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/seqtools-4.44.1+dfsg/blixemApp/detailviewtree.hpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/sequencecellrenderer.cpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/blxview.cpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/blxpanel.cpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/coverageview.cpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/detailviewtree.cpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/blixem_.hpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/blxview.hpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/coverageview.hpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/bigpicturegrid.cpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/exonview.hpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/sequencecellrenderer.hpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/blxFetch.cpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/blxpanel.hpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/blxcontext.cpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/bigpicturegrid.hpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/exonview.cpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.hpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/blxcontext.hpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/bigpicture.hpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/detailview.hpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/blxdotter.hpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/blxFetchDb.cpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/blxdotter.cpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/detailview.cpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/bigpicture.cpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp
Examining data/seqtools-4.44.1+dfsg/blixemApp/blxmain.cpp
Examining data/seqtools-4.44.1+dfsg/belvuApp/belvu_.hpp
Examining data/seqtools-4.44.1+dfsg/belvuApp/belvuAlignment.hpp
Examining data/seqtools-4.44.1+dfsg/belvuApp/belvuConsPlot.hpp
Examining data/seqtools-4.44.1+dfsg/belvuApp/belvuTree.hpp
Examining data/seqtools-4.44.1+dfsg/belvuApp/belvuTree.cpp
Examining data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp
Examining data/seqtools-4.44.1+dfsg/belvuApp/belvuAlignment.cpp
Examining data/seqtools-4.44.1+dfsg/belvuApp/belvuConsPlot.cpp
Examining data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp
Examining data/seqtools-4.44.1+dfsg/belvuApp/belvuWindow.cpp
Examining data/seqtools-4.44.1+dfsg/belvuApp/belvuWindow.hpp
Examining data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxmsp.hpp
Examining data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp
Examining data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.hpp
Examining data/seqtools-4.44.1+dfsg/seqtoolsUtils/seqtoolsWebBrowser.cpp
Examining data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.hpp
Examining data/seqtools-4.44.1+dfsg/seqtoolsUtils/seqtoolsFetch.hpp
Examining data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxGff3Parser.hpp
Examining data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp
Examining data/seqtools-4.44.1+dfsg/seqtoolsUtils/iupac.hpp
Examining data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxmsp.cpp
Examining data/seqtools-4.44.1+dfsg/seqtoolsUtils/translate.cpp
Examining data/seqtools-4.44.1+dfsg/seqtoolsUtils/seqtoolsFetch.cpp
Examining data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxGff3Parser.cpp
Examining data/seqtools-4.44.1+dfsg/seqtoolsUtils/version.hpp
Examining data/seqtools-4.44.1+dfsg/dotterApp/dotplot.cpp
Examining data/seqtools-4.44.1+dfsg/dotterApp/greyramptool.cpp
Examining data/seqtools-4.44.1+dfsg/dotterApp/seqtoolsExonView.hpp
Examining data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp
Examining data/seqtools-4.44.1+dfsg/dotterApp/dotter_.hpp
Examining data/seqtools-4.44.1+dfsg/dotterApp/dotter.cpp
Examining data/seqtools-4.44.1+dfsg/dotterApp/seqtoolsExonView.cpp
Examining data/seqtools-4.44.1+dfsg/dotterApp/dotterKarlin.cpp
Examining data/seqtools-4.44.1+dfsg/dotterApp/alignmenttool.cpp
Examining data/seqtools-4.44.1+dfsg/dotterApp/dotter.hpp
Examining data/seqtools-4.44.1+dfsg/gbtools/src/gbtoolsUtils/gbtoolsUtils.cpp
Examining data/seqtools-4.44.1+dfsg/gbtools/src/gbtoolsCurl/gbtoolsCurl.cpp
Examining data/seqtools-4.44.1+dfsg/gbtools/src/gbtoolsCurl/gbtoolsCurl_P.hpp
Examining data/seqtools-4.44.1+dfsg/gbtools/src/gbtoolsPfetch/gbtoolsPfetch.cpp
Examining data/seqtools-4.44.1+dfsg/gbtools/src/gbtoolsPfetch/gbtoolsPfetchPipe.cpp
Examining data/seqtools-4.44.1+dfsg/gbtools/src/gbtoolsPfetch/gbtoolsPfetchHttp.cpp
Examining data/seqtools-4.44.1+dfsg/gbtools/src/include/gbtools/gbtoolsCurl.hpp
Examining data/seqtools-4.44.1+dfsg/gbtools/src/include/gbtools/gbtoolsGUI.hpp
Examining data/seqtools-4.44.1+dfsg/gbtools/src/include/gbtools/gbtoolsUtils.hpp
Examining data/seqtools-4.44.1+dfsg/gbtools/src/include/gbtools/gbtoolsPfetch.hpp
Examining data/seqtools-4.44.1+dfsg/gbtools/src/include/gbtools/gbtools.hpp
Examining data/seqtools-4.44.1+dfsg/gbtools/src/include/gbtools/gbtoolsTrackhub.hpp
Examining data/seqtools-4.44.1+dfsg/gbtools/src/gbtoolsGUI/gbtoolsGUI.cpp
Examining data/seqtools-4.44.1+dfsg/gbtools/src/gbtoolsTrackhub/gbtoolsTrackhub.cpp
FINAL RESULTS:
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:861:7: [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.
if (sscanf(tmp, "%s%d%d", alnp->name, &alnp->start, &alnp->end) != 3)
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:943:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(bc->treeMethodString, UPGMAstr);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:1173:11: [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(cp + strlen(aln->name), "%d%d%s", &aln->start, &aln->end, GRfeat);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:1177:11: [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(cp + strlen(aln->name), "%s", GRfeat);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:1902:11: [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(cp, "%s", setColor);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:1937:11: [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.
if (sscanf(line, "%c%s", &c, setColor) == 2)
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:2302:7: [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(tmpname, alnp->name);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:2497:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(bc->treeDistString, SCOREDISTstr);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:2498:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(bc->treeMethodString, NJstr);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:2906:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(linecopy, line);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:3183:4: [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(rawseq, line);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:4169:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(name, cp+4);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:4891:2: [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(url, env);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:4893:2: [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(url, DEFAULT_FETCH_URL);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:4921:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(fetchProg, env);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:4923:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(fetchProg, DEFAULT_FETCH_PROG);
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:370:11: [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(suffix, cp + 1);
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:458:7: [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(linecp, line);
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:589:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(treePickString, SWAPstr);
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:677:21: [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(bc->treeMethodString, NJstr);
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:680:21: [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(bc->treeMethodString, UPGMAstr);
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:691:21: [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(bc->treeDistString, JUKESCANTORstr);
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:695:21: [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(bc->treeDistString, KIMURAstr);
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:706:21: [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(bc->treeDistString, STORMSONNstr);
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:710:21: [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(bc->treeDistString, SCOREDISTstr);
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:714:21: [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(bc->treeDistString, UNCORRstr);
data/seqtools-4.44.1+dfsg/belvuApp/belvuTree.cpp:387:15: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(BS->s, ch);
data/seqtools-4.44.1+dfsg/belvuApp/belvuTree.cpp:1400:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(nodes[i]->name, "%s", aln_i->name);
data/seqtools-4.44.1+dfsg/belvuApp/belvuTree.cpp:1402:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(nodes[i]->name, "%s/%d-%d", aln_i->name, aln_i->start, aln_i->end);
data/seqtools-4.44.1+dfsg/blixemApp/bigpicture.cpp:155:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(text, "%1.1f%s", percent, unit);
data/seqtools-4.44.1+dfsg/blixemApp/bigpicture.cpp:159:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(text, "%d%s", (int)percent, unit);
data/seqtools-4.44.1+dfsg/blixemApp/blxFetch.cpp:1074:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(content, "%s\n%s", content1, content2);
data/seqtools-4.44.1+dfsg/blixemApp/blxFetch.cpp:1185:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(tmp, text) ;
data/seqtools-4.44.1+dfsg/blixemApp/blxFetch.cpp:2868:33: [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.
const gboolean success = (system(command->str) == 0);
data/seqtools-4.44.1+dfsg/blixemApp/blxmain.cpp:628:11: [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(xtra_filename, optarg);
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:1156:11: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf(displayText, formatStr, frame);
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:2682:3: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf(messageText, formatStr, group->groupName);
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:6321:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(parseString, "gtk-font-name = \"%s %d\"", origFamily, origSize + DEFAULT_FONT_SIZE_ADJUSTMENT);
data/seqtools-4.44.1+dfsg/blixemApp/detailviewtree.cpp:2131:15: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(displayText, "%s", displayName);
data/seqtools-4.44.1+dfsg/blixemApp/detailviewtree.cpp:3056:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(parseString, "style \"packedTree\"\n"
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:234:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(dest, src);
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:267:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(msp->qname, name);
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:461:13: [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(options.FSfilename, optarg); break;
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:468:13: [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(options.loadfile, optarg); break;
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:471:13: [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(options.mtxfile, optarg); break;
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:484:13: [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(options.winsize, optarg); break;
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:738:77: [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).
options.qname = (char*)g_malloc(strlen(qfilename)+1); strcpy(options.qname, qfilename);
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:794:63: [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).
options.sname = (char*)g_malloc(strlen(sfilename)+1); strcpy(options.sname, sfilename);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxGff3Parser.cpp:317:11: [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.
if (sscanf(line_string->str, "##sequence-region%s%d%d", qName, &qStart, &qEnd) < 3)
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxGff3Parser.cpp:337:11: [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(refSeqName, qName);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxGff3Parser.cpp:803:24: [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.
const int numFound = sscanf(line, ">%s %d %d", seqName, &startCoord, &endCoord);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxGff3Parser.cpp:826:7: [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(refSeqName, seqName);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:348:3: [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(line, "%s", seqName);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:452:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(seqName, curSeq->seqName->str);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:577:7: [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(result + sStart - 1, inputSeq);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:631:7: [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.
if (sscanf(line, "%d%s%d%d%d%d%s",
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:688:4: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(msp->sname, p);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:700:4: [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(msp->sname, db);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:702:4: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(msp->sname, last);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:741:8: [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.
if (sscanf(seq_pos, "%s", sequence) != 1)
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:842:7: [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.
if (sscanf(line, "%d%s%d%d%s%d%d%s",
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:902:4: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(msp->sname, p);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:914:4: [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(msp->sname, db);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:916:4: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat(msp->sname, last);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1240:11: [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.
if (sscanf(startPtr, "%s", result) != 1)
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1395:15: [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.
if (sscanf(line, "# sequence-region%s%d%d", qName, &qStart, &qEnd) < 3)
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1445:7: [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.
if (sscanf(line, "%d%s%s%d%d%s%s%d%d%s",
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1525:7: [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.
if (sscanf(line, "%d%s%s%d%d%s",
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1568:7: [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.
if (sscanf(line, "%s%s%s%d%d%s%s%s",
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1629:7: [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.
if (sscanf(line+13, "%s%s%s", qName, series, look) != 3)
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1722:7: [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.
if (sscanf(line+14, "%s%s", qname, series) != 2)
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1732:7: [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(seq1name, series);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1737:7: [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(seq2name, series);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1776:7: [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(tmp, **readSeq);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1782:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(**readSeq + *readSeqLen, line);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/seqtoolsWebBrowser.cpp:50:17: [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.
const char *system ; /* system name as in "uname -s" */
data/seqtools-4.44.1+dfsg/seqtoolsUtils/seqtoolsWebBrowser.cpp:174:21: [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.
if ((sys_rc = system(sys_cmd->str)) == EXIT_SUCCESS)
data/seqtools-4.44.1+dfsg/seqtoolsUtils/seqtoolsWebBrowser.cpp:226:28: [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.
while (curr_browser->system != NULL)
data/seqtools-4.44.1+dfsg/seqtoolsUtils/seqtoolsWebBrowser.cpp:228:41: [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.
if (g_ascii_strcasecmp(curr_browser->system, unamebuf.sysname) == 0)
data/seqtools-4.44.1+dfsg/seqtoolsUtils/translate.cpp:111:4: [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(aaptr, code[codon]);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:933:5: [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(v[*argc], s);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:1909:3: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf(result, format, value);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:2622:16: [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. If the scanf format is influenceable by an
attacker, it's exploitable.
int fields = sscanf(inputText, format_str, &sequence_name[0], &start, &end, &length);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:2628:16: [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. If the scanf format is influenceable by an
attacker, it's exploitable.
fields = sscanf(inputText, format_str, &sequence_name[0], &start, &end, &length);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:2877:7: [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(tmpStr, len, formatStr, argp);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:2904:7: [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(tmpStr, len, formatStr, argp);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:3071:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(parseString, "style \"detailViewStatusbar\"\n"
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:3802:5: [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(prefixText, warningText);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:3830:5: [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(prefixText, errorText);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:3832:5: [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(prefixText, criticalText);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:4098:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(result, "%s%s%s", timeText, separatorText, msg->text);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.hpp:67:54: [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.
#define DEBUG_OUT(format, args...) debugLogLevel(0); printf(format, ##args); fflush(stdout);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.hpp:73:71: [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.
#define DEBUG_ENTER(format, args...) debugLogLevel(1); printf("-->"); printf(format, ##args); printf("\n"); fflush(stdout);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.hpp:79:71: [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.
#define DEBUG_EXIT(format, args...) debugLogLevel(-1); printf("<--"); printf(format, ##args); printf("\n"); fflush(stdout);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:4890:18: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
if ((env = getenv(FETCH_URL_ENV_VAR)) )
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:4920:18: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
if ((env = getenv(FETCH_PROG_ENV_VAR)) )
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:4929:75: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
g_warning("Executable '%s' not found in path: %s\n", fetchProg, getenv("PATH"));
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:622:18: [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.
while ((optc = getopt_long(argc, argv, optstring, long_options, &optionIndex)) != EOF)
data/seqtools-4.44.1+dfsg/belvuApp/belvuTree.cpp:485:3: [3] (random) srand:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
srand(time(0));
data/seqtools-4.44.1+dfsg/belvuApp/belvuTree.cpp:502:23: [3] (random) drand48:
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.
src = (int)(drand48() * bc->maxLen);
data/seqtools-4.44.1+dfsg/blixemApp/blxFetch.cpp:759:84: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
g_quark_to_string(fetchMethod->name), fetchMethod->location, getenv("PATH"));
data/seqtools-4.44.1+dfsg/blixemApp/blxFetch.cpp:1059:50: [3] (buffer) g_get_home_dir:
This function is synonymous with 'getenv("HOME")';it returns untrustable
input if the environment can beset by an attacker. It can have any content
and length, and the same variable can be set more than once (CWE-807,
CWE-20). Check environment variables carefully before using them.
char *settings_file = g_strdup_printf("%s/%s", g_get_home_dir(), BLIXEM_SETTINGS_FILE);
data/seqtools-4.44.1+dfsg/blixemApp/blxdotter.cpp:1958:124: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
g_set_error(error, BLX_DOTTER_ERROR, BLX_DOTTER_ERROR_NO_EXE, "No dotter executable found in path.\n$PATH=%s\n", getenv("PATH"));
data/seqtools-4.44.1+dfsg/blixemApp/blxmain.cpp:544:18: [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.
while ((optc = getopt_long(argc, argv, optstring, long_options, &optionIndex)) != EOF)
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:5374:45: [3] (buffer) g_get_home_dir:
This function is synonymous with 'getenv("HOME")';it returns untrustable
input if the environment can beset by an attacker. It can have any content
and length, and the same variable can be set more than once (CWE-807,
CWE-20). Check environment variables carefully before using them.
char *filename = g_strdup_printf("%s/%s", g_get_home_dir(), BLIXEM_SETTINGS_FILE);
data/seqtools-4.44.1+dfsg/dotterApp/dotter.cpp:2786:50: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
char *mtxfileText = g_strdup_printf("%s/%s", getenv("BLASTMAT"), mtxfile);
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:413:18: [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.
while ((optc = getopt_long(argc, argv, optstring, long_options, &optionIndex)) != EOF)
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:5249:25: [3] (buffer) g_get_tmp_dir:
This function is synonymous with 'getenv("TMP")';it returns untrustable
input if the environment can beset by an attacker. It can have any content
and length, and the same variable can be set more than once (CWE-807,
CWE-20). Check environment variables carefully before using them.
tmpDir = g_strdup(g_get_tmp_dir());
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:375:14: [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 *colorNames[NUM_TRUECOLORS] = {
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:449:14: [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 *fileFormatNames[BELVU_NUM_FILE_FORMATS] = {
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:1022:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[MAXLENGTH+1];
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:1128:3: [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 line2[MAXLENGTH+1], *cp=line2, *cq, GRfeat[MAXNAMESIZE+1];
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:2291:3: [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 tmpname[MAXNAMESIZE+1], *cp;
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:2830:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[MAXLENGTH+1];
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:2909:7: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (atoi(strtok(linecopy, " ")))
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:2912:35: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
while ( (p = strtok(0, " ")) && atoi(p) )
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:2930:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
seg->qstart = atoi(i ? strtok(0, " ") : strtok(line, " "));
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:2931:19: [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).
seg->qend = atoi(strtok(0, " "));
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:2932:20: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
seg->start = atoi(strtok(0, " "));
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:2933:18: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
seg->end = atoi(strtok(0, " "));
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:3086:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[MAXLENGTH+1];
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:3122:17: [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).
aln->start = atoi(cp);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:3138:15: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
aln->end = atoi(cp);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:4057:3: [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 seq[1001], *cp=NULL, *cq=NULL;
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:4058:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[MAXLENGTH + 1];
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:4366:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[MAXLENGTH+1];
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:4502:3: [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 *cp, *namep, GRname[MAXNAMESIZE*2+2], GRfeat[MAXNAMESIZE+1];
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:4595:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[MAXLENGTH+1];
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:4888:7: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *env, url[1025]="";
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:4918:7: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *env, fetchProg[1025]="";
data/seqtools-4.44.1+dfsg/belvuApp/belvuAlignment.cpp:403:11: [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 displayText[2];
data/seqtools-4.44.1+dfsg/belvuApp/belvuAlignment.cpp:559:3: [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 collapseStr[10],
data/seqtools-4.44.1+dfsg/belvuApp/belvuAlignment.cpp:665:23: [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(collapseStr, "[%3d]", collapseRes);
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.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 line[MAXLENGTH + 1];
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:442:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[MAXLENGTH+1], linecp[MAXLENGTH+1], *cp;
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:452:16: [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).
if (!(file = fopen(filename, "r")))
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:477:25: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (!(aln.start = atoi(cp)))
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:483:23: [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).
if (!(aln.end = atoi(cp)))
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:588:3: [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 treePickString[50];
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:632:42: [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).
case 'b': bc->treebootstraps = atoi(optarg); break;
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:757:24: [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.
if (!*bc->Title) strcpy(bc->Title, "stdin");
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:761:20: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (!(pipe = fopen(argv[optind], "r")))
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:818:20: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (!(file = fopen(readMatchFile, "r")))
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:873:20: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (!(file = fopen(colorCodesFile, "r")))
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:885:20: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if (!(file = fopen(markupColorCodesFile, "r")))
data/seqtools-4.44.1+dfsg/belvuApp/belvuTree.cpp:575:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[MAXLENGTH+1];
data/seqtools-4.44.1+dfsg/belvuApp/belvuWindow.cpp:1038:15: [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 *fil = fopen(filename, "r");
data/seqtools-4.44.1+dfsg/belvuApp/belvuWindow.cpp:1146:15: [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 *fil = fopen(filename, "w");
data/seqtools-4.44.1+dfsg/belvuApp/belvuWindow.cpp:1161:15: [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 *fil = fopen(filename, "w");
data/seqtools-4.44.1+dfsg/belvuApp/belvuWindow.cpp:1175:15: [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 *fil = fopen(filename, "w");
data/seqtools-4.44.1+dfsg/belvuApp/belvuWindow.cpp:1338:15: [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 *fil = fopen(filename, "w");
data/seqtools-4.44.1+dfsg/belvuApp/belvuWindow.cpp:1357:15: [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 *fil = fopen(filename, "r");
data/seqtools-4.44.1+dfsg/belvuApp/belvuWindow.cpp:1449:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *file = fopen(filename, "w");
data/seqtools-4.44.1+dfsg/belvuApp/belvuWindow.cpp:1806:3: [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 rel_path[100] = "../share/doc/seqtools/belvu_quick_start.html";
data/seqtools-4.44.1+dfsg/belvuApp/belvu_.hpp:245:3: [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 name[MAXNAMESIZE + 1];
data/seqtools-4.44.1+dfsg/belvuApp/belvu_.hpp:250:3: [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 fetch[MAXNAMESIZE + 11];
data/seqtools-4.44.1+dfsg/belvuApp/belvu_.hpp:401:3: [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 treeDistString[50];
data/seqtools-4.44.1+dfsg/belvuApp/belvu_.hpp:402:3: [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 treeMethodString[50];
data/seqtools-4.44.1+dfsg/belvuApp/belvu_.hpp:403:3: [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 Title[256];
data/seqtools-4.44.1+dfsg/belvuApp/belvu_.hpp:406:3: [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 organismLabel[3];
data/seqtools-4.44.1+dfsg/blixemApp/bigpicture.cpp:350:7: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char text[bpProperties->leftBorderChars + 3]; /* +3 to include decimal point, 1dp, and terminating nul */
data/seqtools-4.44.1+dfsg/blixemApp/blxFetch.cpp:136:3: [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 sectionId[3]; /* EMBL lines start with a two-letter identifier, which will be parsed into this string */
data/seqtools-4.44.1+dfsg/blixemApp/blxFetch.cpp:942:7: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[RCVBUFSIZE + 1];
data/seqtools-4.44.1+dfsg/blixemApp/blxFetch.cpp:1154:3: [2] (buffer) bcopy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
bcopy((char*)hp->h_addr, (char*) &(servAddr->sin_addr.s_addr), hp->h_length) ;
data/seqtools-4.44.1+dfsg/blixemApp/blxFetch.cpp:2860:26: [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).
FILE *outputFile = fopen(fileName, "w");
data/seqtools-4.44.1+dfsg/blixemApp/blxdotter.cpp:318:20: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
int newVal = atoi(gtk_entry_get_text(GTK_ENTRY(entry)));
data/seqtools-4.44.1+dfsg/blixemApp/blxdotter.cpp:348:20: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
int newVal = atoi(gtk_entry_get_text(GTK_ENTRY(entry)));
data/seqtools-4.44.1+dfsg/blixemApp/blxdotter.cpp:379:26: [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).
const int newVal = atoi(gtk_entry_get_text(GTK_ENTRY(entry)));
data/seqtools-4.44.1+dfsg/blixemApp/blxdotter.cpp:1888:3: [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 *argv[g_slist_length(argList)];
data/seqtools-4.44.1+dfsg/blixemApp/blxmain.cpp:467:3: [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 xtra_filename[1000] = {'\0'} ;
data/seqtools-4.44.1+dfsg/blixemApp/blxmain.cpp:473:3: [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 refSeqName[FULLNAMESIZE+1] = "";
data/seqtools-4.44.1+dfsg/blixemApp/blxmain.cpp:559:32: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
pfetch->port = atoi(strtok(NULL, ":")) ;
data/seqtools-4.44.1+dfsg/blixemApp/blxmain.cpp:598:37: [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).
options.mapCoordsFrom = atoi(optarg); /* will ignore anything after ':', if it exists */
data/seqtools-4.44.1+dfsg/blixemApp/blxmain.cpp:603:37: [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).
options.mapCoordsTo = atoi(cp + 1);
data/seqtools-4.44.1+dfsg/blixemApp/blxmain.cpp:617:32: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
options.startCoord = atoi(optarg);
data/seqtools-4.44.1+dfsg/blixemApp/blxmain.cpp:635:26: [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).
int coord1 = atoi(optarg); /* will ignore anything after ':' */
data/seqtools-4.44.1+dfsg/blixemApp/blxmain.cpp:640:30: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
int coord2 = atoi(cp + 1);
data/seqtools-4.44.1+dfsg/blixemApp/blxmain.cpp:759:36: [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).
else if(FSfilename && !(FSfile = fopen(FSfilename, "r")))
data/seqtools-4.44.1+dfsg/blixemApp/blxmain.cpp:773:3: [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 dummyseqname[FULLNAMESIZE+1] = "";
data/seqtools-4.44.1+dfsg/blixemApp/blxmain.cpp:810:27: [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).
else if(!(seqfile = fopen(seqfilename, "r")))
data/seqtools-4.44.1+dfsg/blixemApp/blxmain.cpp:842:24: [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).
if(!(xtra_file = fopen(xtra_filename, "r")))
data/seqtools-4.44.1+dfsg/blixemApp/blxview.cpp:367:3: [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 dummyseqname1[FULLNAMESIZE+1] = "";
data/seqtools-4.44.1+dfsg/blixemApp/blxview.cpp:369:3: [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 dummyseqname2[FULLNAMESIZE+1] = "";
data/seqtools-4.44.1+dfsg/blixemApp/blxview.cpp:384:20: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *file = fopen(filename, "r");
data/seqtools-4.44.1+dfsg/blixemApp/blxview.cpp:715:7: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char alias[destLen + 1];
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:1155:11: [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 displayText[strlen(formatStr) + numDigitsInInt(frame) + 1];
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:2681:3: [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 messageText[strlen(formatStr) + strlen(group->groupName)];
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:4652:3: [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 rel_path[100] = "../share/doc/seqtools/blixem_quick_start.html";
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:6320:3: [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 parseString[500];
data/seqtools-4.44.1+dfsg/blixemApp/detailview.cpp:2395:7: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char bases[3];
data/seqtools-4.44.1+dfsg/blixemApp/detailview.cpp:2528:7: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char bases[3];
data/seqtools-4.44.1+dfsg/blixemApp/detailview.cpp:2903:3: [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 displayText[displayLen + 1];
data/seqtools-4.44.1+dfsg/blixemApp/detailview.cpp:5687:28: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
int requestedCoord = atoi(inputText);
data/seqtools-4.44.1+dfsg/blixemApp/detailview.cpp:5692:11: [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(defaultInput, "%d", requestedCoord);
data/seqtools-4.44.1+dfsg/blixemApp/detailview.hpp:78:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char donorSite[3]; /* The bases expected at the donor splice site */
data/seqtools-4.44.1+dfsg/blixemApp/detailview.hpp:79:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char acceptorSite[3]; /* The bases expected at the acceptor splice site */
data/seqtools-4.44.1+dfsg/blixemApp/detailview.hpp:81:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char donorSiteRev[3]; /* Same as donorSite but reversed */
data/seqtools-4.44.1+dfsg/blixemApp/detailview.hpp:82:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char acceptorSiteRev[3]; /* Same as acceptorSite but reversed */
data/seqtools-4.44.1+dfsg/blixemApp/detailview.hpp:84:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char donorSiteComp[3]; /* Same as donorSite but complemented */
data/seqtools-4.44.1+dfsg/blixemApp/detailview.hpp:85:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char acceptorSiteComp[3]; /* Same as acceptorSite but complemented */
data/seqtools-4.44.1+dfsg/blixemApp/detailview.hpp:87:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char donorSiteRevComp[3]; /* Same as donorSite but revcomp'd */
data/seqtools-4.44.1+dfsg/blixemApp/detailview.hpp:88:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char acceptorSiteRevComp[3]; /* Same as acceptorSite but revcomp'd */
data/seqtools-4.44.1+dfsg/blixemApp/detailviewtree.cpp:2130:15: [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 displayText[maxLen + 1];
data/seqtools-4.44.1+dfsg/blixemApp/detailviewtree.cpp:2182:11: [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 displayText[numDigitsInInt(coord) + 1];
data/seqtools-4.44.1+dfsg/blixemApp/detailviewtree.cpp:2183:11: [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(displayText, "%d", coord);
data/seqtools-4.44.1+dfsg/blixemApp/detailviewtree.cpp:2225:11: [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 displayText[numDigitsInInt(coord) + 1];
data/seqtools-4.44.1+dfsg/blixemApp/detailviewtree.cpp:2226:11: [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(displayText, "%d", coord);
data/seqtools-4.44.1+dfsg/blixemApp/detailviewtree.cpp:2265:4: [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 displayText[numDigitsInInt((int)score) + 3]; /* +3 to include decimal point, 1 dp, and terminating nul */
data/seqtools-4.44.1+dfsg/blixemApp/detailviewtree.cpp:2268:4: [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(displayText, "%d", (int)score);
data/seqtools-4.44.1+dfsg/blixemApp/detailviewtree.cpp:2305:4: [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 displayText[numDigitsInInt((int)id) + 3]; /* +3 to include decimal point, 1 dp, and terminating nul */
data/seqtools-4.44.1+dfsg/blixemApp/detailviewtree.cpp:2307:11: [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(displayText, "%1.1f", id);
data/seqtools-4.44.1+dfsg/blixemApp/detailviewtree.cpp:2624:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(displayText, "%d", displayVal);
data/seqtools-4.44.1+dfsg/blixemApp/detailviewtree.cpp:2659:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(displayText, "%d", displayVal);
data/seqtools-4.44.1+dfsg/blixemApp/detailviewtree.cpp:3055:3: [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 parseString[500];
data/seqtools-4.44.1+dfsg/dotterApp/alignmenttool.cpp:826:3: [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 seq1Text[atProperties->alignmentLen + 1];
data/seqtools-4.44.1+dfsg/dotterApp/dotplot.cpp:1137:12: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (!atoi(winsizeIn))
data/seqtools-4.44.1+dfsg/dotterApp/dotplot.cpp:1142:36: [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).
properties->slidingWinSize = atoi(winsizeIn);
data/seqtools-4.44.1+dfsg/dotterApp/dotplot.cpp:1605:20: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *loadFile = fopen (loadFileName, "rb");
data/seqtools-4.44.1+dfsg/dotterApp/dotplot.cpp:1689:7: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char matrixName[MAX_MATRIX_NAME_LENGTH + 1];
data/seqtools-4.44.1+dfsg/dotterApp/dotplot.cpp:1827:18: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
saveFile = fopen (fileName, "wb");
data/seqtools-4.44.1+dfsg/dotterApp/dotplot.cpp:3245:10: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char copy[256], *cp;
data/seqtools-4.44.1+dfsg/dotterApp/dotplot.cpp:3249:3: [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(copy, ptr, n); /* Note: strcpy doesn't work - stops at \0 */
data/seqtools-4.44.1+dfsg/dotterApp/dotter.cpp:1132:7: [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(matrixName, "DNA+5/-4");
data/seqtools-4.44.1+dfsg/dotterApp/dotter.cpp:1137:7: [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(matrixName, "BLOSUM62");
data/seqtools-4.44.1+dfsg/dotterApp/dotter.cpp:1149:33: [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).
if (options->savefile && !fopen (options->savefile, "wb"))
data/seqtools-4.44.1+dfsg/dotterApp/dotter.cpp:1152:35: [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).
if (options->exportfile && !fopen (options->exportfile, "wb"))
data/seqtools-4.44.1+dfsg/dotterApp/dotter.cpp:2784:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[1025] = "#", *p;
data/seqtools-4.44.1+dfsg/dotterApp/dotter.cpp:2788:17: [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).
if (!(fil = fopen(mtxfile, "r")) &&
data/seqtools-4.44.1+dfsg/dotterApp/dotter.cpp:2789:17: [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).
!(fil = fopen(mtxfileText, "r")))
data/seqtools-4.44.1+dfsg/dotterApp/dotter.cpp:2820:32: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
MATRIX[row][col] = atoi(p);
data/seqtools-4.44.1+dfsg/dotterApp/dotter.cpp:3035:3: [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 rel_path[100] = "../share/doc/seqtools/dotter_quick_start.html";
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:327:3: [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
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:474:43: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
case 'p': options.pixelFacset = atoi(optarg); break;
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:475:39: [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).
case 'q': options.qoffset = atoi(optarg); break;
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:478:39: [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).
case 's': options.soffset = atoi(optarg); break;
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:486:42: [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).
case 'z': options.dotterZoom = atoi(optarg); break;
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:565:22: [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).
options.qlen = atoi(argv[optind + 1]);
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:567:22: [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).
options.slen = atoi(argv[optind + 3]);
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:655:20: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if(!(qfile = fopen(argv[optind], "r")))
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:665:23: [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.
if ((curChar = (char *)strrchr(argv[optind], '/')))
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:674:21: [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).
if (!(sfile = fopen(argv[optind+1], "r")))
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:684:23: [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.
if ((curChar = (char *)strrchr(argv[optind]+1, '/')))
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:832:24: [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).
else if(!(file = fopen(options.FSfilename, "r")))
data/seqtools-4.44.1+dfsg/gbtools/src/gbtoolsCurl/gbtoolsCurl_P.hpp:67:3: [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 error_message[CURL_ERROR_SIZE];
data/seqtools-4.44.1+dfsg/gbtools/src/gbtoolsGUI/gbtoolsGUI.cpp:204:11: [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(&width, curr, field_size) ;
data/seqtools-4.44.1+dfsg/gbtools/src/gbtoolsGUI/gbtoolsGUI.cpp:205:11: [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(&height, (curr += field_size), field_size) ;
data/seqtools-4.44.1+dfsg/gbtools/src/gbtoolsGUI/gbtoolsGUI.cpp:228:11: [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(&left, curr, field_size) ;
data/seqtools-4.44.1+dfsg/gbtools/src/gbtoolsGUI/gbtoolsGUI.cpp:229:11: [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(&top, (curr += field_size), field_size) ;
data/seqtools-4.44.1+dfsg/gbtools/src/gbtoolsGUI/gbtoolsGUI.cpp:230:11: [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(&right, (curr += field_size), field_size) ;
data/seqtools-4.44.1+dfsg/gbtools/src/gbtoolsGUI/gbtoolsGUI.cpp:231:11: [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(&bottom, (curr += field_size), field_size) ;
data/seqtools-4.44.1+dfsg/gbtools/src/gbtoolsPfetch/gbtoolsPfetchHttp.cpp:214:9: [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 *argv[256] = { tmp_str };
data/seqtools-4.44.1+dfsg/gbtools/src/gbtoolsPfetch/gbtoolsPfetchPipe.cpp:127:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char *argv[256];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxGff3Parser.cpp:311:3: [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 qName[MAXLINE + 1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxGff3Parser.cpp:799:3: [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 seqName[MAXLINE + 1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxmsp.cpp:1212:31: [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).
const int tmp = atoi(inputStr);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:341:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[MAXLINE+1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:377:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[MAXLINE+1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:618:3: [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 sName[MAXLINE+1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:619:3: [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 qframe[8] = "(+1)";
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:641:7: [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(qframe, "(+1)");
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:686:4: [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(msp->sname, "gi");
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:828:3: [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 sName[MAXLINE+1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:829:3: [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 qframe[8] ;
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:830:3: [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 sframe[8] ;
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:852:5: [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(qframe, "(+1)");
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:900:4: [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(msp->sname, "gi");
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1033:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[BLX_BUF_SIZE] ;
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1391:11: [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 qName[MAXLINE + 1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1433:3: [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 qName[MAXLINE+1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1434:3: [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 sName[MAXLINE+1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1435:3: [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 seq[MAXLINE+1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1436:3: [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 qframe[8] = "(+1)";
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1437:3: [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 sframe[8] = "(+1)";
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1517:3: [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 series[MAXLINE+1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1518:3: [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 qName[MAXLINE+1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1519:3: [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 look[MAXLINE+1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1559:3: [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 scorestring[256];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1560:3: [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 series[MAXLINE+1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1561:3: [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 qName[MAXLINE+1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1562:3: [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 look[MAXLINE+1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1563:3: [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 qframe[8] = "(+1)";
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1624:3: [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 series[MAXLINE+1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1625:3: [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 qName[MAXLINE+1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1626:3: [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 look[MAXLINE+1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1719:3: [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 series[MAXLINE+1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1720:3: [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 qname[MAXLINE+1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/iupac.hpp:180:7: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
const char *stdcode1[65] = {
data/seqtools-4.44.1+dfsg/seqtoolsUtils/iupac.hpp:251:7: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
const char *stdcode3[65] = {
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:1231:3: [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(result, "#%x", color->pixel);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:1894:3: [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 result[numDigitsInInt(value) + 1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:1895:3: [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(result, "%d", value);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:1904:3: [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 format[numDp + 5];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:1905:3: [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(format, "%%1.%df", numDp);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:1907:3: [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 result[numDigitsInInt((int)value) + numDp + 2]; /* the +2 includes the and terminating null */
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:1917:10: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
return atoi(inputStr);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:2618:3: [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 sequence_name[1000] = {'\0'};
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:2876:7: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpStr[len];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:2903:7: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char tmpStr[len];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:3070:3: [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 parseString[500];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:3798:3: [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 prefixText[len];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:3826:3: [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 prefixText[len];
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:738:17: [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).
int len = strlen(scoreStr);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:867:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(alnp->name) > MAXNAMESIZE)
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:1075:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(dest->name, src->name, MAXNAMESIZE);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:1081:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(dest->fetch, src->fetch, MAXNAMESIZE+10);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:1131:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(cp, line, MAXLENGTH);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:1154:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(aln->name, cp, MAXNAMESIZE);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:1173:23: [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).
sscanf(cp + strlen(aln->name), "%d%d%s", &aln->start, &aln->end, GRfeat);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:1177:23: [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).
sscanf(cp + strlen(aln->name), "%s", GRfeat);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:1180:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(aln->name)+strlen(GRfeat)+2 > MAXNAMESIZE)
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:1180:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(aln->name)+strlen(GRfeat)+2 > MAXNAMESIZE)
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:1183:7: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
strcat(aln->name, " ");
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:1184:7: [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(aln->name, GRfeat, MAXNAMESIZE-strlen(aln->name));
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:1184:46: [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).
strncat(aln->name, GRfeat, MAXNAMESIZE-strlen(aln->name));
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:2852:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ((int)strlen(labelseq) > seqlen)
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:2855:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
(int)strlen(labelseq), seqlen);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:2857:17: [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).
else if ((int)strlen(labelseq) < seqlen)
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:2860:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
(int)strlen(labelseq), seqlen);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:2905:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
linecopy = (char*)g_malloc(strlen(line)+1);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:3109:4: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(aln->name, line, MAXNAMESIZE);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:3115:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (bc->maxNameLen < (int)strlen(aln->name))
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:3116:23: [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).
bc->maxNameLen = strlen(aln->name);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:3124:13: [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).
if ((len=strlen(cp)) > bc->maxStartLen)
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:3129:33: [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).
if (bc->maxStartLen < (tmp = strlen(tmpStr)))
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:3140:13: [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).
if ((len=strlen(cp)) > bc->maxEndLen)
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:3145:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (bc->maxEndLen < (tmp = strlen(tmpStr)))
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:3167:13: [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).
if ((len=strlen(tmpStr)) > bc->maxScoreLen)
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:3182:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
rawseq = (char*)g_malloc(strlen(line)+1);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:3206:4: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(seqp, rawseq, seglen);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:3219:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(seqp, rawseq + seg->qend, Query_gap);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:3239:8: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(seqp, rawseq + seg->qstart-1, seglen);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:3313:34: [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 (bc->maxNameLen < (int)strlen(alnp->name))
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:3314:26: [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).
bc->maxNameLen = strlen(alnp->name);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:3318:36: [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).
if (bc->maxStartLen < (tmp = strlen(tmpStr)))
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:3326:36: [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).
if (bc->maxEndLen < (tmp = strlen(tmpStr)))
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:4256:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int organismLen = strlen(aln->organism);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:4396:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int lineLen = strlen(line);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:4514:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(namep, aln->name, 50);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:4516:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(GRfeat, cp+1, 50);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:4560:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int curWidth = strlen(mulName);
data/seqtools-4.44.1+dfsg/belvuApp/belvu.cpp:4601:12: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ch = fgetc(pipe);
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:369:42: [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).
char *suffix = (char*)g_malloc(strlen(cp) + 1);
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:389:39: [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).
const int organismLen = strlen(alnp->organism) ;
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:425:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(aln->name, cp, MAXNAMESIZE);
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:471:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(aln.name, cp, MAXNAMESIZE);
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:500:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
scoreLen = strlen(scoreStr);
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:642:21: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
case 'O': strncpy(bc->organismLabel, optarg, 2); break;
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:722:21: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
case 't': strncpy(bc->Title, optarg, 255); break;
data/seqtools-4.44.1+dfsg/belvuApp/belvuMain.cpp:764:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(bc->Title, argv[optind], 255);
data/seqtools-4.44.1+dfsg/belvuApp/belvuTree.cpp:379:23: [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).
ssize += (strlen(g_array_index(right, char*, i)) + 1);
data/seqtools-4.44.1+dfsg/belvuApp/belvuTree.cpp:388:15: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
strcat(BS->s, " ");
data/seqtools-4.44.1+dfsg/belvuApp/belvuTree.cpp:1397:41: [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).
nodes[i]->name = (char*)g_malloc(strlen(aln_i->name) + 50);
data/seqtools-4.44.1+dfsg/belvuApp/belvuTree.cpp:2273:35: [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).
const int defaultLen = min((int)strlen(defaultInput) * 8, 500);
data/seqtools-4.44.1+dfsg/belvuApp/belvuWindow.cpp:2357:48: [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).
gtk_entry_set_width_chars(GTK_ENTRY(entry1), strlen(maxLenText) + 1);
data/seqtools-4.44.1+dfsg/belvuApp/belvuWindow.cpp:2367:48: [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).
gtk_entry_set_width_chars(GTK_ENTRY(entry2), strlen(maxLenText) + 3);
data/seqtools-4.44.1+dfsg/belvuApp/belvuWindow.cpp:2438:48: [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).
gtk_entry_set_width_chars(GTK_ENTRY(entry1), strlen(fromText) + 1);
data/seqtools-4.44.1+dfsg/belvuApp/belvuWindow.cpp:2448:48: [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).
gtk_entry_set_width_chars(GTK_ENTRY(entry2), strlen(toText) + 3);
data/seqtools-4.44.1+dfsg/belvuApp/belvuWindow.cpp:3051:47: [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).
gtk_entry_set_width_chars(GTK_ENTRY(entry), strlen(defaultInput) + 2);
data/seqtools-4.44.1+dfsg/belvuApp/belvuWindow.cpp:3291:39: [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).
const int defaultLen = min((int)strlen(defaultInput) * 8, 500);
data/seqtools-4.44.1+dfsg/belvuApp/belvuWindow.cpp:3591:16: [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).
if ((int)strlen(cp) > maxLen)
data/seqtools-4.44.1+dfsg/belvuApp/belvuWindow.cpp:3592:18: [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).
maxLen = strlen(cp);
data/seqtools-4.44.1+dfsg/blixemApp/bigpicture.cpp:164:27: [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).
const int len = strlen(text);
data/seqtools-4.44.1+dfsg/blixemApp/blxFetch.cpp:716:24: [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).
const int len1 = strlen(str);
data/seqtools-4.44.1+dfsg/blixemApp/blxFetch.cpp:724:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len = min((int)strlen(curStr), len1);
data/seqtools-4.44.1+dfsg/blixemApp/blxFetch.cpp:1183:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(text) ;
data/seqtools-4.44.1+dfsg/blixemApp/blxFetch.cpp:1305:66: [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).
gtk_text_buffer_insert_at_cursor(text_buffer, err_msg, strlen(err_msg));
data/seqtools-4.44.1+dfsg/blixemApp/blxFetch.cpp:1813:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (tmp_str && strlen(tmp_str) == 4)
data/seqtools-4.44.1+dfsg/blixemApp/blxdotter.cpp:1463:21: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
distToSMax = strlen(dotterSSeq) - sSeqMax;
data/seqtools-4.44.1+dfsg/blixemApp/blxdotter.cpp:1666:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
dotterRange->set(1, strlen(result));
data/seqtools-4.44.1+dfsg/blixemApp/blxdotter.cpp:2146:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
IntRange sRange = {1, (int)strlen(dotterSSeq)};
data/seqtools-4.44.1+dfsg/blixemApp/blxdotter.cpp:2293:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
IntRange sRange = {1, (int)strlen(dotterSSeq)};
data/seqtools-4.44.1+dfsg/blixemApp/blxmain.cpp:831:34: [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).
options.refSeqRange.set(1, strlen(options.refSeq));
data/seqtools-4.44.1+dfsg/blixemApp/blxview.cpp:264:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
options->bigPictZoom = strlen(options->refSeq);
data/seqtools-4.44.1+dfsg/blixemApp/blxview.cpp:679:61: [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).
const int numChars = endPtr ? endPtr - startPtr : strlen(startPtr);
data/seqtools-4.44.1+dfsg/blixemApp/blxview.cpp:711:20: [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 srcLen = strlen(organism);
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:613:47: [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).
gtk_entry_set_width_chars(GTK_ENTRY(entry), strlen(value) + 2);
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:630:47: [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).
gtk_entry_set_width_chars(GTK_ENTRY(entry), strlen(displayText) + 2);
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:1155:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
char displayText[strlen(formatStr) + numDigitsInInt(frame) + 1];
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:1552:40: [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).
const int searchStrMax = searchStr ? strlen(searchStr) - 1 : -1;
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:1703:25: [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 (!searchStr || strlen(searchStr) < 1)
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:2062:19: [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).
if (!newName || strlen(newName) < 1)
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:2091:20: [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 (!newOrder || strlen(newOrder) < 1)
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:2681:20: [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).
char messageText[strlen(formatStr) + strlen(group->groupName)];
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:2681:40: [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).
char messageText[strlen(formatStr) + strlen(group->groupName)];
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:3258:51: [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).
gtk_entry_set_width_chars(GTK_ENTRY(entry), strlen(displayText) + 2); /* fudge up width a bit in case user enters longer text */
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:3277:51: [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).
gtk_entry_set_width_chars(GTK_ENTRY(entry), strlen(displayText) + 2);
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:3439:47: [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).
gtk_entry_set_width_chars(GTK_ENTRY(entry), strlen(displayText) + 2);
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:3687:47: [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).
gtk_entry_set_width_chars(GTK_ENTRY(entry), strlen(numStr) + 2); /* fudge up width a bit in case user enters longer text */
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:4489:26: [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).
seqDataSize += strlen(sequence) * sizeof(char);
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:4507:19: [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 refSeqLen = strlen(blxWindowGetRefSeq(blxWindow));
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:5830:23: [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).
const int len = strlen(displayText);
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:5915:37: [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).
const int sourceLen = strlen(sequence);
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:6011:47: [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).
char *tmp = (char*)g_malloc(strlen(result) + 1);
data/seqtools-4.44.1+dfsg/blixemApp/blxwindow.cpp:6512:40: [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).
const int qLen = strlen(refSeqSegment);
data/seqtools-4.44.1+dfsg/blixemApp/detailview.cpp:1141:17: [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).
int len = strlen(value) + 1;
data/seqtools-4.44.1+dfsg/blixemApp/detailview.cpp:1301:32: [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).
const int sLen = strlen(mspGetMatchSeq(firstMsp));
data/seqtools-4.44.1+dfsg/blixemApp/detailview.cpp:1816:27: [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).
const int len = min(strlen(str1), strlen(str2));
data/seqtools-4.44.1+dfsg/blixemApp/detailview.cpp:1816:41: [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).
const int len = min(strlen(str1), strlen(str2));
data/seqtools-4.44.1+dfsg/blixemApp/detailview.cpp:2416:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(donorSite) < 2 || strlen(acceptorSite) < 2)
data/seqtools-4.44.1+dfsg/blixemApp/detailview.cpp:2416:32: [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(donorSite) < 2 || strlen(acceptorSite) < 2)
data/seqtools-4.44.1+dfsg/blixemApp/detailview.cpp:2721:34: [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).
const int comparison_len = strlen(comparison);
data/seqtools-4.44.1+dfsg/blixemApp/detailview.cpp:3003:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int numChars = strlen(mspGetMatchSeq(msp));
data/seqtools-4.44.1+dfsg/blixemApp/detailview.cpp:3626:47: [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).
const int width = ceil((gdouble)strlen(mspGetMatchSeq(msp)) * properties->charWidth());
data/seqtools-4.44.1+dfsg/blixemApp/detailviewtree.cpp:2133:23: [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 i = strlen(displayName);
data/seqtools-4.44.1+dfsg/blixemApp/detailviewtree.cpp:2566:36: [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).
const int numCharsToAppend = strlen(stringToAppend);
data/seqtools-4.44.1+dfsg/blixemApp/sequencecellrenderer.cpp:733:32: [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 (sequence && sIdx <= (int)strlen(sequence))
data/seqtools-4.44.1+dfsg/blixemApp/sequencecellrenderer.cpp:1141:26: [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).
const int segmentLen = strlen(refSeqSegment);
data/seqtools-4.44.1+dfsg/dotterApp/alignmenttool.cpp:814:23: [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).
const int seq1Len = strlen(seq1->sequence);
data/seqtools-4.44.1+dfsg/dotterApp/alignmenttool.cpp:1157:34: [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 (startIdx + numChars > (int)strlen(properties->sequence))
data/seqtools-4.44.1+dfsg/dotterApp/alignmenttool.cpp:1161:18: [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).
numChars = strlen(properties->sequence) - startIdx;
data/seqtools-4.44.1+dfsg/dotterApp/alignmenttool.cpp:1382:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int seq2Len = strlen(seq2->sequence);
data/seqtools-4.44.1+dfsg/dotterApp/dotplot.cpp:1842:24: [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).
const gint32 MNlen = strlen(dc->matrixName);
data/seqtools-4.44.1+dfsg/dotterApp/dotplot.cpp:2677:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (displayText && strlen(displayText) > 0)
data/seqtools-4.44.1+dfsg/dotterApp/dotter.cpp:590:43: [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).
result->refSeqRev = (char*)g_malloc(strlen(result->refSeq) + 1);
data/seqtools-4.44.1+dfsg/dotterApp/dotter.cpp:608:72: [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).
result->refSeqFullRange.set(options->qoffset + 1, options->qoffset + strlen(options->qseq));
data/seqtools-4.44.1+dfsg/dotterApp/dotter.cpp:609:74: [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).
result->matchSeqFullRange.set(options->soffset + 1, options->soffset + strlen(options->sseq));
data/seqtools-4.44.1+dfsg/dotterApp/dotter.cpp:625:45: [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).
result->matchSeqRev = (char*)g_malloc(strlen(result->matchSeq) + 1);
data/seqtools-4.44.1+dfsg/dotterApp/dotter.cpp:1106:20: [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).
const int qlen = strlen(options->qseq);
data/seqtools-4.44.1+dfsg/dotterApp/dotter.cpp:1107:20: [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).
const int slen = strlen(options->sseq);
data/seqtools-4.44.1+dfsg/dotterApp/dotter.cpp:1127:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(matrixName, options->mtxfile, MAX_MATRIX_NAME_LENGTH);
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:266:32: [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).
msp->qname = (char*)g_malloc(strlen(name)+1);
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:460:50: [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).
options.FSfilename = (char*)g_malloc(strlen(optarg)+1);
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:467:48: [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).
options.loadfile = (char*)g_malloc(strlen(optarg)+1);
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:470:47: [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).
options.mtxfile = (char*)g_malloc(strlen(optarg)+1);
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:483:47: [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).
options.winsize = (char*)g_malloc(strlen(optarg)+1);
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:492:5: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
usleep(sleepSecs * 1000);
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:722:51: [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).
options.qname = (char*)g_malloc(strlen(cq)+1); strNamecpy(options.qname, cq);
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:738:55: [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).
options.qname = (char*)g_malloc(strlen(qfilename)+1); strcpy(options.qname, qfilename);
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:781:43: [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).
options.sname = (char*)g_malloc(strlen(cq)+1); strNamecpy(options.sname, cq);
data/seqtools-4.44.1+dfsg/dotterApp/dotterMain.cpp:794:41: [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).
options.sname = (char*)g_malloc(strlen(sfilename)+1); strcpy(options.sname, sfilename);
data/seqtools-4.44.1+dfsg/gbtools/src/gbtoolsCurl/gbtoolsCurl.cpp:43:21: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
#define SHORT_SLEEP usleep(100000)
data/seqtools-4.44.1+dfsg/gbtools/src/gbtoolsPfetch/gbtoolsPfetchHttp.cpp:166:26: [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).
error_size = strlen(curl_object_error);
data/seqtools-4.44.1+dfsg/gbtools/src/gbtoolsTrackhub/gbtoolsTrackhub.cpp:94:16: [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).
sizeleft = strlen(data);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxGff3Parser.cpp:1250:17: [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).
int len = strlen(data);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxGff3Parser.cpp:1257:7: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(gffData->fetchCommand, data, len);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxmsp.cpp:860:27: [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).
const int len = strlen(seq);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxmsp.cpp:1068:18: [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).
result = strlen(sequence);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxmsp.cpp:3689:25: [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).
const int refSeqLen = strlen(refSeq);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:156:23: [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).
const int lineLen = strlen(line);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:265:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
seq1Range->set(1, strlen(*seq1));
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:270:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len = strlen(*seq1);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:352:22: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
char currentChar = fgetc(seqfile);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:363:21: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
currentChar = fgetc(seqfile);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:554:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
cp += strlen(s2)+1;
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:575:41: [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).
result = (char*)g_malloc(sStart + strlen(inputSeq)+1);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:655:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len = strlen(sName);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:687:4: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
strcat(msp->sname, ":");
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:701:4: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
strcat(msp->sname, ":");
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:713:18: [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).
seq_pos = cp + strlen(sName) ;
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:869:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len = strlen(sName);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:901:4: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
strcat(msp->sname, ":");
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:915:4: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
strcat(msp->sname, ":");
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:927:18: [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).
seq_pos = cp + strlen(sName) ;
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1061:19: [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).
line_end = strlen(&buffer[0]) - 1 ;
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1216:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
const int origLen = (int)strlen(startPtr);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1231:39: [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 (validLen < 1 || validLen < (int)strlen(startPtr))
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1646:16: [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).
seqlen = strlen(*seq1);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1655:16: [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).
seqlen = strlen(*seq2);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1771:26: [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 (*readSeqLen + (int)strlen(line) > *readSeqMaxLen)
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1774:35: [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).
*readSeqMaxLen += MAXLINE + strlen(line);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/blxparser.cpp:1785:18: [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).
*readSeqLen += strlen(line);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/seqtoolsWebBrowser.cpp:374:16: [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).
target_len = strlen(target) ;
data/seqtools-4.44.1+dfsg/seqtoolsUtils/seqtoolsWebBrowser.cpp:375:16: [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).
source_len = strlen(source) ;
data/seqtools-4.44.1+dfsg/seqtoolsUtils/translate.cpp:87:32: [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).
aaseq = (char *)g_malloc(strlen(seq) + 1) ;
data/seqtools-4.44.1+dfsg/seqtoolsUtils/translate.cpp:112:13: [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).
aaptr += strlen(code[codon]);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/translate.cpp:169:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
bases = strlen(seq);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/translate.cpp:200:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for (pos = 0; pos < (int)strlen(seq); pos++)
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:436:17: [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).
c = &text[strlen(text) - 1];
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:932:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
v[*argc] = (char *)malloc(strlen(s)+1);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:2547:25: [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 inputStrLen = strlen(inputStr);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:2593:27: [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).
const size_t len1 = strlen(str1);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:2594:17: [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).
result = (strlen(str2) == len1 && !g_ascii_strncasecmp(str1, str2, len1));
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:2875:23: [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).
const int len = strlen(formatStr) + 200;
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:2902:23: [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).
const int len = strlen(formatStr) + 200;
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:3094:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(segment, inputSeq + minIdx, segmentLen);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:3280:52: [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 (g_ascii_strncasecmp(name, pref_font, strlen(pref_font)) == 0
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:3797:19: [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).
const int len = strlen(warningText) + 1;
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:3825:23: [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).
const int len = max(strlen(criticalText), strlen(errorText)) + 1;
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:3825:45: [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).
const int len = max(strlen(criticalText), strlen(errorText)) + 1;
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:4096:34: [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).
char *result = (char*)g_malloc(strlen(msg->text) + strlen(separatorText) + strlen(timeText) + 1);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:4096:54: [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).
char *result = (char*)g_malloc(strlen(msg->text) + strlen(separatorText) + strlen(timeText) + 1);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:4096:78: [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).
char *result = (char*)g_malloc(strlen(msg->text) + strlen(separatorText) + strlen(timeText) + 1);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:4620:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (defaultPath && strlen(defaultPath) > defaultWidth)
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:4621:20: [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).
defaultWidth = strlen(defaultPath);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:4968:47: [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).
gtk_entry_set_width_chars(GTK_ENTRY(entry), strlen(displayText) + 3);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:5005:47: [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).
gtk_entry_set_width_chars(GTK_ENTRY(entry), strlen(displayText) + 3);
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:5251:18: [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 (tmpDir[strlen(tmpDir) - 1] == '/')
data/seqtools-4.44.1+dfsg/seqtoolsUtils/utilities.cpp:5252:16: [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).
tmpDir[strlen(tmpDir) - 1] = '\0';
ANALYSIS SUMMARY:
Hits = 488
Lines analyzed = 83924 in approximately 2.25 seconds (37230 lines/second)
Physical Source Lines of Code (SLOC) = 53102
Hits@level = [0] 56 [1] 187 [2] 193 [3] 14 [4] 94 [5] 0
Hits@level+ = [0+] 544 [1+] 488 [2+] 301 [3+] 108 [4+] 94 [5+] 0
Hits/KSLOC@level+ = [0+] 10.2444 [1+] 9.18986 [2+] 5.66834 [3+] 2.03382 [4+] 1.77018 [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.