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/sift-4.0.3b/src/PN_convert.h
Examining data/sift-4.0.3b/src/queue.c
Examining data/sift-4.0.3b/src/stringlist.h
Examining data/sift-4.0.3b/src/Psiblast.h
Examining data/sift-4.0.3b/src/SortList.h
Examining data/sift-4.0.3b/src/List_Number.h
Examining data/sift-4.0.3b/src/Protdist.h
Examining data/sift-4.0.3b/src/List_Number.c
Examining data/sift-4.0.3b/src/blocklist.h
Examining data/sift-4.0.3b/src/stringhash.h
Examining data/sift-4.0.3b/src/Array_math.c
Examining data/sift-4.0.3b/src/queue.h
Examining data/sift-4.0.3b/src/Alignment.h
Examining data/sift-4.0.3b/src/Psiblast_convert.h
Examining data/sift-4.0.3b/src/PN_blocks.h
Examining data/sift-4.0.3b/src/stringlist.c
Examining data/sift-4.0.3b/src/stringhash.c
Examining data/sift-4.0.3b/src/Matrix_Info.h
Examining data/sift-4.0.3b/src/blocklist.c
Examining data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c
Examining data/sift-4.0.3b/src/consensus_to_seq.c
Examining data/sift-4.0.3b/src/info_on_seqs.c
Examining data/sift-4.0.3b/src/PN_blocks.c
Examining data/sift-4.0.3b/src/Protdist.c
Examining data/sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c
Examining data/sift-4.0.3b/src/seqs_from_psiblast_res.c
Examining data/sift-4.0.3b/src/sift_blimps.h
Examining data/sift-4.0.3b/src/SortList.c
Examining data/sift-4.0.3b/src/Clumping.c
Examining data/sift-4.0.3b/src/Alignment.c
Examining data/sift-4.0.3b/src/PN_convert.c
Examining data/sift-4.0.3b/src/Psiblast.c
Examining data/sift-4.0.3b/src/clump_output_alignedseq.c
Examining data/sift-4.0.3b/src/Matrix_Info.c
FINAL RESULTS:
data/sift-4.0.3b/src/Alignment.c:81:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmp_name, "mablock.%s", desc);
data/sift-4.0.3b/src/Alignment.c:157:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(line, "\\rm %s", tmp_name);
data/sift-4.0.3b/src/Alignment.c:158:4: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(line);
data/sift-4.0.3b/src/Alignment.c:194:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmp_name, "mablock.%s", desc);
data/sift-4.0.3b/src/Alignment.c:270:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(line, "\\rm %s", tmp_name);
data/sift-4.0.3b/src/Alignment.c:271:4: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system(line);
data/sift-4.0.3b/src/Alignment.c:326:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (newseqs[i]->name, seqs[i]->name);
data/sift-4.0.3b/src/Alignment.c:426:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tmp_name, "%s.tmp", desc);
data/sift-4.0.3b/src/Alignment.c:547:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf (line, "\\rm %s", tmp_name);
data/sift-4.0.3b/src/Alignment.c:553:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(line, "\\rm %s", tmp_name);
data/sift-4.0.3b/src/Alignment.c:630:7: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(block->sequences[s].name, seqs[s]->name);
data/sift-4.0.3b/src/Alignment.c:680:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(block->sequences[blockseq].name, seqs[s]->name);
data/sift-4.0.3b/src/Alignment.c:938:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ctemp, seqs[s]->name);
data/sift-4.0.3b/src/Alignment.c:939:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(seqs[s]->name, ctemp+3);
data/sift-4.0.3b/src/Alignment.c:958:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ctemp, seqs[s]->name);
data/sift-4.0.3b/src/Alignment.c:963:11: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(seqs[s]->name, "%s%d", ctemp, s);
data/sift-4.0.3b/src/Alignment.c:993:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ctemp, seqs[s]->name);
data/sift-4.0.3b/src/Alignment.c:994:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(seqs[s]->name, ctemp+3);
data/sift-4.0.3b/src/Alignment.c:1003:9: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat (seqs[s]->name, ctemp);
data/sift-4.0.3b/src/Alignment.c:1024:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (ctemp, seqs[s]->name + startindex);
data/sift-4.0.3b/src/Alignment.c:1026:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (seqs[s]->name, ctemp);
data/sift-4.0.3b/src/Alignment.c:1073:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(ctemp, seqs[s]->name);
data/sift-4.0.3b/src/Alignment.c:1078:11: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(seqs[s]->name, "%s%d", ctemp, s);
data/sift-4.0.3b/src/Alignment.c:1101:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (newseqs[i]->name, seqs[i]->name);
data/sift-4.0.3b/src/Alignment.c:1102:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (newseqs[i]->info, seqs[i]->info);
data/sift-4.0.3b/src/Alignment.c:1177:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (newseq->name, oldseq->name);
data/sift-4.0.3b/src/Alignment.c:1178:10: [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 (newseq->info, oldseq->info);
data/sift-4.0.3b/src/Alignment.c:1392:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (name, &strptr[1]); /* don't need > */
data/sift-4.0.3b/src/Alignment.c:1394:4: [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 (info, strptr);
data/sift-4.0.3b/src/Alignment.c:1442:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (subject->info, info);
data/sift-4.0.3b/src/Alignment.c:1614:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (query_seq, strptr);
data/sift-4.0.3b/src/Alignment.c:1626:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (subject_seq, strptr);
data/sift-4.0.3b/src/Alignment.c:1693:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (subject->name, subject_name);
data/sift-4.0.3b/src/Alignment.c:1706:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (query_seq, strptr);
data/sift-4.0.3b/src/Alignment.c:1721:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (subject_seq, strptr);
data/sift-4.0.3b/src/Alignment.c:2097:9: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat (consensus_sequence->name, comment);
data/sift-4.0.3b/src/Clumping.c:420:9: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
strcat (consensus_sequence->name, comment);
data/sift-4.0.3b/src/Matrix_Info.c:299:11: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (word1, stringp);
data/sift-4.0.3b/src/Matrix_Info.c:301:25: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (result, stringp);
data/sift-4.0.3b/src/Matrix_Info.c:307:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (word2, &word1[1]);
data/sift-4.0.3b/src/Matrix_Info.c:1517:26: [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 (word1, stringp);
data/sift-4.0.3b/src/Matrix_Info.c:1522:17: [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 (word2, &word1[1]);
data/sift-4.0.3b/src/Matrix_Info.c:1580:26: [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 (word1, stringp);
data/sift-4.0.3b/src/Matrix_Info.c:1585:17: [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 (word2, &word1[1]);
data/sift-4.0.3b/src/PN_blocks.c:25:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (newblock->id, block->id);
data/sift-4.0.3b/src/PN_blocks.c:26:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (newblock->ac, block->ac);
data/sift-4.0.3b/src/PN_blocks.c:27:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (newblock->de, block->de);
data/sift-4.0.3b/src/PN_blocks.c:28:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (newblock->bl, block->bl);
data/sift-4.0.3b/src/PN_blocks.c:29:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (newblock->number, block->number);
data/sift-4.0.3b/src/PN_blocks.c:30:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (newblock->motif, block->motif);
data/sift-4.0.3b/src/PN_blocks.c:64:17: [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 (newblock->sequences[i].name,
data/sift-4.0.3b/src/PN_blocks.c:66:17: [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 (newblock->sequences[i].info,
data/sift-4.0.3b/src/PN_blocks.c:193:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (block1->sequences[new_block_index].name,
data/sift-4.0.3b/src/PN_blocks.c:195:13: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (block1->sequences[new_block_index].info,
data/sift-4.0.3b/src/PN_blocks.c:234:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (newblock->id, block->id);
data/sift-4.0.3b/src/PN_blocks.c:235:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (newblock->ac, block->ac);
data/sift-4.0.3b/src/PN_blocks.c:236:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (newblock->de, block->de);
data/sift-4.0.3b/src/PN_blocks.c:237:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (newblock->bl, block->bl);
data/sift-4.0.3b/src/PN_blocks.c:238:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (newblock->number, block->number);
data/sift-4.0.3b/src/PN_blocks.c:239:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (newblock->motif, block->motif);
data/sift-4.0.3b/src/PN_blocks.c:274:4: [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 (newblock->sequences[new_block_index].name,
data/sift-4.0.3b/src/PN_blocks.c:276:25: [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 (newblock->sequences[new_block_index].info,
data/sift-4.0.3b/src/PN_blocks.c:357:8: [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 (block->sequences[newseqindex].name,
data/sift-4.0.3b/src/PN_blocks.c:359:8: [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 (block->sequences[newseqindex].info,
data/sift-4.0.3b/src/PN_blocks.c:396:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (block->sequences[0].name,
data/sift-4.0.3b/src/PN_blocks.c:398:8: [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 (block->sequences[0].info,
data/sift-4.0.3b/src/PN_blocks.c:686:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (newblock->id, block->id);
data/sift-4.0.3b/src/PN_blocks.c:687:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (newblock->ac, block->ac);
data/sift-4.0.3b/src/PN_blocks.c:688:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (newblock->de, block->de);
data/sift-4.0.3b/src/PN_blocks.c:690:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (newblock->number, block->number);
data/sift-4.0.3b/src/PN_blocks.c:691:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (newblock->motif, block->motif);
data/sift-4.0.3b/src/PN_blocks.c:725:17: [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 (newblock->sequences[i].name,
data/sift-4.0.3b/src/PN_blocks.c:727:17: [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 (newblock->sequences[i].info,
data/sift-4.0.3b/src/PN_blocks.c:909:8: [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 (block->sequences[index].name,
data/sift-4.0.3b/src/PN_blocks.c:911:8: [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 (block->sequences[index].info,
data/sift-4.0.3b/src/PN_convert.c:88:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(matrix->ac, block->ac);
data/sift-4.0.3b/src/PN_convert.c:92:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(matrix->number, block->number);
data/sift-4.0.3b/src/PN_convert.c:183:5: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf(ErrorBuffer, /* ^^^^----------------vvvvvvvvvvvvvvvvvvv */
data/sift-4.0.3b/src/PN_convert.c:218:3: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf(ErrorBuffer, /* ^^^^----------------vvvvvvvvvvvvvvvvvvv */ "Using the default conversion method of Altschul's data-dependent method.\n");
data/sift-4.0.3b/src/PN_convert.c:448:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf (matrix_file, "%s/docs/blosum62.bla.new", blimps_dir);
data/sift-4.0.3b/src/PN_convert.c:782:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf (diri_file , "%s/docs/default.diri", blimps_dir);
data/sift-4.0.3b/src/PN_convert.c:999:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf (diri_file , "%s/docs/default.diri", blimps_dir);
data/sift-4.0.3b/src/PN_convert.c:1129:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf (diri_file , "%s/docs/default.diri", blimps_dir);
data/sift-4.0.3b/src/PN_convert.c:1138:3: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf (matrix_file, "%s/docs/default.qij", blimps_dir );
data/sift-4.0.3b/src/PN_convert.c:2172:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(frqname, "%s/docs/default.amino.frq", blimps_dir);
data/sift-4.0.3b/src/PN_convert.c:2173:7: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(qijname, "%s/docs/default.qij", blimps_dir);
data/sift-4.0.3b/src/PN_convert.c:2188:7: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system( "pwd" );
data/sift-4.0.3b/src/PN_convert.c:2235:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf (filename, "%s/docs/default.sij", blimps_dir);
data/sift-4.0.3b/src/Protdist.c:76:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (temp_name, pairwise_distances[i].name);
data/sift-4.0.3b/src/Protdist.c:81:4: [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 (pairwise_distances[j].name, pairwise_distances[j-1].name);
data/sift-4.0.3b/src/Protdist.c:85:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (pairwise_distances[j].name, temp_name);
data/sift-4.0.3b/src/Protdist.c:162:2: [4] (buffer) fscanf:
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.
fscanf (fp, "%s", pairwise_distance[0].name);
data/sift-4.0.3b/src/Protdist.c:176:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (temp_line,line);
data/sift-4.0.3b/src/Protdist.c:179:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (pairwise_distance[i].name, strptr);
data/sift-4.0.3b/src/Psiblast.c:61:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (alignment->subject->info, &Buffer[length +1]);
data/sift-4.0.3b/src/Psiblast.c:237:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf (command_line, "blastpgp -d %s -i %s -o %s -m 6 -R %s",
data/sift-4.0.3b/src/Psiblast.c:241:8: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
ret = system (command_line);
data/sift-4.0.3b/src/Psiblast.c:251:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf (command_line, "\\rm -f %s\n", filename);
data/sift-4.0.3b/src/Psiblast.c:253:2: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system (command_line);
data/sift-4.0.3b/src/Psiblast.c:261:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf (command_line, "formatdb -i %s -o T -p T\n", database);
data/sift-4.0.3b/src/Psiblast.c:263:2: [4] (shell) system:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
system (command_line);
data/sift-4.0.3b/src/blocklist.c:25:4: [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 (new->block_num, block_name);
data/sift-4.0.3b/src/blocklist.c:42:4: [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 (block->number, desc);
data/sift-4.0.3b/src/blocklist.c:51:4: [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 (block->id, desc);
data/sift-4.0.3b/src/blocklist.c:52:4: [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(block->de, desc);
data/sift-4.0.3b/src/blocklist.c:56:4: [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 (ctemp, desc);
data/sift-4.0.3b/src/blocklist.c:85:4: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(block->ac, "%s; distance from previous blocks=(0,0)",
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:114:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (query_filename, pid);
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:133:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (temp_chk_filename, pid);
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:135:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (psiblastres_file, pid);
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:137:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (query_database_file, pid);
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:297:23: [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).
if (argc > 1) strcpy (query_seq_file, argv[1]);
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:305:24: [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).
if ( argc > 2) strcpy (seqfile, argv[2]);
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:317:17: [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).
if ( argc > 3) strcpy (outfile, argv[3]);
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:324:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (errorfilename, outfile);
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:336:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (logfile, outfile);
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:351:16: [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).
if (argc > 5) strcpy (pid, argv[5]);
data/sift-4.0.3b/src/clump_output_alignedseq.c:143:17: [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).
if (argc > 1 ) strcpy (seqfilename, argv[1]);
data/sift-4.0.3b/src/clump_output_alignedseq.c:155:23: [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).
if (argc > 2) strcpy (outfilename, argv[2]);
data/sift-4.0.3b/src/clump_output_alignedseq.c:163:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (errorfilename, outfilename);
data/sift-4.0.3b/src/consensus_to_seq.c:69:3: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (consensus[no_of_items]->title, strptr);
data/sift-4.0.3b/src/consensus_to_seq.c:74:4: [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 (temp_key, strptr);
data/sift-4.0.3b/src/consensus_to_seq.c:119:16: [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).
if (argc > 1) strcpy (seqfilename, argv[1]);
data/sift-4.0.3b/src/consensus_to_seq.c:132:16: [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).
if (argc > 2) strcpy (keyfilename, argv[2]) ;
data/sift-4.0.3b/src/consensus_to_seq.c:143:16: [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).
if (argc > 3) strcpy (outfilename, argv[3]);
data/sift-4.0.3b/src/info_on_seqs.c:109:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (tempname, outfilename);
data/sift-4.0.3b/src/info_on_seqs.c:523:16: [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).
if (argc > 1) strcpy (seqfilename, argv[1]);
data/sift-4.0.3b/src/info_on_seqs.c:536:16: [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).
if (argc > 2) strcpy (substfilename, argv[2]);
data/sift-4.0.3b/src/info_on_seqs.c:553:16: [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).
if (argc > 3) strcpy (outfilename, argv[3]);
data/sift-4.0.3b/src/info_on_seqs.c:560:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (errorfilename, outfilename);
data/sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c:146:16: [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).
if (argc > 1) strcpy (psiblastfilename, argv[1]);
data/sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c:159:16: [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).
if (argc > 2) strcpy (queryaligned_outfilename, argv[2]);
data/sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c:173:2: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (errorfilename, queryaligned_outfilename);
data/sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c:186:24: [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).
if (argc > 4) strcpy (queryfilename, argv[4]);
data/sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c:190:17: [4] (buffer) scanf:
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.
scanf ("%s", queryfilename);
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:154:16: [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).
if (argc > 1) strcpy (psiblastfilename, argv[1]);
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:167:16: [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).
if (argc > 2) strcpy (seqfilename, argv[2]);
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:187:24: [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).
if (argc > 4) strcpy (queryfilename, argv[4]);
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:191:17: [4] (buffer) scanf:
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.
scanf ("%s", queryfilename);
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:194:16: [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).
if (argc > 5) strcpy (outfilename, argv[5]);
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:197:3: [4] (buffer) scanf:
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.
scanf ("%s", outfilename);
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:200:9: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy (errorfilename, outfilename);
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:208:16: [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).
if (argc > 6) strcpy (pid, argv[6]);
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:211:3: [4] (buffer) scanf:
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.
scanf("%s", pid);
data/sift-4.0.3b/src/stringhash.c:142:4: [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 (NewCell->key, Key);
data/sift-4.0.3b/src/stringlist.c:34:4: [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 (cur->next->key, key);
data/sift-4.0.3b/src/PN_convert.c:1732:16: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
double random;
data/sift-4.0.3b/src/PN_convert.c:1737:16: [3] (random) random:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
while (random > P[i] && i < MATRIX_AA_WIDTH) {
data/sift-4.0.3b/src/sift_blimps.h:6:27: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
const char* blimps_dir = getenv ("BLIMPS_DIR");
data/sift-4.0.3b/src/Alignment.c:52:52: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
int try_clustal(FILE* ifp, Sequence* seqs[MAXSEQ], char desc[SMALL_BUFF_LENGTH])
data/sift-4.0.3b/src/Alignment.c:57:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[MAXLEN], tmp_name[30], *name, *residues;
data/sift-4.0.3b/src/Alignment.c:82:8: [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).
tmp=fopen(tmp_name, "w");
data/sift-4.0.3b/src/Alignment.c:109:19: [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 ( (tmp = fopen(tmp_name, "r")) != NULL)
data/sift-4.0.3b/src/Alignment.c:154:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
tmp=fopen(tmp_name, "w");
data/sift-4.0.3b/src/Alignment.c:174:48: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
int try_msf(FILE* ifp, Sequence *seqs[MAXSEQ], char desc[SMALL_BUFF_LENGTH])
data/sift-4.0.3b/src/Alignment.c:179:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[MAXLEN], tmp_name[30], *name, *residues;
data/sift-4.0.3b/src/Alignment.c:195:8: [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).
tmp=fopen(tmp_name, "w");
data/sift-4.0.3b/src/Alignment.c:222:19: [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 ( (tmp = fopen(tmp_name, "r")) != NULL)
data/sift-4.0.3b/src/Alignment.c:267:11: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
tmp=fopen(tmp_name, "w");
data/sift-4.0.3b/src/Alignment.c:406:58: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
int flat_master_slave (FILE* fp, Sequence *seqs[MAXSEQ], char desc[SMALL_BUFF_LENGTH])
data/sift-4.0.3b/src/Alignment.c:411:2: [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[MAXLEN], tmp_name[30], *name, *residues;
data/sift-4.0.3b/src/Alignment.c:427:8: [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).
tmp=fopen(tmp_name, "w");
data/sift-4.0.3b/src/Alignment.c:448:10: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
pos = atoi (startpos);
data/sift-4.0.3b/src/Alignment.c:498:19: [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 ( (tmp = fopen(tmp_name, "r")) != NULL)
data/sift-4.0.3b/src/Alignment.c:545:8: [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).
tmp = fopen (tmp_name, "w");
data/sift-4.0.3b/src/Alignment.c:621:4: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy (block->id, "UNK_ID");
data/sift-4.0.3b/src/Alignment.c:622:4: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy (block->ac, "UNK_AC");
data/sift-4.0.3b/src/Alignment.c:623:4: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy (block->de, "UNK_DE");
data/sift-4.0.3b/src/Alignment.c:624:4: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy (block->bl, "UNK_BL");
data/sift-4.0.3b/src/Alignment.c:625:4: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy (block->number, "UNK_BLNUM");
data/sift-4.0.3b/src/Alignment.c:626:4: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy (block->motif, "UNK_MOTIF");
data/sift-4.0.3b/src/Alignment.c:668:4: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy (block->id, "UNK_ID");
data/sift-4.0.3b/src/Alignment.c:669:4: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy (block->ac, "UNK_AC");
data/sift-4.0.3b/src/Alignment.c:670:4: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy (block->de, "UNK_DE");
data/sift-4.0.3b/src/Alignment.c:671:4: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy (block->bl, "UNK_BL");
data/sift-4.0.3b/src/Alignment.c:672:4: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy (block->number, "UNK_BLNUM");
data/sift-4.0.3b/src/Alignment.c:673:4: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy (block->motif, "UNK_MOTIF");
data/sift-4.0.3b/src/Alignment.c:747:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[MAXLEN];
data/sift-4.0.3b/src/Alignment.c:769:2: [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[LINE_LEN > LARGE_BUFF_LENGTH ? LINE_LEN : LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/Alignment.c:786:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[LINE_LEN];
data/sift-4.0.3b/src/Alignment.c:819:2: [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[MAXLEN];
data/sift-4.0.3b/src/Alignment.c:928:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char ctemp[80];
data/sift-4.0.3b/src/Alignment.c:983:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char ctemp[80];
data/sift-4.0.3b/src/Alignment.c:1002:2: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy (seqs[s]->name, "gi");
data/sift-4.0.3b/src/Alignment.c:1140:2: [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 names[MAXSEQ][SMALL_BUFF_LENGTH],
data/sift-4.0.3b/src/Alignment.c:1374:2: [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[SMALL_BUFF_LENGTH];
data/sift-4.0.3b/src/Alignment.c:1378:2: [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[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/Alignment.c:1379:2: [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 info[SMALL_BUFF_LENGTH];
data/sift-4.0.3b/src/Alignment.c:1535:2: [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[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/Alignment.c:1590:2: [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[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/Alignment.c:1592:2: [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 query_seq[LARGE_BUFF_LENGTH], subject_seq[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/Alignment.c:1611:23: [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).
query_start = atoi (strptr);
data/sift-4.0.3b/src/Alignment.c:1623:25: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
subject_start = atoi (strptr);
data/sift-4.0.3b/src/Alignment.c:1668:40: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
read_1st_4lines_of_pairwise (FILE* fp, char subject_name[SMALL_BUFF_LENGTH],
data/sift-4.0.3b/src/Alignment.c:1672:2: [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[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/Alignment.c:1675:2: [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 query_seq[LARGE_BUFF_LENGTH]; char subject_seq[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/Alignment.c:1675:37: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char query_seq[LARGE_BUFF_LENGTH]; char subject_seq[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/Alignment.c:1703:16: [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).
query_start = atoi (strptr);
data/sift-4.0.3b/src/Alignment.c:1709:14: [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).
query_end = atoi (strptr);
data/sift-4.0.3b/src/Alignment.c:1717:18: [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).
subject_start = atoi(strptr);
data/sift-4.0.3b/src/Alignment.c:1723:16: [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).
subject_end = atoi (strptr);
data/sift-4.0.3b/src/Alignment.c:1961:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char comment[SMALL_BUFF_LENGTH];
data/sift-4.0.3b/src/Alignment.c:2096:2: [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 (comment, "%d", i);
data/sift-4.0.3b/src/Alignment.h:26:52: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
int try_clustal(FILE* ifp, Sequence* seqs[MAXSEQ], char desc[SMALL_BUFF_LENGTH]);
data/sift-4.0.3b/src/Alignment.h:38:48: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
int try_msf(FILE* ifp, Sequence *seqs[MAXSEQ], char desc[SMALL_BUFF_LENGTH]);
data/sift-4.0.3b/src/Alignment.h:68:58: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
int flat_master_slave (FILE* fp, Sequence *seqs[MAXSEQ], char desc[SMALL_BUFF_LENGTH]);
data/sift-4.0.3b/src/Alignment.h:96:80: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
extract_seqs (Sequence* newseqs[MAXSEQ], Sequence* oldseqs[MAXSEQ], int nseqs, char names[MAXSEQ][SMALL_BUFF_LENGTH], int new_no_of_seq);
data/sift-4.0.3b/src/Alignment.h:147:40: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
read_1st_4lines_of_pairwise (FILE* fp, char subject_name[SMALL_BUFF_LENGTH],
data/sift-4.0.3b/src/Clumping.c:50:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char comment[SMALL_BUFF_LENGTH];
data/sift-4.0.3b/src/Clumping.c:262:3: [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 (consensus_seqs[i]->name, "CONSENSUS%d", i);
data/sift-4.0.3b/src/Clumping.c:284:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char comment[SMALL_BUFF_LENGTH];
data/sift-4.0.3b/src/Clumping.c:419:9: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf (comment, "%d", i);
data/sift-4.0.3b/src/List_Number.c:61:2: [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[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/List_Number.c:69:9: [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).
beg = atoi (ptr);
data/sift-4.0.3b/src/List_Number.c:71:9: [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).
end = atoi (ptr);
data/sift-4.0.3b/src/Matrix_Info.c:286:2: [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[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/Matrix_Info.c:288:2: [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 *string_pos, result[10];
data/sift-4.0.3b/src/Matrix_Info.c:290:2: [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 word1[10], word2[10];
data/sift-4.0.3b/src/Matrix_Info.c:308:9: [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).
pos = atoi (word2);
data/sift-4.0.3b/src/Matrix_Info.c:1493:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/Matrix_Info.c:1497:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char word1[10], word2[10];
data/sift-4.0.3b/src/Matrix_Info.c:1523:23: [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).
pos = atoi (word2);
data/sift-4.0.3b/src/Matrix_Info.c:1560:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/Matrix_Info.c:1564:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char word1[10], word2[10];
data/sift-4.0.3b/src/Matrix_Info.c:1586:23: [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).
pos = atoi (word2);
data/sift-4.0.3b/src/PN_blocks.c:222:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char key[SMALL_BUFF_LENGTH];
data/sift-4.0.3b/src/PN_blocks.c:689:9: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf (newblock->bl, "; width=%d; seqs=%d; ", non_X_length, block->num_sequences);
data/sift-4.0.3b/src/PN_blocks.c:749:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat (newblock->de, "updated");
data/sift-4.0.3b/src/PN_blocks.h:20:27: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
Sequence* seq_from_block (char seq_id[30], Block* block);
data/sift-4.0.3b/src/PN_convert.c:63:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffertemp[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/PN_convert.c:178:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(ErrorBuffer,
data/sift-4.0.3b/src/PN_convert.c:213:6: [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(ErrorBuffer,
data/sift-4.0.3b/src/PN_convert.c:442:2: [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 matrix_file[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/PN_convert.c:452:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ( (matrixfp = fopen (matrix_file, "r")) == NULL) {
data/sift-4.0.3b/src/PN_convert.c:768:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char diri_file[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/PN_convert.c:991:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char diri_file[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/PN_convert.c:1118:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char diri_file[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/PN_convert.c:1119:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char matrix_file[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/PN_convert.c:1338:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(ErrorBuffer, "Qij matrix missing, unable to continue.\n");
data/sift-4.0.3b/src/PN_convert.c:1644:2: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy (seq->name, "CONSENSUS");
data/sift-4.0.3b/src/PN_convert.c:1819:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(ErrorBuffer,
data/sift-4.0.3b/src/PN_convert.c:1830:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[132], *ptr;
data/sift-4.0.3b/src/PN_convert.c:1900:41: [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).
scores[row][col] = atoi(ptr);
data/sift-4.0.3b/src/PN_convert.c:1934:30: [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.
void init_frq_qij_for_matrix(char qijname[LARGE_BUFF_LENGTH])
data/sift-4.0.3b/src/PN_convert.c:1942:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ( (fqij=fopen(qijname, "r")) != NULL)
data/sift-4.0.3b/src/PN_convert.c:2071:35: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
struct dirichlet *load_diri_file (char filename[LARGE_BUFF_LENGTH])
data/sift-4.0.3b/src/PN_convert.c:2075:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[MAXLINE], *ptr;
data/sift-4.0.3b/src/PN_convert.c:2080:13: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fin = fopen (filename, "r")) == NULL) {
data/sift-4.0.3b/src/PN_convert.c:2167:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char qijname[80], frqname[80];
data/sift-4.0.3b/src/PN_convert.c:2177:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(frqname, "default.amino.frq");
data/sift-4.0.3b/src/PN_convert.c:2178:7: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(qijname, "default.qij");
data/sift-4.0.3b/src/PN_convert.c:2182:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ( (fqij=fopen(qijname, "r")) != NULL)
data/sift-4.0.3b/src/PN_convert.c:2232:2: [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 filename[80];
data/sift-4.0.3b/src/PN_convert.c:2237:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ( (qijfp = fopen (filename, "r"))
data/sift-4.0.3b/src/PN_convert.h:99:31: [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.
void init_frq_qij_for_matrix (char qijname[LARGE_BUFF_LENGTH]);
data/sift-4.0.3b/src/PN_convert.h:105:35: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
struct dirichlet *load_diri_file (char filename[LARGE_BUFF_LENGTH]);
data/sift-4.0.3b/src/PN_convert.h:109:1: [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 find_min_aa_in_diri (struct working* col, double diri_array[MAXCOMP][AAS], int comp);
data/sift-4.0.3b/src/Protdist.c:72:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char temp_name[15];
data/sift-4.0.3b/src/Protdist.c:146:2: [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[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/Protdist.c:147:2: [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_line[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/Protdist.h:16:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char name[PHYLIP_WIDTH + 1];
data/sift-4.0.3b/src/Psiblast.c:17:33: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
read_psiblast_entry ( FILE* fp, char Buffer[LARGE_BUFF_LENGTH])
data/sift-4.0.3b/src/Psiblast.c:44:26: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
initialize_Aligned_Pair (char Buffer[LARGE_BUFF_LENGTH])
data/sift-4.0.3b/src/Psiblast.c:73:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[LARGE_BUFF_LENGTH], FILE* fp)
data/sift-4.0.3b/src/Psiblast.c:112:25: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
read_4_alignment_lines (char Buffer[LARGE_BUFF_LENGTH], Aligned_Pair* alignment,
data/sift-4.0.3b/src/Psiblast.c:122:46: [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).
alignment->query->position = atoi (strptr);
data/sift-4.0.3b/src/Psiblast.c:132:48: [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).
alignment->subject->position = atoi (strptr);
data/sift-4.0.3b/src/Psiblast.c:205:2: [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 ctemp[12];
data/sift-4.0.3b/src/Psiblast.c:235:2: [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 command_line[LARGE_BUFF_LENGTH * 4];
data/sift-4.0.3b/src/Psiblast.c:249:2: [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 command_line[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/Psiblast.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 command_line[LARGE_BUFF_LENGTH *2];
data/sift-4.0.3b/src/Psiblast.c:275:2: [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[KEY_WIDTH];
data/sift-4.0.3b/src/Psiblast.c:277:2: [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[LINE_LEN];
data/sift-4.0.3b/src/Psiblast.c:280:20: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((psiblastfp = fopen (psiblastres_file, "r")) == NULL)
data/sift-4.0.3b/src/Psiblast.h:28:33: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
read_psiblast_entry ( FILE* fp, char Buffer[LARGE_BUFF_LENGTH]);
data/sift-4.0.3b/src/Psiblast.h:35:25: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
read_4_alignment_lines (char Buffer[LARGE_BUFF_LENGTH], Aligned_Pair* alignment,
data/sift-4.0.3b/src/Psiblast.h:41:40: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
Aligned_Pair* initialize_Aligned_Pair (char Buffer[LARGE_BUFF_LENGTH]);
data/sift-4.0.3b/src/Psiblast.h:44:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char Buffer[LARGE_BUFF_LENGTH], FILE* fp);
data/sift-4.0.3b/src/Psiblast.h:49:28: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void psiblast_system_call (char chkpoint_filename[LARGE_BUFF_LENGTH],
data/sift-4.0.3b/src/Psiblast.h:50:7: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char database[LARGE_BUFF_LENGTH],
data/sift-4.0.3b/src/Psiblast.h:51:7: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char result_file[LARGE_BUFF_LENGTH],
data/sift-4.0.3b/src/Psiblast.h:52:7: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char query_seq_file[LARGE_BUFF_LENGTH],
data/sift-4.0.3b/src/Psiblast.h:55:28: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void formatdb_system_call (char database[LARGE_BUFF_LENGTH]);
data/sift-4.0.3b/src/SortList.c:36:15: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
FILE* outfp; char filename[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/SortList.c:38:2: [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 (filename, "TEMP%d", pos);
data/sift-4.0.3b/src/SortList.c:39:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ( (outfp = fopen (filename, "w")) == NULL) {
data/sift-4.0.3b/src/SortList.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 aa_order[20];
data/sift-4.0.3b/src/blocklist.c:35:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char ctemp[SMALL_BUFF_LENGTH];
data/sift-4.0.3b/src/blocklist.c:53:4: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(block->motif, "UNK");
data/sift-4.0.3b/src/blocklist.c:54:4: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(block->bl, "UNK motif; width=%d; seqs=%d;",
data/sift-4.0.3b/src/blocklist.h:16:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char block_num[10];
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:31:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char query_seq_file[LARGE_BUFF_LENGTH],
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:35:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char pid[SMALL_BUFF_LENGTH],
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:38:29: [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.
int write_seqs_not_in_hash (char query_database_file[LARGE_BUFF_LENGTH],
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:42:25: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void write_seq_to_file (char filename[LARGE_BUFF_LENGTH], Sequence* seq);
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:46:1: [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 errorfilename[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:61:2: [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 seqname[KEY_WIDTH];
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:62:2: [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 pid[SMALL_BUFF_LENGTH];
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:63:2: [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_chk_filename[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:64:2: [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 psiblastres_file[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:65:2: [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 query_database_file[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:66:2: [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 query_seq_file[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:67:2: [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 outfile[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:68:2: [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 string[10]; char query_filename[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:68:19: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char string[10]; char query_filename[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:115:9: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat (query_filename, ".TEMP_QUERY");
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:134:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat (temp_chk_filename, ".TEMP");
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:136:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat (psiblastres_file, ".TEMP_PSIBLAST");
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:138:3: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat (query_database_file, ".TEMP_DB");
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:149:22: [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 ((temp_chk_fp = fopen (temp_chk_filename, "w")) == NULL) {
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:196:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat (query_database_file, ".*");
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:251:25: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
write_seqs_not_in_hash (char query_database_file[LARGE_BUFF_LENGTH],
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:261:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ( (outfp = fopen (query_database_file, "w")) == NULL) {
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:281:2: [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 query_seq_file[LARGE_BUFF_LENGTH],
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:285:2: [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 pid[SMALL_BUFF_LENGTH],
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:288:2: [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 seqfile[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:289:2: [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 outfile[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:290:2: [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 logfile[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:311:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ( (*seqfp = fopen (seqfile, "r")) == NULL )
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:325:9: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat (errorfilename, ".error");
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:326:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((errorfp = fopen (errorfilename, "w")) == NULL) {
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:330:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ( (*outfp = fopen (outfile, "w")) == NULL )
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:337:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat (logfile, ".log");
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:338:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((logfp = fopen (logfile, "w")) == NULL) {
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:369:20: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
write_seq_to_file (char filename[LARGE_BUFF_LENGTH], Sequence* seq)
data/sift-4.0.3b/src/choose_seqs_via_psiblastseedmedian.c:373:12: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen (filename, "w")) == NULL) {
data/sift-4.0.3b/src/clump_output_alignedseq.c:33:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char outfilename[LARGE_BUFF_LENGTH], double* clus,
data/sift-4.0.3b/src/clump_output_alignedseq.c:37:1: [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 errorfilename[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/clump_output_alignedseq.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 outfilename[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/clump_output_alignedseq.c:85:22: [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 ( (outfp = fopen (outfilename, "w")) == NULL)
data/sift-4.0.3b/src/clump_output_alignedseq.c:90:9: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat (outfilename, ".consensuskey");
data/sift-4.0.3b/src/clump_output_alignedseq.c:91:26: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ( (keyoutfp = fopen (outfilename, "w")) == NULL)
data/sift-4.0.3b/src/clump_output_alignedseq.c:133:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char outfilename[LARGE_BUFF_LENGTH], double* clus,
data/sift-4.0.3b/src/clump_output_alignedseq.c:136:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char seqfilename[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/clump_output_alignedseq.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 queryfilename[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/clump_output_alignedseq.c:149:23: [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 ((*seqfp = fopen (seqfilename, "r")) == NULL)
data/sift-4.0.3b/src/clump_output_alignedseq.c:164:9: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat (errorfilename, ".error");
data/sift-4.0.3b/src/clump_output_alignedseq.c:165:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((errorfp = fopen (errorfilename, "w")) == NULL) {
data/sift-4.0.3b/src/clump_output_alignedseq.c:178:26: [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).
if (argc > 4) *option = atoi (argv[4]);
data/sift-4.0.3b/src/consensus_to_seq.c:57:2: [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[LINE_LEN];
data/sift-4.0.3b/src/consensus_to_seq.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 temp_key[KEY_WIDTH];
data/sift-4.0.3b/src/consensus_to_seq.c:110:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char seqfilename[LINE_LEN];
data/sift-4.0.3b/src/consensus_to_seq.c:111:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char outfilename[LINE_LEN];
data/sift-4.0.3b/src/consensus_to_seq.c:112:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char keyfilename[LINE_LEN];
data/sift-4.0.3b/src/consensus_to_seq.c:126:23: [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 ((*seqfp = fopen (seqfilename, "r")) == NULL)
data/sift-4.0.3b/src/consensus_to_seq.c:138:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((*keyfp = fopen (keyfilename, "r")) == NULL)
data/sift-4.0.3b/src/consensus_to_seq.c:149:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ( (*outfp = fopen (outfilename, "w")) == NULL)
data/sift-4.0.3b/src/info_on_seqs.c:26:6: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char outfilename[LARGE_BUFF_LENGTH]);
data/sift-4.0.3b/src/info_on_seqs.c:43:1: [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 errorfilename[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/info_on_seqs.c:54:2: [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 outfilename[LARGE_BUFF_LENGTH], currentoutfile[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/info_on_seqs.c:55:2: [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 tempname[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/info_on_seqs.c:56:2: [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 desc[SMALL_BUFF_LENGTH]; int desc_length; char* strptr;
data/sift-4.0.3b/src/info_on_seqs.c:76:22: [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 ((outfp = fopen (outfilename, "w")) == NULL)
data/sift-4.0.3b/src/info_on_seqs.c:511:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char outfilename[LARGE_BUFF_LENGTH])
data/sift-4.0.3b/src/info_on_seqs.c:513:2: [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 seqfilename[LINE_LEN];
data/sift-4.0.3b/src/info_on_seqs.c:514:2: [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 seq_outfilename[LINE_LEN];
data/sift-4.0.3b/src/info_on_seqs.c:515:2: [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 substfilename[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/info_on_seqs.c:530:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((*seqfp = fopen (seqfilename, "r")) == NULL)
data/sift-4.0.3b/src/info_on_seqs.c:546:27: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
else if ((*polymorphfp = fopen (substfilename, "r")) == NULL)
data/sift-4.0.3b/src/info_on_seqs.c:561:9: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat (errorfilename, ".error");
data/sift-4.0.3b/src/info_on_seqs.c:562:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((errorfp = fopen (errorfilename, "w")) == NULL) {
data/sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c:43:1: [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 errorfilename[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c:49:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char queryfilename[LARGE_BUFF_LENGTH]);
data/sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c:51:41: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
Sequence* read_sequence_from_filename (char filename[LARGE_BUFF_LENGTH]);
data/sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c:63:2: [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 queryfilename[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c:81:2: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy (query_seq->name, "QUERY");
data/sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c:132:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char queryfilename[LARGE_BUFF_LENGTH])
data/sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c:134:2: [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 psiblastfilename[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c:135:2: [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 fasta_outfilename[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c:136:2: [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 queryaligned_outfilename[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c:153:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((*psiblastfp = fopen (psiblastfilename, "r")) == NULL)
data/sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c:168:26: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((*outfpqueryalign = fopen (queryaligned_outfilename, "w")) == NULL)
data/sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c:174:2: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat (errorfilename, ".error");
data/sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c:175:17: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((errorfp = fopen (errorfilename, "w")) == NULL) {
data/sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c:180:41: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (argc > 3) *max_iterations = atoi (argv[3]);
data/sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c:198:30: [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.
read_sequence_from_filename (char filename[LARGE_BUFF_LENGTH])
data/sift-4.0.3b/src/psiblast_res_to_fasta_dbpairwise.c:203:12: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen (filename, "r")) == NULL) {
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:37:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char queryfilename[LARGE_BUFF_LENGTH],
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:38:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char outfilename[LARGE_BUFF_LENGTH],
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:39:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char pid[SMALL_BUFF_LENGTH]);
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:41:41: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
Sequence* read_sequence_from_filename (char filename[LARGE_BUFF_LENGTH]);
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:44:1: [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 errorfilename[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:57:2: [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 queryfilename[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:58:2: [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 outfilename[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/seqs_from_psiblast_res.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 pid[SMALL_BUFF_LENGTH];
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:61:2: [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[LARGE_BUFF_LENGTH]; int converged;
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:67:2: [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 tmpfilename[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:68:2: [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 command_line[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/seqs_from_psiblast_res.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 temp[SMALL_BUFF_LENGTH];
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:81:2: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy (query_seq->name, "QUERY");
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:114:22: [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 ((outfp = fopen (outfilename, "w")) == NULL)
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:139:38: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
int* max_iterations, char queryfilename[LARGE_BUFF_LENGTH],
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:140:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char outfilename[LARGE_BUFF_LENGTH], char pid[SMALL_BUFF_LENGTH])
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:140:41: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char outfilename[LARGE_BUFF_LENGTH], char pid[SMALL_BUFF_LENGTH])
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:142:2: [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 psiblastfilename[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:143:2: [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 seqfilename[LARGE_BUFF_LENGTH];
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:161:21: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((*psiblastfp = fopen (psiblastfilename, "r")) == NULL)
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:175:16: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((*seqfp = fopen (seqfilename, "r")) == NULL)
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:181:41: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
if (argc > 3) *max_iterations = atoi (argv[3]);
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:201:9: [2] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant string.
strcat (errorfilename, ".error");
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:202:24: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((errorfp = fopen (errorfilename, "w")) == NULL) {
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:217:30: [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.
read_sequence_from_filename (char filename[LARGE_BUFF_LENGTH])
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:222:12: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if ((fp = fopen (filename, "r")) == NULL) {
data/sift-4.0.3b/src/stringhash.c:19:6: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char key[KEY_WIDTH];
data/sift-4.0.3b/src/stringhash.c:32:6: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char hash_name[KEY_WIDTH];
data/sift-4.0.3b/src/stringlist.c:26:42: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void insert_stringlist(StringList* list, char key[KEY_WIDTH])
data/sift-4.0.3b/src/stringlist.h:14:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char title[KEY_WIDTH];
data/sift-4.0.3b/src/stringlist.h:15:4: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char key[KEY_WIDTH];
data/sift-4.0.3b/src/stringlist.h:21:42: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
void insert_stringlist(StringList* list, char key[KEY_WIDTH]);
data/sift-4.0.3b/src/Alignment.c:65:11: [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).
strlen(line) < (int) 4 )
data/sift-4.0.3b/src/Alignment.c:88:12: [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).
strlen(line) > (int) 3 )
data/sift-4.0.3b/src/Alignment.c:201:12: [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).
strlen(line) > (int) 3 )
data/sift-4.0.3b/src/Alignment.c:327:3: [1] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant character.
strcpy (newseqs[i]->info, " ");
data/sift-4.0.3b/src/Alignment.c:568:11: [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).
length = strlen (src);
data/sift-4.0.3b/src/Alignment.c:591:12: [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).
length1 = strlen (seq1);
data/sift-4.0.3b/src/Alignment.c:592:12: [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).
length2 = strlen (seq2);
data/sift-4.0.3b/src/Alignment.c:937:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ((int) strlen(seqs[s]->name) > 15) seqs[s]->name[15] = '\0';
data/sift-4.0.3b/src/Alignment.c:959:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(seqs[s]->name);
data/sift-4.0.3b/src/Alignment.c:992:19: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ((int) strlen(seqs[s]->name) > 15) seqs[s]->name[15] = '\0';
data/sift-4.0.3b/src/Alignment.c:999:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy (ctemp, strptr +3 , 8);
data/sift-4.0.3b/src/Alignment.c:1020:14: [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).
len = (int) strlen(seqs[s]->name);
data/sift-4.0.3b/src/Alignment.c:1046:15: [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 ((int) strlen(seqs[s]->name) > SNAMELEN)
data/sift-4.0.3b/src/Alignment.c:1074:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
len = strlen(seqs[s]->name);
data/sift-4.0.3b/src/Alignment.c:1155:20: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
string_length = strlen (oldseqs[i]->name);
data/sift-4.0.3b/src/Alignment.c:1156:8: [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 (names[j]) < string_length) {
data/sift-4.0.3b/src/Alignment.c:1157:21: [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).
string_length = strlen (names[j]);
data/sift-4.0.3b/src/Alignment.c:1615:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
seq_length = strlen (query_seq);
data/sift-4.0.3b/src/Alignment.c:1707:15: [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).
seq_length = strlen (query_seq);
data/sift-4.0.3b/src/PN_convert.c:75:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(Buffertemp, block->id, SMALL_BUFF_LENGTH);
data/sift-4.0.3b/src/PN_convert.c:79:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120). Risk is low because the source is a
constant string.
strncpy(strstr(Buffertemp, "BLOCK"), "MATRIX\0", 7);
data/sift-4.0.3b/src/PN_convert.c:80:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(matrix->id, Buffertemp, SMALL_BUFF_LENGTH);
data/sift-4.0.3b/src/PN_convert.c:83:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(matrix->id,
data/sift-4.0.3b/src/PN_convert.c:84:13: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings. Risk is low because the source is a
constant string.
strncat(Buffertemp, "; MATRIX", SMALL_BUFF_LENGTH - strlen(Buffertemp)),
data/sift-4.0.3b/src/PN_convert.c:84:65: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncat(Buffertemp, "; MATRIX", SMALL_BUFF_LENGTH - strlen(Buffertemp)),
data/sift-4.0.3b/src/PN_convert.c:89:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(matrix->de, block->de, DESC_WIDTH);
data/sift-4.0.3b/src/PN_convert.c:90:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(matrix->ma, block->bl, SMALL_BUFF_LENGTH);
data/sift-4.0.3b/src/PN_convert.c:93:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(matrix->motif, block->motif, 20);
data/sift-4.0.3b/src/PN_convert.c:1836:12: [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).
while ((strlen(line) < (size_t) 1 ||
data/sift-4.0.3b/src/PN_convert.c:1845:27: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for (i=0; i < (int) strlen(line); i++)
data/sift-4.0.3b/src/PN_convert.c:1888:11: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(line) > (size_t) 1 && nrows < 24)
data/sift-4.0.3b/src/PN_convert.c:1896:51: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strspn(ptr, "+-0123456789") == strlen(ptr))
data/sift-4.0.3b/src/Protdist.c:52:26: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
length = strlen (seqs[j]->name);
data/sift-4.0.3b/src/Psiblast.c:54:18: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
length = strlen (stringptr);
data/sift-4.0.3b/src/Psiblast.c:55:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy (alignment->subject->name, &Buffer[1], length-1);
data/sift-4.0.3b/src/Psiblast.c:162:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
estimated_length = strlen(buff);
data/sift-4.0.3b/src/Psiblast.c:294:11: [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).
assert ( strlen(strptr) < KEY_WIDTH);
data/sift-4.0.3b/src/Psiblast.c:295:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy (name, strptr, KEY_WIDTH);
data/sift-4.0.3b/src/Psiblast.c:305:4: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy (name, strptr, KEY_WIDTH);
data/sift-4.0.3b/src/Psiblast.c:310:2: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy (next_seq_to_add, name, KEY_WIDTH);
data/sift-4.0.3b/src/blocklist.c:57:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
if (blist->nblock == 1) strcat(ctemp, "A");
data/sift-4.0.3b/src/blocklist.c:58:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 2) strcat(ctemp, "B");
data/sift-4.0.3b/src/blocklist.c:59:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 3) strcat(ctemp, "C");
data/sift-4.0.3b/src/blocklist.c:60:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 4) strcat(ctemp, "D");
data/sift-4.0.3b/src/blocklist.c:61:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 5) strcat(ctemp, "E");
data/sift-4.0.3b/src/blocklist.c:62:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 6) strcat(ctemp, "F");
data/sift-4.0.3b/src/blocklist.c:63:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 7) strcat(ctemp, "G");
data/sift-4.0.3b/src/blocklist.c:64:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 8) strcat(ctemp, "H");
data/sift-4.0.3b/src/blocklist.c:65:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 9) strcat(ctemp, "I");
data/sift-4.0.3b/src/blocklist.c:66:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 10) strcat(ctemp, "J");
data/sift-4.0.3b/src/blocklist.c:67:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 11) strcat(ctemp, "K");
data/sift-4.0.3b/src/blocklist.c:68:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 12) strcat(ctemp, "L");
data/sift-4.0.3b/src/blocklist.c:69:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 13) strcat(ctemp, "M");
data/sift-4.0.3b/src/blocklist.c:70:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 14) strcat(ctemp, "N");
data/sift-4.0.3b/src/blocklist.c:71:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 15) strcat(ctemp, "O");
data/sift-4.0.3b/src/blocklist.c:72:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 16) strcat(ctemp, "P");
data/sift-4.0.3b/src/blocklist.c:73:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 17) strcat(ctemp, "Q");
data/sift-4.0.3b/src/blocklist.c:74:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 18) strcat(ctemp, "R");
data/sift-4.0.3b/src/blocklist.c:75:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 19) strcat(ctemp, "S");
data/sift-4.0.3b/src/blocklist.c:76:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 20) strcat(ctemp, "T");
data/sift-4.0.3b/src/blocklist.c:77:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 21) strcat(ctemp, "U");
data/sift-4.0.3b/src/blocklist.c:78:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 22) strcat(ctemp, "V");
data/sift-4.0.3b/src/blocklist.c:79:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 23) strcat(ctemp, "W");
data/sift-4.0.3b/src/blocklist.c:80:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 24) strcat(ctemp, "X");
data/sift-4.0.3b/src/blocklist.c:81:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 25) strcat(ctemp, "Y");
data/sift-4.0.3b/src/blocklist.c:82:34: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else if (blist->nblock == 26) strcat(ctemp, "Z");
data/sift-4.0.3b/src/blocklist.c:83:9: [1] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused). Risk is low because the
source is a constant character.
else strcat(ctemp, "*");
data/sift-4.0.3b/src/consensus_to_seq.c:67:10: [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).
strptr[strlen(strptr)] = '\0';
data/sift-4.0.3b/src/consensus_to_seq.c:73:11: [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).
strptr[strlen(strptr)] = '\0';
data/sift-4.0.3b/src/consensus_to_seq.c:86:10: [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).
strptr[strlen(strptr)] = '\0'; done = false;
data/sift-4.0.3b/src/info_on_seqs.c:112:17: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
desc_length = strlen(strptr);
data/sift-4.0.3b/src/info_on_seqs.c:116:3: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy (desc, strptr, desc_length);
data/sift-4.0.3b/src/seqs_from_psiblast_res.c:104:10: [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).
strptr[strlen(strptr)] = '\0';
ANALYSIS SUMMARY:
Hits = 482
Lines analyzed = 11587 in approximately 0.51 seconds (22815 lines/second)
Physical Source Lines of Code (SLOC) = 8324
Hits@level = [0] 516 [1] 73 [2] 260 [3] 3 [4] 146 [5] 0
Hits@level+ = [0+] 998 [1+] 482 [2+] 409 [3+] 149 [4+] 146 [5+] 0
Hits/KSLOC@level+ = [0+] 119.894 [1+] 57.9049 [2+] 49.135 [3+] 17.9 [4+] 17.5396 [5+] 0
Dot directories skipped = 2 (--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.