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/soapdenovo-1.05/src/127mer/arc.c
Examining data/soapdenovo-1.05/src/127mer/attachPEinfo.c
Examining data/soapdenovo-1.05/src/127mer/bubble.c
Examining data/soapdenovo-1.05/src/127mer/check.c
Examining data/soapdenovo-1.05/src/127mer/compactEdge.c
Examining data/soapdenovo-1.05/src/127mer/concatenateEdge.c
Examining data/soapdenovo-1.05/src/127mer/connect.c
Examining data/soapdenovo-1.05/src/127mer/contig.c
Examining data/soapdenovo-1.05/src/127mer/cutTip_graph.c
Examining data/soapdenovo-1.05/src/127mer/cutTipPreGraph.c
Examining data/soapdenovo-1.05/src/127mer/darray.c
Examining data/soapdenovo-1.05/src/127mer/dfib.c
Examining data/soapdenovo-1.05/src/127mer/dfibHeap.c
Examining data/soapdenovo-1.05/src/127mer/fib.c
Examining data/soapdenovo-1.05/src/127mer/fibHeap.c
Examining data/soapdenovo-1.05/src/127mer/hashFunction.c
Examining data/soapdenovo-1.05/src/127mer/inc/check.h
Examining data/soapdenovo-1.05/src/127mer/inc/darray.h
Examining data/soapdenovo-1.05/src/127mer/inc/def.h
Examining data/soapdenovo-1.05/src/127mer/inc/def2.h
Examining data/soapdenovo-1.05/src/127mer/inc/dfib.h
Examining data/soapdenovo-1.05/src/127mer/inc/dfibHeap.h
Examining data/soapdenovo-1.05/src/127mer/inc/dfibpriv.h
Examining data/soapdenovo-1.05/src/127mer/inc/extfunc.h
Examining data/soapdenovo-1.05/src/127mer/inc/extfunc2.h
Examining data/soapdenovo-1.05/src/127mer/inc/extvab.h
Examining data/soapdenovo-1.05/src/127mer/inc/fib.h
Examining data/soapdenovo-1.05/src/127mer/inc/fibHeap.h
Examining data/soapdenovo-1.05/src/127mer/inc/fibpriv.h
Examining data/soapdenovo-1.05/src/127mer/inc/global.h
Examining data/soapdenovo-1.05/src/127mer/inc/newhash.h
Examining data/soapdenovo-1.05/src/127mer/inc/nuc.h
Examining data/soapdenovo-1.05/src/127mer/inc/stack.h
Examining data/soapdenovo-1.05/src/127mer/inc/stdinc.h
Examining data/soapdenovo-1.05/src/127mer/inc/types.h
Examining data/soapdenovo-1.05/src/127mer/kmer.c
Examining data/soapdenovo-1.05/src/127mer/lib.c
Examining data/soapdenovo-1.05/src/127mer/loadGraph.c
Examining data/soapdenovo-1.05/src/127mer/loadPath.c
Examining data/soapdenovo-1.05/src/127mer/loadPreGraph.c
Examining data/soapdenovo-1.05/src/127mer/localAsm.c
Examining data/soapdenovo-1.05/src/127mer/main.c
Examining data/soapdenovo-1.05/src/127mer/map.c
Examining data/soapdenovo-1.05/src/127mer/mem_manager.c
Examining data/soapdenovo-1.05/src/127mer/newhash.c
Examining data/soapdenovo-1.05/src/127mer/node2edge.c
Examining data/soapdenovo-1.05/src/127mer/orderContig.c
Examining data/soapdenovo-1.05/src/127mer/output_contig.c
Examining data/soapdenovo-1.05/src/127mer/output_pregraph.c
Examining data/soapdenovo-1.05/src/127mer/output_scaffold.c
Examining data/soapdenovo-1.05/src/127mer/pregraph.c
Examining data/soapdenovo-1.05/src/127mer/prlHashCtg.c
Examining data/soapdenovo-1.05/src/127mer/prlHashReads.c
Examining data/soapdenovo-1.05/src/127mer/prlRead2Ctg.c
Examining data/soapdenovo-1.05/src/127mer/prlRead2path.c
Examining data/soapdenovo-1.05/src/127mer/prlReadFillGap.c
Examining data/soapdenovo-1.05/src/127mer/read2scaf.c
Examining data/soapdenovo-1.05/src/127mer/readInterval.c
Examining data/soapdenovo-1.05/src/127mer/readseq1by1.c
Examining data/soapdenovo-1.05/src/127mer/scaffold.c
Examining data/soapdenovo-1.05/src/127mer/searchPath.c
Examining data/soapdenovo-1.05/src/127mer/seq.c
Examining data/soapdenovo-1.05/src/127mer/splitReps.c
Examining data/soapdenovo-1.05/src/127mer/stack.c
Examining data/soapdenovo-1.05/src/31mer/arc.c
Examining data/soapdenovo-1.05/src/31mer/attachPEinfo.c
Examining data/soapdenovo-1.05/src/31mer/bubble.c
Examining data/soapdenovo-1.05/src/31mer/check.c
Examining data/soapdenovo-1.05/src/31mer/compactEdge.c
Examining data/soapdenovo-1.05/src/31mer/concatenateEdge.c
Examining data/soapdenovo-1.05/src/31mer/connect.c
Examining data/soapdenovo-1.05/src/31mer/contig.c
Examining data/soapdenovo-1.05/src/31mer/cutTip_graph.c
Examining data/soapdenovo-1.05/src/31mer/cutTipPreGraph.c
Examining data/soapdenovo-1.05/src/31mer/darray.c
Examining data/soapdenovo-1.05/src/31mer/dfib.c
Examining data/soapdenovo-1.05/src/31mer/dfibHeap.c
Examining data/soapdenovo-1.05/src/31mer/fib.c
Examining data/soapdenovo-1.05/src/31mer/fibHeap.c
Examining data/soapdenovo-1.05/src/31mer/hashFunction.c
Examining data/soapdenovo-1.05/src/31mer/inc/check.h
Examining data/soapdenovo-1.05/src/31mer/inc/darray.h
Examining data/soapdenovo-1.05/src/31mer/inc/def.h
Examining data/soapdenovo-1.05/src/31mer/inc/def2.h
Examining data/soapdenovo-1.05/src/31mer/inc/dfib.h
Examining data/soapdenovo-1.05/src/31mer/inc/dfibHeap.h
Examining data/soapdenovo-1.05/src/31mer/inc/dfibpriv.h
Examining data/soapdenovo-1.05/src/31mer/inc/extfunc.h
Examining data/soapdenovo-1.05/src/31mer/inc/extfunc2.h
Examining data/soapdenovo-1.05/src/31mer/inc/extvab.h
Examining data/soapdenovo-1.05/src/31mer/inc/fib.h
Examining data/soapdenovo-1.05/src/31mer/inc/fibHeap.h
Examining data/soapdenovo-1.05/src/31mer/inc/fibpriv.h
Examining data/soapdenovo-1.05/src/31mer/inc/global.h
Examining data/soapdenovo-1.05/src/31mer/inc/newhash.h
Examining data/soapdenovo-1.05/src/31mer/inc/nuc.h
Examining data/soapdenovo-1.05/src/31mer/inc/stack.h
Examining data/soapdenovo-1.05/src/31mer/inc/stdinc.h
Examining data/soapdenovo-1.05/src/31mer/inc/types.h
Examining data/soapdenovo-1.05/src/31mer/kmer.c
Examining data/soapdenovo-1.05/src/31mer/lib.c
Examining data/soapdenovo-1.05/src/31mer/loadGraph.c
Examining data/soapdenovo-1.05/src/31mer/loadPath.c
Examining data/soapdenovo-1.05/src/31mer/loadPreGraph.c
Examining data/soapdenovo-1.05/src/31mer/localAsm.c
Examining data/soapdenovo-1.05/src/31mer/main.c
Examining data/soapdenovo-1.05/src/31mer/map.c
Examining data/soapdenovo-1.05/src/31mer/mem_manager.c
Examining data/soapdenovo-1.05/src/31mer/newhash.c
Examining data/soapdenovo-1.05/src/31mer/node2edge.c
Examining data/soapdenovo-1.05/src/31mer/orderContig.c
Examining data/soapdenovo-1.05/src/31mer/output_contig.c
Examining data/soapdenovo-1.05/src/31mer/output_pregraph.c
Examining data/soapdenovo-1.05/src/31mer/output_scaffold.c
Examining data/soapdenovo-1.05/src/31mer/pregraph.c
Examining data/soapdenovo-1.05/src/31mer/prlHashCtg.c
Examining data/soapdenovo-1.05/src/31mer/prlHashReads.c
Examining data/soapdenovo-1.05/src/31mer/prlRead2Ctg.c
Examining data/soapdenovo-1.05/src/31mer/prlRead2path.c
Examining data/soapdenovo-1.05/src/31mer/prlReadFillGap.c
Examining data/soapdenovo-1.05/src/31mer/read2scaf.c
Examining data/soapdenovo-1.05/src/31mer/readInterval.c
Examining data/soapdenovo-1.05/src/31mer/readseq1by1.c
Examining data/soapdenovo-1.05/src/31mer/scaffold.c
Examining data/soapdenovo-1.05/src/31mer/searchPath.c
Examining data/soapdenovo-1.05/src/31mer/seq.c
Examining data/soapdenovo-1.05/src/31mer/splitReps.c
Examining data/soapdenovo-1.05/src/31mer/stack.c
Examining data/soapdenovo-1.05/src/63mer/arc.c
Examining data/soapdenovo-1.05/src/63mer/attachPEinfo.c
Examining data/soapdenovo-1.05/src/63mer/bubble.c
Examining data/soapdenovo-1.05/src/63mer/check.c
Examining data/soapdenovo-1.05/src/63mer/compactEdge.c
Examining data/soapdenovo-1.05/src/63mer/concatenateEdge.c
Examining data/soapdenovo-1.05/src/63mer/connect.c
Examining data/soapdenovo-1.05/src/63mer/contig.c
Examining data/soapdenovo-1.05/src/63mer/cutTip_graph.c
Examining data/soapdenovo-1.05/src/63mer/cutTipPreGraph.c
Examining data/soapdenovo-1.05/src/63mer/darray.c
Examining data/soapdenovo-1.05/src/63mer/dfib.c
Examining data/soapdenovo-1.05/src/63mer/dfibHeap.c
Examining data/soapdenovo-1.05/src/63mer/fib.c
Examining data/soapdenovo-1.05/src/63mer/fibHeap.c
Examining data/soapdenovo-1.05/src/63mer/hashFunction.c
Examining data/soapdenovo-1.05/src/63mer/inc/check.h
Examining data/soapdenovo-1.05/src/63mer/inc/darray.h
Examining data/soapdenovo-1.05/src/63mer/inc/def.h
Examining data/soapdenovo-1.05/src/63mer/inc/def2.h
Examining data/soapdenovo-1.05/src/63mer/inc/dfib.h
Examining data/soapdenovo-1.05/src/63mer/inc/dfibHeap.h
Examining data/soapdenovo-1.05/src/63mer/inc/dfibpriv.h
Examining data/soapdenovo-1.05/src/63mer/inc/extfunc.h
Examining data/soapdenovo-1.05/src/63mer/inc/extfunc2.h
Examining data/soapdenovo-1.05/src/63mer/inc/extvab.h
Examining data/soapdenovo-1.05/src/63mer/inc/fib.h
Examining data/soapdenovo-1.05/src/63mer/inc/fibHeap.h
Examining data/soapdenovo-1.05/src/63mer/inc/fibpriv.h
Examining data/soapdenovo-1.05/src/63mer/inc/global.h
Examining data/soapdenovo-1.05/src/63mer/inc/newhash.h
Examining data/soapdenovo-1.05/src/63mer/inc/nuc.h
Examining data/soapdenovo-1.05/src/63mer/inc/stack.h
Examining data/soapdenovo-1.05/src/63mer/inc/stdinc.h
Examining data/soapdenovo-1.05/src/63mer/inc/types.h
Examining data/soapdenovo-1.05/src/63mer/kmer.c
Examining data/soapdenovo-1.05/src/63mer/lib.c
Examining data/soapdenovo-1.05/src/63mer/loadGraph.c
Examining data/soapdenovo-1.05/src/63mer/loadPath.c
Examining data/soapdenovo-1.05/src/63mer/loadPreGraph.c
Examining data/soapdenovo-1.05/src/63mer/localAsm.c
Examining data/soapdenovo-1.05/src/63mer/main.c
Examining data/soapdenovo-1.05/src/63mer/map.c
Examining data/soapdenovo-1.05/src/63mer/mem_manager.c
Examining data/soapdenovo-1.05/src/63mer/newhash.c
Examining data/soapdenovo-1.05/src/63mer/node2edge.c
Examining data/soapdenovo-1.05/src/63mer/orderContig.c
Examining data/soapdenovo-1.05/src/63mer/output_contig.c
Examining data/soapdenovo-1.05/src/63mer/output_pregraph.c
Examining data/soapdenovo-1.05/src/63mer/output_scaffold.c
Examining data/soapdenovo-1.05/src/63mer/pregraph.c
Examining data/soapdenovo-1.05/src/63mer/prlHashCtg.c
Examining data/soapdenovo-1.05/src/63mer/prlHashReads.c
Examining data/soapdenovo-1.05/src/63mer/prlRead2Ctg.c
Examining data/soapdenovo-1.05/src/63mer/prlRead2path.c
Examining data/soapdenovo-1.05/src/63mer/prlReadFillGap.c
Examining data/soapdenovo-1.05/src/63mer/read2scaf.c
Examining data/soapdenovo-1.05/src/63mer/readInterval.c
Examining data/soapdenovo-1.05/src/63mer/readseq1by1.c
Examining data/soapdenovo-1.05/src/63mer/scaffold.c
Examining data/soapdenovo-1.05/src/63mer/searchPath.c
Examining data/soapdenovo-1.05/src/63mer/seq.c
Examining data/soapdenovo-1.05/src/63mer/splitReps.c
Examining data/soapdenovo-1.05/src/63mer/stack.c
FINAL RESULTS:
data/soapdenovo-1.05/src/127mer/arc.c:83:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.arc.gvz", outfile );
data/soapdenovo-1.05/src/127mer/attachPEinfo.c:62:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.peGrads", infile );
data/soapdenovo-1.05/src/127mer/bubble.c:1868:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( temp, "%s.pathpair", outfile );
data/soapdenovo-1.05/src/127mer/connect.c:74:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.scaffold.gvz", outfile );
data/soapdenovo-1.05/src/127mer/contig.c:113:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/127mer/contig.c:118:5: [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 ( optarg, "%s", graphfile ); //
data/soapdenovo-1.05/src/127mer/lib.c:300:4: [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 ( lib_array[i].a1_fname[index], tabs[1] );
data/soapdenovo-1.05/src/127mer/lib.c:305:4: [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 ( lib_array[i].q1_fname[index], tabs[1] );
data/soapdenovo-1.05/src/127mer/lib.c:310:4: [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 ( lib_array[i].a2_fname[index], tabs[1] );
data/soapdenovo-1.05/src/127mer/lib.c:315:4: [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 ( lib_array[i].q2_fname[index], tabs[1] );
data/soapdenovo-1.05/src/127mer/lib.c:320:4: [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 ( lib_array[i].s_a_fname[index], tabs[1] );
data/soapdenovo-1.05/src/127mer/lib.c:325:4: [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 ( lib_array[i].s_q_fname[index], tabs[1] );
data/soapdenovo-1.05/src/127mer/lib.c:330:4: [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 ( lib_array[i].p_fname[index], tabs[1] );
data/soapdenovo-1.05/src/127mer/loadGraph.c:182:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.preGraphBasic", graphfile );
data/soapdenovo-1.05/src/127mer/loadGraph.c:199:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.updated.edge", graphfile );
data/soapdenovo-1.05/src/127mer/loadGraph.c:201:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.newContigIndex", outfile );
data/soapdenovo-1.05/src/127mer/loadGraph.c:363:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.Arc", graphfile );
data/soapdenovo-1.05/src/127mer/loadGraph.c:394:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.contig", graphfile );
data/soapdenovo-1.05/src/127mer/loadGraph.c:409:4: [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 + 1, "%d %s %d", &edgeno, name, &length );
data/soapdenovo-1.05/src/127mer/loadPath.c:47:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.markOnEdge", graphfile );
data/soapdenovo-1.05/src/127mer/loadPath.c:106:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.path", graphfile );
data/soapdenovo-1.05/src/127mer/loadPath.c:150:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.markOnEdge", graphfile );
data/soapdenovo-1.05/src/127mer/loadPath.c:212:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.path", graphfile );
data/soapdenovo-1.05/src/127mer/loadPreGraph.c:51:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.preGraphBasic", graphfile );
data/soapdenovo-1.05/src/127mer/loadPreGraph.c:72:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.vertex", graphfile );
data/soapdenovo-1.05/src/127mer/loadPreGraph.c:235:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.edge", graphfile );
data/soapdenovo-1.05/src/127mer/loadPreGraph.c:270:4: [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 + 7, "%d,%llx %llx %llx %llx,%llx %llx %llx %llx,%s %d,%d",
data/soapdenovo-1.05/src/127mer/loadPreGraph.c:399:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.preArc", graphfile );
data/soapdenovo-1.05/src/127mer/main.c:102:5: [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 ( optarg, "%s", readfile );
data/soapdenovo-1.05/src/127mer/main.c:106:5: [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 ( optarg, "%s", outfile ); //
data/soapdenovo-1.05/src/127mer/main.c:110:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/127mer/main.c:114:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/127mer/main.c:118:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/127mer/main.c:123:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/127mer/main.c:128:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/127mer/map.c:40:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.preGraphBasic", gfile );
data/soapdenovo-1.05/src/127mer/map.c:113:5: [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 ( optarg, "%s", shortrdsfile );
data/soapdenovo-1.05/src/127mer/map.c:117:5: [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 ( optarg, "%s", graphfile ); //
data/soapdenovo-1.05/src/127mer/map.c:120:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/127mer/map.c:124:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/127mer/node2edge.c:49:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( temp, "%s.edge", outfile );
data/soapdenovo-1.05/src/127mer/orderContig.c:2213:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.scaf", outfile );
data/soapdenovo-1.05/src/127mer/orderContig.c:2215:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.scaf_gap", outfile );
data/soapdenovo-1.05/src/127mer/orderContig.c:2749:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.links", infile );
data/soapdenovo-1.05/src/127mer/orderContig.c:2761:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.readOnContig", infile );
data/soapdenovo-1.05/src/127mer/orderContig.c:2884:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.links", infile );
data/soapdenovo-1.05/src/127mer/output_contig.c:35:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.edge.gvz", outfile );
data/soapdenovo-1.05/src/127mer/output_contig.c:111:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( temp, "%s.contig", outfile );
data/soapdenovo-1.05/src/127mer/output_contig.c:192:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( temp, "%s.ContigIndex", outfile );
data/soapdenovo-1.05/src/127mer/output_contig.c:221:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.updated.edge", outfile );
data/soapdenovo-1.05/src/127mer/output_contig.c:260:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.Arc", outfile );
data/soapdenovo-1.05/src/127mer/output_pregraph.c:55:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( temp, "%s.vertex", outfile );
data/soapdenovo-1.05/src/127mer/output_pregraph.c:78:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( temp, "%s.preGraphBasic", outfile );
data/soapdenovo-1.05/src/127mer/output_scaffold.c:33:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.contig.gvz", outfile );
data/soapdenovo-1.05/src/127mer/output_scaffold.c:53:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.scaffold.gvz", outfile );
data/soapdenovo-1.05/src/127mer/pregraph.c:120:5: [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 ( optarg, "%s", shortrdsfile );
data/soapdenovo-1.05/src/127mer/pregraph.c:124:5: [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 ( optarg, "%s", graphfile ); //
data/soapdenovo-1.05/src/127mer/pregraph.c:127:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/127mer/pregraph.c:131:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/127mer/prlHashCtg.c:269:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.contig", grapfile );
data/soapdenovo-1.05/src/127mer/prlHashReads.c:375:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.peGrads", outfile );
data/soapdenovo-1.05/src/127mer/prlHashReads.c:600:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.kmerFreq", outfile );
data/soapdenovo-1.05/src/127mer/prlRead2Ctg.c:491:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.ContigIndex", infile );
data/soapdenovo-1.05/src/127mer/prlRead2Ctg.c:583:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.readInGap", outfile );
data/soapdenovo-1.05/src/127mer/prlRead2Ctg.c:585:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.readOnContig", outfile );
data/soapdenovo-1.05/src/127mer/prlRead2Ctg.c:648:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.peGrads", outfile );
data/soapdenovo-1.05/src/127mer/prlRead2Ctg.c:781:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.longReadInGap", outfile );
data/soapdenovo-1.05/src/127mer/prlRead2path.c:328:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.preArc", outfile );
data/soapdenovo-1.05/src/127mer/prlRead2path.c:333:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.markOnEdge", outfile );
data/soapdenovo-1.05/src/127mer/prlRead2path.c:591:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.path", outfile );
data/soapdenovo-1.05/src/127mer/prlReadFillGap.c:139:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.readInGap", graphfile );
data/soapdenovo-1.05/src/127mer/prlReadFillGap.c:141:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.longReadInGap", graphfile );
data/soapdenovo-1.05/src/127mer/prlReadFillGap.c:1054:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( line, "%s.scaf_gap", graphfile );
data/soapdenovo-1.05/src/127mer/prlReadFillGap.c:1056:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( line, "%s.scafSeq", graphfile );
data/soapdenovo-1.05/src/127mer/prlReadFillGap.c:1058:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( line, "%s.gapSeq", graphfile );
data/soapdenovo-1.05/src/127mer/read2scaf.c:139:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( line, "%s.scaf_gap", graphfile );
data/soapdenovo-1.05/src/127mer/read2scaf.c:275:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.readOnContig", graphfile );
data/soapdenovo-1.05/src/127mer/read2scaf.c:277:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.readOnScaf", graphfile );
data/soapdenovo-1.05/src/127mer/readseq1by1.c:51:4: [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 ( &str[1], "%s", src_name );
data/soapdenovo-1.05/src/127mer/readseq1by1.c:163:4: [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 ( &str[1], "%s", src_name );
data/soapdenovo-1.05/src/127mer/readseq1by1.c:196:4: [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 ( &str[1], "%s", src_name );
data/soapdenovo-1.05/src/127mer/readseq1by1.c:327:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( cmd, "gzip -dc %s", fname );
data/soapdenovo-1.05/src/127mer/readseq1by1.c:328:8: [4] (shell) popen:
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.
fp = popen ( cmd, "r" );
data/soapdenovo-1.05/src/127mer/scaffold.c:96:5: [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 ( optarg, "%s", graphfile ); //
data/soapdenovo-1.05/src/127mer/scaffold.c:99:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/127mer/scaffold.c:103:5: [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 ( optarg, "%s", temp );
data/soapdenovo-1.05/src/127mer/scaffold.c:116:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/31mer/arc.c:83:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.arc.gvz", outfile );
data/soapdenovo-1.05/src/31mer/attachPEinfo.c:62:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.peGrads", infile );
data/soapdenovo-1.05/src/31mer/bubble.c:1925:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( temp, "%s.pathpair", outfile );
data/soapdenovo-1.05/src/31mer/connect.c:74:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.scaffold.gvz", outfile );
data/soapdenovo-1.05/src/31mer/contig.c:117:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/31mer/contig.c:121:5: [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 ( optarg, "%s", temp );
data/soapdenovo-1.05/src/31mer/contig.c:126:5: [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 ( optarg, "%s", graphfile ); //
data/soapdenovo-1.05/src/31mer/lib.c:279:4: [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 ( lib_array[i].a1_fname[index], tabs[1] );
data/soapdenovo-1.05/src/31mer/lib.c:284:4: [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 ( lib_array[i].q1_fname[index], tabs[1] );
data/soapdenovo-1.05/src/31mer/lib.c:289:4: [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 ( lib_array[i].a2_fname[index], tabs[1] );
data/soapdenovo-1.05/src/31mer/lib.c:294:4: [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 ( lib_array[i].q2_fname[index], tabs[1] );
data/soapdenovo-1.05/src/31mer/lib.c:299:4: [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 ( lib_array[i].s_a_fname[index], tabs[1] );
data/soapdenovo-1.05/src/31mer/lib.c:304:4: [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 ( lib_array[i].s_q_fname[index], tabs[1] );
data/soapdenovo-1.05/src/31mer/lib.c:309:4: [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 ( lib_array[i].p_fname[index], tabs[1] );
data/soapdenovo-1.05/src/31mer/loadGraph.c:40:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.updated.vertex", graphfile );
data/soapdenovo-1.05/src/31mer/loadGraph.c:189:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.preGraphBasic", graphfile );
data/soapdenovo-1.05/src/31mer/loadGraph.c:206:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.updated.edge", graphfile );
data/soapdenovo-1.05/src/31mer/loadGraph.c:208:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.newContigIndex", outfile );
data/soapdenovo-1.05/src/31mer/loadGraph.c:371:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.Arc", graphfile );
data/soapdenovo-1.05/src/31mer/loadGraph.c:402:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.contig", graphfile );
data/soapdenovo-1.05/src/31mer/loadGraph.c:417:4: [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 + 1, "%d %s %d", &edgeno, name, &length );
data/soapdenovo-1.05/src/31mer/loadPath.c:47:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.markOnEdge", graphfile );
data/soapdenovo-1.05/src/31mer/loadPath.c:106:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.path", graphfile );
data/soapdenovo-1.05/src/31mer/loadPath.c:150:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.markOnEdge", graphfile );
data/soapdenovo-1.05/src/31mer/loadPath.c:212:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.path", graphfile );
data/soapdenovo-1.05/src/31mer/loadPreGraph.c:51:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.preGraphBasic", graphfile );
data/soapdenovo-1.05/src/31mer/loadPreGraph.c:72:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.vertex", graphfile );
data/soapdenovo-1.05/src/31mer/loadPreGraph.c:203:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.edge", graphfile );
data/soapdenovo-1.05/src/31mer/loadPreGraph.c:238:4: [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 + 7, "%d,%llx,%llx,%s %d,%d", &length, &from_kmer, &to_kmer, str, &cvg, &bal_ed );
data/soapdenovo-1.05/src/31mer/loadPreGraph.c:371:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.preArc", graphfile );
data/soapdenovo-1.05/src/31mer/main.c:111:5: [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 ( optarg, "%s", readfile );
data/soapdenovo-1.05/src/31mer/main.c:115:5: [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 ( optarg, "%s", outfile ); //
data/soapdenovo-1.05/src/31mer/main.c:119:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/31mer/main.c:123:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/31mer/main.c:127:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/31mer/main.c:132:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/31mer/main.c:137:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/31mer/main.c:148:5: [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 ( optarg, "%s", temp );
data/soapdenovo-1.05/src/31mer/main.c:153:5: [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 ( optarg, "%s", temp );
data/soapdenovo-1.05/src/31mer/map.c:40:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.preGraphBasic", gfile );
data/soapdenovo-1.05/src/31mer/map.c:112:5: [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 ( optarg, "%s", shortrdsfile );
data/soapdenovo-1.05/src/31mer/map.c:116:5: [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 ( optarg, "%s", graphfile ); //
data/soapdenovo-1.05/src/31mer/map.c:119:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/31mer/map.c:123:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/31mer/node2edge.c:49:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( temp, "%s.edge", outfile );
data/soapdenovo-1.05/src/31mer/orderContig.c:2213:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.scaf", outfile );
data/soapdenovo-1.05/src/31mer/orderContig.c:2215:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.scaf_gap", outfile );
data/soapdenovo-1.05/src/31mer/orderContig.c:2749:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.links", infile );
data/soapdenovo-1.05/src/31mer/orderContig.c:2761:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.readOnContig", infile );
data/soapdenovo-1.05/src/31mer/orderContig.c:2885:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.links", infile );
data/soapdenovo-1.05/src/31mer/output_contig.c:35:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.edge.gvz", outfile );
data/soapdenovo-1.05/src/31mer/output_contig.c:130:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( temp, "%s.contig", outfile );
data/soapdenovo-1.05/src/31mer/output_contig.c:206:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( temp, "%s.ContigIndex", outfile );
data/soapdenovo-1.05/src/31mer/output_contig.c:235:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.updated.edge", outfile );
data/soapdenovo-1.05/src/31mer/output_contig.c:270:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.Arc", outfile );
data/soapdenovo-1.05/src/31mer/output_pregraph.c:53:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( temp, "%s.vertex", outfile );
data/soapdenovo-1.05/src/31mer/output_pregraph.c:76:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( temp, "%s.preGraphBasic", outfile );
data/soapdenovo-1.05/src/31mer/output_scaffold.c:33:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.contig.gvz", outfile );
data/soapdenovo-1.05/src/31mer/output_scaffold.c:53:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.scaffold.gvz", outfile );
data/soapdenovo-1.05/src/31mer/pregraph.c:121:5: [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 ( optarg, "%s", shortrdsfile );
data/soapdenovo-1.05/src/31mer/pregraph.c:125:5: [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 ( optarg, "%s", graphfile ); //
data/soapdenovo-1.05/src/31mer/pregraph.c:128:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/31mer/pregraph.c:132:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/31mer/pregraph.c:139:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/31mer/prlHashCtg.c:268:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.contig", grapfile );
data/soapdenovo-1.05/src/31mer/prlHashReads.c:374:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.peGrads", outfile );
data/soapdenovo-1.05/src/31mer/prlHashReads.c:618:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.kmerFreq", outfile );
data/soapdenovo-1.05/src/31mer/prlRead2Ctg.c:492:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.ContigIndex", infile );
data/soapdenovo-1.05/src/31mer/prlRead2Ctg.c:587:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.readInGap", outfile );
data/soapdenovo-1.05/src/31mer/prlRead2Ctg.c:589:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.readOnContig", outfile );
data/soapdenovo-1.05/src/31mer/prlRead2Ctg.c:655:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.peGrads", outfile );
data/soapdenovo-1.05/src/31mer/prlRead2Ctg.c:791:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.longReadInGap", outfile );
data/soapdenovo-1.05/src/31mer/prlRead2path.c:326:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.preArc", outfile );
data/soapdenovo-1.05/src/31mer/prlRead2path.c:331:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.markOnEdge", outfile );
data/soapdenovo-1.05/src/31mer/prlRead2path.c:583:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.path", outfile );
data/soapdenovo-1.05/src/31mer/prlReadFillGap.c:139:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.readInGap", graphfile );
data/soapdenovo-1.05/src/31mer/prlReadFillGap.c:141:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.longReadInGap", graphfile );
data/soapdenovo-1.05/src/31mer/prlReadFillGap.c:1042:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( line, "%s.scaf_gap", graphfile );
data/soapdenovo-1.05/src/31mer/prlReadFillGap.c:1044:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( line, "%s.scafSeq", graphfile );
data/soapdenovo-1.05/src/31mer/prlReadFillGap.c:1046:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( line, "%s.gapSeq", graphfile );
data/soapdenovo-1.05/src/31mer/read2scaf.c:139:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( line, "%s.scaf_gap", graphfile );
data/soapdenovo-1.05/src/31mer/read2scaf.c:271:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.readOnContig", graphfile );
data/soapdenovo-1.05/src/31mer/read2scaf.c:273:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.readOnScaf", graphfile );
data/soapdenovo-1.05/src/31mer/readseq1by1.c:51:4: [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 ( &str[1], "%s", src_name );
data/soapdenovo-1.05/src/31mer/readseq1by1.c:163:4: [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 ( &str[1], "%s", src_name );
data/soapdenovo-1.05/src/31mer/readseq1by1.c:196:4: [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 ( &str[1], "%s", src_name );
data/soapdenovo-1.05/src/31mer/readseq1by1.c:327:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( cmd, "gzip -dc %s", fname );
data/soapdenovo-1.05/src/31mer/readseq1by1.c:328:8: [4] (shell) popen:
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.
fp = popen ( cmd, "r" );
data/soapdenovo-1.05/src/31mer/scaffold.c:96:5: [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 ( optarg, "%s", graphfile ); //
data/soapdenovo-1.05/src/31mer/scaffold.c:99:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/31mer/scaffold.c:103:5: [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 ( optarg, "%s", temp );
data/soapdenovo-1.05/src/31mer/scaffold.c:116:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/63mer/arc.c:83:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.arc.gvz", outfile );
data/soapdenovo-1.05/src/63mer/attachPEinfo.c:62:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.peGrads", infile );
data/soapdenovo-1.05/src/63mer/bubble.c:1868:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( temp, "%s.pathpair", outfile );
data/soapdenovo-1.05/src/63mer/connect.c:74:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.scaffold.gvz", outfile );
data/soapdenovo-1.05/src/63mer/contig.c:113:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/63mer/contig.c:118:5: [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 ( optarg, "%s", graphfile ); //
data/soapdenovo-1.05/src/63mer/lib.c:300:4: [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 ( lib_array[i].a1_fname[index], tabs[1] );
data/soapdenovo-1.05/src/63mer/lib.c:305:4: [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 ( lib_array[i].q1_fname[index], tabs[1] );
data/soapdenovo-1.05/src/63mer/lib.c:310:4: [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 ( lib_array[i].a2_fname[index], tabs[1] );
data/soapdenovo-1.05/src/63mer/lib.c:315:4: [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 ( lib_array[i].q2_fname[index], tabs[1] );
data/soapdenovo-1.05/src/63mer/lib.c:320:4: [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 ( lib_array[i].s_a_fname[index], tabs[1] );
data/soapdenovo-1.05/src/63mer/lib.c:325:4: [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 ( lib_array[i].s_q_fname[index], tabs[1] );
data/soapdenovo-1.05/src/63mer/lib.c:330:4: [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 ( lib_array[i].p_fname[index], tabs[1] );
data/soapdenovo-1.05/src/63mer/loadGraph.c:182:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.preGraphBasic", graphfile );
data/soapdenovo-1.05/src/63mer/loadGraph.c:199:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.updated.edge", graphfile );
data/soapdenovo-1.05/src/63mer/loadGraph.c:201:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.newContigIndex", outfile );
data/soapdenovo-1.05/src/63mer/loadGraph.c:363:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.Arc", graphfile );
data/soapdenovo-1.05/src/63mer/loadGraph.c:394:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.contig", graphfile );
data/soapdenovo-1.05/src/63mer/loadGraph.c:409:4: [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 + 1, "%d %s %d", &edgeno, name, &length );
data/soapdenovo-1.05/src/63mer/loadPath.c:47:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.markOnEdge", graphfile );
data/soapdenovo-1.05/src/63mer/loadPath.c:106:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.path", graphfile );
data/soapdenovo-1.05/src/63mer/loadPath.c:150:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.markOnEdge", graphfile );
data/soapdenovo-1.05/src/63mer/loadPath.c:212:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.path", graphfile );
data/soapdenovo-1.05/src/63mer/loadPreGraph.c:51:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.preGraphBasic", graphfile );
data/soapdenovo-1.05/src/63mer/loadPreGraph.c:72:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.vertex", graphfile );
data/soapdenovo-1.05/src/63mer/loadPreGraph.c:214:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.edge", graphfile );
data/soapdenovo-1.05/src/63mer/loadPreGraph.c:249:4: [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 + 7, "%d,%llx %llx,%llx %llx,%s %d,%d",
data/soapdenovo-1.05/src/63mer/loadPreGraph.c:378:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.preArc", graphfile );
data/soapdenovo-1.05/src/63mer/main.c:102:5: [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 ( optarg, "%s", readfile );
data/soapdenovo-1.05/src/63mer/main.c:106:5: [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 ( optarg, "%s", outfile ); //
data/soapdenovo-1.05/src/63mer/main.c:110:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/63mer/main.c:114:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/63mer/main.c:118:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/63mer/main.c:123:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/63mer/main.c:128:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/63mer/map.c:40:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.preGraphBasic", gfile );
data/soapdenovo-1.05/src/63mer/map.c:113:5: [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 ( optarg, "%s", shortrdsfile );
data/soapdenovo-1.05/src/63mer/map.c:117:5: [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 ( optarg, "%s", graphfile ); //
data/soapdenovo-1.05/src/63mer/map.c:120:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/63mer/map.c:124:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/63mer/node2edge.c:49:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( temp, "%s.edge", outfile );
data/soapdenovo-1.05/src/63mer/orderContig.c:2213:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.scaf", outfile );
data/soapdenovo-1.05/src/63mer/orderContig.c:2215:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.scaf_gap", outfile );
data/soapdenovo-1.05/src/63mer/orderContig.c:2749:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.links", infile );
data/soapdenovo-1.05/src/63mer/orderContig.c:2761:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.readOnContig", infile );
data/soapdenovo-1.05/src/63mer/orderContig.c:2884:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.links", infile );
data/soapdenovo-1.05/src/63mer/output_contig.c:35:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.edge.gvz", outfile );
data/soapdenovo-1.05/src/63mer/output_contig.c:121:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( temp, "%s.contig", outfile );
data/soapdenovo-1.05/src/63mer/output_contig.c:200:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( temp, "%s.ContigIndex", outfile );
data/soapdenovo-1.05/src/63mer/output_contig.c:229:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.updated.edge", outfile );
data/soapdenovo-1.05/src/63mer/output_contig.c:265:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.Arc", outfile );
data/soapdenovo-1.05/src/63mer/output_pregraph.c:55:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( temp, "%s.vertex", outfile );
data/soapdenovo-1.05/src/63mer/output_pregraph.c:78:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( temp, "%s.preGraphBasic", outfile );
data/soapdenovo-1.05/src/63mer/output_scaffold.c:33:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.contig.gvz", outfile );
data/soapdenovo-1.05/src/63mer/output_scaffold.c:53:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.scaffold.gvz", outfile );
data/soapdenovo-1.05/src/63mer/pregraph.c:121:5: [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 ( optarg, "%s", shortrdsfile );
data/soapdenovo-1.05/src/63mer/pregraph.c:125:5: [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 ( optarg, "%s", graphfile ); //
data/soapdenovo-1.05/src/63mer/pregraph.c:128:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/63mer/pregraph.c:132:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/63mer/prlHashCtg.c:269:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.contig", grapfile );
data/soapdenovo-1.05/src/63mer/prlHashReads.c:374:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.peGrads", outfile );
data/soapdenovo-1.05/src/63mer/prlHashReads.c:599:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.kmerFreq", outfile );
data/soapdenovo-1.05/src/63mer/prlRead2Ctg.c:491:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.ContigIndex", infile );
data/soapdenovo-1.05/src/63mer/prlRead2Ctg.c:583:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.readInGap", outfile );
data/soapdenovo-1.05/src/63mer/prlRead2Ctg.c:585:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.readOnContig", outfile );
data/soapdenovo-1.05/src/63mer/prlRead2Ctg.c:648:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.peGrads", outfile );
data/soapdenovo-1.05/src/63mer/prlRead2Ctg.c:781:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.longReadInGap", outfile );
data/soapdenovo-1.05/src/63mer/prlRead2path.c:328:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.preArc", outfile );
data/soapdenovo-1.05/src/63mer/prlRead2path.c:333:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.markOnEdge", outfile );
data/soapdenovo-1.05/src/63mer/prlRead2path.c:591:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.path", outfile );
data/soapdenovo-1.05/src/63mer/prlReadFillGap.c:139:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.readInGap", graphfile );
data/soapdenovo-1.05/src/63mer/prlReadFillGap.c:141:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.longReadInGap", graphfile );
data/soapdenovo-1.05/src/63mer/prlReadFillGap.c:1054:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( line, "%s.scaf_gap", graphfile );
data/soapdenovo-1.05/src/63mer/prlReadFillGap.c:1056:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( line, "%s.scafSeq", graphfile );
data/soapdenovo-1.05/src/63mer/prlReadFillGap.c:1058:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( line, "%s.gapSeq", graphfile );
data/soapdenovo-1.05/src/63mer/read2scaf.c:139:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( line, "%s.scaf_gap", graphfile );
data/soapdenovo-1.05/src/63mer/read2scaf.c:275:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.readOnContig", graphfile );
data/soapdenovo-1.05/src/63mer/read2scaf.c:277:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( name, "%s.readOnScaf", graphfile );
data/soapdenovo-1.05/src/63mer/readseq1by1.c:51:4: [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 ( &str[1], "%s", src_name );
data/soapdenovo-1.05/src/63mer/readseq1by1.c:163:4: [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 ( &str[1], "%s", src_name );
data/soapdenovo-1.05/src/63mer/readseq1by1.c:196:4: [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 ( &str[1], "%s", src_name );
data/soapdenovo-1.05/src/63mer/readseq1by1.c:327:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf ( cmd, "gzip -dc %s", fname );
data/soapdenovo-1.05/src/63mer/readseq1by1.c:328:8: [4] (shell) popen:
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.
fp = popen ( cmd, "r" );
data/soapdenovo-1.05/src/63mer/scaffold.c:96:5: [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 ( optarg, "%s", graphfile ); //
data/soapdenovo-1.05/src/63mer/scaffold.c:99:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/63mer/scaffold.c:103:5: [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 ( optarg, "%s", temp );
data/soapdenovo-1.05/src/63mer/scaffold.c:116:5: [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 ( optarg, "%s", temp ); //
data/soapdenovo-1.05/src/127mer/contig.c:108:19: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ( ( copt = getopt ( argc, argv, "g:M:R" ) ) != EOF )
data/soapdenovo-1.05/src/127mer/main.c:96:19: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ( ( copt = getopt ( argc, argv, "s:o:K:M:L:p:G:dDRua:" ) ) != EOF )
data/soapdenovo-1.05/src/127mer/map.c:106:19: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ( ( copt = getopt ( argc, argv, "s:g:K:p:" ) ) != EOF )
data/soapdenovo-1.05/src/127mer/pregraph.c:113:19: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ( ( copt = getopt ( argc, argv, "s:o:K:p:a:dDR" ) ) != EOF )
data/soapdenovo-1.05/src/127mer/scaffold.c:90:19: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ( ( copt = getopt ( argc, argv, "g:L:p:G:FuS" ) ) != EOF )
data/soapdenovo-1.05/src/31mer/contig.c:112:19: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ( ( copt = getopt ( argc, argv, "g:M:D:R" ) ) != EOF )
data/soapdenovo-1.05/src/31mer/main.c:105:19: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ( ( copt = getopt ( argc, argv, "a:s:o:K:M:L:p:G:d:D:Ru" ) ) != EOF )
data/soapdenovo-1.05/src/31mer/map.c:105:19: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ( ( copt = getopt ( argc, argv, "s:g:K:p:" ) ) != EOF )
data/soapdenovo-1.05/src/31mer/pregraph.c:114:19: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ( ( copt = getopt ( argc, argv, "a:s:o:K:p:d:DR" ) ) != EOF )
data/soapdenovo-1.05/src/31mer/scaffold.c:90:19: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ( ( copt = getopt ( argc, argv, "g:L:p:G:FuS" ) ) != EOF )
data/soapdenovo-1.05/src/63mer/contig.c:108:19: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ( ( copt = getopt ( argc, argv, "g:M:R" ) ) != EOF )
data/soapdenovo-1.05/src/63mer/main.c:96:19: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ( ( copt = getopt ( argc, argv, "s:o:K:M:L:p:G:dDRua:" ) ) != EOF )
data/soapdenovo-1.05/src/63mer/map.c:106:19: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ( ( copt = getopt ( argc, argv, "s:g:K:p:" ) ) != EOF )
data/soapdenovo-1.05/src/63mer/pregraph.c:114:19: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ( ( copt = getopt ( argc, argv, "s:o:K:p:a:dDR" ) ) != EOF )
data/soapdenovo-1.05/src/63mer/scaffold.c:90:19: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
while ( ( copt = getopt ( argc, argv, "g:L:p:G:FuS" ) ) != EOF )
data/soapdenovo-1.05/src/127mer/arc.c:80:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/127mer/attachPEinfo.c:59:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], line[1024];
data/soapdenovo-1.05/src/127mer/attachPEinfo.c:63:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen ( name, "r" );
data/soapdenovo-1.05/src/127mer/bubble.c:62:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char fastSequence[MAXREADLENGTH];
data/soapdenovo-1.05/src/127mer/bubble.c:63:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char slowSequence[MAXREADLENGTH];
data/soapdenovo-1.05/src/127mer/bubble.c:1867:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[256];
data/soapdenovo-1.05/src/127mer/check.c:32:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ( ( fp = fopen ( name, mode ) ) == NULL )
data/soapdenovo-1.05/src/127mer/check.c:75:2: [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 ( p, q, old_size );
data/soapdenovo-1.05/src/127mer/connect.c:69:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/127mer/contig.c:30:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char shortrdsfile[256], graphfile[256];
data/soapdenovo-1.05/src/127mer/contig.c:104:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[100];
data/soapdenovo-1.05/src/127mer/contig.c:114:9: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
M = atoi ( temp );
data/soapdenovo-1.05/src/127mer/cutTipPreGraph.c:458:11: [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.
unsigned char thrdSignal[thrd_num + 1];
data/soapdenovo-1.05/src/127mer/inc/nuc.h:24:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char na_name[17] = {'g', 'a', 't', 'c',
data/soapdenovo-1.05/src/127mer/kmer.c:320:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char kmerSeq[128];
data/soapdenovo-1.05/src/127mer/lib.c:28:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char tabs[2][1024];
data/soapdenovo-1.05/src/127mer/lib.c:102:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[1024], ch;
data/soapdenovo-1.05/src/127mer/lib.c:126:20: [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).
{ maxReadLen = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/127mer/lib.c:205:31: [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.
lib_array[i].s_a_fname = ( char ** ) ckalloc ( lib_array[i].num_s_a_file * sizeof ( char * ) );
data/soapdenovo-1.05/src/127mer/lib.c:213:31: [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.
lib_array[i].s_q_fname = ( char ** ) ckalloc ( lib_array[i].num_s_q_file * sizeof ( char * ) );
data/soapdenovo-1.05/src/127mer/lib.c:221:29: [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.
lib_array[i].p_fname = ( char ** ) ckalloc ( lib_array[i].num_p_file * sizeof ( char * ) );
data/soapdenovo-1.05/src/127mer/lib.c:229:30: [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.
lib_array[i].a1_fname = ( char ** ) ckalloc ( lib_array[i].num_a1_file * sizeof ( char * ) );
data/soapdenovo-1.05/src/127mer/lib.c:237:30: [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.
lib_array[i].a2_fname = ( char ** ) ckalloc ( lib_array[i].num_a2_file * sizeof ( char * ) );
data/soapdenovo-1.05/src/127mer/lib.c:245:30: [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.
lib_array[i].q1_fname = ( char ** ) ckalloc ( lib_array[i].num_q1_file * sizeof ( char * ) );
data/soapdenovo-1.05/src/127mer/lib.c:253:30: [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.
lib_array[i].q2_fname = ( char ** ) ckalloc ( lib_array[i].num_q2_file * sizeof ( char * ) );
data/soapdenovo-1.05/src/127mer/lib.c:333:29: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
{ lib_array[i].min_ins = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/127mer/lib.c:335:29: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
{ lib_array[i].max_ins = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/127mer/lib.c:337:29: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
{ lib_array[i].avg_ins = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/127mer/lib.c:339:35: [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).
{ lib_array[i].rd_len_cutoff = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/127mer/lib.c:341:29: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
{ lib_array[i].reverse = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/127mer/lib.c:343:30: [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).
{ lib_array[i].asm_flag = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/127mer/lib.c:345:26: [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).
{ lib_array[i].rank = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/127mer/lib.c:347:34: [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).
{ lib_array[i].pair_num_cut = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/127mer/lib.c:349:35: [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).
{ lib_array[i].rd_len_cutoff = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/127mer/lib.c:351:29: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
{ lib_array[i].map_len = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/127mer/loadGraph.c:171:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char c, name[256], line[1024];
data/soapdenovo-1.05/src/127mer/loadGraph.c:359:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], line[1024];
data/soapdenovo-1.05/src/127mer/loadGraph.c:371:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
from_ed = atoi ( seg );
data/soapdenovo-1.05/src/127mer/loadGraph.c:376:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
target = atoi ( seg );
data/soapdenovo-1.05/src/127mer/loadGraph.c:378:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
weight = atoi ( seg );
data/soapdenovo-1.05/src/127mer/loadGraph.c:389:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char c, name[256], line[1024], *tightSeq = NULL;
data/soapdenovo-1.05/src/127mer/loadPath.c:43:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], line[1024];
data/soapdenovo-1.05/src/127mer/loadPath.c:48:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen ( name, "r" );
data/soapdenovo-1.05/src/127mer/loadPath.c:107:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen ( name, "r" );
data/soapdenovo-1.05/src/127mer/loadPath.c:120:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
edgeno = atoi ( seg );
data/soapdenovo-1.05/src/127mer/loadPath.c:145:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/127mer/loadPath.c:151:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen ( name, "r" );
data/soapdenovo-1.05/src/127mer/loadPath.c:213:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen ( name, "rb" );
data/soapdenovo-1.05/src/127mer/loadPreGraph.c:46:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], line[256];
data/soapdenovo-1.05/src/127mer/loadPreGraph.c:228:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char c, name[256], line[1024], str[32];
data/soapdenovo-1.05/src/127mer/loadPreGraph.c:395:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], line[1024];
data/soapdenovo-1.05/src/127mer/loadPreGraph.c:406:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
from_ed = atoi ( seg );
data/soapdenovo-1.05/src/127mer/loadPreGraph.c:410:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
target = atoi ( seg );
data/soapdenovo-1.05/src/127mer/loadPreGraph.c:412:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
weight = atoi ( seg );
data/soapdenovo-1.05/src/127mer/localAsm.c:314:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char kmerSeq[128];
data/soapdenovo-1.05/src/127mer/localAsm.c:1414:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char fastSequence[MAXREADLENGTH];
data/soapdenovo-1.05/src/127mer/localAsm.c:1415:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char slowSequence[MAXREADLENGTH];
data/soapdenovo-1.05/src/127mer/main.c:83:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char * options[16];
data/soapdenovo-1.05/src/127mer/main.c:85:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char readfile[256], outfile[256];
data/soapdenovo-1.05/src/127mer/main.c:86:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[128];
data/soapdenovo-1.05/src/127mer/main.c:89:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char kmer_s[16], len_s[16], ncpu_s[16], M_s[16];
data/soapdenovo-1.05/src/127mer/main.c:111:12: [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).
kmer = atoi ( temp );
data/soapdenovo-1.05/src/127mer/main.c:115:14: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
GLDiff = atoi ( temp );
data/soapdenovo-1.05/src/127mer/main.c:119:9: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
M = atoi ( temp );
data/soapdenovo-1.05/src/127mer/main.c:124:12: [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).
ncpu = atoi ( temp );
data/soapdenovo-1.05/src/127mer/main.c:129:18: [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).
cutoff_len = atoi ( temp );
data/soapdenovo-1.05/src/127mer/main.c:144:23: [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).
initKmerSetSize = atoi ( optarg );
data/soapdenovo-1.05/src/127mer/main.c:175:3: [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 ( kmer_s, "%d", kmer );
data/soapdenovo-1.05/src/127mer/main.c:182:3: [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 ( ncpu_s, "%d", ncpu );
data/soapdenovo-1.05/src/127mer/main.c:209:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf ( M_s, "%d", M );
data/soapdenovo-1.05/src/127mer/main.c:231:3: [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 ( ncpu_s, "%d", ncpu );
data/soapdenovo-1.05/src/127mer/main.c:250:3: [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 ( len_s, "%d", cutoff_len );
data/soapdenovo-1.05/src/127mer/map.c:29:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char shortrdsfile[256];
data/soapdenovo-1.05/src/127mer/map.c:30:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char graphfile[256];
data/soapdenovo-1.05/src/127mer/map.c:36:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], ch;
data/soapdenovo-1.05/src/127mer/map.c:39:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[1024];
data/soapdenovo-1.05/src/127mer/map.c:41:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen ( name, "r" );
data/soapdenovo-1.05/src/127mer/map.c:102:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[100];
data/soapdenovo-1.05/src/127mer/map.c:121:18: [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).
overlaplen = atoi ( temp );
data/soapdenovo-1.05/src/127mer/map.c:125:16: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
thrd_num = atoi ( temp );
data/soapdenovo-1.05/src/127mer/node2edge.c:36:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char edge_seq[100000];
data/soapdenovo-1.05/src/127mer/node2edge.c:48:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[256];
data/soapdenovo-1.05/src/127mer/orderContig.c:2187:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/127mer/orderContig.c:2744:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], *line;
data/soapdenovo-1.05/src/127mer/orderContig.c:2875:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], *line;
data/soapdenovo-1.05/src/127mer/output_contig.c:32:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/127mer/output_contig.c:103:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[256];
data/soapdenovo-1.05/src/127mer/output_contig.c:218:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/127mer/output_contig.c:257:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/127mer/output_pregraph.c:50:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[256];
data/soapdenovo-1.05/src/127mer/output_scaffold.c:30:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/127mer/output_scaffold.c:48:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/127mer/pregraph.c:29:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char shortrdsfile[256];
data/soapdenovo-1.05/src/127mer/pregraph.c:30:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char graphfile[256];
data/soapdenovo-1.05/src/127mer/pregraph.c:109:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[100];
data/soapdenovo-1.05/src/127mer/pregraph.c:128:18: [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).
overlaplen = atoi ( temp );
data/soapdenovo-1.05/src/127mer/pregraph.c:132:16: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
thrd_num = atoi ( temp );
data/soapdenovo-1.05/src/127mer/pregraph.c:144:23: [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).
initKmerSetSize = atoi ( optarg );
data/soapdenovo-1.05/src/127mer/prlHashCtg.c:79:21: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ( unsigned char ) ( hashBanBuffer[i] % thrd_num ) != id )
data/soapdenovo-1.05/src/127mer/prlHashCtg.c:251:12: [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).
{ return atoi ( & ( name[0] ) ); }
data/soapdenovo-1.05/src/127mer/prlHashCtg.c:259:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], *next_name;
data/soapdenovo-1.05/src/127mer/prlHashCtg.c:263:11: [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.
unsigned char thrdSignal[thrd_num + 1];
data/soapdenovo-1.05/src/127mer/prlHashReads.c:252:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char * next_name, name[256];
data/soapdenovo-1.05/src/127mer/prlHashReads.c:258:11: [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.
unsigned char thrdSignal[thrd_num + 1];
data/soapdenovo-1.05/src/127mer/prlHashReads.c:597:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/127mer/prlRead2Ctg.c:488:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], lldne[1024];
data/soapdenovo-1.05/src/127mer/prlRead2Ctg.c:523:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char * src_name, *next_name, name[256];
data/soapdenovo-1.05/src/127mer/prlRead2Ctg.c:528:11: [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.
unsigned char thrdSignal[thrd_num + 1];
data/soapdenovo-1.05/src/127mer/prlRead2Ctg.c:716:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char * src_name, *next_name, name[256];
data/soapdenovo-1.05/src/127mer/prlRead2Ctg.c:721:11: [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.
unsigned char thrdSignal[thrd_num + 1];
data/soapdenovo-1.05/src/127mer/prlRead2path.c:325:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/127mer/prlRead2path.c:570:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], *src_name, *next_name;
data/soapdenovo-1.05/src/127mer/prlRead2path.c:575:11: [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.
unsigned char thrdSignal[thrd_num + 1];
data/soapdenovo-1.05/src/127mer/prlReadFillGap.c:125:3: [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 ( freadBuf, pt, len / 4 + 1 );
data/soapdenovo-1.05/src/127mer/prlReadFillGap.c:137:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[1024];
data/soapdenovo-1.05/src/127mer/prlReadFillGap.c:140:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen ( name, "rb" );
data/soapdenovo-1.05/src/127mer/prlReadFillGap.c:142:8: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp2 = fopen ( name, "rb" );
data/soapdenovo-1.05/src/127mer/prlReadFillGap.c:241:11: [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).
length = atoi ( tp );
data/soapdenovo-1.05/src/127mer/prlReadFillGap.c:243:8: [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 = atoi ( tp );
data/soapdenovo-1.05/src/127mer/prlReadFillGap.c:251:9: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
ctg = atoi ( tp );
data/soapdenovo-1.05/src/127mer/prlReadFillGap.c:1038:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[1024];
data/soapdenovo-1.05/src/127mer/prlReadFillGap.c:1046:11: [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.
unsigned char thrdSignal[thrd_num + 1];
data/soapdenovo-1.05/src/127mer/read2scaf.c:125:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[1024];
data/soapdenovo-1.05/src/127mer/read2scaf.c:269:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[1024], line[1024];
data/soapdenovo-1.05/src/127mer/readseq1by1.c:28:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char src_rc_seq[1024];
data/soapdenovo-1.05/src/127mer/readseq1by1.c:34:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[5000];
data/soapdenovo-1.05/src/127mer/readseq1by1.c:121:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[5000];
data/soapdenovo-1.05/src/127mer/readseq1by1.c:144:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[5000], src_name[5000];
data/soapdenovo-1.05/src/127mer/readseq1by1.c:188:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[5000];
data/soapdenovo-1.05/src/127mer/scaffold.c:32:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char graphfile[256];
data/soapdenovo-1.05/src/127mer/scaffold.c:84:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[256];
data/soapdenovo-1.05/src/127mer/scaffold.c:100:14: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
GLDiff = atoi ( temp );
data/soapdenovo-1.05/src/127mer/scaffold.c:104:17: [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).
ctg_short = atoi ( temp );
data/soapdenovo-1.05/src/127mer/scaffold.c:117:16: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
thrd_num = atoi ( temp );
data/soapdenovo-1.05/src/127mer/splitReps.c:31:17: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static unsigned char gothrough[4][4];
data/soapdenovo-1.05/src/31mer/arc.c:80:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/31mer/attachPEinfo.c:59:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], line[1024];
data/soapdenovo-1.05/src/31mer/attachPEinfo.c:63:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen ( name, "r" );
data/soapdenovo-1.05/src/31mer/bubble.c:62:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char fastSequence[MAXREADLENGTH];
data/soapdenovo-1.05/src/31mer/bubble.c:63:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char slowSequence[MAXREADLENGTH];
data/soapdenovo-1.05/src/31mer/bubble.c:106:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char kmerSeq[32];
data/soapdenovo-1.05/src/31mer/bubble.c:1049:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char kmerSeq[32], ch;
data/soapdenovo-1.05/src/31mer/bubble.c:1924:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[256];
data/soapdenovo-1.05/src/31mer/check.c:32:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ( ( fp = fopen ( name, mode ) ) == NULL )
data/soapdenovo-1.05/src/31mer/check.c:75:2: [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 ( p, q, old_size );
data/soapdenovo-1.05/src/31mer/connect.c:69:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/31mer/contig.c:30:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char shortrdsfile[256], graphfile[256];
data/soapdenovo-1.05/src/31mer/contig.c:108:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[100];
data/soapdenovo-1.05/src/31mer/contig.c:118:9: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
M = atoi ( temp );
data/soapdenovo-1.05/src/31mer/contig.c:122:17: [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).
deLowEdge = atoi ( temp ) >= 0 ? atoi ( temp ) : 0;
data/soapdenovo-1.05/src/31mer/contig.c:122:38: [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).
deLowEdge = atoi ( temp ) >= 0 ? atoi ( temp ) : 0;
data/soapdenovo-1.05/src/31mer/cutTipPreGraph.c:37:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char kmerSeq[32], ch;
data/soapdenovo-1.05/src/31mer/cutTipPreGraph.c:463:11: [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.
unsigned char thrdSignal[thrd_num + 1];
data/soapdenovo-1.05/src/31mer/inc/nuc.h:24:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char na_name[17] = {'g', 'a', 't', 'c',
data/soapdenovo-1.05/src/31mer/kmer.c:28:17: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static unsigned char filter_array[8] = { ( unsigned char ) 1, ( ( unsigned char ) 1 ) << 1, ( ( unsigned char ) 1 ) << 2, ( ( unsigned char ) 1 ) << 3, ( ( unsigned char ) 1 ) << 4, ( ( unsigned char ) 1 ) << 5, ( ( unsigned char ) 1 ) << 6, ( ( unsigned char ) 1 ) << 7};
data/soapdenovo-1.05/src/31mer/lib.c:28:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char tabs[2][1024];
data/soapdenovo-1.05/src/31mer/lib.c:81:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[1024], ch;
data/soapdenovo-1.05/src/31mer/lib.c:105:20: [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).
{ maxReadLen = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/31mer/lib.c:184:31: [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.
lib_array[i].s_a_fname = ( char ** ) ckalloc ( lib_array[i].num_s_a_file * sizeof ( char * ) );
data/soapdenovo-1.05/src/31mer/lib.c:192:31: [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.
lib_array[i].s_q_fname = ( char ** ) ckalloc ( lib_array[i].num_s_q_file * sizeof ( char * ) );
data/soapdenovo-1.05/src/31mer/lib.c:200:29: [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.
lib_array[i].p_fname = ( char ** ) ckalloc ( lib_array[i].num_p_file * sizeof ( char * ) );
data/soapdenovo-1.05/src/31mer/lib.c:208:30: [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.
lib_array[i].a1_fname = ( char ** ) ckalloc ( lib_array[i].num_a1_file * sizeof ( char * ) );
data/soapdenovo-1.05/src/31mer/lib.c:216:30: [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.
lib_array[i].a2_fname = ( char ** ) ckalloc ( lib_array[i].num_a2_file * sizeof ( char * ) );
data/soapdenovo-1.05/src/31mer/lib.c:224:30: [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.
lib_array[i].q1_fname = ( char ** ) ckalloc ( lib_array[i].num_q1_file * sizeof ( char * ) );
data/soapdenovo-1.05/src/31mer/lib.c:232:30: [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.
lib_array[i].q2_fname = ( char ** ) ckalloc ( lib_array[i].num_q2_file * sizeof ( char * ) );
data/soapdenovo-1.05/src/31mer/lib.c:312:29: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
{ lib_array[i].min_ins = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/31mer/lib.c:314:29: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
{ lib_array[i].max_ins = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/31mer/lib.c:316:29: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
{ lib_array[i].avg_ins = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/31mer/lib.c:318:35: [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).
{ lib_array[i].rd_len_cutoff = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/31mer/lib.c:320:29: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
{ lib_array[i].reverse = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/31mer/lib.c:322:30: [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).
{ lib_array[i].asm_flag = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/31mer/lib.c:324:26: [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).
{ lib_array[i].rank = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/31mer/lib.c:326:34: [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).
{ lib_array[i].pair_num_cut = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/31mer/lib.c:328:35: [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).
{ lib_array[i].rd_len_cutoff = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/31mer/lib.c:330:29: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
{ lib_array[i].map_len = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/31mer/loadGraph.c:35:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], line[256];
data/soapdenovo-1.05/src/31mer/loadGraph.c:177:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char c, name[256], line[1024];
data/soapdenovo-1.05/src/31mer/loadGraph.c:367:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], line[1024];
data/soapdenovo-1.05/src/31mer/loadGraph.c:379:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
from_ed = atoi ( seg );
data/soapdenovo-1.05/src/31mer/loadGraph.c:384:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
target = atoi ( seg );
data/soapdenovo-1.05/src/31mer/loadGraph.c:386:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
weight = atoi ( seg );
data/soapdenovo-1.05/src/31mer/loadGraph.c:397:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char c, name[256], line[1024], *tightSeq = NULL;
data/soapdenovo-1.05/src/31mer/loadPath.c:43:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], line[1024];
data/soapdenovo-1.05/src/31mer/loadPath.c:48:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen ( name, "r" );
data/soapdenovo-1.05/src/31mer/loadPath.c:107:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen ( name, "r" );
data/soapdenovo-1.05/src/31mer/loadPath.c:120:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
edgeno = atoi ( seg );
data/soapdenovo-1.05/src/31mer/loadPath.c:145:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/31mer/loadPath.c:151:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen ( name, "r" );
data/soapdenovo-1.05/src/31mer/loadPath.c:213:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen ( name, "rb" );
data/soapdenovo-1.05/src/31mer/loadPreGraph.c:46:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], line[256];
data/soapdenovo-1.05/src/31mer/loadPreGraph.c:196:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char c, name[256], line[1024], str[32];
data/soapdenovo-1.05/src/31mer/loadPreGraph.c:367:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], line[1024];
data/soapdenovo-1.05/src/31mer/loadPreGraph.c:378:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
from_ed = atoi ( seg );
data/soapdenovo-1.05/src/31mer/loadPreGraph.c:382:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
target = atoi ( seg );
data/soapdenovo-1.05/src/31mer/loadPreGraph.c:384:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
weight = atoi ( seg );
data/soapdenovo-1.05/src/31mer/localAsm.c:293:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char kmerSeq[32], ch;
data/soapdenovo-1.05/src/31mer/localAsm.c:1355:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char fastSequence[MAXREADLENGTH];
data/soapdenovo-1.05/src/31mer/localAsm.c:1356:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char slowSequence[MAXREADLENGTH];
data/soapdenovo-1.05/src/31mer/main.c:92:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char * options[16];
data/soapdenovo-1.05/src/31mer/main.c:94:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char readfile[256], outfile[256];
data/soapdenovo-1.05/src/31mer/main.c:95:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[128];
data/soapdenovo-1.05/src/31mer/main.c:98:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char kmer_s[16], len_s[16], ncpu_s[16], M_s[16], lowK_s[16], lowC_s[16];
data/soapdenovo-1.05/src/31mer/main.c:120:12: [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).
kmer = atoi ( temp );
data/soapdenovo-1.05/src/31mer/main.c:124:14: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
GLDiff = atoi ( temp );
data/soapdenovo-1.05/src/31mer/main.c:128:9: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
M = atoi ( temp );
data/soapdenovo-1.05/src/31mer/main.c:133:12: [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).
ncpu = atoi ( temp );
data/soapdenovo-1.05/src/31mer/main.c:138:18: [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).
cutoff_len = atoi ( temp );
data/soapdenovo-1.05/src/31mer/main.c:149:12: [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).
lowK = atoi ( temp );
data/soapdenovo-1.05/src/31mer/main.c:154:12: [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).
lowC = atoi ( temp );
data/soapdenovo-1.05/src/31mer/main.c:157:23: [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).
initKmerSetSize = atoi ( optarg );
data/soapdenovo-1.05/src/31mer/main.c:191:3: [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 ( kmer_s, "%d", kmer );
data/soapdenovo-1.05/src/31mer/main.c:198:3: [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 ( ncpu_s, "%d", ncpu );
data/soapdenovo-1.05/src/31mer/main.c:205:3: [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 ( lowK_s, "%d", lowK );
data/soapdenovo-1.05/src/31mer/main.c:226:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf ( M_s, "%d", M );
data/soapdenovo-1.05/src/31mer/main.c:235:3: [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 ( lowC_s, "%d", lowC );
data/soapdenovo-1.05/src/31mer/main.c:255:3: [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 ( ncpu_s, "%d", ncpu );
data/soapdenovo-1.05/src/31mer/main.c:278:3: [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 ( ncpu_s, "%d", ncpu );
data/soapdenovo-1.05/src/31mer/main.c:285:3: [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 ( len_s, "%d", cutoff_len );
data/soapdenovo-1.05/src/31mer/map.c:29:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char shortrdsfile[256];
data/soapdenovo-1.05/src/31mer/map.c:30:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char graphfile[256];
data/soapdenovo-1.05/src/31mer/map.c:36:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], ch;
data/soapdenovo-1.05/src/31mer/map.c:39:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[1024];
data/soapdenovo-1.05/src/31mer/map.c:41:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen ( name, "r" );
data/soapdenovo-1.05/src/31mer/map.c:101:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[100];
data/soapdenovo-1.05/src/31mer/map.c:120:18: [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).
overlaplen = atoi ( temp );
data/soapdenovo-1.05/src/31mer/map.c:124:16: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
thrd_num = atoi ( temp );
data/soapdenovo-1.05/src/31mer/node2edge.c:36:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char edge_seq[100000];
data/soapdenovo-1.05/src/31mer/node2edge.c:48:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[256];
data/soapdenovo-1.05/src/31mer/orderContig.c:2187:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/31mer/orderContig.c:2744:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], *line;
data/soapdenovo-1.05/src/31mer/orderContig.c:2876:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], *line;
data/soapdenovo-1.05/src/31mer/output_contig.c:32:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/31mer/output_contig.c:122:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[256];
data/soapdenovo-1.05/src/31mer/output_contig.c:232:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/31mer/output_contig.c:267:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/31mer/output_pregraph.c:48:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[256];
data/soapdenovo-1.05/src/31mer/output_scaffold.c:30:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/31mer/output_scaffold.c:48:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/31mer/pregraph.c:29:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char shortrdsfile[256];
data/soapdenovo-1.05/src/31mer/pregraph.c:30:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char graphfile[256];
data/soapdenovo-1.05/src/31mer/pregraph.c:110:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[100];
data/soapdenovo-1.05/src/31mer/pregraph.c:129:18: [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).
overlaplen = atoi ( temp );
data/soapdenovo-1.05/src/31mer/pregraph.c:133:16: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
thrd_num = atoi ( temp );
data/soapdenovo-1.05/src/31mer/pregraph.c:140:17: [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).
deLowKmer = atoi ( temp ) >= 0 ? atoi ( temp ) : 0;
data/soapdenovo-1.05/src/31mer/pregraph.c:140:38: [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).
deLowKmer = atoi ( temp ) >= 0 ? atoi ( temp ) : 0;
data/soapdenovo-1.05/src/31mer/pregraph.c:146:23: [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).
initKmerSetSize = atoi ( optarg );
data/soapdenovo-1.05/src/31mer/prlHashCtg.c:78:21: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ( unsigned char ) ( hashBanBuffer[i] % thrd_num ) != id )
data/soapdenovo-1.05/src/31mer/prlHashCtg.c:250:12: [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).
{ return atoi ( & ( name[0] ) ); }
data/soapdenovo-1.05/src/31mer/prlHashCtg.c:258:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], *next_name;
data/soapdenovo-1.05/src/31mer/prlHashCtg.c:262:11: [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.
unsigned char thrdSignal[thrd_num + 1];
data/soapdenovo-1.05/src/31mer/prlHashReads.c:251:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char * next_name, name[256];
data/soapdenovo-1.05/src/31mer/prlHashReads.c:257:11: [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.
unsigned char thrdSignal[thrd_num + 1];
data/soapdenovo-1.05/src/31mer/prlHashReads.c:519:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char kmerSeq[32], ch;
data/soapdenovo-1.05/src/31mer/prlHashReads.c:615:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/31mer/prlRead2Ctg.c:489:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], lldne[1024];
data/soapdenovo-1.05/src/31mer/prlRead2Ctg.c:524:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char * src_name, *next_name, name[256];
data/soapdenovo-1.05/src/31mer/prlRead2Ctg.c:529:11: [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.
unsigned char thrdSignal[thrd_num + 1];
data/soapdenovo-1.05/src/31mer/prlRead2Ctg.c:726:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char * src_name, *next_name, name[256];
data/soapdenovo-1.05/src/31mer/prlRead2Ctg.c:731:11: [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.
unsigned char thrdSignal[thrd_num + 1];
data/soapdenovo-1.05/src/31mer/prlRead2path.c:323:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/31mer/prlRead2path.c:562:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], *src_name, *next_name;
data/soapdenovo-1.05/src/31mer/prlRead2path.c:567:11: [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.
unsigned char thrdSignal[thrd_num + 1];
data/soapdenovo-1.05/src/31mer/prlReadFillGap.c:125:3: [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 ( freadBuf, pt, len / 4 + 1 );
data/soapdenovo-1.05/src/31mer/prlReadFillGap.c:137:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[1024];
data/soapdenovo-1.05/src/31mer/prlReadFillGap.c:140:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen ( name, "rb" );
data/soapdenovo-1.05/src/31mer/prlReadFillGap.c:142:8: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp2 = fopen ( name, "rb" );
data/soapdenovo-1.05/src/31mer/prlReadFillGap.c:241:11: [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).
length = atoi ( tp );
data/soapdenovo-1.05/src/31mer/prlReadFillGap.c:243:8: [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 = atoi ( tp );
data/soapdenovo-1.05/src/31mer/prlReadFillGap.c:251:9: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
ctg = atoi ( tp );
data/soapdenovo-1.05/src/31mer/prlReadFillGap.c:1026:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[1024];
data/soapdenovo-1.05/src/31mer/prlReadFillGap.c:1034:11: [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.
unsigned char thrdSignal[thrd_num + 1];
data/soapdenovo-1.05/src/31mer/read2scaf.c:125:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[1024];
data/soapdenovo-1.05/src/31mer/read2scaf.c:265:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[1024], line[1024];
data/soapdenovo-1.05/src/31mer/readseq1by1.c:28:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char src_rc_seq[1024];
data/soapdenovo-1.05/src/31mer/readseq1by1.c:34:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[5000];
data/soapdenovo-1.05/src/31mer/readseq1by1.c:121:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[5000];
data/soapdenovo-1.05/src/31mer/readseq1by1.c:144:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[5000], src_name[5000];
data/soapdenovo-1.05/src/31mer/readseq1by1.c:188:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[5000];
data/soapdenovo-1.05/src/31mer/scaffold.c:32:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char graphfile[256];
data/soapdenovo-1.05/src/31mer/scaffold.c:84:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[256];
data/soapdenovo-1.05/src/31mer/scaffold.c:100:14: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
GLDiff = atoi ( temp );
data/soapdenovo-1.05/src/31mer/scaffold.c:104:17: [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).
ctg_short = atoi ( temp );
data/soapdenovo-1.05/src/31mer/scaffold.c:117:16: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
thrd_num = atoi ( temp );
data/soapdenovo-1.05/src/31mer/splitReps.c:31:17: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static unsigned char gothrough[4][4];
data/soapdenovo-1.05/src/63mer/arc.c:80:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/63mer/attachPEinfo.c:59:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], line[1024];
data/soapdenovo-1.05/src/63mer/attachPEinfo.c:63:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen ( name, "r" );
data/soapdenovo-1.05/src/63mer/bubble.c:62:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char fastSequence[MAXREADLENGTH];
data/soapdenovo-1.05/src/63mer/bubble.c:63:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char slowSequence[MAXREADLENGTH];
data/soapdenovo-1.05/src/63mer/bubble.c:1867:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[256];
data/soapdenovo-1.05/src/63mer/check.c:32:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ( ( fp = fopen ( name, mode ) ) == NULL )
data/soapdenovo-1.05/src/63mer/check.c:75:2: [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 ( p, q, old_size );
data/soapdenovo-1.05/src/63mer/connect.c:69:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/63mer/contig.c:30:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char shortrdsfile[256], graphfile[256];
data/soapdenovo-1.05/src/63mer/contig.c:104:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[100];
data/soapdenovo-1.05/src/63mer/contig.c:114:9: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
M = atoi ( temp );
data/soapdenovo-1.05/src/63mer/cutTipPreGraph.c:454:11: [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.
unsigned char thrdSignal[thrd_num + 1];
data/soapdenovo-1.05/src/63mer/inc/nuc.h:24:1: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char na_name[17] = {'g', 'a', 't', 'c',
data/soapdenovo-1.05/src/63mer/kmer.c:186:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char kmerSeq[64];
data/soapdenovo-1.05/src/63mer/lib.c:28:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char tabs[2][1024];
data/soapdenovo-1.05/src/63mer/lib.c:102:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[1024], ch;
data/soapdenovo-1.05/src/63mer/lib.c:126:20: [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).
{ maxReadLen = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/63mer/lib.c:205:31: [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.
lib_array[i].s_a_fname = ( char ** ) ckalloc ( lib_array[i].num_s_a_file * sizeof ( char * ) );
data/soapdenovo-1.05/src/63mer/lib.c:213:31: [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.
lib_array[i].s_q_fname = ( char ** ) ckalloc ( lib_array[i].num_s_q_file * sizeof ( char * ) );
data/soapdenovo-1.05/src/63mer/lib.c:221:29: [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.
lib_array[i].p_fname = ( char ** ) ckalloc ( lib_array[i].num_p_file * sizeof ( char * ) );
data/soapdenovo-1.05/src/63mer/lib.c:229:30: [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.
lib_array[i].a1_fname = ( char ** ) ckalloc ( lib_array[i].num_a1_file * sizeof ( char * ) );
data/soapdenovo-1.05/src/63mer/lib.c:237:30: [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.
lib_array[i].a2_fname = ( char ** ) ckalloc ( lib_array[i].num_a2_file * sizeof ( char * ) );
data/soapdenovo-1.05/src/63mer/lib.c:245:30: [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.
lib_array[i].q1_fname = ( char ** ) ckalloc ( lib_array[i].num_q1_file * sizeof ( char * ) );
data/soapdenovo-1.05/src/63mer/lib.c:253:30: [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.
lib_array[i].q2_fname = ( char ** ) ckalloc ( lib_array[i].num_q2_file * sizeof ( char * ) );
data/soapdenovo-1.05/src/63mer/lib.c:333:29: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
{ lib_array[i].min_ins = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/63mer/lib.c:335:29: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
{ lib_array[i].max_ins = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/63mer/lib.c:337:29: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
{ lib_array[i].avg_ins = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/63mer/lib.c:339:35: [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).
{ lib_array[i].rd_len_cutoff = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/63mer/lib.c:341:29: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
{ lib_array[i].reverse = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/63mer/lib.c:343:30: [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).
{ lib_array[i].asm_flag = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/63mer/lib.c:345:26: [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).
{ lib_array[i].rank = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/63mer/lib.c:347:34: [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).
{ lib_array[i].pair_num_cut = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/63mer/lib.c:349:35: [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).
{ lib_array[i].rd_len_cutoff = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/63mer/lib.c:351:29: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
{ lib_array[i].map_len = atoi ( tabs[1] ); }
data/soapdenovo-1.05/src/63mer/loadGraph.c:171:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char c, name[256], line[1024];
data/soapdenovo-1.05/src/63mer/loadGraph.c:359:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], line[1024];
data/soapdenovo-1.05/src/63mer/loadGraph.c:371:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
from_ed = atoi ( seg );
data/soapdenovo-1.05/src/63mer/loadGraph.c:376:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
target = atoi ( seg );
data/soapdenovo-1.05/src/63mer/loadGraph.c:378:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
weight = atoi ( seg );
data/soapdenovo-1.05/src/63mer/loadGraph.c:389:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char c, name[256], line[1024], *tightSeq = NULL;
data/soapdenovo-1.05/src/63mer/loadPath.c:43:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], line[1024];
data/soapdenovo-1.05/src/63mer/loadPath.c:48:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen ( name, "r" );
data/soapdenovo-1.05/src/63mer/loadPath.c:107:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen ( name, "r" );
data/soapdenovo-1.05/src/63mer/loadPath.c:120:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
edgeno = atoi ( seg );
data/soapdenovo-1.05/src/63mer/loadPath.c:145:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/63mer/loadPath.c:151:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen ( name, "r" );
data/soapdenovo-1.05/src/63mer/loadPath.c:213:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen ( name, "rb" );
data/soapdenovo-1.05/src/63mer/loadPreGraph.c:46:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], line[256];
data/soapdenovo-1.05/src/63mer/loadPreGraph.c:207:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char c, name[256], line[1024], str[32];
data/soapdenovo-1.05/src/63mer/loadPreGraph.c:374:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], line[1024];
data/soapdenovo-1.05/src/63mer/loadPreGraph.c:385:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
from_ed = atoi ( seg );
data/soapdenovo-1.05/src/63mer/loadPreGraph.c:389:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
target = atoi ( seg );
data/soapdenovo-1.05/src/63mer/loadPreGraph.c:391:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
weight = atoi ( seg );
data/soapdenovo-1.05/src/63mer/localAsm.c:307:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char kmerSeq[64];
data/soapdenovo-1.05/src/63mer/localAsm.c:1387:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char fastSequence[MAXREADLENGTH];
data/soapdenovo-1.05/src/63mer/localAsm.c:1388:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char slowSequence[MAXREADLENGTH];
data/soapdenovo-1.05/src/63mer/main.c:83:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char * options[16];
data/soapdenovo-1.05/src/63mer/main.c:85:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char readfile[256], outfile[256];
data/soapdenovo-1.05/src/63mer/main.c:86:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[128];
data/soapdenovo-1.05/src/63mer/main.c:89:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char kmer_s[16], len_s[16], ncpu_s[16], M_s[16];
data/soapdenovo-1.05/src/63mer/main.c:111:12: [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).
kmer = atoi ( temp );
data/soapdenovo-1.05/src/63mer/main.c:115:14: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
GLDiff = atoi ( temp );
data/soapdenovo-1.05/src/63mer/main.c:119:9: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
M = atoi ( temp );
data/soapdenovo-1.05/src/63mer/main.c:124:12: [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).
ncpu = atoi ( temp );
data/soapdenovo-1.05/src/63mer/main.c:129:18: [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).
cutoff_len = atoi ( temp );
data/soapdenovo-1.05/src/63mer/main.c:144:23: [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).
initKmerSetSize = atoi ( optarg );
data/soapdenovo-1.05/src/63mer/main.c:178:3: [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 ( kmer_s, "%d", kmer );
data/soapdenovo-1.05/src/63mer/main.c:185:3: [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 ( ncpu_s, "%d", ncpu );
data/soapdenovo-1.05/src/63mer/main.c:212:2: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf ( M_s, "%d", M );
data/soapdenovo-1.05/src/63mer/main.c:234:3: [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 ( ncpu_s, "%d", ncpu );
data/soapdenovo-1.05/src/63mer/main.c:257:3: [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 ( ncpu_s, "%d", ncpu );
data/soapdenovo-1.05/src/63mer/main.c:264:3: [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 ( len_s, "%d", cutoff_len );
data/soapdenovo-1.05/src/63mer/map.c:29:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char shortrdsfile[256];
data/soapdenovo-1.05/src/63mer/map.c:30:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char graphfile[256];
data/soapdenovo-1.05/src/63mer/map.c:36:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], ch;
data/soapdenovo-1.05/src/63mer/map.c:39:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[1024];
data/soapdenovo-1.05/src/63mer/map.c:41:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen ( name, "r" );
data/soapdenovo-1.05/src/63mer/map.c:102:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[100];
data/soapdenovo-1.05/src/63mer/map.c:121:18: [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).
overlaplen = atoi ( temp );
data/soapdenovo-1.05/src/63mer/map.c:125:16: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
thrd_num = atoi ( temp );
data/soapdenovo-1.05/src/63mer/node2edge.c:36:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char edge_seq[100000];
data/soapdenovo-1.05/src/63mer/node2edge.c:48:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[256];
data/soapdenovo-1.05/src/63mer/orderContig.c:2187:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/63mer/orderContig.c:2744:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], *line;
data/soapdenovo-1.05/src/63mer/orderContig.c:2875:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], *line;
data/soapdenovo-1.05/src/63mer/output_contig.c:32:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/63mer/output_contig.c:113:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[256];
data/soapdenovo-1.05/src/63mer/output_contig.c:226:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/63mer/output_contig.c:262:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/63mer/output_pregraph.c:50:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[256];
data/soapdenovo-1.05/src/63mer/output_scaffold.c:30:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/63mer/output_scaffold.c:48:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/63mer/pregraph.c:29:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char shortrdsfile[256];
data/soapdenovo-1.05/src/63mer/pregraph.c:30:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char graphfile[256];
data/soapdenovo-1.05/src/63mer/pregraph.c:110:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[100];
data/soapdenovo-1.05/src/63mer/pregraph.c:129:18: [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).
overlaplen = atoi ( temp );
data/soapdenovo-1.05/src/63mer/pregraph.c:133:16: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
thrd_num = atoi ( temp );
data/soapdenovo-1.05/src/63mer/pregraph.c:145:23: [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).
initKmerSetSize = atoi ( optarg );
data/soapdenovo-1.05/src/63mer/prlHashCtg.c:79:21: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
if ( ( unsigned char ) ( hashBanBuffer[i] % thrd_num ) != id )
data/soapdenovo-1.05/src/63mer/prlHashCtg.c:251:12: [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).
{ return atoi ( & ( name[0] ) ); }
data/soapdenovo-1.05/src/63mer/prlHashCtg.c:259:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], *next_name;
data/soapdenovo-1.05/src/63mer/prlHashCtg.c:263:11: [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.
unsigned char thrdSignal[thrd_num + 1];
data/soapdenovo-1.05/src/63mer/prlHashReads.c:252:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char * next_name, name[256];
data/soapdenovo-1.05/src/63mer/prlHashReads.c:258:11: [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.
unsigned char thrdSignal[thrd_num + 1];
data/soapdenovo-1.05/src/63mer/prlHashReads.c:596:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/63mer/prlRead2Ctg.c:488:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], lldne[1024];
data/soapdenovo-1.05/src/63mer/prlRead2Ctg.c:523:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char * src_name, *next_name, name[256];
data/soapdenovo-1.05/src/63mer/prlRead2Ctg.c:528:11: [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.
unsigned char thrdSignal[thrd_num + 1];
data/soapdenovo-1.05/src/63mer/prlRead2Ctg.c:716:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char * src_name, *next_name, name[256];
data/soapdenovo-1.05/src/63mer/prlRead2Ctg.c:721:11: [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.
unsigned char thrdSignal[thrd_num + 1];
data/soapdenovo-1.05/src/63mer/prlRead2path.c:325:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256];
data/soapdenovo-1.05/src/63mer/prlRead2path.c:570:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[256], *src_name, *next_name;
data/soapdenovo-1.05/src/63mer/prlRead2path.c:575:11: [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.
unsigned char thrdSignal[thrd_num + 1];
data/soapdenovo-1.05/src/63mer/prlReadFillGap.c:125:3: [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 ( freadBuf, pt, len / 4 + 1 );
data/soapdenovo-1.05/src/63mer/prlReadFillGap.c:137:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[1024];
data/soapdenovo-1.05/src/63mer/prlReadFillGap.c:140:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen ( name, "rb" );
data/soapdenovo-1.05/src/63mer/prlReadFillGap.c:142:8: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp2 = fopen ( name, "rb" );
data/soapdenovo-1.05/src/63mer/prlReadFillGap.c:241:11: [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).
length = atoi ( tp );
data/soapdenovo-1.05/src/63mer/prlReadFillGap.c:243:8: [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 = atoi ( tp );
data/soapdenovo-1.05/src/63mer/prlReadFillGap.c:251:9: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
ctg = atoi ( tp );
data/soapdenovo-1.05/src/63mer/prlReadFillGap.c:1038:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[1024];
data/soapdenovo-1.05/src/63mer/prlReadFillGap.c:1046:11: [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.
unsigned char thrdSignal[thrd_num + 1];
data/soapdenovo-1.05/src/63mer/read2scaf.c:125:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[1024];
data/soapdenovo-1.05/src/63mer/read2scaf.c:269:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[1024], line[1024];
data/soapdenovo-1.05/src/63mer/readseq1by1.c:28:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char src_rc_seq[1024];
data/soapdenovo-1.05/src/63mer/readseq1by1.c:34:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[5000];
data/soapdenovo-1.05/src/63mer/readseq1by1.c:121:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[5000];
data/soapdenovo-1.05/src/63mer/readseq1by1.c:144:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[5000], src_name[5000];
data/soapdenovo-1.05/src/63mer/readseq1by1.c:188:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char str[5000];
data/soapdenovo-1.05/src/63mer/scaffold.c:32:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char graphfile[256];
data/soapdenovo-1.05/src/63mer/scaffold.c:84:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp[256];
data/soapdenovo-1.05/src/63mer/scaffold.c:100:14: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
GLDiff = atoi ( temp );
data/soapdenovo-1.05/src/63mer/scaffold.c:104:17: [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).
ctg_short = atoi ( temp );
data/soapdenovo-1.05/src/63mer/scaffold.c:117:16: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
thrd_num = atoi ( temp );
data/soapdenovo-1.05/src/63mer/splitReps.c:31:17: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static unsigned char gothrough[4][4];
data/soapdenovo-1.05/src/127mer/attachPEinfo.c:303:7: [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 ( line ) )
data/soapdenovo-1.05/src/127mer/cutTipPreGraph.c:369:3: [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 ( 1 );
data/soapdenovo-1.05/src/127mer/cutTipPreGraph.c:442:3: [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 ( 10 );
data/soapdenovo-1.05/src/127mer/lib.c:53:12: [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).
int len = strlen ( line );
data/soapdenovo-1.05/src/127mer/loadGraph.c:415:21: [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).
for ( i = 0; i < strlen ( line ); i++ )
data/soapdenovo-1.05/src/127mer/loadPreGraph.c:277:14: [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).
linelen = strlen ( line );
data/soapdenovo-1.05/src/127mer/localAsm.c:88:41: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
static void getSeqFromRead ( READNEARBY read, char * src_seq )
data/soapdenovo-1.05/src/127mer/localAsm.c:90:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int len_seq = read.len;
data/soapdenovo-1.05/src/127mer/localAsm.c:92:57: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
char * tightSeq = ( char * ) darrayGet ( readSeqInGap, read.seqStarter );
data/soapdenovo-1.05/src/127mer/orderContig.c:2811:7: [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 ( line ) )
data/soapdenovo-1.05/src/127mer/prlHashCtg.c:109:3: [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 ( 1 );
data/soapdenovo-1.05/src/127mer/prlHashCtg.c:237:3: [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 ( 10 );
data/soapdenovo-1.05/src/127mer/prlHashReads.c:113:3: [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 ( 1 );
data/soapdenovo-1.05/src/127mer/prlHashReads.c:238:3: [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 ( 10 );
data/soapdenovo-1.05/src/127mer/prlRead2Ctg.c:132:3: [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 ( 1 );
data/soapdenovo-1.05/src/127mer/prlRead2Ctg.c:325:3: [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 ( 10 );
data/soapdenovo-1.05/src/127mer/prlRead2path.c:193:3: [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 ( 1 );
data/soapdenovo-1.05/src/127mer/prlRead2path.c:556:3: [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 ( 10 );
data/soapdenovo-1.05/src/127mer/prlReadFillGap.c:917:3: [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 ( 1 );
data/soapdenovo-1.05/src/127mer/prlReadFillGap.c:947:3: [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 ( 10 );
data/soapdenovo-1.05/src/127mer/readseq1by1.c:56:11: [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).
strL = strlen ( str );
data/soapdenovo-1.05/src/127mer/readseq1by1.c:130:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
slen = strlen ( str );
data/soapdenovo-1.05/src/127mer/readseq1by1.c:165:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ( ( l = strlen ( src_name ) ) > *max_name_leg )
data/soapdenovo-1.05/src/127mer/readseq1by1.c:170:9: [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).
n += strlen ( str ) - 1;
data/soapdenovo-1.05/src/127mer/readseq1by1.c:219:11: [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).
strL = strlen ( str );
data/soapdenovo-1.05/src/127mer/readseq1by1.c:324:7: [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 ( fname ) > 3 && strcmp ( fname + strlen ( fname ) - 3, ".gz" ) == 0 )
data/soapdenovo-1.05/src/127mer/readseq1by1.c:324:48: [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).
if ( strlen ( fname ) > 3 && strcmp ( fname + strlen ( fname ) - 3, ".gz" ) == 0 )
data/soapdenovo-1.05/src/127mer/readseq1by1.c:326:39: [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).
char * cmd = ( char * ) ckalloc ( ( strlen ( fname ) + 20 ) * sizeof ( char ) );
data/soapdenovo-1.05/src/127mer/readseq1by1.c:421:7: [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 ( fname ) > 3 && strcmp ( fname + strlen ( fname ) - 3, ".gz" ) == 0 )
data/soapdenovo-1.05/src/127mer/readseq1by1.c:421:48: [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).
if ( strlen ( fname ) > 3 && strcmp ( fname + strlen ( fname ) - 3, ".gz" ) == 0 )
data/soapdenovo-1.05/src/127mer/readseq1by1.c:440:7: [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 ( fname ) > 3 && strcmp ( fname + strlen ( fname ) - 3, ".gz" ) == 0 )
data/soapdenovo-1.05/src/127mer/readseq1by1.c:440:48: [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).
if ( strlen ( fname ) > 3 && strcmp ( fname + strlen ( fname ) - 3, ".gz" ) == 0 )
data/soapdenovo-1.05/src/31mer/attachPEinfo.c:303:7: [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 ( line ) )
data/soapdenovo-1.05/src/31mer/cutTipPreGraph.c:374:3: [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 ( 1 );
data/soapdenovo-1.05/src/31mer/cutTipPreGraph.c:447:3: [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 ( 10 );
data/soapdenovo-1.05/src/31mer/lib.c:32:12: [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).
int len = strlen ( line );
data/soapdenovo-1.05/src/31mer/loadGraph.c:423:21: [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).
for ( i = 0; i < strlen ( line ); i++ )
data/soapdenovo-1.05/src/31mer/loadPreGraph.c:243:14: [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).
linelen = strlen ( line );
data/soapdenovo-1.05/src/31mer/localAsm.c:79:41: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
static void getSeqFromRead ( READNEARBY read, char * src_seq )
data/soapdenovo-1.05/src/31mer/localAsm.c:81:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int len_seq = read.len;
data/soapdenovo-1.05/src/31mer/localAsm.c:83:57: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
char * tightSeq = ( char * ) darrayGet ( readSeqInGap, read.seqStarter );
data/soapdenovo-1.05/src/31mer/orderContig.c:2811:7: [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 ( line ) )
data/soapdenovo-1.05/src/31mer/prlHashCtg.c:108:3: [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 ( 1 );
data/soapdenovo-1.05/src/31mer/prlHashCtg.c:236:3: [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 ( 10 );
data/soapdenovo-1.05/src/31mer/prlHashReads.c:112:3: [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 ( 1 );
data/soapdenovo-1.05/src/31mer/prlHashReads.c:237:3: [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 ( 10 );
data/soapdenovo-1.05/src/31mer/prlRead2Ctg.c:134:3: [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 ( 1 );
data/soapdenovo-1.05/src/31mer/prlRead2Ctg.c:337:3: [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 ( 10 );
data/soapdenovo-1.05/src/31mer/prlRead2path.c:191:3: [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 ( 1 );
data/soapdenovo-1.05/src/31mer/prlRead2path.c:548:3: [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 ( 10 );
data/soapdenovo-1.05/src/31mer/prlReadFillGap.c:905:3: [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 ( 1 );
data/soapdenovo-1.05/src/31mer/prlReadFillGap.c:935:3: [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 ( 10 );
data/soapdenovo-1.05/src/31mer/readseq1by1.c:56:11: [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).
strL = strlen ( str );
data/soapdenovo-1.05/src/31mer/readseq1by1.c:130:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
slen = strlen ( str );
data/soapdenovo-1.05/src/31mer/readseq1by1.c:165:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ( ( l = strlen ( src_name ) ) > *max_name_leg )
data/soapdenovo-1.05/src/31mer/readseq1by1.c:170:9: [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).
n += strlen ( str ) - 1;
data/soapdenovo-1.05/src/31mer/readseq1by1.c:219:11: [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).
strL = strlen ( str );
data/soapdenovo-1.05/src/31mer/readseq1by1.c:324:7: [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 ( fname ) > 3 && strcmp ( fname + strlen ( fname ) - 3, ".gz" ) == 0 )
data/soapdenovo-1.05/src/31mer/readseq1by1.c:324:48: [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).
if ( strlen ( fname ) > 3 && strcmp ( fname + strlen ( fname ) - 3, ".gz" ) == 0 )
data/soapdenovo-1.05/src/31mer/readseq1by1.c:326:39: [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).
char * cmd = ( char * ) ckalloc ( ( strlen ( fname ) + 20 ) * sizeof ( char ) );
data/soapdenovo-1.05/src/31mer/readseq1by1.c:421:7: [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 ( fname ) > 3 && strcmp ( fname + strlen ( fname ) - 3, ".gz" ) == 0 )
data/soapdenovo-1.05/src/31mer/readseq1by1.c:421:48: [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).
if ( strlen ( fname ) > 3 && strcmp ( fname + strlen ( fname ) - 3, ".gz" ) == 0 )
data/soapdenovo-1.05/src/31mer/readseq1by1.c:440:7: [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 ( fname ) > 3 && strcmp ( fname + strlen ( fname ) - 3, ".gz" ) == 0 )
data/soapdenovo-1.05/src/31mer/readseq1by1.c:440:48: [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).
if ( strlen ( fname ) > 3 && strcmp ( fname + strlen ( fname ) - 3, ".gz" ) == 0 )
data/soapdenovo-1.05/src/63mer/attachPEinfo.c:303:7: [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 ( line ) )
data/soapdenovo-1.05/src/63mer/cutTipPreGraph.c:365:3: [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 ( 1 );
data/soapdenovo-1.05/src/63mer/cutTipPreGraph.c:438:3: [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 ( 10 );
data/soapdenovo-1.05/src/63mer/lib.c:53:12: [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).
int len = strlen ( line );
data/soapdenovo-1.05/src/63mer/loadGraph.c:415:21: [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).
for ( i = 0; i < strlen ( line ); i++ )
data/soapdenovo-1.05/src/63mer/loadPreGraph.c:256:14: [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).
linelen = strlen ( line );
data/soapdenovo-1.05/src/63mer/localAsm.c:81:41: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
static void getSeqFromRead ( READNEARBY read, char * src_seq )
data/soapdenovo-1.05/src/63mer/localAsm.c:83:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int len_seq = read.len;
data/soapdenovo-1.05/src/63mer/localAsm.c:85:57: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
char * tightSeq = ( char * ) darrayGet ( readSeqInGap, read.seqStarter );
data/soapdenovo-1.05/src/63mer/orderContig.c:2811:7: [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 ( line ) )
data/soapdenovo-1.05/src/63mer/prlHashCtg.c:109:3: [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 ( 1 );
data/soapdenovo-1.05/src/63mer/prlHashCtg.c:237:3: [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 ( 10 );
data/soapdenovo-1.05/src/63mer/prlHashReads.c:113:3: [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 ( 1 );
data/soapdenovo-1.05/src/63mer/prlHashReads.c:238:3: [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 ( 10 );
data/soapdenovo-1.05/src/63mer/prlRead2Ctg.c:132:3: [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 ( 1 );
data/soapdenovo-1.05/src/63mer/prlRead2Ctg.c:325:3: [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 ( 10 );
data/soapdenovo-1.05/src/63mer/prlRead2path.c:193:3: [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 ( 1 );
data/soapdenovo-1.05/src/63mer/prlRead2path.c:556:3: [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 ( 10 );
data/soapdenovo-1.05/src/63mer/prlReadFillGap.c:917:3: [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 ( 1 );
data/soapdenovo-1.05/src/63mer/prlReadFillGap.c:947:3: [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 ( 10 );
data/soapdenovo-1.05/src/63mer/readseq1by1.c:56:11: [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).
strL = strlen ( str );
data/soapdenovo-1.05/src/63mer/readseq1by1.c:130:10: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
slen = strlen ( str );
data/soapdenovo-1.05/src/63mer/readseq1by1.c:165:15: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ( ( l = strlen ( src_name ) ) > *max_name_leg )
data/soapdenovo-1.05/src/63mer/readseq1by1.c:170:9: [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).
n += strlen ( str ) - 1;
data/soapdenovo-1.05/src/63mer/readseq1by1.c:219:11: [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).
strL = strlen ( str );
data/soapdenovo-1.05/src/63mer/readseq1by1.c:324:7: [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 ( fname ) > 3 && strcmp ( fname + strlen ( fname ) - 3, ".gz" ) == 0 )
data/soapdenovo-1.05/src/63mer/readseq1by1.c:324:48: [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).
if ( strlen ( fname ) > 3 && strcmp ( fname + strlen ( fname ) - 3, ".gz" ) == 0 )
data/soapdenovo-1.05/src/63mer/readseq1by1.c:326:39: [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).
char * cmd = ( char * ) ckalloc ( ( strlen ( fname ) + 20 ) * sizeof ( char ) );
data/soapdenovo-1.05/src/63mer/readseq1by1.c:421:7: [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 ( fname ) > 3 && strcmp ( fname + strlen ( fname ) - 3, ".gz" ) == 0 )
data/soapdenovo-1.05/src/63mer/readseq1by1.c:421:48: [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).
if ( strlen ( fname ) > 3 && strcmp ( fname + strlen ( fname ) - 3, ".gz" ) == 0 )
data/soapdenovo-1.05/src/63mer/readseq1by1.c:440:7: [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 ( fname ) > 3 && strcmp ( fname + strlen ( fname ) - 3, ".gz" ) == 0 )
data/soapdenovo-1.05/src/63mer/readseq1by1.c:440:48: [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).
if ( strlen ( fname ) > 3 && strcmp ( fname + strlen ( fname ) - 3, ".gz" ) == 0 )
ANALYSIS SUMMARY:
Hits = 797
Lines analyzed = 71654 in approximately 1.67 seconds (42954 lines/second)
Physical Source Lines of Code (SLOC) = 51547
Hits@level = [0] 1607 [1] 96 [2] 420 [3] 15 [4] 266 [5] 0
Hits@level+ = [0+] 2404 [1+] 797 [2+] 701 [3+] 281 [4+] 266 [5+] 0
Hits/KSLOC@level+ = [0+] 46.637 [1+] 15.4616 [2+] 13.5992 [3+] 5.45134 [4+] 5.16034 [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.