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/mothur-1.44.3/TestMothur/catch.hpp
Examining data/mothur-1.44.3/TestMothur/dataset.cpp
Examining data/mothur-1.44.3/TestMothur/dataset.h
Examining data/mothur-1.44.3/TestMothur/distcdataset.cpp
Examining data/mothur-1.44.3/TestMothur/distcdataset.h
Examining data/mothur-1.44.3/TestMothur/distpdataset.cpp
Examining data/mothur-1.44.3/TestMothur/distpdataset.h
Examining data/mothur-1.44.3/TestMothur/fakes/fakemcc.hpp
Examining data/mothur-1.44.3/TestMothur/fakes/fakeoligos.h
Examining data/mothur-1.44.3/TestMothur/fakes/fakeoptimatrix.cpp
Examining data/mothur-1.44.3/TestMothur/fakes/fakeoptimatrix.hpp
Examining data/mothur-1.44.3/TestMothur/fastqdataset.cpp
Examining data/mothur-1.44.3/TestMothur/fastqdataset.h
Examining data/mothur-1.44.3/TestMothur/main.cpp
Examining data/mothur-1.44.3/TestMothur/testbiominfocommand.cpp
Examining data/mothur-1.44.3/TestMothur/testbiominfocommand.h
Examining data/mothur-1.44.3/TestMothur/testclassifier/testphylotree.cpp
Examining data/mothur-1.44.3/TestMothur/testclassifier/testphylotree.hpp
Examining data/mothur-1.44.3/TestMothur/testclustercalcs.cpp
Examining data/mothur-1.44.3/TestMothur/testclustercalcs.hpp
Examining data/mothur-1.44.3/TestMothur/testcommands/testgetgroupscommand.cpp
Examining data/mothur-1.44.3/TestMothur/testcommands/testgetgroupscommand.h
Examining data/mothur-1.44.3/TestMothur/testcommands/testmergegroupscommand.cpp
Examining data/mothur-1.44.3/TestMothur/testcommands/testmergegroupscommand.h
Examining data/mothur-1.44.3/TestMothur/testcommands/testremovegroupscommand.cpp
Examining data/mothur-1.44.3/TestMothur/testcommands/testremovegroupscommand.h
Examining data/mothur-1.44.3/TestMothur/testcommands/testrenamefilecommand.cpp
Examining data/mothur-1.44.3/TestMothur/testcommands/testrenamefilecommand.h
Examining data/mothur-1.44.3/TestMothur/testcommands/testrenameseqscommand.cpp
Examining data/mothur-1.44.3/TestMothur/testcommands/testrenameseqscommand.h
Examining data/mothur-1.44.3/TestMothur/testcommands/testsetseedcommand.cpp
Examining data/mothur-1.44.3/TestMothur/testcontainers/testOligos.cpp
Examining data/mothur-1.44.3/TestMothur/testcontainers/testOligos.hpp
Examining data/mothur-1.44.3/TestMothur/testcontainers/testcounttable.cpp
Examining data/mothur-1.44.3/TestMothur/testcontainers/testcounttable.hpp
Examining data/mothur-1.44.3/TestMothur/testcontainers/testfastqread.cpp
Examining data/mothur-1.44.3/TestMothur/testcontainers/testfastqread.h
Examining data/mothur-1.44.3/TestMothur/testcontainers/testoptimatrix.cpp
Examining data/mothur-1.44.3/TestMothur/testcontainers/testoptimatrix.h
Examining data/mothur-1.44.3/TestMothur/testcontainers/testsequence.cpp
Examining data/mothur-1.44.3/TestMothur/testcontainers/testsequence.h
Examining data/mothur-1.44.3/TestMothur/testcontainers/testsharedrabundfloatvector.cpp
Examining data/mothur-1.44.3/TestMothur/testcontainers/testsharedrabundfloatvector.hpp
Examining data/mothur-1.44.3/TestMothur/testcontainers/testsharedrabundfloatvectors.cpp
Examining data/mothur-1.44.3/TestMothur/testcontainers/testsharedrabundfloatvectors.hpp
Examining data/mothur-1.44.3/TestMothur/testcontainers/testsharedrabundvector.cpp
Examining data/mothur-1.44.3/TestMothur/testcontainers/testsharedrabundvector.hpp
Examining data/mothur-1.44.3/TestMothur/testcontainers/testsharedrabundvectors.cpp
Examining data/mothur-1.44.3/TestMothur/testcontainers/testsharedrabundvectors.hpp
Examining data/mothur-1.44.3/TestMothur/testopticluster.cpp
Examining data/mothur-1.44.3/TestMothur/testopticluster.h
Examining data/mothur-1.44.3/TestMothur/testoptirefmatrix.cpp
Examining data/mothur-1.44.3/TestMothur/testoptirefmatrix.hpp
Examining data/mothur-1.44.3/TestMothur/testsubsample.cpp
Examining data/mothur-1.44.3/TestMothur/testsubsample.hpp
Examining data/mothur-1.44.3/TestMothur/testtrimoligos.cpp
Examining data/mothur-1.44.3/TestMothur/testtrimoligos.hpp
Examining data/mothur-1.44.3/TestMothur/testvsearchfileparser.cpp
Examining data/mothur-1.44.3/TestMothur/testvsearchfileparser.h
Examining data/mothur-1.44.3/source/averagelinkage.cpp
Examining data/mothur-1.44.3/source/calcsparcc.cpp
Examining data/mothur-1.44.3/source/calcsparcc.h
Examining data/mothur-1.44.3/source/calculators/accuracy.cpp
Examining data/mothur-1.44.3/source/calculators/accuracy.hpp
Examining data/mothur-1.44.3/source/calculators/ace.cpp
Examining data/mothur-1.44.3/source/calculators/ace.h
Examining data/mothur-1.44.3/source/calculators/bergerparker.cpp
Examining data/mothur-1.44.3/source/calculators/bergerparker.h
Examining data/mothur-1.44.3/source/calculators/boneh.cpp
Examining data/mothur-1.44.3/source/calculators/boneh.h
Examining data/mothur-1.44.3/source/calculators/bootstrap.cpp
Examining data/mothur-1.44.3/source/calculators/bootstrap.h
Examining data/mothur-1.44.3/source/calculators/bstick.cpp
Examining data/mothur-1.44.3/source/calculators/bstick.h
Examining data/mothur-1.44.3/source/calculators/calculator.cpp
Examining data/mothur-1.44.3/source/calculators/calculator.h
Examining data/mothur-1.44.3/source/calculators/canberra.cpp
Examining data/mothur-1.44.3/source/calculators/canberra.h
Examining data/mothur-1.44.3/source/calculators/chao1.cpp
Examining data/mothur-1.44.3/source/calculators/chao1.h
Examining data/mothur-1.44.3/source/calculators/coverage.cpp
Examining data/mothur-1.44.3/source/calculators/coverage.h
Examining data/mothur-1.44.3/source/calculators/dayhoff.h
Examining data/mothur-1.44.3/source/calculators/diversitycalc.h
Examining data/mothur-1.44.3/source/calculators/diversityutils.cpp
Examining data/mothur-1.44.3/source/calculators/diversityutils.hpp
Examining data/mothur-1.44.3/source/calculators/eachgapdist.cpp
Examining data/mothur-1.44.3/source/calculators/eachgapdist.h
Examining data/mothur-1.44.3/source/calculators/eachgapignore.cpp
Examining data/mothur-1.44.3/source/calculators/eachgapignore.h
Examining data/mothur-1.44.3/source/calculators/efron.cpp
Examining data/mothur-1.44.3/source/calculators/efron.h
Examining data/mothur-1.44.3/source/calculators/erarefaction.cpp
Examining data/mothur-1.44.3/source/calculators/erarefaction.hpp
Examining data/mothur-1.44.3/source/calculators/f1score.cpp
Examining data/mothur-1.44.3/source/calculators/f1score.hpp
Examining data/mothur-1.44.3/source/calculators/fdr.cpp
Examining data/mothur-1.44.3/source/calculators/fdr.hpp
Examining data/mothur-1.44.3/source/calculators/filters.h
Examining data/mothur-1.44.3/source/calculators/fn.cpp
Examining data/mothur-1.44.3/source/calculators/fn.hpp
Examining data/mothur-1.44.3/source/calculators/fp.cpp
Examining data/mothur-1.44.3/source/calculators/fp.hpp
Examining data/mothur-1.44.3/source/calculators/fpfn.cpp
Examining data/mothur-1.44.3/source/calculators/fpfn.hpp
Examining data/mothur-1.44.3/source/calculators/geom.cpp
Examining data/mothur-1.44.3/source/calculators/geom.h
Examining data/mothur-1.44.3/source/calculators/goodscoverage.cpp
Examining data/mothur-1.44.3/source/calculators/goodscoverage.h
Examining data/mothur-1.44.3/source/calculators/gower.cpp
Examining data/mothur-1.44.3/source/calculators/gower.h
Examining data/mothur-1.44.3/source/calculators/hamming.cpp
Examining data/mothur-1.44.3/source/calculators/hamming.h
Examining data/mothur-1.44.3/source/calculators/heip.cpp
Examining data/mothur-1.44.3/source/calculators/heip.h
Examining data/mothur-1.44.3/source/calculators/hellinger.cpp
Examining data/mothur-1.44.3/source/calculators/hellinger.h
Examining data/mothur-1.44.3/source/calculators/igabundance.cpp
Examining data/mothur-1.44.3/source/calculators/igabundance.hpp
Examining data/mothur-1.44.3/source/calculators/ignoregaps.cpp
Examining data/mothur-1.44.3/source/calculators/ignoregaps.h
Examining data/mothur-1.44.3/source/calculators/igrarefaction.cpp
Examining data/mothur-1.44.3/source/calculators/igrarefaction.hpp
Examining data/mothur-1.44.3/source/calculators/invsimpson.cpp
Examining data/mothur-1.44.3/source/calculators/invsimpson.h
Examining data/mothur-1.44.3/source/calculators/jackknife.cpp
Examining data/mothur-1.44.3/source/calculators/jackknife.h
Examining data/mothur-1.44.3/source/calculators/lnabundance.cpp
Examining data/mothur-1.44.3/source/calculators/lnabundance.hpp
Examining data/mothur-1.44.3/source/calculators/lnrarefaction.cpp
Examining data/mothur-1.44.3/source/calculators/lnrarefaction.hpp
Examining data/mothur-1.44.3/source/calculators/lnshift.cpp
Examining data/mothur-1.44.3/source/calculators/lnshift.hpp
Examining data/mothur-1.44.3/source/calculators/logsd.cpp
Examining data/mothur-1.44.3/source/calculators/logsd.h
Examining data/mothur-1.44.3/source/calculators/lsabundance.cpp
Examining data/mothur-1.44.3/source/calculators/lsabundance.hpp
Examining data/mothur-1.44.3/source/calculators/lsrarefaction.cpp
Examining data/mothur-1.44.3/source/calculators/lsrarefaction.hpp
Examining data/mothur-1.44.3/source/calculators/manhattan.cpp
Examining data/mothur-1.44.3/source/calculators/manhattan.h
Examining data/mothur-1.44.3/source/calculators/mcc.cpp
Examining data/mothur-1.44.3/source/calculators/mcc.hpp
Examining data/mothur-1.44.3/source/calculators/memchi2.cpp
Examining data/mothur-1.44.3/source/calculators/memchi2.h
Examining data/mothur-1.44.3/source/calculators/memchord.cpp
Examining data/mothur-1.44.3/source/calculators/memchord.h
Examining data/mothur-1.44.3/source/calculators/memeuclidean.cpp
Examining data/mothur-1.44.3/source/calculators/memeuclidean.h
Examining data/mothur-1.44.3/source/calculators/mempearson.cpp
Examining data/mothur-1.44.3/source/calculators/mempearson.h
Examining data/mothur-1.44.3/source/calculators/metroig.cpp
Examining data/mothur-1.44.3/source/calculators/metroig.hpp
Examining data/mothur-1.44.3/source/calculators/metrolognormal.cpp
Examining data/mothur-1.44.3/source/calculators/metrolognormal.hpp
Examining data/mothur-1.44.3/source/calculators/metrologstudent.cpp
Examining data/mothur-1.44.3/source/calculators/metrologstudent.hpp
Examining data/mothur-1.44.3/source/calculators/metrosichel.cpp
Examining data/mothur-1.44.3/source/calculators/metrosichel.hpp
Examining data/mothur-1.44.3/source/calculators/npshannon.cpp
Examining data/mothur-1.44.3/source/calculators/npshannon.h
Examining data/mothur-1.44.3/source/calculators/npv.cpp
Examining data/mothur-1.44.3/source/calculators/npv.hpp
Examining data/mothur-1.44.3/source/calculators/nseqs.h
Examining data/mothur-1.44.3/source/calculators/odum.cpp
Examining data/mothur-1.44.3/source/calculators/odum.h
Examining data/mothur-1.44.3/source/calculators/onegapdist.cpp
Examining data/mothur-1.44.3/source/calculators/onegapdist.h
Examining data/mothur-1.44.3/source/calculators/onegapignore.cpp
Examining data/mothur-1.44.3/source/calculators/onegapignore.h
Examining data/mothur-1.44.3/source/calculators/parsimony.cpp
Examining data/mothur-1.44.3/source/calculators/parsimony.h
Examining data/mothur-1.44.3/source/calculators/ppv.cpp
Examining data/mothur-1.44.3/source/calculators/ppv.hpp
Examining data/mothur-1.44.3/source/calculators/prng.cpp
Examining data/mothur-1.44.3/source/calculators/prng.h
Examining data/mothur-1.44.3/source/calculators/qstat.cpp
Examining data/mothur-1.44.3/source/calculators/qstat.h
Examining data/mothur-1.44.3/source/calculators/sensitivity.cpp
Examining data/mothur-1.44.3/source/calculators/sensitivity.hpp
Examining data/mothur-1.44.3/source/calculators/shannon.cpp
Examining data/mothur-1.44.3/source/calculators/shannon.h
Examining data/mothur-1.44.3/source/calculators/shannoneven.cpp
Examining data/mothur-1.44.3/source/calculators/shannoneven.h
Examining data/mothur-1.44.3/source/calculators/shannonrange.cpp
Examining data/mothur-1.44.3/source/calculators/shannonrange.h
Examining data/mothur-1.44.3/source/calculators/sharedace.cpp
Examining data/mothur-1.44.3/source/calculators/sharedace.h
Examining data/mothur-1.44.3/source/calculators/sharedanderbergs.cpp
Examining data/mothur-1.44.3/source/calculators/sharedanderbergs.h
Examining data/mothur-1.44.3/source/calculators/sharedbraycurtis.cpp
Examining data/mothur-1.44.3/source/calculators/sharedbraycurtis.h
Examining data/mothur-1.44.3/source/calculators/sharedchao1.cpp
Examining data/mothur-1.44.3/source/calculators/sharedchao1.h
Examining data/mothur-1.44.3/source/calculators/sharedjabund.cpp
Examining data/mothur-1.44.3/source/calculators/sharedjabund.h
Examining data/mothur-1.44.3/source/calculators/sharedjackknife.cpp
Examining data/mothur-1.44.3/source/calculators/sharedjackknife.h
Examining data/mothur-1.44.3/source/calculators/sharedjclass.cpp
Examining data/mothur-1.44.3/source/calculators/sharedjclass.h
Examining data/mothur-1.44.3/source/calculators/sharedjest.cpp
Examining data/mothur-1.44.3/source/calculators/sharedjest.h
Examining data/mothur-1.44.3/source/calculators/sharedjsd.cpp
Examining data/mothur-1.44.3/source/calculators/sharedjsd.h
Examining data/mothur-1.44.3/source/calculators/sharedkstest.cpp
Examining data/mothur-1.44.3/source/calculators/sharedkstest.h
Examining data/mothur-1.44.3/source/calculators/sharedkulczynski.cpp
Examining data/mothur-1.44.3/source/calculators/sharedkulczynski.h
Examining data/mothur-1.44.3/source/calculators/sharedkulczynskicody.cpp
Examining data/mothur-1.44.3/source/calculators/sharedkulczynskicody.h
Examining data/mothur-1.44.3/source/calculators/sharedlennon.cpp
Examining data/mothur-1.44.3/source/calculators/sharedlennon.h
Examining data/mothur-1.44.3/source/calculators/sharedmarczewski.cpp
Examining data/mothur-1.44.3/source/calculators/sharedmarczewski.h
Examining data/mothur-1.44.3/source/calculators/sharedmorisitahorn.cpp
Examining data/mothur-1.44.3/source/calculators/sharedmorisitahorn.h
Examining data/mothur-1.44.3/source/calculators/sharednseqs.h
Examining data/mothur-1.44.3/source/calculators/sharedochiai.cpp
Examining data/mothur-1.44.3/source/calculators/sharedochiai.h
Examining data/mothur-1.44.3/source/calculators/sharedrjsd.cpp
Examining data/mothur-1.44.3/source/calculators/sharedrjsd.h
Examining data/mothur-1.44.3/source/calculators/sharedsobs.cpp
Examining data/mothur-1.44.3/source/calculators/sharedsobs.h
Examining data/mothur-1.44.3/source/calculators/sharedsobscollectsummary.cpp
Examining data/mothur-1.44.3/source/calculators/sharedsobscollectsummary.h
Examining data/mothur-1.44.3/source/calculators/sharedsorabund.cpp
Examining data/mothur-1.44.3/source/calculators/sharedsorabund.h
Examining data/mothur-1.44.3/source/calculators/sharedsorclass.cpp
Examining data/mothur-1.44.3/source/calculators/sharedsorclass.h
Examining data/mothur-1.44.3/source/calculators/sharedsorest.cpp
Examining data/mothur-1.44.3/source/calculators/sharedsorest.h
Examining data/mothur-1.44.3/source/calculators/sharedthetan.cpp
Examining data/mothur-1.44.3/source/calculators/sharedthetan.h
Examining data/mothur-1.44.3/source/calculators/sharedthetayc.cpp
Examining data/mothur-1.44.3/source/calculators/sharedthetayc.h
Examining data/mothur-1.44.3/source/calculators/shen.cpp
Examining data/mothur-1.44.3/source/calculators/shen.h
Examining data/mothur-1.44.3/source/calculators/siabundance.cpp
Examining data/mothur-1.44.3/source/calculators/siabundance.hpp
Examining data/mothur-1.44.3/source/calculators/simpson.cpp
Examining data/mothur-1.44.3/source/calculators/simpson.h
Examining data/mothur-1.44.3/source/calculators/simpsoneven.cpp
Examining data/mothur-1.44.3/source/calculators/simpsoneven.h
Examining data/mothur-1.44.3/source/calculators/sirarefaction.cpp
Examining data/mothur-1.44.3/source/calculators/sirarefaction.hpp
Examining data/mothur-1.44.3/source/calculators/sishift.cpp
Examining data/mothur-1.44.3/source/calculators/sishift.hpp
Examining data/mothur-1.44.3/source/calculators/smithwilson.cpp
Examining data/mothur-1.44.3/source/calculators/smithwilson.h
Examining data/mothur-1.44.3/source/calculators/sobs.h
Examining data/mothur-1.44.3/source/calculators/soergel.cpp
Examining data/mothur-1.44.3/source/calculators/soergel.h
Examining data/mothur-1.44.3/source/calculators/solow.cpp
Examining data/mothur-1.44.3/source/calculators/solow.h
Examining data/mothur-1.44.3/source/calculators/spearman.cpp
Examining data/mothur-1.44.3/source/calculators/spearman.h
Examining data/mothur-1.44.3/source/calculators/speciesprofile.cpp
Examining data/mothur-1.44.3/source/calculators/speciesprofile.h
Examining data/mothur-1.44.3/source/calculators/specificity.cpp
Examining data/mothur-1.44.3/source/calculators/specificity.hpp
Examining data/mothur-1.44.3/source/calculators/structchi2.cpp
Examining data/mothur-1.44.3/source/calculators/structchi2.h
Examining data/mothur-1.44.3/source/calculators/structchord.cpp
Examining data/mothur-1.44.3/source/calculators/structchord.h
Examining data/mothur-1.44.3/source/calculators/structeuclidean.cpp
Examining data/mothur-1.44.3/source/calculators/structeuclidean.h
Examining data/mothur-1.44.3/source/calculators/structkulczynski.cpp
Examining data/mothur-1.44.3/source/calculators/structkulczynski.h
Examining data/mothur-1.44.3/source/calculators/structpearson.cpp
Examining data/mothur-1.44.3/source/calculators/structpearson.h
Examining data/mothur-1.44.3/source/calculators/tn.cpp
Examining data/mothur-1.44.3/source/calculators/tn.hpp
Examining data/mothur-1.44.3/source/calculators/tp.cpp
Examining data/mothur-1.44.3/source/calculators/tp.hpp
Examining data/mothur-1.44.3/source/calculators/tptn.cpp
Examining data/mothur-1.44.3/source/calculators/tptn.hpp
Examining data/mothur-1.44.3/source/calculators/treecalculator.h
Examining data/mothur-1.44.3/source/calculators/unweighted.cpp
Examining data/mothur-1.44.3/source/calculators/unweighted.h
Examining data/mothur-1.44.3/source/calculators/uvest.cpp
Examining data/mothur-1.44.3/source/calculators/uvest.h
Examining data/mothur-1.44.3/source/calculators/weighted.cpp
Examining data/mothur-1.44.3/source/calculators/weighted.h
Examining data/mothur-1.44.3/source/calculators/whittaker.cpp
Examining data/mothur-1.44.3/source/calculators/whittaker.h
Examining data/mothur-1.44.3/source/checked.h
Examining data/mothur-1.44.3/source/chimera/bellerophon.cpp
Examining data/mothur-1.44.3/source/chimera/bellerophon.h
Examining data/mothur-1.44.3/source/chimera/ccode.cpp
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Examining data/mothur-1.44.3/source/chimera/chimeracheckrdp.cpp
Examining data/mothur-1.44.3/source/chimera/chimeracheckrdp.h
Examining data/mothur-1.44.3/source/chimera/chimerarealigner.cpp
Examining data/mothur-1.44.3/source/chimera/chimerarealigner.h
Examining data/mothur-1.44.3/source/chimera/chimeraslayer.cpp
Examining data/mothur-1.44.3/source/chimera/chimeraslayer.h
Examining data/mothur-1.44.3/source/chimera/decalc.cpp
Examining data/mothur-1.44.3/source/chimera/decalc.h
Examining data/mothur-1.44.3/source/chimera/maligner.cpp
Examining data/mothur-1.44.3/source/chimera/maligner.h
Examining data/mothur-1.44.3/source/chimera/mothurchimera.cpp
Examining data/mothur-1.44.3/source/chimera/mothurchimera.h
Examining data/mothur-1.44.3/source/chimera/myPerseus.cpp
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Examining data/mothur-1.44.3/source/chimera/pintail.cpp
Examining data/mothur-1.44.3/source/chimera/pintail.h
Examining data/mothur-1.44.3/source/chimera/slayer.cpp
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Examining data/mothur-1.44.3/source/classifier/alignnode.cpp
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Examining data/mothur-1.44.3/source/classifier/aligntree.cpp
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Examining data/mothur-1.44.3/source/classifier/bayesian.cpp
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Examining data/mothur-1.44.3/source/classifier/classify.cpp
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Examining data/mothur-1.44.3/source/classifier/kmernode.cpp
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Examining data/mothur-1.44.3/source/classifier/opticlassifier.cpp
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Examining data/mothur-1.44.3/source/classifier/phylosummary.cpp
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Examining data/mothur-1.44.3/source/classifier/taxonomyequalizer.cpp
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Examining data/mothur-1.44.3/source/clearcut/clearcut.cpp
Examining data/mothur-1.44.3/source/clearcut/clearcut.h
Examining data/mothur-1.44.3/source/clearcut/cmdargs.cpp
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Examining data/mothur-1.44.3/source/clearcut/common.h
Examining data/mothur-1.44.3/source/clearcut/distclearcut.cpp
Examining data/mothur-1.44.3/source/clearcut/distclearcut.h
Examining data/mothur-1.44.3/source/clearcut/dmat.cpp
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Examining data/mothur-1.44.3/source/clearcut/fasta.cpp
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Examining data/mothur-1.44.3/source/clearcut/getopt_long.cpp
Examining data/mothur-1.44.3/source/clearcut/getopt_long.h
Examining data/mothur-1.44.3/source/cluster.cpp
Examining data/mothur-1.44.3/source/cluster.hpp
Examining data/mothur-1.44.3/source/clusterclassic.cpp
Examining data/mothur-1.44.3/source/clusterclassic.h
Examining data/mothur-1.44.3/source/collect.cpp
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Examining data/mothur-1.44.3/source/commandfactory.cpp
Examining data/mothur-1.44.3/source/commandfactory.hpp
Examining data/mothur-1.44.3/source/commandoptionparser.cpp
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Examining data/mothur-1.44.3/source/commandparameter.h
Examining data/mothur-1.44.3/source/commands/aligncheckcommand.cpp
Examining data/mothur-1.44.3/source/commands/aligncheckcommand.h
Examining data/mothur-1.44.3/source/commands/aligncommand.cpp
Examining data/mothur-1.44.3/source/commands/aligncommand.h
Examining data/mothur-1.44.3/source/commands/amovacommand.cpp
Examining data/mothur-1.44.3/source/commands/amovacommand.h
Examining data/mothur-1.44.3/source/commands/anosimcommand.cpp
Examining data/mothur-1.44.3/source/commands/anosimcommand.h
Examining data/mothur-1.44.3/source/commands/binsequencecommand.cpp
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Examining data/mothur-1.44.3/source/commands/biominfocommand.cpp
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Examining data/mothur-1.44.3/source/commands/chimerabellerophoncommand.cpp
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Examining data/mothur-1.44.3/source/commands/chimeraccodecommand.cpp
Examining data/mothur-1.44.3/source/commands/chimeraccodecommand.h
Examining data/mothur-1.44.3/source/commands/chimeracheckcommand.cpp
Examining data/mothur-1.44.3/source/commands/chimeracheckcommand.h
Examining data/mothur-1.44.3/source/commands/chimeraperseuscommand.cpp
Examining data/mothur-1.44.3/source/commands/chimeraperseuscommand.h
Examining data/mothur-1.44.3/source/commands/chimerapintailcommand.cpp
Examining data/mothur-1.44.3/source/commands/chimerapintailcommand.h
Examining data/mothur-1.44.3/source/commands/chimeraslayercommand.cpp
Examining data/mothur-1.44.3/source/commands/chimeraslayercommand.h
Examining data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp
Examining data/mothur-1.44.3/source/commands/chimerauchimecommand.h
Examining data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp
Examining data/mothur-1.44.3/source/commands/chimeravsearchcommand.h
Examining data/mothur-1.44.3/source/commands/chopseqscommand.cpp
Examining data/mothur-1.44.3/source/commands/chopseqscommand.h
Examining data/mothur-1.44.3/source/commands/classifyotucommand.cpp
Examining data/mothur-1.44.3/source/commands/classifyotucommand.h
Examining data/mothur-1.44.3/source/commands/classifyseqscommand.cpp
Examining data/mothur-1.44.3/source/commands/classifyseqscommand.h
Examining data/mothur-1.44.3/source/commands/classifysvmsharedcommand.cpp
Examining data/mothur-1.44.3/source/commands/classifysvmsharedcommand.h
Examining data/mothur-1.44.3/source/commands/classifytreecommand.cpp
Examining data/mothur-1.44.3/source/commands/classifytreecommand.h
Examining data/mothur-1.44.3/source/commands/clearcutcommand.cpp
Examining data/mothur-1.44.3/source/commands/clearcutcommand.h
Examining data/mothur-1.44.3/source/commands/clustercommand.cpp
Examining data/mothur-1.44.3/source/commands/clustercommand.h
Examining data/mothur-1.44.3/source/commands/clusterdoturcommand.cpp
Examining data/mothur-1.44.3/source/commands/clusterdoturcommand.h
Examining data/mothur-1.44.3/source/commands/clusterfitcommand.cpp
Examining data/mothur-1.44.3/source/commands/clusterfitcommand.hpp
Examining data/mothur-1.44.3/source/commands/clusterfragmentscommand.cpp
Examining data/mothur-1.44.3/source/commands/clusterfragmentscommand.h
Examining data/mothur-1.44.3/source/commands/clustersplitcommand.cpp
Examining data/mothur-1.44.3/source/commands/clustersplitcommand.h
Examining data/mothur-1.44.3/source/commands/collectcommand.cpp
Examining data/mothur-1.44.3/source/commands/collectcommand.h
Examining data/mothur-1.44.3/source/commands/collectsharedcommand.cpp
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Examining data/mothur-1.44.3/source/commands/command.hpp
Examining data/mothur-1.44.3/source/commands/consensusseqscommand.cpp
Examining data/mothur-1.44.3/source/commands/consensusseqscommand.h
Examining data/mothur-1.44.3/source/commands/cooccurrencecommand.cpp
Examining data/mothur-1.44.3/source/commands/cooccurrencecommand.h
Examining data/mothur-1.44.3/source/commands/corraxescommand.cpp
Examining data/mothur-1.44.3/source/commands/corraxescommand.h
Examining data/mothur-1.44.3/source/commands/countgroupscommand.cpp
Examining data/mothur-1.44.3/source/commands/countgroupscommand.h
Examining data/mothur-1.44.3/source/commands/countseqscommand.cpp
Examining data/mothur-1.44.3/source/commands/countseqscommand.h
Examining data/mothur-1.44.3/source/commands/createdatabasecommand.cpp
Examining data/mothur-1.44.3/source/commands/createdatabasecommand.h
Examining data/mothur-1.44.3/source/commands/deconvolutecommand.cpp
Examining data/mothur-1.44.3/source/commands/deconvolutecommand.h
Examining data/mothur-1.44.3/source/commands/degapseqscommand.cpp
Examining data/mothur-1.44.3/source/commands/degapseqscommand.h
Examining data/mothur-1.44.3/source/commands/deuniqueseqscommand.cpp
Examining data/mothur-1.44.3/source/commands/deuniqueseqscommand.h
Examining data/mothur-1.44.3/source/commands/deuniquetreecommand.cpp
Examining data/mothur-1.44.3/source/commands/deuniquetreecommand.h
Examining data/mothur-1.44.3/source/commands/distancecommand.cpp
Examining data/mothur-1.44.3/source/commands/distancecommand.h
Examining data/mothur-1.44.3/source/commands/distsharedcommand.cpp
Examining data/mothur-1.44.3/source/commands/distsharedcommand.h
Examining data/mothur-1.44.3/source/commands/diversityestimatorcommand.cpp
Examining data/mothur-1.44.3/source/commands/diversityestimatorcommand.hpp
Examining data/mothur-1.44.3/source/commands/filterseqscommand.cpp
Examining data/mothur-1.44.3/source/commands/filterseqscommand.h
Examining data/mothur-1.44.3/source/commands/filtersharedcommand.cpp
Examining data/mothur-1.44.3/source/commands/filtersharedcommand.h
Examining data/mothur-1.44.3/source/commands/getcoremicrobiomecommand.cpp
Examining data/mothur-1.44.3/source/commands/getcoremicrobiomecommand.h
Examining data/mothur-1.44.3/source/commands/getcurrentcommand.cpp
Examining data/mothur-1.44.3/source/commands/getcurrentcommand.h
Examining data/mothur-1.44.3/source/commands/getdistscommand.cpp
Examining data/mothur-1.44.3/source/commands/getdistscommand.h
Examining data/mothur-1.44.3/source/commands/getgroupcommand.cpp
Examining data/mothur-1.44.3/source/commands/getgroupcommand.h
Examining data/mothur-1.44.3/source/commands/getgroupscommand.cpp
Examining data/mothur-1.44.3/source/commands/getgroupscommand.h
Examining data/mothur-1.44.3/source/commands/getlabelcommand.cpp
Examining data/mothur-1.44.3/source/commands/getlabelcommand.h
Examining data/mothur-1.44.3/source/commands/getlineagecommand.cpp
Examining data/mothur-1.44.3/source/commands/getlineagecommand.h
Examining data/mothur-1.44.3/source/commands/getlistcountcommand.cpp
Examining data/mothur-1.44.3/source/commands/getlistcountcommand.h
Examining data/mothur-1.44.3/source/commands/getmetacommunitycommand.cpp
Examining data/mothur-1.44.3/source/commands/getmetacommunitycommand.h
Examining data/mothur-1.44.3/source/commands/getmimarkspackagecommand.cpp
Examining data/mothur-1.44.3/source/commands/getmimarkspackagecommand.h
Examining data/mothur-1.44.3/source/commands/getoturepcommand.cpp
Examining data/mothur-1.44.3/source/commands/getoturepcommand.h
Examining data/mothur-1.44.3/source/commands/getotuscommand.cpp
Examining data/mothur-1.44.3/source/commands/getotuscommand.h
Examining data/mothur-1.44.3/source/commands/getrabundcommand.cpp
Examining data/mothur-1.44.3/source/commands/getrabundcommand.h
Examining data/mothur-1.44.3/source/commands/getrelabundcommand.cpp
Examining data/mothur-1.44.3/source/commands/getrelabundcommand.h
Examining data/mothur-1.44.3/source/commands/getsabundcommand.cpp
Examining data/mothur-1.44.3/source/commands/getsabundcommand.h
Examining data/mothur-1.44.3/source/commands/getseqscommand.cpp
Examining data/mothur-1.44.3/source/commands/getseqscommand.h
Examining data/mothur-1.44.3/source/commands/getsharedotucommand.cpp
Examining data/mothur-1.44.3/source/commands/getsharedotucommand.h
Examining data/mothur-1.44.3/source/commands/heatmapcommand.cpp
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Examining data/mothur-1.44.3/source/commands/heatmapsimcommand.cpp
Examining data/mothur-1.44.3/source/commands/heatmapsimcommand.h
Examining data/mothur-1.44.3/source/commands/helpcommand.cpp
Examining data/mothur-1.44.3/source/commands/helpcommand.h
Examining data/mothur-1.44.3/source/commands/homovacommand.cpp
Examining data/mothur-1.44.3/source/commands/homovacommand.h
Examining data/mothur-1.44.3/source/commands/indicatorcommand.cpp
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Examining data/mothur-1.44.3/source/commands/kruskalwalliscommand.cpp
Examining data/mothur-1.44.3/source/commands/kruskalwalliscommand.h
Examining data/mothur-1.44.3/source/commands/lefsecommand.cpp
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Examining data/mothur-1.44.3/source/commands/libshuffcommand.cpp
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Examining data/mothur-1.44.3/source/commands/listotuscommand.cpp
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Examining data/mothur-1.44.3/source/commands/listseqscommand.cpp
Examining data/mothur-1.44.3/source/commands/listseqscommand.h
Examining data/mothur-1.44.3/source/commands/makebiomcommand.cpp
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Examining data/mothur-1.44.3/source/commands/makeclrcommand.cpp
Examining data/mothur-1.44.3/source/commands/makeclrcommand.hpp
Examining data/mothur-1.44.3/source/commands/makecontigscommand.cpp
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Examining data/mothur-1.44.3/source/commands/makefastqcommand.cpp
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Examining data/mothur-1.44.3/source/commands/makefilecommand.cpp
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Examining data/mothur-1.44.3/source/commands/makegroupcommand.cpp
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Examining data/mothur-1.44.3/source/commands/makelefsecommand.cpp
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Examining data/mothur-1.44.3/source/commands/makelookupcommand.cpp
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Examining data/mothur-1.44.3/source/commands/makesharedcommand.cpp
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Examining data/mothur-1.44.3/source/commands/mantelcommand.cpp
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Examining data/mothur-1.44.3/source/commands/mergecountcommand.cpp
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Examining data/mothur-1.44.3/source/commands/mergefilecommand.cpp
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Examining data/mothur-1.44.3/source/commands/mergegroupscommand.cpp
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Examining data/mothur-1.44.3/source/commands/mergeotuscommand.cpp
Examining data/mothur-1.44.3/source/commands/mergeotuscommand.hpp
Examining data/mothur-1.44.3/source/commands/mergesfffilecommand.cpp
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Examining data/mothur-1.44.3/source/commands/mergetaxsummarycommand.cpp
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Examining data/mothur-1.44.3/source/commands/metastatscommand.cpp
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Examining data/mothur-1.44.3/source/commands/mgclustercommand.cpp
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Examining data/mothur-1.44.3/source/commands/mimarksattributescommand.cpp
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Examining data/mothur-1.44.3/source/commands/newcommandtemplate.cpp
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Examining data/mothur-1.44.3/source/commands/otuhierarchycommand.cpp
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Examining data/mothur-1.44.3/source/commands/pairwiseseqscommand.cpp
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Examining data/mothur-1.44.3/source/commands/parsefastaqcommand.cpp
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Examining data/mothur-1.44.3/source/commands/parsimonycommand.cpp
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Examining data/mothur-1.44.3/source/commands/pcacommand.cpp
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Examining data/mothur-1.44.3/source/commands/phylodiversitycommand.cpp
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Examining data/mothur-1.44.3/source/commands/phylotypecommand.cpp
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Examining data/mothur-1.44.3/source/commands/preclustercommand.cpp
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Examining data/mothur-1.44.3/source/commands/primerdesigncommand.cpp
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Examining data/mothur-1.44.3/source/commands/quitcommand.cpp
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Examining data/mothur-1.44.3/source/commands/rarefactcommand.cpp
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Examining data/mothur-1.44.3/source/commands/removedistscommand.cpp
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Examining data/mothur-1.44.3/source/commands/removegroupscommand.cpp
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Examining data/mothur-1.44.3/source/commands/removelineagecommand.cpp
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Examining data/mothur-1.44.3/source/commands/removeotuscommand.cpp
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Examining data/mothur-1.44.3/source/commands/removerarecommand.cpp
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Examining data/mothur-1.44.3/source/commands/removeseqscommand.cpp
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Examining data/mothur-1.44.3/source/commands/renamefilecommand.cpp
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Examining data/mothur-1.44.3/source/uchime_src/hspfinder.h
Examining data/mothur-1.44.3/source/uchime_src/make3way.cpp
Examining data/mothur-1.44.3/source/uchime_src/mx.cpp
Examining data/mothur-1.44.3/source/uchime_src/mx.h
Examining data/mothur-1.44.3/source/uchime_src/myopts.h
Examining data/mothur-1.44.3/source/uchime_src/myutils.cpp
Examining data/mothur-1.44.3/source/uchime_src/myutils.h
Examining data/mothur-1.44.3/source/uchime_src/orf.h
Examining data/mothur-1.44.3/source/uchime_src/out.h
Examining data/mothur-1.44.3/source/uchime_src/path.cpp
Examining data/mothur-1.44.3/source/uchime_src/path.h
Examining data/mothur-1.44.3/source/uchime_src/searchchime.cpp
Examining data/mothur-1.44.3/source/uchime_src/seq.h
Examining data/mothur-1.44.3/source/uchime_src/seqdb.cpp
Examining data/mothur-1.44.3/source/uchime_src/seqdb.h
Examining data/mothur-1.44.3/source/uchime_src/setnucmx.cpp
Examining data/mothur-1.44.3/source/uchime_src/sfasta.cpp
Examining data/mothur-1.44.3/source/uchime_src/sfasta.h
Examining data/mothur-1.44.3/source/uchime_src/svnmods.h
Examining data/mothur-1.44.3/source/uchime_src/svnversion.h
Examining data/mothur-1.44.3/source/uchime_src/timers.h
Examining data/mothur-1.44.3/source/uchime_src/timing.h
Examining data/mothur-1.44.3/source/uchime_src/tracebackbit.cpp
Examining data/mothur-1.44.3/source/uchime_src/uc.h
Examining data/mothur-1.44.3/source/uchime_src/uchime_main.cpp
Examining data/mothur-1.44.3/source/uchime_src/ultra.h
Examining data/mothur-1.44.3/source/uchime_src/usort.cpp
Examining data/mothur-1.44.3/source/uchime_src/viterbifast.cpp
Examining data/mothur-1.44.3/source/uchime_src/windex.h
Examining data/mothur-1.44.3/source/uchime_src/writechhit.cpp
Examining data/mothur-1.44.3/source/unchecked.h
Examining data/mothur-1.44.3/source/utf8.h
Examining data/mothur-1.44.3/source/utils.cpp
Examining data/mothur-1.44.3/source/utils.hpp
Examining data/mothur-1.44.3/source/validcalculator.cpp
Examining data/mothur-1.44.3/source/validcalculator.h
Examining data/mothur-1.44.3/source/validparameter.cpp
Examining data/mothur-1.44.3/source/validparameter.h
Examining data/mothur-1.44.3/source/venn.cpp
Examining data/mothur-1.44.3/source/venn.h
Examining data/mothur-1.44.3/source/vsearchfileparser.cpp
Examining data/mothur-1.44.3/source/vsearchfileparser.h
Examining data/mothur-1.44.3/source/weightedlinkage.cpp
Examining data/mothur-1.44.3/source/wilcox.cpp
Examining data/mothur-1.44.3/source/wilcox.h
Examining data/mothur-1.44.3/source/writer.h
FINAL RESULTS:
data/mothur-1.44.3/source/clearcut/clearcut.cpp:1986:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dest->taxaname[i], src->taxaname[i]);
data/mothur-1.44.3/source/clearcut/dmat.cpp:540:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dmat->taxaname[row], token->buf);
data/mothur-1.44.3/source/clearcut/fasta.cpp:468:2: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
sscanf(ptr, "%s", alignment->titles[seq]); /* get the first word and use as the title */
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:607:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(commandString.c_str());
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:480:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(commandString.c_str());
data/mothur-1.44.3/source/commands/clustercommand.cpp:557:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(commandString.c_str());
data/mothur-1.44.3/source/commands/clustersplitcommand.cpp:1188:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(commandString.c_str());
data/mothur-1.44.3/source/commands/distancecommand.cpp:332:4: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(("gzip -v " + outputFile).c_str());
data/mothur-1.44.3/source/commands/makecontigscommand.cpp:500:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(unzipCommand.c_str());
data/mothur-1.44.3/source/commands/makecontigscommand.cpp:502:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(unzipCommand.c_str());
data/mothur-1.44.3/source/commands/makecontigscommand.cpp:520:25: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(unzipCommand.c_str());
data/mothur-1.44.3/source/commands/makecontigscommand.cpp:526:25: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(unzipCommand.c_str());
data/mothur-1.44.3/source/commands/makefilecommand.cpp:353:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(findCommand.c_str());
data/mothur-1.44.3/source/commands/makefilecommand.cpp:360:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(findCommand.c_str());
data/mothur-1.44.3/source/commands/pairwiseseqscommand.cpp:268:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(("gzip -v " + outputFile).c_str());
data/mothur-1.44.3/source/commands/systemcommand.cpp:99:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(command.c_str());
data/mothur-1.44.3/source/datastructures/blastalign.cpp:65:2: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(blastCommand.c_str()); // Here we assume that "bl2seq" is in the users path or in the same folder as
data/mothur-1.44.3/source/datastructures/blastdb.cpp:164:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(blastCommand.c_str());
data/mothur-1.44.3/source/datastructures/blastdb.cpp:227:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(blastCommand.c_str());
data/mothur-1.44.3/source/datastructures/blastdb.cpp:294:3: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(formatdbCommand.c_str()); // to get the right sequence names, i think. -p F
data/mothur-1.44.3/source/uchime_src/myutils.cpp:518:2: [4] (format) vsnprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
vsnprintf(szStr, MAX_FORMATTED_STRING_LENGTH-1, Format, ArgList);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:555:2: [4] (format) vfprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
vfprintf(g_fLog, Format, ArgList);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:582:3: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
fprintf(stderr, (i == 0) ? "%s" : " %s", g_Argv[i].c_str());
data/mothur-1.44.3/source/uchime_src/path.cpp:128:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(Front, rhs.Front);
data/mothur-1.44.3/source/uchime_src/path.cpp:137:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(Front, PathStr);
data/mothur-1.44.3/source/uchime_src/uchime_main.cpp:28:2: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
printf(
data/mothur-1.44.3/source/utils.cpp:771:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(versionTestCommand.c_str());
data/mothur-1.44.3/source/utils.cpp:1319:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(command.c_str());
data/mothur-1.44.3/source/utils.cpp:1346:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(command.c_str());
data/mothur-1.44.3/source/utils.cpp:1935:9: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(makeDirectoryCommand.c_str());
data/mothur-1.44.3/source/utils.cpp:2054:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system("clear");
data/mothur-1.44.3/source/utils.cpp:2056:13: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system("CLS");
data/mothur-1.44.3/TestMothur/catch.hpp:7923:18: [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/mothur-1.44.3/source/clearcut/cmdargs.cpp:136:9: [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.
c = getopt_long(argc,
data/mothur-1.44.3/source/clearcut/getopt_long.cpp:272:1: [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.
getopt_long(int argc, char **argv,
data/mothur-1.44.3/source/clearcut/getopt_long.cpp:495:9: [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.
c = getopt_long(argc, argv, shortopts, longopts, indexptr);
data/mothur-1.44.3/source/clearcut/getopt_long.h:51:5: [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.
int getopt_long(int argc, char **argv,
data/mothur-1.44.3/source/commandfactory.cpp:386:36: [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.
bool seed = false; int random;
data/mothur-1.44.3/source/commandfactory.cpp:391:87: [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.
if (util.isNumeric1(intputOption)) { util.mothurConvert(intputOption, random); seed=true; }
data/mothur-1.44.3/source/commandfactory.cpp:395:76: [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.
if (seed) { m->mothurOut("Setting random seed to " + toString(random) + ".\n\n"); m->setRandomSeed(random); }
data/mothur-1.44.3/source/commandfactory.cpp:395:113: [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.
if (seed) { m->mothurOut("Setting random seed to " + toString(random) + ".\n\n"); m->setRandomSeed(random); }
data/mothur-1.44.3/source/commands/setdircommand.cpp:114:70: [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.
if (util.isInteger(temp)) { util.mothurConvert(temp, random); seed = true; }
data/mothur-1.44.3/source/commands/setdircommand.cpp:120:34: [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.
m->setRandomSeed(random);
data/mothur-1.44.3/source/commands/setdircommand.cpp:121:67: [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.
m->mothurOut("Setting random seed to " + toString(random) + ".\n\n");
data/mothur-1.44.3/source/commands/setdircommand.h:39:9: [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.
int random;
data/mothur-1.44.3/source/commands/setseedcommand.cpp:65:70: [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.
if (util.isInteger(temp)) { util.mothurConvert(temp, random); seed = true; }
data/mothur-1.44.3/source/commands/setseedcommand.cpp:82:26: [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.
m->setRandomSeed(random);
data/mothur-1.44.3/source/commands/setseedcommand.cpp:83:59: [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.
m->mothurOut("Setting random seed to " + toString(random) + ".\n\n");
data/mothur-1.44.3/source/commands/setseedcommand.h:37:9: [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.
int random;
data/mothur-1.44.3/source/commands/unifracunweightedcommand.cpp:187:21: [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.
if (subsample && random) { m->mothurOut("[ERROR]: random must be false, if subsample=t.\n"); abort=true; }
data/mothur-1.44.3/source/commands/unifracunweightedcommand.cpp:201:9: [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.
if (!random) { iters = 0; } //turn off random calcs
data/mothur-1.44.3/source/commands/unifracunweightedcommand.cpp:271:7: [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.
if (random) { outSum << "UWSig"; m->mothurOut("UWSig"); }
data/mothur-1.44.3/source/commands/unifracunweightedcommand.cpp:294:22: [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.
if (!random) { UWScoreSig[k].push_back(0.0); }
data/mothur-1.44.3/source/commands/unifracunweightedcommand.cpp:297:17: [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.
if (random) { runRandomCalcs(T[i], userData); }
data/mothur-1.44.3/source/commands/unifracunweightedcommand.cpp:344:8: [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.
if (random) { printUnweightedFile(i+1); }
data/mothur-1.44.3/source/commands/unifracunweightedcommand.cpp:715:8: [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.
if (random) {
data/mothur-1.44.3/source/commands/unifracunweightedcommand.h:50:23: [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.
bool abort, phylip, random, includeRoot, consensus, subsample;
data/mothur-1.44.3/source/commands/unifracweightedcommand.cpp:190:21: [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.
if (subsample && random) { m->mothurOut("[ERROR]: random must be false, if subsample=t.\n"); abort=true; }
data/mothur-1.44.3/source/commands/unifracweightedcommand.cpp:276:17: [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.
if (random) { runRandomCalcs(T[i], ct, userData, (i+1), WScoreSig, groupComb); }
data/mothur-1.44.3/source/commands/unifracweightedcommand.cpp:735:7: [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.
if (random) { outSum << "WSig"; m->mothurOut("WSig"); }
data/mothur-1.44.3/source/commands/unifracweightedcommand.cpp:744:17: [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.
if (random) {
data/mothur-1.44.3/source/commands/unifracweightedcommand.h:40:23: [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.
bool abort, phylip, random, includeRoot, subsample, consensus, withReplacement;
data/mothur-1.44.3/source/subsample.cpp:33:33: [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.
vector<int> random;
data/mothur-1.44.3/source/subsample.cpp:36:57: [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.
for (int k = 0; k < num; k++) { random.push_back(j); }
data/mothur-1.44.3/source/subsample.cpp:38:46: [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.
util.mothurRandomShuffle(random);
data/mothur-1.44.3/source/subsample.cpp:41:68: [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.
for (int j = 0; j < size; j++) { sampleRandoms[random[j]]++; }
data/mothur-1.44.3/source/subsample.cpp:46:75: [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.
for (int j = size; j < thisSize; j++) { sampleRandoms[random[j]]++; }
data/mothur-1.44.3/source/subsample.cpp:89:29: [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.
vector<int> random;
data/mothur-1.44.3/source/subsample.cpp:92:53: [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.
for (int k = 0; k < num; k++) { random.push_back(j); }
data/mothur-1.44.3/source/subsample.cpp:96:43: [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.
long long totalNumReads = random.size()-1;
data/mothur-1.44.3/source/subsample.cpp:101:35: [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.
sampleRandoms[random[randomRead]]++;
data/mothur-1.44.3/source/subsample.cpp:110:43: [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.
for (long long j = 0; j < random.size(); j++) {
data/mothur-1.44.3/source/subsample.cpp:112:39: [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.
sampleRandoms[random[j]]++;
data/mothur-1.44.3/source/utils.cpp:38:42: [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.
mersenne_twister_engine.seed(s); srand(s);
data/mothur-1.44.3/source/utils.cpp:255:16: [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.
return random;
data/mothur-1.44.3/source/utils.cpp:270:16: [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.
return random;
data/mothur-1.44.3/source/utils.cpp:285:16: [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.
return random;
data/mothur-1.44.3/source/utils.cpp:300:16: [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.
return random;
data/mothur-1.44.3/TestMothur/catch.hpp:1620:23: [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/mothur-1.44.3/TestMothur/catch.hpp:1621:24: [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/mothur-1.44.3/TestMothur/catch.hpp:2816:9: [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/mothur-1.44.3/TestMothur/catch.hpp:5700:14: [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/mothur-1.44.3/TestMothur/catch.hpp:5780:26: [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/mothur-1.44.3/TestMothur/catch.hpp:5816:26: [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/mothur-1.44.3/TestMothur/catch.hpp:6895:9: [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/mothur-1.44.3/TestMothur/catch.hpp:6932:15: [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/mothur-1.44.3/TestMothur/catch.hpp:8091:21: [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/mothur-1.44.3/TestMothur/catch.hpp:8855:16: [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/mothur-1.44.3/source/clearcut/clearcut.cpp:1484:12: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen(nj_args->outfilename, "w"); /* open for writing */
data/mothur-1.44.3/source/clearcut/clearcut.cpp:1486:12: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen(nj_args->outfilename, "a"); /* open for appending */
data/mothur-1.44.3/source/clearcut/clearcut.cpp:1990:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dest->val, src->valhandle, NJ_NCELLS(src->ntaxa)*sizeof(float));
data/mothur-1.44.3/source/clearcut/clearcut.cpp:1993:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dest->r, src->rhandle, src->ntaxa*sizeof(float));
data/mothur-1.44.3/source/clearcut/clearcut.cpp:1994:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dest->r2, src->r2handle, src->ntaxa*sizeof(float));
data/mothur-1.44.3/source/clearcut/cmdargs.cpp:169:22: [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).
nj_args.seed = atoi(optarg);
data/mothur-1.44.3/source/clearcut/cmdargs.cpp:177:24: [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).
nj_args.ntrees = atoi(optarg);
data/mothur-1.44.3/source/clearcut/cmdargs.cpp:411:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char input_mode[32];
data/mothur-1.44.3/source/clearcut/cmdargs.cpp:415:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(input_mode, "Distance Matrix");
data/mothur-1.44.3/source/clearcut/cmdargs.cpp:418:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(input_mode, "Unaligned Sequences");
data/mothur-1.44.3/source/clearcut/cmdargs.cpp:421:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(input_mode, "Aligned Sequences");
data/mothur-1.44.3/source/clearcut/cmdargs.cpp:424:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(input_mode, "UNKNOWN");
data/mothur-1.44.3/source/clearcut/dmat.cpp:447:10: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen(nj_args->infilename, "r");
data/mothur-1.44.3/source/clearcut/dmat.cpp:777:8: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen(nj_args->matrixout, "w");
data/mothur-1.44.3/source/clearcut/fasta.cpp:61:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static const char NJ_dna_ambiguity_syms[NJ_NUM_DNA_AMBIGUITY_SYMS] =
data/mothur-1.44.3/source/clearcut/fasta.cpp:70:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static const char NJ_protein_ambiguity_syms[NJ_NUM_PROTEIN_AMBIGUITY_SYMS] =
data/mothur-1.44.3/source/clearcut/fasta.cpp:76:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static const char NJ_dna_syms[NJ_NUM_DNA_SYMS] =
data/mothur-1.44.3/source/clearcut/fasta.cpp:83:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static const char NJ_protein_syms[NJ_NUM_PROTEIN_SYMS] =
data/mothur-1.44.3/source/clearcut/fasta.cpp:342:10: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen(nj_args->infilename, "r");
data/mothur-1.44.3/source/clearcut/getopt_long.cpp:474:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *argv[50];
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:578:13: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(tempucl, "--ucl");
data/mothur-1.44.3/source/commands/countseqscommand.cpp:291:9: [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 buffer[4096];
data/mothur-1.44.3/source/commands/countseqscommand.cpp:368:9: [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 buffer[4096];
data/mothur-1.44.3/source/commands/distancecommand.cpp:288:14: [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).
fileHandle.open(outputFile.c_str());
data/mothur-1.44.3/source/commands/filterseqscommand.cpp:156:26: [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).
else { soft = (float)atoi(temp.c_str()) / 100.0; }
data/mothur-1.44.3/source/commands/getdistscommand.cpp:312:13: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[4096];
data/mothur-1.44.3/source/commands/getgroupscommand.cpp:941:13: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[4096];
data/mothur-1.44.3/source/commands/makecontigscommand.cpp:2335:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
pFile = fopen (fasta[1].c_str(),"rb");
data/mothur-1.44.3/source/commands/makecontigscommand.cpp:2407:25: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
pFile = fopen (qual[0].c_str(),"rb");
data/mothur-1.44.3/source/commands/makecontigscommand.cpp:2466:26: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
pFile2 = fopen (qual[1].c_str(),"rb");
data/mothur-1.44.3/source/commands/pairwiseseqscommand.cpp:244:20: [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).
fileHandle.open(outputFile.c_str());
data/mothur-1.44.3/source/commands/removedistscommand.cpp:315:13: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[4096];
data/mothur-1.44.3/source/commands/removegroupscommand.cpp:998:13: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[4096];
data/mothur-1.44.3/source/commands/shhhercommand.cpp:258:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
pFile = fopen (filename.c_str(),"rb");
data/mothur-1.44.3/source/commands/shhhercommand.cpp:272:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
pFile2 = fopen (filename.c_str(),"rb");
data/mothur-1.44.3/source/commands/trimflowscommand.cpp:636:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
pFile = fopen (flowFileName.c_str(),"rb");
data/mothur-1.44.3/source/commands/trimseqscommand.cpp:1159:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
pFile = fopen (qfilename.c_str(),"rb");
data/mothur-1.44.3/source/datastructures/groupmap.cpp:133:9: [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 buffer[4096];
data/mothur-1.44.3/source/datastructures/groupmap.cpp:226:9: [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 buffer[4096];
data/mothur-1.44.3/source/datastructures/groupmap.cpp:308:9: [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 buffer[4096];
data/mothur-1.44.3/source/datastructures/groupmap.cpp:383:9: [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 buffer[4096];
data/mothur-1.44.3/source/datastructures/sffheader.cpp:67:13: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer2 [8];
data/mothur-1.44.3/source/datastructures/sffheader.cpp:72:13: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer3 [4];
data/mothur-1.44.3/source/datastructures/sffheader.cpp:77:13: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char rnumReads[4];
data/mothur-1.44.3/source/datastructures/sffheader.cpp:84:33: [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* hlength = new char [2];
data/mothur-1.44.3/source/datastructures/sffheader.cpp:90:33: [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* klength = new char [2];
data/mothur-1.44.3/source/datastructures/sffheader.cpp:96:32: [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.
char* nflows = new char [2];
data/mothur-1.44.3/source/datastructures/sffheader.cpp:157:9: [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 offsetBuffer[8];
data/mothur-1.44.3/source/datastructures/sffheader.cpp:170:9: [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 readIndexLength[4];
data/mothur-1.44.3/source/datastructures/sffheader.cpp:179:9: [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 numSampleReads[4];
data/mothur-1.44.3/source/datastructures/sffread.cpp:90:42: [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* rclipAdapterLeft = new char [2];
data/mothur-1.44.3/source/datastructures/sffread.cpp:96:43: [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* rclipAdapterRight = new char [2];
data/mothur-1.44.3/source/datastructures/sffread.cpp:126:17: [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 rflowgram [2];
data/mothur-1.44.3/source/datastructures/sffread.cpp:139:17: [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 flowINdex[1];
data/mothur-1.44.3/source/datastructures/sffread.cpp:157:17: [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 score[1];
data/mothur-1.44.3/source/datastructures/treemap.cpp:39:9: [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 buffer[4096];
data/mothur-1.44.3/source/datastructures/treemap.cpp:118:9: [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 buffer[4096];
data/mothur-1.44.3/source/read/readtree.cpp:237:4: [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 name[MAX_LINE];
data/mothur-1.44.3/source/read/splitmatrix.cpp:416:15: [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).
outFile.open(fileName.c_str(), ios::app);
data/mothur-1.44.3/source/read/splitmatrix.cpp:505:13: [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).
outFile.open(fileName.c_str(), ios::app);
data/mothur-1.44.3/source/read/splitmatrix.cpp:601:24: [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).
fileHandle.open(tempDistFile.c_str());
data/mothur-1.44.3/source/read/splitmatrix.cpp:747:24: [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).
fileHandle.open(tempDistFile.c_str());
data/mothur-1.44.3/source/read/splitmatrix.cpp:902:13: [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).
outFile.open(fileName.c_str(), ios::ate);
data/mothur-1.44.3/source/read/splitmatrix.cpp:934:10: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
pFile = fopen (filename.c_str(),"rb");
data/mothur-1.44.3/source/read/splitmatrix.cpp:948:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
pFile2 = fopen (filename.c_str(),"rb");
data/mothur-1.44.3/source/seqnoise.cpp:179:45: [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(number.c_str());
data/mothur-1.44.3/source/seqnoise.cpp:186:37: [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(number.c_str());
data/mothur-1.44.3/source/seqnoise.cpp:238:19: [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 index = atoi(number.c_str());
data/mothur-1.44.3/source/seqnoise.cpp:245:17: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
int index = atoi(number.c_str());
data/mothur-1.44.3/source/uchime_src/alpha.cpp:523:10: [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.
unsigned char g_LetterToCharAmino[256] =
data/mothur-1.44.3/source/uchime_src/alpha.cpp:1043:10: [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.
unsigned char g_LetterToCharNucleo[256] =
data/mothur-1.44.3/source/uchime_src/alpha.cpp:1371:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char g_CodonWordToAminoChar[4*4*4] =
data/mothur-1.44.3/source/uchime_src/alpha.cpp:1439:10: [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.
unsigned char g_CharToCompChar[256] =
data/mothur-1.44.3/source/uchime_src/alpha2.cpp:12:9: [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.
static char Str[32];
data/mothur-1.44.3/source/uchime_src/alpha2.cpp:37:9: [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.
static char Str[32];
data/mothur-1.44.3/source/uchime_src/fractid.cpp:15:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(ptrDesc, "(term gap in Query)");
data/mothur-1.44.3/source/uchime_src/fractid.cpp:57:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(ptrDesc, "(ids=%u/cols=%u)", Ids, Cols);
data/mothur-1.44.3/source/uchime_src/fractid.cpp:97:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(ptrDesc, "(ids=%u/cols=%u)", Ids, Cols);
data/mothur-1.44.3/source/uchime_src/fractid.cpp:120:4: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(ptrDesc, "(no matches)");
data/mothur-1.44.3/source/uchime_src/fractid.cpp:166:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(ptrDesc, "(ids=%u/cols=%u)", Ids, Cols);
data/mothur-1.44.3/source/uchime_src/fractid.cpp:192:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(ptrDesc, "Gap opens %u, Id=1 - [(diffs=%u)/(target_length=%u)]",
data/mothur-1.44.3/source/uchime_src/fractid.cpp:233:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(ptrDesc, "(ids=%u/cols=%u)", Ids, Cols);
data/mothur-1.44.3/source/uchime_src/fractid.cpp:267:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(ptrDesc, "(ids=%u/shorter_length=%u)", Ids, MinLen);
data/mothur-1.44.3/source/uchime_src/fractid.cpp:282:4: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(ptrDesc, "(NULL path)");
data/mothur-1.44.3/source/uchime_src/fractid.cpp:295:5: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(ptrDesc, "(leftjust)");
data/mothur-1.44.3/source/uchime_src/fractid.cpp:305:5: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(ptrDesc, "(rightjust)");
data/mothur-1.44.3/source/uchime_src/fractid.cpp:365:9: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(ptrDesc, "(maxtgap)");
data/mothur-1.44.3/source/uchime_src/fractid.cpp:374:9: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(ptrDesc, "(maxqgap)");
data/mothur-1.44.3/source/uchime_src/globalalign2.cpp:39:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(PD.Front, Path.c_str(), n);
data/mothur-1.44.3/source/uchime_src/mx.h:26:9: [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.
static char s[16];
data/mothur-1.44.3/source/uchime_src/mx.h:28:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(s, "%12u", f);
data/mothur-1.44.3/source/uchime_src/mx.h:34:9: [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.
static char s[16];
data/mothur-1.44.3/source/uchime_src/mx.h:36:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(s, "%12d", f);
data/mothur-1.44.3/source/uchime_src/mx.h:42:9: [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.
static char s[16];
data/mothur-1.44.3/source/uchime_src/mx.h:44:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(s, "%5d", f);
data/mothur-1.44.3/source/uchime_src/mx.h:50:9: [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.
static char s[16];
data/mothur-1.44.3/source/uchime_src/mx.h:53:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(s, "%12.12s", "?");
data/mothur-1.44.3/source/uchime_src/mx.h:55:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(s, "%12.12s", "*");
data/mothur-1.44.3/source/uchime_src/mx.h:57:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(s, "%12.12s", ".");
data/mothur-1.44.3/source/uchime_src/mx.h:59:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(s, "%12.5f", f);
data/mothur-1.44.3/source/uchime_src/mx.h:61:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(s, "%12.4g", f);
data/mothur-1.44.3/source/uchime_src/mx.h:67:9: [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.
static char s[16];
data/mothur-1.44.3/source/uchime_src/mx.h:70:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(s, "%12.12s", "*");
data/mothur-1.44.3/source/uchime_src/mx.h:72:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(s, "%12.12s", ".");
data/mothur-1.44.3/source/uchime_src/mx.h:74:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(s, "%12.5f", f);
data/mothur-1.44.3/source/uchime_src/mx.h:76:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(s, "%12.4g", f);
data/mothur-1.44.3/source/uchime_src/mx.h:88:9: [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.
static char s[2];
data/mothur-1.44.3/source/uchime_src/mx.h:95:9: [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.
static char s[2];
data/mothur-1.44.3/source/uchime_src/mx.h:102:9: [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.
static char s[2];
data/mothur-1.44.3/source/uchime_src/mx.h:116:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char m_Name[32];
data/mothur-1.44.3/source/uchime_src/mx.h:117:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char m_Alpha[32];
data/mothur-1.44.3/source/uchime_src/mx.h:118:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char m_Alpha2[32];
data/mothur-1.44.3/source/uchime_src/myutils.cpp:42:8: [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 *g_IOBuffers[256];
data/mothur-1.44.3/source/uchime_src/myutils.cpp:178:12: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *f = fopen(FileName.c_str(), Mode);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:198:12: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *f = fopen(FileName.c_str(), "wb+");
data/mothur-1.44.3/source/uchime_src/myutils.cpp:335:10: [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).
int h = open(FileName.c_str(), O_RDONLY);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:517:9: [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.
static char szStr[MAX_FORMATTED_STRING_LENGTH];
data/mothur-1.44.3/source/uchime_src/myutils.cpp:641:9: [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.
static char statm[64];
data/mothur-1.44.3/source/uchime_src/myutils.cpp:647:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(statm, "/proc/%d/statm", (int) pid);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:650:11: [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).
int fd = open(statm, O_RDONLY);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:653:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[64];
data/mothur-1.44.3/source/uchime_src/myutils.cpp:725:9: [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.
static char Str[16];
data/mothur-1.44.3/source/uchime_src/myutils.cpp:727:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%02d:%02d", MM, SS);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:729:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%02d:%02d:%02d", HH, MM, SS);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:738:9: [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.
static char Str[16];
data/mothur-1.44.3/source/uchime_src/myutils.cpp:740:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.2gs", Secs);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:742:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.2fms", Secs*1e3);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:744:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.3fs", Secs);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:750:9: [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.
static char Str[32];
data/mothur-1.44.3/source/uchime_src/myutils.cpp:753:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.1fkb", Bytes/1e3);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:755:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.1fMb", Bytes/1e6);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:757:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.0fMb", Bytes/1e6);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:759:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.1fGb", Bytes/1e9);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:761:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.0fGb", Bytes/1e9);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:763:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.3gb", Bytes);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:769:9: [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.
static char Str[32];
data/mothur-1.44.3/source/uchime_src/myutils.cpp:773:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%u", i);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:775:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.1fk", d/1e3);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:777:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.1fM", d/1e6);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:779:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.0fM", d/1e6);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:781:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.1fG", d/1e9);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:783:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.0fG", d/1e9);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:785:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.3g", d);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:791:9: [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.
static char Str[32];
data/mothur-1.44.3/source/uchime_src/myutils.cpp:795:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.3g", a);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:797:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.3f", a);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:802:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.0f", d);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:804:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.1f", d);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:807:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.0f", d);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:809:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.1fk", d/1e3);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:811:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.1fM", d/1e6);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:813:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.0fM", d/1e6);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:815:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.1fG", d/1e9);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:817:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.0fG", d/1e9);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:819:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%.3g", d);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:856:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Str[32];
data/mothur-1.44.3/source/uchime_src/myutils.cpp:857:3: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%5.5s", MemBytesToStr(Bytes));
data/mothur-1.44.3/source/uchime_src/myutils.cpp:963:9: [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.
static char Str[16];
data/mothur-1.44.3/source/uchime_src/myutils.cpp:965:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Str, "%5.1f%%", p);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:979:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Tmp[16];
data/mothur-1.44.3/source/uchime_src/myutils.cpp:980:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(Tmp, "%u", Index);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:1323:23: [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).
EnumValues[Name] = atoi(Value.c_str());
data/mothur-1.44.3/source/uchime_src/myutils.cpp:1391:24: [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).
*(int *) Opt.Value = atoi(Value.c_str());
data/mothur-1.44.3/source/uchime_src/myutils.cpp:1676:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(t, s, n+1);
data/mothur-1.44.3/source/uchime_src/out.h:24:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char IdDesc[256];
data/mothur-1.44.3/source/uchime_src/seqdb.cpp:253:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(m_Seqs[Index], Seq, L);
data/mothur-1.44.3/source/uchime_src/seqdb.cpp:257:2: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(m_Labels[Index], Label, n);
data/mothur-1.44.3/source/uchime_src/setnucmx.cpp:24:2: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(g_SubstMxf.m_Alpha, "ACGT");
data/mothur-1.44.3/source/utils.cpp:559:13: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[MAX_PATH];
data/mothur-1.44.3/source/utils.cpp:813:20: [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).
fileHandle.open(completeFileName.c_str());
data/mothur-1.44.3/source/utils.cpp:835:20: [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).
fileHandle.open(completeFileName.c_str());
data/mothur-1.44.3/source/utils.cpp:857:20: [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).
fileHandle.open(completeFileName.c_str(), ios::binary);
data/mothur-1.44.3/source/utils.cpp:877:20: [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).
fileHandle.open(completeFileName.c_str(), ios::binary);
data/mothur-1.44.3/source/utils.cpp:894:14: [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(completeFileName.c_str(), ios_base::in | ios_base::binary);
data/mothur-1.44.3/source/utils.cpp:917:14: [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(completeFileName.c_str(), ios_base::in | ios_base::binary);
data/mothur-1.44.3/source/utils.cpp:1100:20: [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).
fileHandle.open(completeFileName.c_str(), ios::trunc);
data/mothur-1.44.3/source/utils.cpp:1116:20: [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).
fileHandle.open(completeFileName.c_str(), ios::trunc | ios::binary);
data/mothur-1.44.3/source/utils.cpp:1139:13: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[4096];
data/mothur-1.44.3/source/utils.cpp:1164:13: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[4096];
data/mothur-1.44.3/source/utils.cpp:1190:13: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[4096];
data/mothur-1.44.3/source/utils.cpp:1223:13: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[4096];
data/mothur-1.44.3/source/utils.cpp:1248:16: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
output.open(fullFileName.c_str(), ios::app | ios::binary);
data/mothur-1.44.3/source/utils.cpp:1258:17: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[4096];
data/mothur-1.44.3/source/utils.cpp:1289:13: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[4096];
data/mothur-1.44.3/source/utils.cpp:1379:20: [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).
fileHandle.open(fileName.c_str(), ios::app);
data/mothur-1.44.3/source/utils.cpp:1393:20: [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).
fileHandle.open(fileName.c_str(), ios::app | ios::binary);
data/mothur-1.44.3/source/utils.cpp:1889:13: [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).
out.open(outTemp.c_str(), ios::trunc);
data/mothur-1.44.3/source/utils.cpp:1916:13: [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).
out.open(outTemp.c_str(), ios::trunc);
data/mothur-1.44.3/source/utils.cpp:2003:9: [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 buffer[80];
data/mothur-1.44.3/source/utils.cpp:2193:20: [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).
fileHandle.open(fileName.c_str());
data/mothur-1.44.3/source/utils.cpp:2261:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
pFile = fopen (completeFileName.c_str(),"rb");
data/mothur-1.44.3/source/utils.cpp:2303:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
pFile = fopen (completeFileName.c_str(),"rb");
data/mothur-1.44.3/source/utils.cpp:2454:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
pFile = fopen (filename.c_str(),"rb");
data/mothur-1.44.3/source/utils.cpp:2508:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
pFile = fopen (filename.c_str(),"rb");
data/mothur-1.44.3/source/utils.cpp:2539:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
pFile = fopen (filename.c_str(),"rb");
data/mothur-1.44.3/source/utils.cpp:2620:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
pFile = fopen (filename.c_str(),"rb");
data/mothur-1.44.3/source/utils.cpp:2723:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
pFile = fopen (filename.c_str(),"rb");
data/mothur-1.44.3/source/utils.cpp:3057:9: [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 buffer[4096];
data/mothur-1.44.3/source/utils.cpp:3122:9: [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 buffer[4096];
data/mothur-1.44.3/source/utils.cpp:3180:9: [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 buffer[4096];
data/mothur-1.44.3/source/utils.cpp:3245:9: [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 buffer[4096];
data/mothur-1.44.3/source/utils.cpp:3347:9: [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 buffer[4096];
data/mothur-1.44.3/source/utils.cpp:3468:9: [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 buffer[4096];
data/mothur-1.44.3/source/utils.cpp:3527:9: [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 buffer[4096];
data/mothur-1.44.3/source/utils.cpp:3649:9: [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 buffer[4096];
data/mothur-1.44.3/source/utils.cpp:3789:9: [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 buffer[4096];
data/mothur-1.44.3/source/validparameter.cpp:91:9: [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).
a = atoi(range.at(1).c_str());
data/mothur-1.44.3/source/validparameter.cpp:96:9: [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).
b = atoi(range.at(3).c_str());
data/mothur-1.44.3/TestMothur/dataset.cpp:134:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
Sequence read(in); util.gobble(in);
data/mothur-1.44.3/TestMothur/dataset.cpp:135:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
seqs.push_back(read);
data/mothur-1.44.3/TestMothur/fastqdataset.cpp:44:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
FastqRead read(in, ignore, format); util.gobble(in);
data/mothur-1.44.3/TestMothur/fastqdataset.cpp:45:50: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (!ignore) { ffastqReads.push_back(read); count++; }
data/mothur-1.44.3/TestMothur/fastqdataset.cpp:66:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
FastqRead read(in, ignore, format); util.gobble(in);
data/mothur-1.44.3/TestMothur/fastqdataset.cpp:67:50: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (!ignore) { rfastqReads.push_back(read); count++; }
data/mothur-1.44.3/TestMothur/testcontainers/testOligos.cpp:62:57: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
Oligos pairedOligosNoReverse; pairedOligosNoReverse.read(test.oligosfiles[1], false);
data/mothur-1.44.3/TestMothur/testcontainers/testfastqread.cpp:32:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
FastqRead read(seq, qual);
data/mothur-1.44.3/TestMothur/testcontainers/testfastqread.cpp:34:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
EXPECT_EQ(read.getSeq(), "ATGCGTCATC");
data/mothur-1.44.3/TestMothur/testcontainers/testfastqread.cpp:35:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
EXPECT_EQ(read.getScores()[0], 31);
data/mothur-1.44.3/TestMothur/testcontainers/testfastqread.cpp:44:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
FastqRead read(in, ignore, format);
data/mothur-1.44.3/TestMothur/testcontainers/testfastqread.cpp:46:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
EXPECT_EQ(read.getSeq(), (testFastq.reads[0]).getSeq());
data/mothur-1.44.3/TestMothur/testcontainers/testfastqread.cpp:47:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
EXPECT_EQ(read.getScores()[0], testFastq.reads[0].getScores()[0]);
data/mothur-1.44.3/source/chimera/myPerseus.cpp:1044:18: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
return (double)mismatch / (double)counter;
data/mothur-1.44.3/source/clearcut/clearcut.cpp:1966:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
dest->taxaname[i] = (char *)calloc(strlen(src->taxaname[i])+1, sizeof(char));
data/mothur-1.44.3/source/clearcut/distclearcut.cpp:149:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
dmat->taxaname[i] = (char *)calloc(strlen(alignment->titles[i])+1, sizeof(char));
data/mothur-1.44.3/source/clearcut/distclearcut.cpp:155:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(dmat->taxaname[i], alignment->titles[i], strlen(alignment->titles[i]));
data/mothur-1.44.3/source/clearcut/distclearcut.cpp:155:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(dmat->taxaname[i], alignment->titles[i], strlen(alignment->titles[i]));
data/mothur-1.44.3/source/clearcut/dmat.cpp:183:6: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(token) == 1) {
data/mothur-1.44.3/source/clearcut/dmat.cpp:189:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for(i=0;i<strlen(token);i++) {
data/mothur-1.44.3/source/clearcut/dmat.cpp:269:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(!NJ_is_number(token[strlen(token)-1])) {
data/mothur-1.44.3/source/clearcut/dmat.cpp:306:7: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c = fgetc(fp);
data/mothur-1.44.3/source/clearcut/dmat.cpp:335:9: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c = fgetc(fp);
data/mothur-1.44.3/source/clearcut/dmat.cpp:534:44: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
dmat->taxaname[row] = (char *)calloc(strlen(token->buf)+1, sizeof(char));
data/mothur-1.44.3/source/clearcut/fasta.cpp:380:9: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
c = fgetc(fp);
data/mothur-1.44.3/source/clearcut/fasta.cpp:452:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
alignment->titles[seq] = (char *)calloc(strlen(buf), sizeof(char));
data/mothur-1.44.3/source/clearcut/getopt_long.cpp:210:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len = strlen(arg);
data/mothur-1.44.3/source/clearcut/getopt_long.cpp:386:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len = strlen(opt);
data/mothur-1.44.3/source/commands/aligncheckcommand.cpp:161:15: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
vector<int> equal;
data/mothur-1.44.3/source/commands/aligncheckcommand.cpp:190:6: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
equal.push_back(data.equal);
data/mothur-1.44.3/source/commands/aligncheckcommand.cpp:190:27: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
equal.push_back(data.equal);
data/mothur-1.44.3/source/commands/aligncheckcommand.cpp:197:106: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
out << seq.getName() << '\t' << data.pound << '\t' << data.dash << '\t' << data.plus << '\t' << data.equal << '\t';
data/mothur-1.44.3/source/commands/aligncheckcommand.cpp:210:8: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
sort(equal.begin(), equal.end());
data/mothur-1.44.3/source/commands/aligncheckcommand.cpp:210:23: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
sort(equal.begin(), equal.end());
data/mothur-1.44.3/source/commands/aligncheckcommand.cpp:226:122: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
m->mothurOut("Minimum:\t" + toString(pound[0]) + "\t" + toString(dash[0]) + "\t" + toString(plus[0]) + "\t" + toString(equal[0]) + "\t" + toString(loop[0]) + "\t" + toString(tilde[0]) + "\t" + toString(total[0])+ "\n");
data/mothur-1.44.3/source/commands/aligncheckcommand.cpp:227:148: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
m->mothurOut("2.5%-tile:\t" + toString(pound[ptile0_25]) + "\t" + toString(dash[ptile0_25]) + "\t" + toString(plus[ptile0_25]) + "\t" + toString(equal[ptile0_25]) + "\t"+ toString(loop[ptile0_25]) + "\t"+ toString(tilde[ptile0_25]) + "\t"+ toString(total[ptile0_25])+ "\n");
data/mothur-1.44.3/source/commands/aligncheckcommand.cpp:228:141: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
m->mothurOut("25%-tile:\t" + toString(pound[ptile25]) + "\t" + toString(dash[ptile25]) + "\t" + toString(plus[ptile25]) + "\t" + toString(equal[ptile25]) + "\t" + toString(loop[ptile25]) + "\t" + toString(tilde[ptile25]) + "\t" + toString(total[ptile25])+ "\n");
data/mothur-1.44.3/source/commands/aligncheckcommand.cpp:229:140: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
m->mothurOut("Median: \t" + toString(pound[ptile50]) + "\t" + toString(dash[ptile50]) + "\t" + toString(plus[ptile50]) + "\t" + toString(equal[ptile50]) + "\t" + toString(loop[ptile50]) + "\t" + toString(tilde[ptile50]) + "\t" + toString(total[ptile50])+ "\n");
data/mothur-1.44.3/source/commands/aligncheckcommand.cpp:230:141: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
m->mothurOut("75%-tile:\t" + toString(pound[ptile75]) + "\t" + toString(dash[ptile75]) + "\t" + toString(plus[ptile75]) + "\t" + toString(equal[ptile75]) + "\t" + toString(loop[ptile75]) + "\t" + toString(tilde[ptile75]) + "\t" + toString(total[ptile75])+ "\n");
data/mothur-1.44.3/source/commands/aligncheckcommand.cpp:231:149: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
m->mothurOut("97.5%-tile:\t" + toString(pound[ptile97_5]) + "\t" + toString(dash[ptile97_5]) + "\t" + toString(plus[ptile97_5]) + "\t" + toString(equal[ptile97_5]) + "\t" + toString(loop[ptile97_5]) + "\t" + toString(tilde[ptile97_5]) + "\t" + toString(total[ptile97_5])+ "\n");
data/mothur-1.44.3/source/commands/aligncheckcommand.cpp:232:143: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
m->mothurOut("Maximum:\t" + toString(pound[ptile100]) + "\t" + toString(dash[ptile100]) + "\t" + toString(plus[ptile100]) + "\t" + toString(equal[ptile100]) + "\t" + toString(loop[ptile100]) + "\t" + toString(tilde[ptile100]) + "\t" + toString(total[ptile100])+ "\n");
data/mothur-1.44.3/source/commands/aligncheckcommand.h:22:6: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
int equal;
data/mothur-1.44.3/source/commands/aligncheckcommand.h:25:62: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
statData() : pound(0), loop(0), tilde(0), dash(0), plus(0), equal(0), total(0) {};
data/mothur-1.44.3/source/commands/amovacommand.cpp:162:43: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
vector<string> sampleNames = readMatrix.read(distanceMatrix);
data/mothur-1.44.3/source/commands/anosimcommand.cpp:136:43: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
vector<string> sampleNames = readMatrix.read(distanceMatrix);
data/mothur-1.44.3/source/commands/biominfocommand.cpp:233:31: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
attribute.read(attributeType, biomTableId);
data/mothur-1.44.3/source/commands/biominfocommand.cpp:241:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
attribute.read(attributeType, &data);
data/mothur-1.44.3/source/commands/biominfocommand.cpp:246:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
attribute.read(attributeType, data);
data/mothur-1.44.3/source/commands/biominfocommand.cpp:259:31: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
attribute.read(attributeType, &data);
data/mothur-1.44.3/source/commands/biominfocommand.cpp:263:31: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
attribute.read(attributeType, data);
data/mothur-1.44.3/source/commands/biominfocommand.cpp:307:37: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
dataset.read((void*)data, str_type);
data/mothur-1.44.3/source/commands/biominfocommand.cpp:329:37: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
dataset.read((void*)data, str_type);
data/mothur-1.44.3/source/commands/biominfocommand.cpp:350:37: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
dataset.read(data, H5::PredType::NATIVE_INT, data_mspace, dataSpace);
data/mothur-1.44.3/source/commands/biominfocommand.cpp:370:37: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
dataset.read(data, H5::PredType::NATIVE_FLOAT, data_mspace, dataSpace);
data/mothur-1.44.3/source/commands/chimeraslayercommand.cpp:200:29: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
util.mothurConvert(temp, mismatch);
data/mothur-1.44.3/source/commands/chimeraslayercommand.cpp:775:84: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
chimera = new ChimeraSlayer(filename, templatefile, trim, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, util.getRandomNumber());
data/mothur-1.44.3/source/commands/chimeraslayercommand.cpp:777:94: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
chimera = new ChimeraSlayer(filename, templatefile, trim, priority, search, ksize, match, mismatch, window, divR, minSimilarity, minCoverage, minBS, minSNP, parents, iters, increment, numwanted, realign, blastlocation, util.getRandomNumber());
data/mothur-1.44.3/source/commands/chimeraslayercommand.h:57:57: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
int window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, templateSeqsLength;
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:358:9: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
strncat(tempUchime, uchimeCommand.c_str(), uchimeCommand.length());
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:384:30: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempRef = '\0'; strncat(tempRef, "--db", 4);
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:388:28: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempR = '\0'; strncat(tempR, params->templatefile.c_str(), params->templatefile.length());
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:393:25: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempIn = '\0'; strncat(tempIn, "--input", 7);
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:397:23: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*temp = '\0'; strncat(temp, params->formattedFastaFilename.c_str(), params->formattedFastaFilename.length());
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:402:24: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempO = '\0'; strncat(tempO, "--uchimeout", 11);
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:407:26: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempout = '\0'; strncat(tempout, params->driverOutputFName.c_str(), params->driverOutputFName.length());
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:412:28: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempA = '\0'; strncat(tempA, "--uchimealns", 12);
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:417:28: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempa = '\0'; strncat(tempa, params->driverAlns.c_str(), params->driverAlns.length());
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:423:28: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempA = '\0'; strncat(tempA, "--strand", 8);
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:426:28: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempa = '\0'; strncat(tempa, params->vars->strand.c_str(), params->vars->strand.length());
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:432:31: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempskew = '\0'; strncat(tempskew, "--abskew", 8);
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:437:31: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempSkew = '\0'; strncat(tempSkew, params->vars->abskew.c_str(), params->vars->abskew.length());
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:443:31: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempminh = '\0'; strncat(tempminh, "--minh", 6);
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:447:31: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempMinH = '\0'; strncat(tempMinH, params->vars->minh.c_str(), params->vars->minh.length());
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:454:33: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempmindiv = '\0'; strncat(tempmindiv, "--mindiv", 8);
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:458:33: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempMindiv = '\0'; strncat(tempMindiv, params->vars->mindiv.c_str(), params->vars->mindiv.length());
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:466:29: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempxn = '\0'; strncat(tempxn, "--xn", 4);
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:470:29: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempXn = '\0'; strncat(tempXn, params->vars->xn.c_str(), params->vars->xn.length());
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:477:29: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempdn = '\0'; strncat(tempdn, "--dn", 4);
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:480:29: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempDn = '\0'; strncat(tempDn, params->vars->dn.c_str(), params->vars->dn.length());
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:488:29: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempxa = '\0'; strncat(tempxa, "--xa", 4);
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:491:29: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempXa = '\0'; strncat(tempXa, params->vars->xa.c_str(), params->vars->xa.length());
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:499:33: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempchunks = '\0'; strncat(tempchunks, "--chunks", 8);
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:502:33: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempChunks = '\0'; strncat(tempChunks, params->vars->chunks.c_str(), params->vars->chunks.length());
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:510:35: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempminchunk = '\0'; strncat(tempminchunk, "--minchunk", 10);
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:513:35: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempMinchunk = '\0'; strncat(tempMinchunk, params->vars->minchunk.c_str(), params->vars->minchunk.length());
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:520:41: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempidsmoothwindow = '\0'; strncat(tempidsmoothwindow, "--idsmoothwindow", 16);
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:524:41: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempIdsmoothwindow = '\0'; strncat(tempIdsmoothwindow, params->vars->idsmoothwindow.c_str(), params->vars->idsmoothwindow.length());
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:532:31: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempmaxp = '\0'; strncat(tempmaxp, "--maxp", 6);
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:535:31: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempMaxp = '\0'; strncat(tempMaxp, params->vars->maxp.c_str(), params->vars->maxp.length());
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:543:35: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempskipgaps = '\0'; strncat(tempskipgaps, "--noskipgaps", 12);
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:550:36: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempskipgaps2 = '\0'; strncat(tempskipgaps2, "--noskipgaps2", 13);
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:556:33: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempminlen = '\0'; strncat(tempminlen, "--minlen", 8);
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:561:33: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempMinlen = '\0'; strncat(tempMinlen, params->vars->minlen.c_str(), params->vars->minlen.length());
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:568:33: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempmaxlen = '\0'; strncat(tempmaxlen, "--maxlen", 8);
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:571:33: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempMaxlen = '\0'; strncat(tempMaxlen, params->vars->maxlen.c_str(), params->vars->maxlen.length());
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:584:37: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempqueryfract = '\0'; strncat(tempqueryfract, "--queryfract", 12);
data/mothur-1.44.3/source/commands/chimerauchimecommand.cpp:588:37: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempQueryfract = '\0'; strncat(tempQueryfract, params->vars->queryfract.c_str(), params->vars->queryfract.length());
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:306:9: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
strncat(tempVsearch, vsearchCommand.c_str(), vsearchCommand.length());
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:334:30: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempRef = '\0'; strncat(tempRef, "--db", 4);
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:338:28: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempR = '\0'; strncat(tempR, params->templatefile.c_str(), params->templatefile.length());
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:342:29: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempIn = '\0'; strncat(tempIn, "--uchime_ref", 12);
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:345:27: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*temp = '\0'; strncat(temp, params->formattedFastaFilename.c_str(), params->formattedFastaFilename.length());
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:350:29: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempIn = '\0'; strncat(tempIn, "--uchime_denovo", 15);
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:353:27: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*temp = '\0'; strncat(temp, params->formattedFastaFilename.c_str(), params->formattedFastaFilename.length());
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:366:24: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempO = '\0'; strncat(tempO, "--chimeras", 10);
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:369:26: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempout = '\0'; strncat(tempout, outputFNamec.c_str(), outputFNamec.length());
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:373:33: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempchimeraout = '\0'; strncat(tempchimeraout, "--uchimeout", 11);
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:376:27: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempoutc = '\0'; strncat(tempoutc, params->driverOutputFName.c_str(), params->driverOutputFName.length());
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:380:28: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempxsize = '\0'; strncat(tempxsize, "--xsize", 7);
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:385:28: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempA = '\0'; strncat(tempA, "--uchimealns", 12);
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:390:28: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempa = '\0'; strncat(tempa, params->driverAlns.c_str(), params->driverAlns.length());
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:397:31: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempskew = '\0'; strncat(tempskew, "--abskew", 8);
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:402:31: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempSkew = '\0'; strncat(tempSkew, params->vars->abskew.c_str(), params->vars->abskew.length());
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:408:31: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempminh = '\0'; strncat(tempminh, "--minh", 6);
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:412:31: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempMinH = '\0'; strncat(tempMinH, params->vars->minh.c_str(), params->vars->minh.length());
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:419:33: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempmindiv = '\0'; strncat(tempmindiv, "--mindiv", 8);
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:423:33: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempMindiv = '\0'; strncat(tempMindiv, params->vars->mindiv.c_str(), params->vars->mindiv.length());
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:430:33: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempmindiv = '\0'; strncat(tempmindiv, "--mindiffs", 10);
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:433:33: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempMindiv = '\0'; strncat(tempMindiv, params->vars->mindiffs.c_str(), params->vars->mindiffs.length());
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:440:29: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempxn = '\0'; strncat(tempxn, "--xn", 4);
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:444:29: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempXn = '\0'; strncat(tempXn, params->vars->xn.c_str(), params->vars->xn.length());
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:451:29: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*tempdn = '\0'; strncat(tempdn, "--dn", 4);
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:454:29: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempDn = '\0'; strncat(tempDn, params->vars->dn.c_str(), params->vars->dn.length());
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:460:59: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
char* threads = new char[10]; threads[0] = '\0'; strncat(threads, "--threads", 9);
data/mothur-1.44.3/source/commands/chimeravsearchcommand.cpp:464:30: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempThreads = '\0'; strncat(tempThreads, numProcessors.c_str(), numProcessors.length());
data/mothur-1.44.3/source/commands/classifysvmsharedcommand.cpp:331:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
designMap.read(designfile);
data/mothur-1.44.3/source/commands/classifysvmsharedcommand.cpp:370:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
designMap.read(designFilePath);
data/mothur-1.44.3/source/commands/clearcutcommand.cpp:232:34: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*clearcutParameters[0] = '\0'; strncat(clearcutParameters[0], "clearcut", 8);
data/mothur-1.44.3/source/commands/clearcutcommand.cpp:235:104: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
if (phylipfile != "") { clearcutParameters[1] = new char[11]; *clearcutParameters[1] = '\0'; strncat(clearcutParameters[1], "--distance", 10); }
data/mothur-1.44.3/source/commands/clearcutcommand.cpp:238:96: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
if (fastafile != "") { clearcutParameters[1] = new char[12]; *clearcutParameters[1] = '\0'; strncat(clearcutParameters[1], "--alignment", 11); }
data/mothur-1.44.3/source/commands/clearcutcommand.cpp:241:117: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
if (version) { clearcutParameters[parameterCount] = new char[10]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--version", 9); parameterCount++; }
data/mothur-1.44.3/source/commands/clearcutcommand.cpp:242:117: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
if (verbose) { clearcutParameters[parameterCount] = new char[10]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--verbose", 9); parameterCount++; }
data/mothur-1.44.3/source/commands/clearcutcommand.cpp:243:115: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
if (quiet) { clearcutParameters[parameterCount] = new char[8]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--quiet", 7); parameterCount++; }
data/mothur-1.44.3/source/commands/clearcutcommand.cpp:247:48: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], tempSeed.c_str(), tempSeed.length());
data/mothur-1.44.3/source/commands/clearcutcommand.cpp:250:118: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
if (norandom) { clearcutParameters[parameterCount] = new char[11]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--norandom", 10); parameterCount++; }
data/mothur-1.44.3/source/commands/clearcutcommand.cpp:251:117: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
if (shuffle) { clearcutParameters[parameterCount] = new char[10]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--shuffle", 9); parameterCount++; }
data/mothur-1.44.3/source/commands/clearcutcommand.cpp:252:118: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
if (neighbor) { clearcutParameters[parameterCount] = new char[11]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--neighbor", 10); parameterCount++; }
data/mothur-1.44.3/source/commands/clearcutcommand.cpp:256:47: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], tempIn.c_str(), tempIn.length());
data/mothur-1.44.3/source/commands/clearcutcommand.cpp:259:120: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
if (stdoutWanted) { clearcutParameters[parameterCount] = new char[9]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--stdout", 8); parameterCount++; }
data/mothur-1.44.3/source/commands/clearcutcommand.cpp:263:48: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], tempOut.c_str(), tempOut.length());
data/mothur-1.44.3/source/commands/clearcutcommand.cpp:268:113: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
if (DNA) { clearcutParameters[parameterCount] = new char[6]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--DNA", 5); parameterCount++; }
data/mothur-1.44.3/source/commands/clearcutcommand.cpp:269:117: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
if (protein) { clearcutParameters[parameterCount] = new char[10]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--protein", 9); parameterCount++; }
data/mothur-1.44.3/source/commands/clearcutcommand.cpp:270:115: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
if (jukes) { clearcutParameters[parameterCount] = new char[8]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--jukes", 7); parameterCount++; }
data/mothur-1.44.3/source/commands/clearcutcommand.cpp:271:115: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
if (kimura) { clearcutParameters[parameterCount] = new char[9]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--kimura", 8); parameterCount++; }
data/mothur-1.44.3/source/commands/clearcutcommand.cpp:275:48: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], tempMatrix.c_str(), tempMatrix.length());
data/mothur-1.44.3/source/commands/clearcutcommand.cpp:284:48: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], tempNtrees.c_str(), tempNtrees.length());
data/mothur-1.44.3/source/commands/clearcutcommand.cpp:288:116: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
if (expblen) { clearcutParameters[parameterCount] = new char[10]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--expblen", 9); parameterCount++; }
data/mothur-1.44.3/source/commands/clearcutcommand.cpp:289:116: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
if (expdist) { clearcutParameters[parameterCount] = new char[10]; *clearcutParameters[parameterCount] = '\0'; strncat(clearcutParameters[parameterCount], "--expdist", 9); parameterCount++; }
data/mothur-1.44.3/source/commands/clustercommand.cpp:485:100: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
char* vsearchParameter = new char[vsearchCommand.length()+1]; vsearchParameter[0] = '\0'; strncat(vsearchParameter, vsearchCommand.c_str(), vsearchCommand.length());
data/mothur-1.44.3/source/commands/clustercommand.cpp:489:65: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
char* maxaccepts = new char[16]; maxaccepts[0] = '\0'; strncat(maxaccepts, "--maxaccepts=16", 15);
data/mothur-1.44.3/source/commands/clustercommand.cpp:494:108: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
char* processorsParameter = new char[processorsString.length()+1]; processorsParameter[0] = '\0'; strncat(processorsParameter, processorsString.c_str(), processorsString.length());
data/mothur-1.44.3/source/commands/clustercommand.cpp:498:61: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
char* usersort = new char[11]; usersort[0] = '\0'; strncat(usersort, "--usersort", 10);
data/mothur-1.44.3/source/commands/clustercommand.cpp:507:96: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
char* cutoffParameter = new char[cutoffString.length()+1]; cutoffParameter[0] = '\0'; strncat(cutoffParameter, cutoffString.c_str(), cutoffString.length());
data/mothur-1.44.3/source/commands/clustercommand.cpp:511:69: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
char* minseqlength = new char[18]; minseqlength[0] = '\0'; strncat(minseqlength, "--minseqlength=30", 17);
data/mothur-1.44.3/source/commands/clustercommand.cpp:515:65: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
char* wordlength = new char[15]; wordlength[0] = '\0'; strncat(wordlength, "--wordlength=8", 14);
data/mothur-1.44.3/source/commands/clustercommand.cpp:520:64: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
char* uc = new char[tempIn.length()+1]; uc[0] = '\0'; strncat(uc, tempIn.c_str(), tempIn.length());
data/mothur-1.44.3/source/commands/clustercommand.cpp:525:96: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
char* cluster_smallmen = new char[tempSorted.length()+1]; cluster_smallmen[0] = '\0'; strncat(cluster_smallmen, tempSorted.c_str(), tempSorted.length());
data/mothur-1.44.3/source/commands/clustercommand.cpp:529:65: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
char* maxrejects = new char[16]; maxrejects[0] = '\0'; strncat(maxrejects, "--maxrejects=64", 15);
data/mothur-1.44.3/source/commands/clustercommand.cpp:533:57: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
char* strand = new char[14]; strand[0] = '\0'; strncat(strand, "--strand=both", 13);
data/mothur-1.44.3/source/commands/clustercommand.cpp:538:67: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
char* log = new char[tempLog.length()+1]; log[0] = '\0'; strncat(log, tempLog.c_str(), tempLog.length());
data/mothur-1.44.3/source/commands/clustercommand.cpp:543:67: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
char* sizeorder = new char[12]; sizeorder[0] = '\0'; strncat(sizeorder, "--sizeorder", 11);
data/mothur-1.44.3/source/commands/clustercommand.cpp:579:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ReadMatrix* read;
data/mothur-1.44.3/source/commands/clustercommand.cpp:592:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read->read(nameMap);
data/mothur-1.44.3/source/commands/clustercommand.cpp:596:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read->read(ct);
data/mothur-1.44.3/source/commands/clustercommand.cpp:598:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
}else { read->read(nameMap); }
data/mothur-1.44.3/source/commands/clustercommand.cpp:608:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
delete read;
data/mothur-1.44.3/source/commands/clustersplitcommand.cpp:461:30: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
convert->read(nameMap);
data/mothur-1.44.3/source/commands/clustersplitcommand.cpp:1116:100: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
char* vsearchParameter = new char[vsearchCommand.length()+1]; vsearchParameter[0] = '\0'; strncat(vsearchParameter, vsearchCommand.c_str(), vsearchCommand.length());
data/mothur-1.44.3/source/commands/clustersplitcommand.cpp:1120:65: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
char* maxaccepts = new char[16]; maxaccepts[0] = '\0'; strncat(maxaccepts, "--maxaccepts=16", 15);
data/mothur-1.44.3/source/commands/clustersplitcommand.cpp:1124:59: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
char* threads = new char[12]; threads[0] = '\0'; strncat(threads, "--threads=1", 11);
data/mothur-1.44.3/source/commands/clustersplitcommand.cpp:1128:61: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
char* usersort = new char[11]; usersort[0] = '\0'; strncat(usersort, "--usersort", 10);
data/mothur-1.44.3/source/commands/clustersplitcommand.cpp:1137:96: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
char* cutoffParameter = new char[cutoffString.length()+1]; cutoffParameter[0] = '\0'; strncat(cutoffParameter, cutoffString.c_str(), cutoffString.length());
data/mothur-1.44.3/source/commands/clustersplitcommand.cpp:1141:69: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
char* minseqlength = new char[18]; minseqlength[0] = '\0'; strncat(minseqlength, "--minseqlength=30", 17);
data/mothur-1.44.3/source/commands/clustersplitcommand.cpp:1145:65: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
char* wordlength = new char[15]; wordlength[0] = '\0'; strncat(wordlength, "--wordlength=8", 14);
data/mothur-1.44.3/source/commands/clustersplitcommand.cpp:1150:64: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
char* uc = new char[tempIn.length()+1]; uc[0] = '\0'; strncat(uc, tempIn.c_str(), tempIn.length());
data/mothur-1.44.3/source/commands/clustersplitcommand.cpp:1155:96: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
char* cluster_smallmen = new char[tempSorted.length()+1]; cluster_smallmen[0] = '\0'; strncat(cluster_smallmen, tempSorted.c_str(), tempSorted.length());
data/mothur-1.44.3/source/commands/clustersplitcommand.cpp:1159:65: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
char* maxrejects = new char[16]; maxrejects[0] = '\0'; strncat(maxrejects, "--maxrejects=64", 15);
data/mothur-1.44.3/source/commands/clustersplitcommand.cpp:1163:57: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
char* strand = new char[14]; strand[0] = '\0'; strncat(strand, "--strand=both", 13);
data/mothur-1.44.3/source/commands/clustersplitcommand.cpp:1168:67: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
char* log = new char[tempLog.length()+1]; log[0] = '\0'; strncat(log, tempLog.c_str(), tempLog.length());
data/mothur-1.44.3/source/commands/clustersplitcommand.cpp:1173:67: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
char* sizeorder = new char[12]; sizeorder[0] = '\0'; strncat(sizeorder, "--sizeorder", 11);
data/mothur-1.44.3/source/commands/clustersplitcommand.cpp:1290:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read->read(nameMap);
data/mothur-1.44.3/source/commands/clustersplitcommand.cpp:1294:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read->read(ct);
data/mothur-1.44.3/source/commands/clustersplitcommand.cpp:1295:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
}else { read->read(nameMap); }
data/mothur-1.44.3/source/commands/clustersplitcommand.cpp:1306:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
delete read; read = NULL;
data/mothur-1.44.3/source/commands/countseqscommand.cpp:300:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(buffer, 4096);
data/mothur-1.44.3/source/commands/countseqscommand.cpp:377:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(buffer, 4096);
data/mothur-1.44.3/source/commands/getdistscommand.cpp:314:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in3.read(buffer, 4096);
data/mothur-1.44.3/source/commands/getgroupscommand.cpp:943:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in3.read(buffer, 4096);
data/mothur-1.44.3/source/commands/getmimarkspackagecommand.cpp:406:39: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
Oligos oligos; oligos.read(oligosfile);
data/mothur-1.44.3/source/commands/homovacommand.cpp:145:43: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
vector<string> sampleNames = readMatrix.read(distanceMatrix);
data/mothur-1.44.3/source/commands/indicatorcommand.cpp:229:8: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
if (mismatch) { //cleanup and exit
data/mothur-1.44.3/source/commands/indicatorcommand.cpp:234:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int readOk = read->read(&ct); if (readOk != 0) { m->mothurOut("Read Terminated.\n"); delete read; return 0; }
data/mothur-1.44.3/source/commands/indicatorcommand.cpp:234:99: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int readOk = read->read(&ct); if (readOk != 0) { m->mothurOut("Read Terminated.\n"); delete read; return 0; }
data/mothur-1.44.3/source/commands/indicatorcommand.cpp:235:48: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
vector<Tree*> T = read->getTrees(); delete read;
data/mothur-1.44.3/source/commands/makecontigscommand.cpp:1389:6: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool read(Sequence& fSeq, Sequence& rSeq, QualityScores*& fQual, QualityScores*& rQual, Sequence& findexBarcode, Sequence& rindexBarcode, char delim, boost::iostreams::filtering_istream& inFF, boost::iostreams::filtering_istream& inRF, boost::iostreams::filtering_istream& inFQ, boost::iostreams::filtering_istream& inRQ, string thisfqualindexfile, string thisrqualindexfile, string format, int nameType, int offByOneTrimLength, MothurOut* m) {
data/mothur-1.44.3/source/commands/makecontigscommand.cpp:1471:6: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool read(Sequence& fSeq, Sequence& rSeq, QualityScores*& fQual, QualityScores*& rQual,Sequence& findexBarcode, Sequence& rindexBarcode, char delim, ifstream& inFFasta, ifstream& inRFasta, ifstream& inFQualIndex, ifstream& inRQualIndex, string thisfqualindexfile, string thisrqualindexfile, string format, int nameType, int offByOneTrimLength, MothurOut* m) {
data/mothur-1.44.3/source/commands/makecontigscommand.cpp:1757:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ignore = read(fSeq, rSeq, fQual, rQual, findexBarcode, rindexBarcode, params->delim, inFF, inRF, inFQ, inRQ, thisfqualindexfile, thisrqualindexfile, params->format, params->nameType, params->offByOneTrimLength, params->m);
data/mothur-1.44.3/source/commands/makecontigscommand.cpp:1760:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ignore = read(fSeq, rSeq, fQual, rQual, findexBarcode, rindexBarcode, params->delim, inFFasta, inRFasta, inFQualIndex, inRQualIndex, thisfqualindexfile, thisrqualindexfile, params->format, params->nameType, params->offByOneTrimLength, params->m);
data/mothur-1.44.3/source/commands/makecontigscommand.cpp:2623:31: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
Oligos oligos; oligos.read(oligosfile, false);
data/mothur-1.44.3/source/commands/mantelcommand.cpp:122:38: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
vector<string> names1 = readMatrix.read(matrix1);
data/mothur-1.44.3/source/commands/mantelcommand.cpp:129:39: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
vector<string> names2 = readMatrix2.read(matrix2);
data/mothur-1.44.3/source/commands/mergesfffilecommand.cpp:218:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool goodHeader = header->read(in);
data/mothur-1.44.3/source/commands/mergesfffilecommand.cpp:236:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
delete read;
data/mothur-1.44.3/source/commands/mgclustercommand.cpp:487:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read->read(nameMap);
data/mothur-1.44.3/source/commands/mgclustercommand.cpp:499:84: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (m->getControl_pressed()) { outputTypes.clear(); delete nameMap; delete read; delete list; delete rabund; return 0; }
data/mothur-1.44.3/source/commands/mgclustercommand.cpp:513:36: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
delete nameMap; delete read; delete list; delete rabund;
data/mothur-1.44.3/source/commands/mgclustercommand.cpp:525:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
delete read;
data/mothur-1.44.3/source/commands/mgclustercommand.h:45:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ReadBlast* read;
data/mothur-1.44.3/source/commands/nmdscommand.cpp:147:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
names = readFile.read(matrix);
data/mothur-1.44.3/source/commands/parsefastaqcommand.cpp:1066:38: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (fileOption > 0) { oligos.read(oligosfile, false); } // like make.contigs
data/mothur-1.44.3/source/commands/parsefastaqcommand.cpp:1067:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
else { oligos.read(oligosfile); }
data/mothur-1.44.3/source/commands/pcoacommand.cpp:123:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
names = readFile.read(D);
data/mothur-1.44.3/source/commands/pcrseqscommand.cpp:372:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
oligos.read(oligosfile);
data/mothur-1.44.3/source/commands/preclustercommand.cpp:508:82: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
void mergeSeqs(seqPNode* representative, seqPNode* duplicate, string& chunk, int mismatch, int originalCount, preClusterData* params){
data/mothur-1.44.3/source/commands/preclustercommand.cpp:518:115: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
chunk += representative->name + "\t" + duplicate->name + "\t" + toString(originalCount) + "\t" + toString(mismatch) + "\t" + duplicate->sequence + "\n";
data/mothur-1.44.3/source/commands/preclustercommand.cpp:520:28: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
duplicate->diffs = mismatch;
data/mothur-1.44.3/source/commands/preclustercommand.cpp:566:33: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
if (mismatch <= params->diffs) { mergeSeqs(params->alignSeqs[i], params->alignSeqs[j], chunk, mismatch, originalCount[j], params); count++; }
data/mothur-1.44.3/source/commands/preclustercommand.cpp:566:123: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
if (mismatch <= params->diffs) { mergeSeqs(params->alignSeqs[i], params->alignSeqs[j], chunk, mismatch, originalCount[j], params); count++; }
data/mothur-1.44.3/source/commands/preclustercommand.cpp:601:33: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
if (mismatch <= params->diffs && skew <= beta[mismatch]) { mergeSeqs(params->alignSeqs[i], params->alignSeqs[j], chunk, mismatch, originalCount[j], params); count++; }
data/mothur-1.44.3/source/commands/preclustercommand.cpp:601:75: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
if (mismatch <= params->diffs && skew <= beta[mismatch]) { mergeSeqs(params->alignSeqs[i], params->alignSeqs[j], chunk, mismatch, originalCount[j], params); count++; }
data/mothur-1.44.3/source/commands/preclustercommand.cpp:601:149: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
if (mismatch <= params->diffs && skew <= beta[mismatch]) { mergeSeqs(params->alignSeqs[i], params->alignSeqs[j], chunk, mismatch, originalCount[j], params); count++; }
data/mothur-1.44.3/source/commands/rarefactsharedcommand.cpp:214:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
designMap.read(designfile);
data/mothur-1.44.3/source/commands/removedistscommand.cpp:317:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in3.read(buffer, 4096);
data/mothur-1.44.3/source/commands/removegroupscommand.cpp:1000:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in3.read(buffer, 4096);
data/mothur-1.44.3/source/commands/seqerrorcommand.cpp:576:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
report.read(reportFile);
data/mothur-1.44.3/source/commands/seqerrorcommand.cpp:581:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
quality.read(qualFile);
data/mothur-1.44.3/source/commands/seqerrorcommand.cpp:591:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
quality.read(qualFile);
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:311:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool goodHeader = header->read(in);
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:329:45: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (split > 1) { assignToSample(read, trimOligos, rtrimOligos); }
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:343:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
delete read;
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:467:47: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void SffInfoCommand::assignToSample(SffRead*& read, TrimOligos*& trimOligos, TrimOligos*& rtrimOligos){
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:472:60: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (hasOligos) { trashCodeLength = findGroup(read, barcodeIndex, primerIndex, trimOligos, rtrimOligos); }
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:473:60: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
else if (hasGroup) { trashCodeLength = findGroup(read, barcodeIndex, primerIndex, "groupMode"); }
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:493:41: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int SffInfoCommand::findGroup(SffRead*& read, int& barcode, int& primer, TrimOligos*& trimOligos, TrimOligos*& rtrimOligos) {
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:611:41: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int SffInfoCommand::findGroup(SffRead*& read, int& barcode, int& primer, string groupMode) {
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:682:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
SffRead read(numFlows);
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:688:4: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.setName(seqName);
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:690:56: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
string runPrefix = parseHeaderLineToString(inSFF); read.setTimeStamp(runPrefix);
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:691:58: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
string regionNumber = parseHeaderLineToString(inSFF); read.setRegion(regionNumber);
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:692:57: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
string xyLocation = parseHeaderLineToString(inSFF); read.setXY(xyLocation);
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:700:75: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
unsigned short readHeaderLen = parseHeaderLineToShort(inSFF); read.setHeaderLength(readHeaderLen);
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:701:72: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
unsigned short nameLength = parseHeaderLineToShort(inSFF); read.setNameLength(nameLength);
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:702:48: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int numBases = parseHeaderLineToInt(inSFF); read.setNumBases(numBases);
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:703:74: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
unsigned short clipQualLeft = parseHeaderLineToShort(inSFF); read.setClipQualLeft(clipQualLeft);
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:704:66: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
unsigned short clipQualRight = parseHeaderLineToShort(inSFF); read.setClipQualRight(clipQualRight);
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:705:74: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
unsigned short clipAdapLeft = parseHeaderLineToShort(inSFF); read.setClipAdapterLeft(clipAdapLeft);
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:706:75: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
unsigned short clipAdapRight = parseHeaderLineToShort(inSFF); read.setClipAdapterRight(clipAdapRight);
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:710:96: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
vector<unsigned short> flowVector = parseHeaderLineToFloatVector(inSFF, numFlows); read.setFlowgrams(flowVector);
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:716:4: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.setFlowIndex(flowIndicesAdjusted);
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:718:51: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
string bases = parseHeaderLineToString(inSFF); read.setBases(bases);
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:719:86: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
vector<unsigned int> qualityScores = parseHeaderLineToIntVector(inSFF, numBases); read.setQualScores(qualityScores);
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:724:53: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (seqNames.size() != 0) { if (seqNames.count(read.getName()) == 0) { print = false; } }
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:728:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (fasta) { read.printFasta(outFasta, trim); }
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:729:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (qual) { read.printQuality(outQual, trim); }
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:730:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (flow) { read.printFlow(outFlow); }
data/mothur-1.44.3/source/commands/sffinfocommand.cpp:863:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
oligosObject->read(oligoFile);
data/mothur-1.44.3/source/commands/sffinfocommand.h:60:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int findGroup(SffRead*& read, int& barcode, int& primer, TrimOligos*&, TrimOligos*&);
data/mothur-1.44.3/source/commands/shhhercommand.cpp:834:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read->read(clusterNameMap);
data/mothur-1.44.3/source/commands/shhhercommand.cpp:839:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
delete read;
data/mothur-1.44.3/source/commands/sracommand.cpp:1231:62: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ((fileOption == 3) || (fileOption == 5)) { oligos.read(oligosfile, false); } //like make.contigs
data/mothur-1.44.3/source/commands/sracommand.cpp:1232:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
else { oligos.read(oligosfile); }
data/mothur-1.44.3/source/commands/srainfocommand.cpp:264:9: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
strncat(tempPrefetch, prefetchCommand.c_str(), prefetchCommand.length());
data/mothur-1.44.3/source/commands/srainfocommand.cpp:269:59: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
char* maxs = new char[3]; maxs[0] = '\0'; strncat(maxs, "-X", 2);
data/mothur-1.44.3/source/commands/srainfocommand.cpp:273:31: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempSize = '\0'; strncat(tempSize, msize.c_str(), msize.length());
data/mothur-1.44.3/source/commands/srainfocommand.cpp:278:67: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
char* outputFile = new char[3]; outputFile[0] = '\0'; strncat(outputFile, "-o", 2);
data/mothur-1.44.3/source/commands/srainfocommand.cpp:284:30: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempoutfile = '\0'; strncat(tempoutfile, outputFileName.c_str(), outputFileName.length());
data/mothur-1.44.3/source/commands/srainfocommand.cpp:335:9: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
strncat(tempFasterQ, fasterQCommand.c_str(), fasterQCommand.length());
data/mothur-1.44.3/source/commands/srainfocommand.cpp:345:65: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
splitFiles = new char[3]; splitFiles[0] = '\0'; strncat(splitFiles, "-S", 2);
data/mothur-1.44.3/source/commands/srainfocommand.cpp:347:66: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
splitFiles = new char[14]; splitFiles[0] = '\0'; strncat(splitFiles, "--split-files", 13);
data/mothur-1.44.3/source/commands/srainfocommand.cpp:355:31: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
splitSingleFiles[0] = '\0'; strncat(splitSingleFiles, "-3", 2);
data/mothur-1.44.3/source/commands/srainfocommand.cpp:358:31: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
splitSingleFiles[0] = '\0'; strncat(splitSingleFiles, "--split-3", 9);
data/mothur-1.44.3/source/commands/srainfocommand.cpp:364:59: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
char* threads = new char[10]; threads[0] = '\0'; strncat(threads, "--threads", 9);
data/mothur-1.44.3/source/commands/srainfocommand.cpp:368:30: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempThreads = '\0'; strncat(tempThreads, numProcessors.c_str(), numProcessors.length());
data/mothur-1.44.3/source/commands/srainfocommand.cpp:374:63: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
char* gzip = new char[7]; gzip[0] = '\0'; strncat(gzip, "--gzip", 6);
data/mothur-1.44.3/source/commands/srainfocommand.cpp:382:56: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
outputFile = new char[3]; outputFile[0] = '\0'; strncat(outputFile, "-o", 2);
data/mothur-1.44.3/source/commands/srainfocommand.cpp:387:25: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempoutfile = '\0'; strncat(tempoutfile, outputFileName.c_str(), outputFileName.length());
data/mothur-1.44.3/source/commands/srainfocommand.cpp:392:57: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
outputFile = new char[9]; outputFile[0] = '\0'; strncat(outputFile, "--outdir", 8);
data/mothur-1.44.3/source/commands/srainfocommand.cpp:395:26: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
*tempoutfile = '\0'; strncat(tempoutfile, outputFileName.c_str(), outputFileName.length());
data/mothur-1.44.3/source/commands/treesharedcommand.cpp:304:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
readMatrix->read(nameMap);
data/mothur-1.44.3/source/commands/treesharedcommand.cpp:310:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
readMatrix->read(ct);
data/mothur-1.44.3/source/commands/treesharedcommand.cpp:313:65: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
}else { NameAssignment* nameMap = NULL; readMatrix->read(nameMap); list = readMatrix->getListVector(); }
data/mothur-1.44.3/source/commands/trimflowscommand.cpp:594:31: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
Oligos oligos; oligos.read(oligoFileName);
data/mothur-1.44.3/source/commands/trimseqscommand.cpp:849:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
oligos.read(oligoFile);
data/mothur-1.44.3/source/datastructures/blastalign.cpp:23:4: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
mismatch(mm) // This is the penalty to assess for a mismatch (mismatch <= 0)
data/mothur-1.44.3/source/datastructures/blastalign.cpp:62:63: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
blastCommand += " -r " + toString(match) + " -q " + toString(mismatch);
data/mothur-1.44.3/source/datastructures/blastalign.hpp:38:8: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
float mismatch;
data/mothur-1.44.3/source/datastructures/blastdb.cpp:201:19: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
float numBases, mismatch, gap, startQuery, endQuery, startRef, endRef, score, searchScore;
data/mothur-1.44.3/source/datastructures/blastdb.cpp:237:77: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
m8FileHandle >> dummy >> templateAccession >> searchScore >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
data/mothur-1.44.3/source/datastructures/designmap.cpp:16:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(file);
data/mothur-1.44.3/source/datastructures/designmap.cpp:24:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int DesignMap::read(string file) {
data/mothur-1.44.3/source/datastructures/designmap.h:32:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int read(string);
data/mothur-1.44.3/source/datastructures/filefile.cpp:26:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(f, mode);
data/mothur-1.44.3/source/datastructures/filefile.cpp:86:36: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
vector< vector<string> > FileFile::read(string f, string mode){
data/mothur-1.44.3/source/datastructures/filefile.hpp:85:30: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
vector< vector<string> > read(string, string); //read file, used with () constructor
data/mothur-1.44.3/source/datastructures/groupmap.cpp:162:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
fileHandle.read(buffer, 4096);
data/mothur-1.44.3/source/datastructures/groupmap.cpp:239:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
fileHandle.read(buffer, 4096);
data/mothur-1.44.3/source/datastructures/groupmap.cpp:315:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
fileHandle.read(buffer, 4096);
data/mothur-1.44.3/source/datastructures/groupmap.cpp:390:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
fileHandle.read(buffer, 4096);
data/mothur-1.44.3/source/datastructures/kmeralign.cpp:120:29: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
int unknown, match, mismatch; unknown = 0; match = 0; mismatch = 0;
data/mothur-1.44.3/source/datastructures/kmeralign.cpp:142:59: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
prob = (-1.38629 * unknown + match * pmatch + mismatch * pmismatch);
data/mothur-1.44.3/source/datastructures/kmeralign.cpp:144:95: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
prob = (-1.38629 * (aLength + bLength - 2 * overlap + unknown) + match * pmatch + mismatch * pmismatch);
data/mothur-1.44.3/source/datastructures/oligos.cpp:50:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int Oligos::read(string o){
data/mothur-1.44.3/source/datastructures/oligos.cpp:69:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int Oligos::read(string o, bool reverse){
data/mothur-1.44.3/source/datastructures/oligos.h:25:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int read(string);
data/mothur-1.44.3/source/datastructures/oligos.h:26:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int read(string, bool); //read without reversing the paired barcodes, for make.contigs.
data/mothur-1.44.3/source/datastructures/optiblastmatrix.cpp:61:25: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
float numBases, mismatch, gap, startQuery, endQuery, startRef, endRef, score, lengthThisSeq;
data/mothur-1.44.3/source/datastructures/optiblastmatrix.cpp:76:79: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
fileHandle >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
data/mothur-1.44.3/source/datastructures/optiblastmatrix.cpp:114:79: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
fileHandle >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
data/mothur-1.44.3/source/datastructures/optiblastmatrix.cpp:290:71: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
in >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
data/mothur-1.44.3/source/datastructures/optiblastmatrix.cpp:340:71: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
in >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
data/mothur-1.44.3/source/datastructures/qualityscores.cpp:140:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int QualityScores::read(ifstream& qFile){
data/mothur-1.44.3/source/datastructures/qualityscores.h:33:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int read(ifstream&);
data/mothur-1.44.3/source/datastructures/reportfile.cpp:43:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int ReportFile::read(ifstream& repFile){
data/mothur-1.44.3/source/datastructures/reportfile.h:22:6: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int read(ifstream&);
data/mothur-1.44.3/source/datastructures/sffheader.cpp:34:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read(in);
data/mothur-1.44.3/source/datastructures/sffheader.cpp:44:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool SffCommonHeader::read(ifstream& in){
data/mothur-1.44.3/source/datastructures/sffheader.cpp:55:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(&(*magic), 4);
data/mothur-1.44.3/source/datastructures/sffheader.cpp:61:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(&(*cversion), 4);
data/mothur-1.44.3/source/datastructures/sffheader.cpp:68:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(buffer2, 8);
data/mothur-1.44.3/source/datastructures/sffheader.cpp:73:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(buffer3, 4);
data/mothur-1.44.3/source/datastructures/sffheader.cpp:78:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(rnumReads, 4);
data/mothur-1.44.3/source/datastructures/sffheader.cpp:85:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(&(*hlength), 2);
data/mothur-1.44.3/source/datastructures/sffheader.cpp:91:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(&(*klength), 2);
data/mothur-1.44.3/source/datastructures/sffheader.cpp:97:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(&(*nflows), 2);
data/mothur-1.44.3/source/datastructures/sffheader.cpp:103:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(&(*fcode), 1);
data/mothur-1.44.3/source/datastructures/sffheader.cpp:109:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(&(*tempBuffer), numFlows);
data/mothur-1.44.3/source/datastructures/sffheader.cpp:116:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(&(*tempBuffer2), keyLength);
data/mothur-1.44.3/source/datastructures/sffheader.hpp:74:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool read(ifstream& in);
data/mothur-1.44.3/source/datastructures/sffread.cpp:61:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(&(*readHeaderLength), 2);
data/mothur-1.44.3/source/datastructures/sffread.cpp:67:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(&(*readNameLength), 2);
data/mothur-1.44.3/source/datastructures/sffread.cpp:73:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(&(*readNumBases), 4);
data/mothur-1.44.3/source/datastructures/sffread.cpp:79:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(&(*rclipQualLeft), 2);
data/mothur-1.44.3/source/datastructures/sffread.cpp:85:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(&(*rclipQualRight), 2);
data/mothur-1.44.3/source/datastructures/sffread.cpp:91:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(&(*rclipAdapterLeft), 2);
data/mothur-1.44.3/source/datastructures/sffread.cpp:97:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(&(*rclipAdapterRight), 2);
data/mothur-1.44.3/source/datastructures/sffread.cpp:103:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(&(*readName), nameLength);
data/mothur-1.44.3/source/datastructures/sffread.cpp:127:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(rflowgram, 2);
data/mothur-1.44.3/source/datastructures/sffread.cpp:140:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(flowINdex, 1);
data/mothur-1.44.3/source/datastructures/sffread.cpp:148:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(&(*readBases), numBases);
data/mothur-1.44.3/source/datastructures/sffread.cpp:158:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(score, 1);
data/mothur-1.44.3/source/datastructures/treemap.cpp:46:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
fileHandle.read(buffer, 4096);
data/mothur-1.44.3/source/datastructures/treemap.cpp:125:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
fileHandle.read(buffer, 4096);
data/mothur-1.44.3/source/gotohoverlap.cpp:29:40: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
gapOpen(gO), gapExtend(gE), match(f), mismatch(mm), Alignment(r) {
data/mothur-1.44.3/source/gotohoverlap.cpp:63:56: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
else { diagonal = alignment[i-1][j-1].cValue + mismatch; }
data/mothur-1.44.3/source/gotohoverlap.hpp:40:8: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
float mismatch;
data/mothur-1.44.3/source/mothur.cpp:107:31: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
*temp = '\0'; strncat(temp, "#help();quit();", 15);
data/mothur-1.44.3/source/nast.cpp:384:34: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
float similarity = 100 * (1. - mismatch / (float)denominator);
data/mothur-1.44.3/source/needlemanoverlap.cpp:28:20: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
gap(gO), match(f), mismatch(mm), Alignment(r) { // the gap openning penalty is assessed for
data/mothur-1.44.3/source/needlemanoverlap.cpp:67:56: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
else { diagonal = alignment[i-1][j-1].cValue + mismatch; }
data/mothur-1.44.3/source/needlemanoverlap.cpp:123:83: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
else { diagonal = alignment[i-1][j-1].cValue + mismatch; }
data/mothur-1.44.3/source/needlemanoverlap.hpp:40:8: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
float mismatch;
data/mothur-1.44.3/source/read/readblast.cpp:33:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int ReadBlast::read(NameAssignment* nameMap) {
data/mothur-1.44.3/source/read/readblast.cpp:50:19: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
float numBases, mismatch, gap, startQuery, endQuery, startRef, endRef, score, lengthThisSeq;
data/mothur-1.44.3/source/read/readblast.cpp:68:70: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
fileHandle >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
data/mothur-1.44.3/source/read/readblast.cpp:103:70: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
fileHandle >> firstName >> secondName >> percentId >> numBases >> mismatch >> gap >> startQuery >> endQuery >> startRef >> endRef >> eScore >> score;
data/mothur-1.44.3/source/read/readblast.h:28:6: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int read(NameAssignment*);
data/mothur-1.44.3/source/read/readcluster.cpp:25:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int ReadCluster::read(NameAssignment*& nameMap){
data/mothur-1.44.3/source/read/readcluster.cpp:45:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int ReadCluster::read(CountTable*& ct){
data/mothur-1.44.3/source/read/readcluster.h:27:6: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int read(NameAssignment*&);
data/mothur-1.44.3/source/read/readcluster.h:28:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int read(CountTable*&);
data/mothur-1.44.3/source/read/readcolumn.cpp:31:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int ReadColumnMatrix::read(NameAssignment* nameMap){
data/mothur-1.44.3/source/read/readcolumn.cpp:151:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int ReadColumnMatrix::read(CountTable* countTable){
data/mothur-1.44.3/source/read/readcolumn.h:22:6: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int read(NameAssignment*);
data/mothur-1.44.3/source/read/readcolumn.h:23:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int read(CountTable*);
data/mothur-1.44.3/source/read/readmatrix.hpp:26:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
virtual int read(NameAssignment*){ return 1; }
data/mothur-1.44.3/source/read/readmatrix.hpp:27:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
virtual int read(CountTable*){ return 1; }
data/mothur-1.44.3/source/read/readphylip.cpp:32:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int ReadPhylipMatrix::read(NameAssignment* nameMap){
data/mothur-1.44.3/source/read/readphylip.cpp:202:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int ReadPhylipMatrix::read(CountTable* countTable){
data/mothur-1.44.3/source/read/readphylip.h:22:6: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int read(NameAssignment*);
data/mothur-1.44.3/source/read/readphylip.h:23:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int read(CountTable*);
data/mothur-1.44.3/source/read/readphylipvector.cpp:25:34: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
vector<string> ReadPhylipVector::read(vector< vector<double> >& matrix) {
data/mothur-1.44.3/source/read/readphylipvector.cpp:112:34: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
vector<string> ReadPhylipVector::read(vector<seqDist>& matrix) {
data/mothur-1.44.3/source/read/readphylipvector.h:24:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
vector<string> read(vector< vector<double> >&); //pass in matrix to fill with values, returns vector of strings containing names in phylipfile
data/mothur-1.44.3/source/read/readphylipvector.h:25:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
vector<string> read(vector<seqDist>&); //pass in matrix to fill with values, returns vector of strings containing names in phylipfile
data/mothur-1.44.3/source/read/readtree.cpp:98:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int ReadNewickTree::read(CountTable* ct) {
data/mothur-1.44.3/source/read/readtree.h:29:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
virtual int read(CountTable*) = 0;
data/mothur-1.44.3/source/read/readtree.h:54:6: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int read(CountTable*);
data/mothur-1.44.3/source/read/treereader.cpp:82:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int readOk = read->read(ct);
data/mothur-1.44.3/source/read/treereader.cpp:84:66: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if (readOk != 0) { m->mothurOut("Read Terminated.\n"); delete read; m->setControl_pressed(true); return 0; }
data/mothur-1.44.3/source/read/treereader.cpp:88:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
delete read;
data/mothur-1.44.3/source/refchimeratest.cpp:651:17: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
return (double)mismatch / (double)(mismatch + match);
data/mothur-1.44.3/source/uchime_src/fractid.cpp:286:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
unsigned ColCount = (unsigned) strlen(Path);
data/mothur-1.44.3/source/uchime_src/mx.cpp:143:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(m_Name, Name, n);
data/mothur-1.44.3/source/uchime_src/mx.cpp:181:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
unsigned Width = strlen(z);
data/mothur-1.44.3/source/uchime_src/mx.cpp:190:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
unsigned n = strlen(m_Alpha);
data/mothur-1.44.3/source/uchime_src/mx.cpp:209:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
unsigned n = strlen(m_Alpha2);
data/mothur-1.44.3/source/uchime_src/mx.h:188:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(m_Alpha, Alpha, n);
data/mothur-1.44.3/source/uchime_src/myopts.h:146:10: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
FLT_OPT( mismatch, -2.0, 0.0, FLT_MAX)
data/mothur-1.44.3/source/uchime_src/myutils.cpp:349:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
size_t n = read(h, Buffer, stBytes);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:404:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
unsigned n = strlen(Line);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:420:11: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int c = fgetc(f);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:654:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int n = read(fd, Buffer, sizeof(Buffer) - 1);
data/mothur-1.44.3/source/uchime_src/myutils.cpp:1674:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
unsigned n = unsigned(strlen(s));
data/mothur-1.44.3/source/uchime_src/path.cpp:135:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
unsigned NeededBytes = (unsigned) strlen(PathStr) + 1;
data/mothur-1.44.3/source/uchime_src/path.h:44:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
unsigned L = (unsigned) strlen(Start);
data/mothur-1.44.3/source/uchime_src/seqdb.cpp:42:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
unsigned n = strlen(m_Labels[i]);
data/mothur-1.44.3/source/uchime_src/seqdb.cpp:143:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
unsigned L = (unsigned) strlen(m_Labels[Index]);
data/mothur-1.44.3/source/uchime_src/seqdb.cpp:255:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
unsigned n = strlen(Label) + 1;
data/mothur-1.44.3/source/uchime_src/setnucmx.cpp:21:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
unsigned N = unsigned(strlen(Alphabet));
data/mothur-1.44.3/source/utils.cpp:1141:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
input.read(buffer, 4096);
data/mothur-1.44.3/source/utils.cpp:1167:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
input.read(buffer, 4096);
data/mothur-1.44.3/source/utils.cpp:1192:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
input.read(buffer, 4096);
data/mothur-1.44.3/source/utils.cpp:1225:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
input.read(buffer, 4096);
data/mothur-1.44.3/source/utils.cpp:1260:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
input.read(buffer, 4096);
data/mothur-1.44.3/source/utils.cpp:1291:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
input.read(buffer, 4096);
data/mothur-1.44.3/source/utils.cpp:2800:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(chunk, size);
data/mothur-1.44.3/source/utils.cpp:3065:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(buffer, 4096);
data/mothur-1.44.3/source/utils.cpp:3130:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(buffer, 4096);
data/mothur-1.44.3/source/utils.cpp:3188:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(buffer, 4096);
data/mothur-1.44.3/source/utils.cpp:3253:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(buffer, 4096);
data/mothur-1.44.3/source/utils.cpp:3355:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(buffer, 4096);
data/mothur-1.44.3/source/utils.cpp:3476:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(buffer, 4096);
data/mothur-1.44.3/source/utils.cpp:3535:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(buffer, 4096);
data/mothur-1.44.3/source/utils.cpp:3657:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(buffer, 4096);
data/mothur-1.44.3/source/utils.cpp:3794:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(buffer, 4096);
data/mothur-1.44.3/source/utils.cpp:4222:16: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
return equal;
data/mothur-1.44.3/source/utils.cpp:4236:16: [1] (buffer) equal:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
return equal;
ANALYSIS SUMMARY:
Hits = 713
Lines analyzed = 226745 in approximately 6.48 seconds (35005 lines/second)
Physical Source Lines of Code (SLOC) = 161381
Hits@level = [0] 336 [1] 417 [2] 218 [3] 46 [4] 32 [5] 0
Hits@level+ = [0+] 1049 [1+] 713 [2+] 296 [3+] 78 [4+] 32 [5+] 0
Hits/KSLOC@level+ = [0+] 6.50015 [1+] 4.41812 [2+] 1.83417 [3+] 0.483328 [4+] 0.198289 [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.