dfsg/multichoose/multichoose.c:15:9:  [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).
    n = atoi(argv[1]);
data/libvcflib-1.0.1+dfsg/multichoose/multichoose.cpp:50:13:  [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 k = atoi(argv[1]);
data/libvcflib-1.0.1+dfsg/src/BedReader.h:45:24:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
            startPos = atoi(region.substr(foundFirstColon + 1).c_str());
data/libvcflib-1.0.1+dfsg/src/BedReader.h:50:24:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
            startPos = atoi(region.substr(foundFirstColon + 1, foundRangeSep - foundFirstColon).c_str());
data/libvcflib-1.0.1+dfsg/src/BedReader.h:53:27:  [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).
                stopPos = atoi(region.substr(foundRangeSep + sep.size()).c_str()); // end-exclusive, bed-format
data/libvcflib-1.0.1+dfsg/src/BedReader.h:111:29:  [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).
                            atoi(strip(fields[1]).c_str()),
data/libvcflib-1.0.1+dfsg/src/BedReader.h:112:29:  [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).
                            atoi(strip(fields[2]).c_str()),
data/libvcflib-1.0.1+dfsg/src/BedReader.h:145:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        open(fname);
data/libvcflib-1.0.1+dfsg/src/BedReader.h:158:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    void open(const string& fname) {
data/libvcflib-1.0.1+dfsg/src/BedReader.h:159:14:  [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(fname.c_str());
data/libvcflib-1.0.1+dfsg/src/Variant.cpp:6:8:  [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 rev_arr [26] = {84, 66, 71, 68, 69, 70, 67, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 65,
data/libvcflib-1.0.1+dfsg/src/Variant.cpp:2533:43:  [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).
                cigar.push_back(make_pair(atoi(number.c_str()), type));
data/libvcflib-1.0.1+dfsg/src/Variant.cpp:2543:35:  [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).
        cigar.push_back(make_pair(atoi(number.c_str()), type));
data/libvcflib-1.0.1+dfsg/src/Variant.cpp:2560:43:  [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).
                cigar.push_back(make_pair(atoi(number.c_str()), type));
data/libvcflib-1.0.1+dfsg/src/Variant.cpp:2570:35:  [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).
        cigar.push_back(make_pair(atoi(number.c_str()), type));
data/libvcflib-1.0.1+dfsg/src/Variant.h:96:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    bool open(string& filename) {
data/libvcflib-1.0.1+dfsg/src/Variant.h:107:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        _file.open(filename.c_str(), ifstream::in);
data/libvcflib-1.0.1+dfsg/src/Variant.h:119:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    bool open(istream& stream) {
data/libvcflib-1.0.1+dfsg/src/Variant.h:125:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    bool open(ifstream& stream) {
data/libvcflib-1.0.1+dfsg/src/abba-baba.cpp:131:16:  [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).
    int indx = atoi((*it).c_str());
data/libvcflib-1.0.1+dfsg/src/abba-baba.cpp:227:17:  [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).
    variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/bFst.cpp:336:12:  [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).
    index[ atoi( (*it).c_str() ) ] = 1;
data/libvcflib-1.0.1+dfsg/src/bFst.cpp:473:17:  [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).
    variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:1789:10:  [2] (integer) atol:
  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).
# define atol (1.0e-50)
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:1946:14:  [2] (integer) atol:
  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).
        T4 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:1994:15:  [2] (integer) atol:
  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).
        T10 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:2030:15:  [2] (integer) atol:
  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).
        T14 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:2061:9:  [2] (integer) atol:
  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).
# undef atol
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:2149:10:  [2] (integer) atol:
  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).
# define atol (1.0e-50)
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:2313:14:  [2] (integer) atol:
  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).
        T5 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:2349:14:  [2] (integer) atol:
  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).
        T9 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:2382:15:  [2] (integer) atol:
  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).
        T12 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:2424:9:  [2] (integer) atol:
  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).
# undef atol
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:2510:10:  [2] (integer) atol:
  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).
# define atol (1.0e-50)
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:2635:14:  [2] (integer) atol:
  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).
        T6 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:2675:15:  [2] (integer) atol:
  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).
        T10 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:2710:9:  [2] (integer) atol:
  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).
# undef atol
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:2805:10:  [2] (integer) atol:
  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).
# define atol (1.0e-50)
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:2893:14:  [2] (integer) atol:
  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).
        T5 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:2924:14:  [2] (integer) atol:
  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).
        T9 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:2954:15:  [2] (integer) atol:
  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).
        T12 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:2981:9:  [2] (integer) atol:
  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).
# undef atol
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:3069:10:  [2] (integer) atol:
  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).
# define atol (1.0e-50)
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:3190:14:  [2] (integer) atol:
  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).
        T6 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:3232:11:  [2] (integer) atol:
  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).
    T10 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:3285:11:  [2] (integer) atol:
  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).
    T14 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:3326:9:  [2] (integer) atol:
  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).
# undef atol
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:3445:10:  [2] (integer) atol:
  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).
# define atol (1.0e-50)
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:3543:14:  [2] (integer) atol:
  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).
        T5 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:3574:14:  [2] (integer) atol:
  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).
        T9 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:3605:15:  [2] (integer) atol:
  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).
        T13 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:3635:15:  [2] (integer) atol:
  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).
        T16 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:3662:9:  [2] (integer) atol:
  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).
# undef atol
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:3745:10:  [2] (integer) atol:
  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).
# define atol (1.0e-50)
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:3895:14:  [2] (integer) atol:
  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).
        T7 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:3945:9:  [2] (integer) atol:
  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).
# undef atol
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:4033:10:  [2] (integer) atol:
  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).
# define atol (1.0e-50)
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:4191:14:  [2] (integer) atol:
  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).
        T6 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:4226:14:  [2] (integer) atol:
  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).
        T9 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:4259:15:  [2] (integer) atol:
  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).
        T12 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:4302:9:  [2] (integer) atol:
  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).
# undef atol
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:4564:10:  [2] (integer) atol:
  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).
# define atol (1.0e-50)
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:4674:14:  [2] (integer) atol:
  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).
        T6 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:4709:14:  [2] (integer) atol:
  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).
        T9 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:4740:9:  [2] (integer) atol:
  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).
# undef atol
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:4815:10:  [2] (integer) atol:
  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).
# define atol (1.0e-50)
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:4918:14:  [2] (integer) atol:
  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).
        T6 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:4954:15:  [2] (integer) atol:
  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).
        T10 = atol;
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:4985:9:  [2] (integer) atol:
  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).
# undef atol
data/libvcflib-1.0.1+dfsg/src/cdflib.cpp:10856:10:  [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 time_buffer[TIME_SIZE];
data/libvcflib-1.0.1+dfsg/src/dumpContigsFromHeader.cpp:19:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/genotypeSummary.cpp:69:12:  [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).
    index[ atoi( (*it).c_str() ) ] = 1;
data/libvcflib-1.0.1+dfsg/src/genotypeSummary.cpp:197:29:  [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).
        is_open=variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/genotypeSummary.cpp:201:26:  [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).
    	is_open=variantFile.open(filename); 
data/libvcflib-1.0.1+dfsg/src/gl-XPEHH.cpp:184:12:  [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).
    index[ atoi( (*it).c_str() ) ] = 1;
data/libvcflib-1.0.1+dfsg/src/gl-XPEHH.cpp:505:15:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	    phased = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/gl-XPEHH.cpp:543:17:  [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).
    variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/hapLrt.cpp:66:12:  [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).
    index[ atoi( (*it).c_str() ) ] = 1;
data/libvcflib-1.0.1+dfsg/src/hapLrt.cpp:418:17:  [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).
    variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/iHS.cpp:121:19:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
      int   pos = atoi(region[3].c_str()) ;
data/libvcflib-1.0.1+dfsg/src/iHS.cpp:172:12:  [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).
    index[ atoi( (*it).c_str() ) ] = 1;
data/libvcflib-1.0.1+dfsg/src/iHS.cpp:444:29:  [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).
	      globalOpts.threads = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/iHS.cpp:533:17:  [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).
    variantFile.open(globalOpts.filename);
data/libvcflib-1.0.1+dfsg/src/meltEHH.cpp:117:19:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
      int   pos = atoi(region[3].c_str()) ;
data/libvcflib-1.0.1+dfsg/src/meltEHH.cpp:168:12:  [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).
    index[ atoi( (*it).c_str() ) ] = 1;
data/libvcflib-1.0.1+dfsg/src/meltEHH.cpp:416:25:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	      globalOpts.pos = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/meltEHH.cpp:427:29:  [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).
	      globalOpts.threads = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/meltEHH.cpp:518:17:  [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).
    variantFile.open(globalOpts.filename);
data/libvcflib-1.0.1+dfsg/src/pFst.cpp:65:12:  [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).
    index[ atoi( (*it).c_str() ) ] = 1;
data/libvcflib-1.0.1+dfsg/src/pFst.cpp:186:17:  [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).
    variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/pVst.cpp:235:12:  [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).
    index[ atoi( (*it).c_str() ) ] = 1;
data/libvcflib-1.0.1+dfsg/src/pVst.cpp:331:15:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	      nper = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/pVst.cpp:349:14:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	      cpu = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/pVst.cpp:399:17:  [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).
    variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/pVst.cpp:460:16:  [2] (integer) atol:
  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).
	varDat->end = atol(var.info["END"].front().c_str());
data/libvcflib-1.0.1+dfsg/src/permuteGPAT++.cpp:81:30:  [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).
	  globalOpts.npermutation = atoi(((string)optarg).c_str());
data/libvcflib-1.0.1+dfsg/src/permuteGPAT++.cpp:87:22:  [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).
	  globalOpts.nsuc = atoi(((string)optarg).c_str());
data/libvcflib-1.0.1+dfsg/src/permuteGPATsmoother.cpp:82:30:  [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).
	  globalOpts.npermutation = atoi(((string)optarg).c_str());
data/libvcflib-1.0.1+dfsg/src/permuteGPATsmoother.cpp:88:22:  [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).
	  globalOpts.nsuc = atoi(((string)optarg).c_str());
data/libvcflib-1.0.1+dfsg/src/permuteRegions.cpp:142:23:  [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).
	globalOpts.threads = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/permuteRegions.cpp:336:18:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
     sp->pos   = atoi(region[1].c_str());
data/libvcflib-1.0.1+dfsg/src/permuteRegions.cpp:365:18:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
     sp->n     = atoi(region[globalOpts.nIndex].c_str());
data/libvcflib-1.0.1+dfsg/src/permuteSmooth.cpp:144:32:  [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).
          globalOpts.threads = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/permuteSmooth.cpp:352:18:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
     sp->pos   = atoi(region[1].c_str());
data/libvcflib-1.0.1+dfsg/src/permuteSmooth.cpp:381:18:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
     sp->n     = atoi(region[globalOpts.nIndex].c_str());
data/libvcflib-1.0.1+dfsg/src/plotHaps.cpp:56:12:  [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).
    index[ atoi( (*it).c_str() ) ] = 1;
data/libvcflib-1.0.1+dfsg/src/plotHaps.cpp:269:17:  [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).
    variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/popStats.cpp:68:12:  [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).
    index[ atoi( (*it).c_str() ) ] = 1;
data/libvcflib-1.0.1+dfsg/src/popStats.cpp:158:21:  [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(!variantFile.open(filename)){
data/libvcflib-1.0.1+dfsg/src/rnglib.cpp:1792:10:  [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 time_buffer[TIME_SIZE];
data/libvcflib-1.0.1+dfsg/src/segmentFst.cpp:277:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	    if(atoi(lineDat[1].c_str()) < lastPos){
data/libvcflib-1.0.1+dfsg/src/segmentFst.cpp:281:16:  [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).
	    lastPos = atoi(lineDat[1].c_str());
data/libvcflib-1.0.1+dfsg/src/segmentFst.cpp:283:20:  [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).
	    pos.push_back(atoi(lineDat[1].c_str()));
data/libvcflib-1.0.1+dfsg/src/segmentIhs.cpp:275:9:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
	    if(atoi(lineDat[1].c_str()) < lastPos){
data/libvcflib-1.0.1+dfsg/src/segmentIhs.cpp:279:16:  [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).
	    lastPos = atoi(lineDat[1].c_str());
data/libvcflib-1.0.1+dfsg/src/segmentIhs.cpp:281:20:  [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).
	    pos.push_back(atoi(lineDat[1].c_str()));
data/libvcflib-1.0.1+dfsg/src/sequenceDiversity.cpp:66:12:  [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).
    index[ atoi( (*it).c_str() ) ] = 1;
data/libvcflib-1.0.1+dfsg/src/sequenceDiversity.cpp:329:17:  [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).
    variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/smoother.cpp:130:24:  [2] (integer) atol:
  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).
    current.position = atol( sline[opt.pos].c_str() );
data/libvcflib-1.0.1+dfsg/src/smoother.cpp:258:13:  [2] (integer) atol:
  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).
	opt.step = atol(optarg);
data/libvcflib-1.0.1+dfsg/src/smoother.cpp:264:13:  [2] (integer) atol:
  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).
	opt.size = atol(optarg);
data/libvcflib-1.0.1+dfsg/src/splitUniqStarts.cpp:127:23:  [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(!variantFile.open(filename)){
data/libvcflib-1.0.1+dfsg/src/splitUniqStarts.cpp:196:23:  [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(!variantFile.open(filename)){
data/libvcflib-1.0.1+dfsg/src/splitUniqStarts.cpp:207:6:  [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).
	oz->open(fname.str().c_str());
data/libvcflib-1.0.1+dfsg/src/vcf2dag.cpp:79:21:  [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).
        variantFile.open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcf2dag.cpp:81:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcf2dag.cpp:94:19:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        reference.open(fastaFileName);
data/libvcflib-1.0.1+dfsg/src/vcf2fasta.cpp:38:10:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    void open(string& m_filename, string& m_seqname, int m_linewidth = 80) {
data/libvcflib-1.0.1+dfsg/src/vcf2fasta.cpp:44:19:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        fastafile.open(filename.c_str());
data/libvcflib-1.0.1+dfsg/src/vcf2fasta.cpp:107:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            f.open(fileName, thisSeqName);
data/libvcflib-1.0.1+dfsg/src/vcf2fasta.cpp:242:29:  [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).
            defaultPloidy = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/vcf2fasta.cpp:265:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    reference.open(fastaFileName);
data/libvcflib-1.0.1+dfsg/src/vcf2fasta.cpp:269:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcf2fasta.cpp:271:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcf2tsv.cpp:148:21:  [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).
        variantFile.open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcf2tsv.cpp:150:26:  [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 (!variantFile.open(std::cin)) {
data/libvcflib-1.0.1+dfsg/src/vcfToHap.cpp:117:19:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
      int   pos = atoi(region[3].c_str()) ;
data/libvcflib-1.0.1+dfsg/src/vcfToHap.cpp:172:12:  [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).
    index[ atoi( (*it).c_str() ) ] = 1;
data/libvcflib-1.0.1+dfsg/src/vcfToHap.cpp:228:29:  [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).
	      globalOpts.threads = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/vcfToHap.cpp:317:17:  [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).
    variantFile.open(globalOpts.filename);
data/libvcflib-1.0.1+dfsg/src/vcfaddinfo.cpp:37:22:  [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).
        variantFileA.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfaddinfo.cpp:39:22:  [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).
        variantFileA.open(filenameA);
data/libvcflib-1.0.1+dfsg/src/vcfaddinfo.cpp:44:22:  [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).
        variantFileB.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfaddinfo.cpp:46:22:  [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).
        variantFileB.open(filenameB);
data/libvcflib-1.0.1+dfsg/src/vcfafpath.cpp:15:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfafpath.cpp:17:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfallelicprimitives.cpp:98:25:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
            maxLength = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/vcfallelicprimitives.cpp:113:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfallelicprimitives.cpp:115:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfaltcount.cpp:21:17:  [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).
    variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfannotate.cpp:92:21:  [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).
        variantFile.open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcfannotate.cpp:94:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfannotategenotypes.cpp:112:22:  [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).
        variantFileA.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfannotategenotypes.cpp:114:22:  [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).
        variantFileA.open(filenameA);
data/libvcflib-1.0.1+dfsg/src/vcfannotategenotypes.cpp:119:22:  [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).
        variantFileB.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfannotategenotypes.cpp:121:22:  [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).
        variantFileB.open(filenameB);
data/libvcflib-1.0.1+dfsg/src/vcfbreakmulti.cpp:67:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfbreakmulti.cpp:69:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfcat.cpp:16:25:  [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).
            variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfcheck.cpp:115:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ref.open(fastaRef);
data/libvcflib-1.0.1+dfsg/src/vcfcheck.cpp:121:21:  [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).
        variantFile.open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcfcheck.cpp:123:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfclassify.cpp:97:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfclassify.cpp:99:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfcleancomplex.cpp:25:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfcleancomplex.cpp:27:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfcombine.cpp:109:14:  [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).
        vcf->open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcfcommonsamples.cpp:47:22:  [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).
        variantFileA.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfcommonsamples.cpp:49:22:  [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).
        variantFileA.open(filenameA);
data/libvcflib-1.0.1+dfsg/src/vcfcommonsamples.cpp:54:22:  [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).
        variantFileB.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfcommonsamples.cpp:56:22:  [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).
        variantFileB.open(filenameB);
data/libvcflib-1.0.1+dfsg/src/vcfcountalleles.cpp:12:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfcountalleles.cpp:14:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfcreatemulti.cpp:136:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfcreatemulti.cpp:138:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfdistance.cpp:27:17:  [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).
    variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfecho.cpp:12:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfecho.cpp:14:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfentropy.cpp:72:26:  [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).
            windowSize = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/vcfentropy.cpp:101:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ref.open(fastaRef);
data/libvcflib-1.0.1+dfsg/src/vcfentropy.cpp:107:21:  [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).
        variantFile.open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcfentropy.cpp:109:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfevenregions.cpp:97:33:  [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).
            number_of_regions = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/vcfevenregions.cpp:101:35:  [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).
            number_of_positions = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/vcfevenregions.cpp:105:22:  [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).
            offset = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/vcfevenregions.cpp:109:23:  [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).
            overlap = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/vcfevenregions.cpp:138:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ref.open(fastaRef);
data/libvcflib-1.0.1+dfsg/src/vcfevenregions.cpp:144:21:  [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).
        variantFile.open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcfevenregions.cpp:146:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcffilter.cpp:214:19:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      variantFile.open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcffilter.cpp:216:19:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
      variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcffixup.cpp:54:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcffixup.cpp:61:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfflatten.cpp:31:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfflatten.cpp:33:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfgeno2alleles.cpp:20:17:  [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).
    variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfgeno2alleles.cpp:42:29:  [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 index = atoi(g->c_str());
data/libvcflib-1.0.1+dfsg/src/vcfgeno2haplo.cpp:89:26:  [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).
            windowsize = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/vcfgeno2haplo.cpp:117:21:  [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).
        variantFile.open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcfgeno2haplo.cpp:119:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfgeno2haplo.cpp:132:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    reference.open(fastaFileName);
data/libvcflib-1.0.1+dfsg/src/vcfgenosamplenames.cpp:12:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfgenosamplenames.cpp:14:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfgenosummarize.cpp:25:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfgenosummarize.cpp:28:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfgenotypecompare.cpp:43:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfgenotypecompare.cpp:45:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfgenotypes.cpp:23:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfgenotypes.cpp:25:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfglbound.cpp:93:21:  [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).
        variantFile.open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcfglbound.cpp:95:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfglxgt.cpp:81:21:  [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).
        variantFile.open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcfglxgt.cpp:83:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfhetcount.cpp:24:21:  [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).
        variantFile.open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcfhetcount.cpp:26:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfhethomratio.cpp:22:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfhethomratio.cpp:24:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfindex.cpp:14:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfindex.cpp:16:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfinfo2qual.cpp:22:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfinfo2qual.cpp:24:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfinfosummarize.cpp:152:21:  [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).
        variantFile.open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcfinfosummarize.cpp:154:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfintersect.cpp:109:26:  [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).
            windowsize = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/vcfintersect.cpp:195:21:  [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).
        variantFile.open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcfintersect.cpp:197:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfintersect.cpp:220:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        bed.open(bedFileName);
data/libvcflib-1.0.1+dfsg/src/vcfintersect.cpp:235:34:  [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).
                otherVariantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfintersect.cpp:238:30:  [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).
            otherVariantFile.open(vcfFileName);
data/libvcflib-1.0.1+dfsg/src/vcfintersect.cpp:278:19:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        reference.open(fastaFileName);
data/libvcflib-1.0.1+dfsg/src/vcfkeepgeno.cpp:32:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfkeepgeno.cpp:34:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfkeepinfo.cpp:27:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfkeepinfo.cpp:29:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfkeepsamples.cpp:26:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfkeepsamples.cpp:28:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfld.cpp:56:12:  [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).
    index[ atoi( (*it).c_str() ) ] = 1;
data/libvcflib-1.0.1+dfsg/src/vcfld.cpp:260:21:  [2] (integer) atol:
  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).
	      windowSize = atol( win.c_str() );
data/libvcflib-1.0.1+dfsg/src/vcfld.cpp:293:17:  [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).
    variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfleftalign.cpp:519:22:  [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).
            window = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/vcfleftalign.cpp:538:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfleftalign.cpp:540:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfleftalign.cpp:553:24:  [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).
        fastaReference.open(fastaFileName);
data/libvcflib-1.0.1+dfsg/src/vcflength.cpp:14:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcflength.cpp:16:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfnormalizesvs.cpp:71:17:  [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).
    variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfnormalizesvs.cpp:81:18:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            ins->open(x);
data/libvcflib-1.0.1+dfsg/src/vcfnormalizesvs.cpp:87:13:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
        ref.open(ref_file);
data/libvcflib-1.0.1+dfsg/src/vcfnull2ref.cpp:23:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfnull2ref.cpp:25:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfnumalt.cpp:22:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfnumalt.cpp:24:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfoverlay.cpp:83:31:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
            if (!variantFile->open(inputFilename)) {
data/libvcflib-1.0.1+dfsg/src/vcfparsealts.cpp:12:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfparsealts.cpp:14:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfprimers.cpp:79:28:  [2] (integer) atoi:
  Unless checked, the resulting number can exceed the expected range
  (CWE-190). If source untrusted, check both minimum and maximum, even if the
  input had no minus sign (large numbers can roll over into negative number;
  consider saving to an unsigned value if that is intended).
            primerLength = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/vcfprimers.cpp:108:9:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    ref.open(fastaRef);
data/libvcflib-1.0.1+dfsg/src/vcfprimers.cpp:114:21:  [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).
        variantFile.open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcfprimers.cpp:116:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfqual2info.cpp:21:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfqual2info.cpp:23:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfrandomsample.cpp:67:20:  [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).
            seed = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/vcfrandomsample.cpp:92:21:  [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).
        variantFile.open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcfrandomsample.cpp:94:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfrandomsample.cpp:106:20:  [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).
            random.open("/dev/urandom", fstream::in);
data/libvcflib-1.0.1+dfsg/src/vcfrandomsample.cpp:108:20:  [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).
            random.open("/dev/random", fstream::in);
data/libvcflib-1.0.1+dfsg/src/vcfremap.cpp:90:26:  [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).
            windowsize = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/vcfremap.cpp:123:29:  [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).
            altwindowsize = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/vcfremap.cpp:149:21:  [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).
        variantFile.open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcfremap.cpp:151:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfremap.cpp:164:20:  [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).
        freference.open(fastaFileName);
data/libvcflib-1.0.1+dfsg/src/vcfremap.cpp:228:27:  [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).
                    len = atoi(slen.c_str());
data/libvcflib-1.0.1+dfsg/src/vcfremap.cpp:240:27:  [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).
                    len = atoi(slen.c_str());
data/libvcflib-1.0.1+dfsg/src/vcfremap.cpp:251:27:  [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).
                    len = atoi(slen.c_str());
data/libvcflib-1.0.1+dfsg/src/vcfremap.cpp:276:27:  [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).
                    len = atoi(slen.c_str());
data/libvcflib-1.0.1+dfsg/src/vcfremoveaberrantgenotypes.cpp:46:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfremoveaberrantgenotypes.cpp:48:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfremovesamples.cpp:46:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfremovesamples.cpp:48:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfroc.cpp:152:26:  [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).
            windowsize = atoi(optarg);
data/libvcflib-1.0.1+dfsg/src/vcfroc.cpp:186:21:  [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).
        variantFile.open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcfroc.cpp:188:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfroc.cpp:204:34:  [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).
                truthVariantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfroc.cpp:207:30:  [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).
            truthVariantFile.open(truthVcfFileName);
data/libvcflib-1.0.1+dfsg/src/vcfroc.cpp:220:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
    reference.open(fastaFileName);
data/libvcflib-1.0.1+dfsg/src/vcfsample2info.cpp:136:21:  [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).
        variantFile.open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcfsample2info.cpp:138:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfsamplediff.cpp:125:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfsamplediff.cpp:127:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfsamplenames.cpp:12:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfsamplenames.cpp:14:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfsamplestats.cpp:93:21:  [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).
        variantFile.open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcfsamplestats.cpp:95:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfsitesummarize.cpp:12:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfsitesummarize.cpp:14:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfsom.cpp:354:21:  [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).
        variantFile.open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcfsom.cpp:356:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfsom.cpp:521:29:  [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).
            trueVariantFile.open(trueVCF);
data/libvcflib-1.0.1+dfsg/src/vcfsom.cpp:543:30:  [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).
            falseVariantFile.open(falseVCF);
data/libvcflib-1.0.1+dfsg/src/vcfstats.cpp:181:21:  [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).
        variantFile.open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcfstats.cpp:183:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfstreamsort.cpp:83:21:  [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).
        variantFile.open(inputFilename);
data/libvcflib-1.0.1+dfsg/src/vcfstreamsort.cpp:85:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfuniq.cpp:12:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfuniq.cpp:14:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfuniqalleles.cpp:13:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfuniqalleles.cpp:15:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfunphase.cpp:23:21:  [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).
        variantFile.open(std::cin);
data/libvcflib-1.0.1+dfsg/src/vcfunphase.cpp:25:21:  [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).
        variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/vcfunphase.cpp:49:35:  [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).
                    gti.push_back(atoi(g->c_str()));
data/libvcflib-1.0.1+dfsg/src/vec128int.h:326:32:  [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 vector unsigned char permute_selector[4] = {
data/libvcflib-1.0.1+dfsg/src/vec128int.h:346:32:  [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 vector unsigned char permute_selector[2] = {
data/libvcflib-1.0.1+dfsg/src/vec128int.h:369:32:  [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 vector unsigned char permute_selector[8] = {
data/libvcflib-1.0.1+dfsg/src/vec128int.h:399:32:  [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 vector unsigned char permute_selector[16] = {
data/libvcflib-1.0.1+dfsg/src/vec128int.h:476:34:  [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 vector unsigned char permute_selector[8] = {
data/libvcflib-1.0.1+dfsg/src/vec128int.h:1493:32:  [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 vector unsigned char permute_selector[16] = {
data/libvcflib-1.0.1+dfsg/src/veclib_types.h:170:5:  [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                      as_char              [8];
data/libvcflib-1.0.1+dfsg/src/veclib_types.h:171:12:  [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.
    signed char               as_signed_char       [8];
data/libvcflib-1.0.1+dfsg/src/veclib_types.h: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.
    signed char               as_char              [8];
data/libvcflib-1.0.1+dfsg/src/veclib_types.h:184:14:  [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.
    unsigned char             as_unsigned_char     [8];
data/libvcflib-1.0.1+dfsg/src/veclib_types.h:185:12:  [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.
    signed char               as_signed_char       [8];
data/libvcflib-1.0.1+dfsg/src/veclib_types.h:211:5:  [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                      as_char              [16];
data/libvcflib-1.0.1+dfsg/src/veclib_types.h:245:5:  [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                      as_char              [16];
data/libvcflib-1.0.1+dfsg/src/veclib_types.h:278:21:  [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.
    vector signed   char      as_vector_signed_char         [2];
data/libvcflib-1.0.1+dfsg/src/veclib_types.h:279:21:  [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.
    vector unsigned char      as_vector_unsigned_char       [2];
data/libvcflib-1.0.1+dfsg/src/veclib_types.h:280:21:  [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.
    vector bool     char      as_vector_bool_char           [2];
data/libvcflib-1.0.1+dfsg/src/veclib_types.h:290:5:  [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                      as_char                       [32];
data/libvcflib-1.0.1+dfsg/src/veclib_types.h:317:21:  [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.
    vector signed   char      as_vector_signed_char         [2];
data/libvcflib-1.0.1+dfsg/src/veclib_types.h:318:21:  [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.
    vector unsigned char      as_vector_unsigned_char       [2];
data/libvcflib-1.0.1+dfsg/src/veclib_types.h:319:21:  [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.
    vector bool     char      as_vector_bool_char           [2];
data/libvcflib-1.0.1+dfsg/src/veclib_types.h:330:5:  [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                      as_char                       [32];
data/libvcflib-1.0.1+dfsg/src/wcFst.cpp:67:12:  [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).
    index[ atoi( (*it).c_str() ) ] = 1;
data/libvcflib-1.0.1+dfsg/src/wcFst.cpp:170:17:  [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).
    variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/src/xpEHH.cpp:67:12:  [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).
    index[ atoi( (*it).c_str() ) ] = 1;
data/libvcflib-1.0.1+dfsg/src/xpEHH.cpp:305:17:  [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).
    variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/test/tests/variantFileTests.h:7:23:  [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).
TEST(VariantCallFile, open){
data/libvcflib-1.0.1+dfsg/test/tests/variantFileTests.h:13:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/test/tests/variantFileTests.h:25:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/test/tests/variantFileTests.h:40:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/test/tests/variantFileTests.h:54:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  variantFile.open(filename);
data/libvcflib-1.0.1+dfsg/test/tests/variantTests.h:17:15:  [2] (misc) open:
  Check when opening files - can an attacker redirect it (via symlinks),
  force the opening of special file type (e.g., device files), move things
  around to create a race condition, control its ancestors, or change its
  contents? (CWE-362).
  variantFile.open(filename);  

ANALYSIS SUMMARY:

Hits = 437
Lines analyzed = 56413 in approximately 1.54 seconds (36561 lines/second)
Physical Source Lines of Code (SLOC) = 38938
Hits@level = [0]  49 [1]   0 [2] 351 [3]  86 [4]   0 [5]   0
Hits@level+ = [0+] 486 [1+] 437 [2+] 437 [3+]  86 [4+]   0 [5+]   0
Hits/KSLOC@level+ = [0+] 12.4814 [1+] 11.223 [2+] 11.223 [3+] 2.20864 [4+]   0 [5+]   0
Dot directories skipped = 1 (--followdotdir overrides)
Minimum risk level = 1
Not every hit is necessarily a security vulnerability.
There may be other security vulnerabilities; review your code!
See 'Secure Programming HOWTO'
(https://dwheeler.com/secure-programs) for more information.