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/hisat2-2.2.1/aligner_bt.cpp
Examining data/hisat2-2.2.1/aligner_bt.h
Examining data/hisat2-2.2.1/aligner_cache.cpp
Examining data/hisat2-2.2.1/aligner_cache.h
Examining data/hisat2-2.2.1/aligner_driver.cpp
Examining data/hisat2-2.2.1/aligner_driver.h
Examining data/hisat2-2.2.1/aligner_metrics.h
Examining data/hisat2-2.2.1/aligner_report.h
Examining data/hisat2-2.2.1/aligner_result.cpp
Examining data/hisat2-2.2.1/aligner_result.h
Examining data/hisat2-2.2.1/aligner_seed.cpp
Examining data/hisat2-2.2.1/aligner_seed.h
Examining data/hisat2-2.2.1/aligner_seed2.cpp
Examining data/hisat2-2.2.1/aligner_seed2.h
Examining data/hisat2-2.2.1/aligner_seed_policy.cpp
Examining data/hisat2-2.2.1/aligner_seed_policy.h
Examining data/hisat2-2.2.1/aligner_sw.cpp
Examining data/hisat2-2.2.1/aligner_sw_common.h
Examining data/hisat2-2.2.1/aligner_sw_driver.cpp
Examining data/hisat2-2.2.1/aligner_sw_driver.h
Examining data/hisat2-2.2.1/aligner_sw_nuc.h
Examining data/hisat2-2.2.1/aligner_swsse.cpp
Examining data/hisat2-2.2.1/aligner_swsse.h
Examining data/hisat2-2.2.1/aligner_swsse_ee_i16.cpp
Examining data/hisat2-2.2.1/aligner_swsse_ee_u8.cpp
Examining data/hisat2-2.2.1/aligner_swsse_loc_i16.cpp
Examining data/hisat2-2.2.1/aligner_swsse_loc_u8.cpp
Examining data/hisat2-2.2.1/aln_sink.cpp
Examining data/hisat2-2.2.1/aln_sink.h
Examining data/hisat2-2.2.1/alphabet.cpp
Examining data/hisat2-2.2.1/alphabet.h
Examining data/hisat2-2.2.1/alt.h
Examining data/hisat2-2.2.1/assert_helpers.h
Examining data/hisat2-2.2.1/banded.cpp
Examining data/hisat2-2.2.1/banded.h
Examining data/hisat2-2.2.1/binary_sa_search.h
Examining data/hisat2-2.2.1/bit_packed_array.cpp
Examining data/hisat2-2.2.1/bit_packed_array.h
Examining data/hisat2-2.2.1/bitpack.h
Examining data/hisat2-2.2.1/blockwise_sa.h
Examining data/hisat2-2.2.1/bp_aligner.h
Examining data/hisat2-2.2.1/btypes.h
Examining data/hisat2-2.2.1/ccnt_lut.cpp
Examining data/hisat2-2.2.1/diff_sample.cpp
Examining data/hisat2-2.2.1/diff_sample.h
Examining data/hisat2-2.2.1/dp_framer.cpp
Examining data/hisat2-2.2.1/dp_framer.h
Examining data/hisat2-2.2.1/ds.cpp
Examining data/hisat2-2.2.1/ds.h
Examining data/hisat2-2.2.1/edit.cpp
Examining data/hisat2-2.2.1/edit.h
Examining data/hisat2-2.2.1/endian_swap.h
Examining data/hisat2-2.2.1/fast_mutex.h
Examining data/hisat2-2.2.1/filebuf.h
Examining data/hisat2-2.2.1/formats.h
Examining data/hisat2-2.2.1/gbwt_graph.h
Examining data/hisat2-2.2.1/gfm.cpp
Examining data/hisat2-2.2.1/gfm.h
Examining data/hisat2-2.2.1/gp.h
Examining data/hisat2-2.2.1/group_walk.cpp
Examining data/hisat2-2.2.1/group_walk.h
Examining data/hisat2-2.2.1/hgfm.h
Examining data/hisat2-2.2.1/hi_aligner.h
Examining data/hisat2-2.2.1/hier_idx_common.h
Examining data/hisat2-2.2.1/hisat2.cpp
Examining data/hisat2-2.2.1/hisat2_build.cpp
Examining data/hisat2-2.2.1/hisat2_build_main.cpp
Examining data/hisat2-2.2.1/hisat2_inspect.cpp
Examining data/hisat2-2.2.1/hisat2_main.cpp
Examining data/hisat2-2.2.1/hisat2_repeat.cpp
Examining data/hisat2-2.2.1/hisat2_repeat_main.cpp
Examining data/hisat2-2.2.1/hisat2lib/ht2.h
Examining data/hisat2-2.2.1/hisat2lib/ht2_alignment.cpp
Examining data/hisat2-2.2.1/hisat2lib/ht2_handle.h
Examining data/hisat2-2.2.1/hisat2lib/ht2_index.cpp
Examining data/hisat2-2.2.1/hisat2lib/ht2_init.cpp
Examining data/hisat2-2.2.1/hisat2lib/ht2_repeat.cpp
Examining data/hisat2-2.2.1/hisat2lib/java_jni/ht2module.c
Examining data/hisat2-2.2.1/hisat2lib/pymodule/ht2module.c
Examining data/hisat2-2.2.1/hisat_bp.cpp
Examining data/hisat2-2.2.1/ival_list.cpp
Examining data/hisat2-2.2.1/ival_list.h
Examining data/hisat2-2.2.1/li_hla/alignments.hpp
Examining data/hisat2-2.2.1/li_hla/defs.h
Examining data/hisat2-2.2.1/li_hla/main.cpp
Examining data/hisat2-2.2.1/limit.cpp
Examining data/hisat2-2.2.1/limit.h
Examining data/hisat2-2.2.1/ls.cpp
Examining data/hisat2-2.2.1/ls.h
Examining data/hisat2-2.2.1/mask.cpp
Examining data/hisat2-2.2.1/mask.h
Examining data/hisat2-2.2.1/mem_ids.h
Examining data/hisat2-2.2.1/mm.h
Examining data/hisat2-2.2.1/msvcc/codeStubs/getopt.c
Examining data/hisat2-2.2.1/msvcc/codeStubs/getopt.h
Examining data/hisat2-2.2.1/msvcc/codeStubs/getopt1.c
Examining data/hisat2-2.2.1/msvcc/codeStubs/sys/time.cpp
Examining data/hisat2-2.2.1/msvcc/codeStubs/sys/time.h
Examining data/hisat2-2.2.1/msvcc/codeStubs/unistd.h
Examining data/hisat2-2.2.1/multikey_qsort.cpp
Examining data/hisat2-2.2.1/multikey_qsort.h
Examining data/hisat2-2.2.1/opts.h
Examining data/hisat2-2.2.1/outq.cpp
Examining data/hisat2-2.2.1/outq.h
Examining data/hisat2-2.2.1/pat.cpp
Examining data/hisat2-2.2.1/pat.h
Examining data/hisat2-2.2.1/pe.cpp
Examining data/hisat2-2.2.1/pe.h
Examining data/hisat2-2.2.1/presets.cpp
Examining data/hisat2-2.2.1/presets.h
Examining data/hisat2-2.2.1/qual.cpp
Examining data/hisat2-2.2.1/qual.h
Examining data/hisat2-2.2.1/radix_sort.h
Examining data/hisat2-2.2.1/random_source.cpp
Examining data/hisat2-2.2.1/random_source.h
Examining data/hisat2-2.2.1/random_util.cpp
Examining data/hisat2-2.2.1/random_util.h
Examining data/hisat2-2.2.1/read.h
Examining data/hisat2-2.2.1/read_qseq.cpp
Examining data/hisat2-2.2.1/ref_coord.cpp
Examining data/hisat2-2.2.1/ref_coord.h
Examining data/hisat2-2.2.1/ref_read.cpp
Examining data/hisat2-2.2.1/ref_read.h
Examining data/hisat2-2.2.1/reference.cpp
Examining data/hisat2-2.2.1/reference.h
Examining data/hisat2-2.2.1/repeat.h
Examining data/hisat2-2.2.1/repeat_builder.cpp
Examining data/hisat2-2.2.1/repeat_builder.h
Examining data/hisat2-2.2.1/repeat_kmer.h
Examining data/hisat2-2.2.1/rfm.h
Examining data/hisat2-2.2.1/sam.h
Examining data/hisat2-2.2.1/scoring.cpp
Examining data/hisat2-2.2.1/scoring.h
Examining data/hisat2-2.2.1/search_globals.h
Examining data/hisat2-2.2.1/sequence_io.h
Examining data/hisat2-2.2.1/shmem.cpp
Examining data/hisat2-2.2.1/shmem.h
Examining data/hisat2-2.2.1/simple_func.cpp
Examining data/hisat2-2.2.1/simple_func.h
Examining data/hisat2-2.2.1/splice_site.cpp
Examining data/hisat2-2.2.1/splice_site.h
Examining data/hisat2-2.2.1/splice_site_mem.h
Examining data/hisat2-2.2.1/splice_site_new.cpp
Examining data/hisat2-2.2.1/spliced_aligner.h
Examining data/hisat2-2.2.1/sse_util.cpp
Examining data/hisat2-2.2.1/sstring.cpp
Examining data/hisat2-2.2.1/sstring.h
Examining data/hisat2-2.2.1/str_util.h
Examining data/hisat2-2.2.1/third_party/cpuid.h
Examining data/hisat2-2.2.1/threading.h
Examining data/hisat2-2.2.1/timer.h
Examining data/hisat2-2.2.1/tinythread.cpp
Examining data/hisat2-2.2.1/tinythread.h
Examining data/hisat2-2.2.1/tokenize.h
Examining data/hisat2-2.2.1/tp.h
Examining data/hisat2-2.2.1/unique.cpp
Examining data/hisat2-2.2.1/unique.h
Examining data/hisat2-2.2.1/util.h
Examining data/hisat2-2.2.1/word_io.h
Examining data/hisat2-2.2.1/zbox.h
Examining data/hisat2-2.2.1/aligner_sw.h
Examining data/hisat2-2.2.1/sse_util.h
Examining data/hisat2-2.2.1/processor_support.h
FINAL RESULTS:
data/hisat2-2.2.1/filebuf.h:222:9: [5] (buffer) gets:
Does not check for buffer overflows (CWE-120, CWE-20). Use fgets() instead.
size_t gets(char *buf, size_t len) {
data/hisat2-2.2.1/pat.h:1013:22: [5] (buffer) gets:
Does not check for buffer overflows (CWE-120, CWE-20). Use fgets() instead.
size_t rd = filebuf.gets(buf, buflen);
data/hisat2-2.2.1/gfm.h:2807:9: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
sscanf(HISAT2_VERSION, "%d.%d.%d-%s",
data/hisat2-2.2.1/hisat2lib/ht2_index.cpp:73:9: [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(result->names[i], hp->gfm->_refnames[i].c_str());
data/hisat2-2.2.1/hisat2lib/java_jni/ht2module.c:32:33: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
#define DEBUGLOG(fmt, ...) do { fprintf(stderr, "%s:%d:%s(): " fmt, __FILE__, __LINE__, __func__, ##__VA_ARGS__); } while(0)
data/hisat2-2.2.1/hisat2lib/pymodule/ht2module.c:27:33: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
#define DEBUGLOG(fmt, ...) do { fprintf(stderr, "%s:%d:%s(): " fmt, __FILE__, __LINE__, __func__, ##__VA_ARGS__); } while(0)
data/hisat2-2.2.1/li_hla/alignments.hpp:51:3: [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( fileName, file ) ;
data/hisat2-2.2.1/li_hla/main.cpp:113:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf( buffer, "%s.snp", argv[1] ) ;
data/hisat2-2.2.1/li_hla/main.cpp:162:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf( buffer, "%s_backbone.fa", argv[1] ) ;
data/hisat2-2.2.1/li_hla/main.cpp:205:2: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf( buffer, "%s.link", argv[1] ) ;
data/hisat2-2.2.1/aligner_cache.cpp:168:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
next_option = getopt_long(argc, argv, short_opts, long_opts, &option_index);
data/hisat2-2.2.1/aligner_seed.cpp:427:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
next_option = getopt_long(
data/hisat2-2.2.1/aligner_sw.cpp:3097:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
next_option = getopt_long(argc, argv, short_opts, long_opts, &option_index);
data/hisat2-2.2.1/aligner_sw.cpp:3150:2: [3] (random) srand:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
srand(seed);
data/hisat2-2.2.1/fast_mutex.h:116:7: [3] (misc) InitializeCriticalSection:
Exceptions can be thrown in low-memory situations. Use
InitializeCriticalSectionAndSpinCount instead.
InitializeCriticalSection(mHandle);
data/hisat2-2.2.1/fast_mutex.h:171:7: [3] (misc) EnterCriticalSection:
On some versions of Windows, exceptions can be thrown in low-memory
situations. Use InitializeCriticalSectionAndSpinCount instead.
EnterCriticalSection(mHandle);
data/hisat2-2.2.1/gfm.cpp:55:12: [3] (buffer) getenv:
Environment variables are untrustable input if they can be set by an
attacker. They can have any content and length, and the same variable can
be set more than once (CWE-807, CWE-20). Check environment variables
carefully before using them.
if(getenv("HISAT2_INDEXES") != NULL) {
data/hisat2-2.2.1/gfm.cpp:56:26: [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.
str = string(getenv("HISAT2_INDEXES")) + "/" + gfmFileBase;
data/hisat2-2.2.1/hisat2.cpp:1806:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
next_option = getopt_long(
data/hisat2-2.2.1/hisat2_build.cpp:291:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
next_option = getopt_long(
data/hisat2-2.2.1/hisat2_build.cpp:779:9: [3] (random) srand:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
srand(seed);
data/hisat2-2.2.1/hisat2_inspect.cpp:145:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
next_option = getopt_long(argc, argv, short_options, long_options, &option_index);
data/hisat2-2.2.1/hisat2_repeat.cpp:350:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
next_option = getopt_long(
data/hisat2-2.2.1/hisat2_repeat.cpp:853:9: [3] (random) srand:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
srand(seed);
data/hisat2-2.2.1/hisat_bp.cpp:1501:17: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
next_option = getopt_long(
data/hisat2-2.2.1/msvcc/codeStubs/getopt.c:224:16: [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.
#elif !defined(getenv)
data/hisat2-2.2.1/msvcc/codeStubs/getopt.c:228:14: [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.
extern char *getenv (const char *);
data/hisat2-2.2.1/msvcc/codeStubs/getopt.c:419:21: [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.
posixly_correct = getenv ("POSIXLY_CORRECT");
data/hisat2-2.2.1/msvcc/codeStubs/getopt.c:980:1: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
getopt (int argc, char *const *argv, const char *optstring)
data/hisat2-2.2.1/msvcc/codeStubs/getopt.c:1005:11: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
c = getopt (argc, argv, "abc:d:0123456789");
data/hisat2-2.2.1/msvcc/codeStubs/getopt.h:118:12: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
extern int getopt (int argc, char *const *argv, const char *shortopts);
data/hisat2-2.2.1/msvcc/codeStubs/getopt.h:121:12: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
extern int getopt ();
data/hisat2-2.2.1/msvcc/codeStubs/getopt.h:126:12: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
extern int getopt_long (int argc, char *const *argv, const char *shortopts,
data/hisat2-2.2.1/msvcc/codeStubs/getopt.h:138:12: [3] (buffer) getopt:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
extern int getopt ();
data/hisat2-2.2.1/msvcc/codeStubs/getopt.h:139:12: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
extern int getopt_long ();
data/hisat2-2.2.1/msvcc/codeStubs/getopt1.c:69:1: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
getopt_long (int argc, char *const *argv, const char *options,
data/hisat2-2.2.1/msvcc/codeStubs/getopt1.c:115:11: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
c = getopt_long (argc, argv, "abc:d:0123456789",
data/hisat2-2.2.1/tinythread.cpp:61:3: [3] (misc) InitializeCriticalSection:
Exceptions can be thrown in low-memory situations. Use
InitializeCriticalSectionAndSpinCount instead.
InitializeCriticalSection(&mWaitersCountLock);
data/hisat2-2.2.1/tinythread.cpp:82:3: [3] (misc) EnterCriticalSection:
On some versions of Windows, exceptions can be thrown in low-memory
situations. Use InitializeCriticalSectionAndSpinCount instead.
EnterCriticalSection(&mWaitersCountLock);
data/hisat2-2.2.1/tinythread.cpp:98:3: [3] (misc) EnterCriticalSection:
On some versions of Windows, exceptions can be thrown in low-memory
situations. Use InitializeCriticalSectionAndSpinCount instead.
EnterCriticalSection(&mWaitersCountLock);
data/hisat2-2.2.1/tinythread.cpp:112:3: [3] (misc) EnterCriticalSection:
On some versions of Windows, exceptions can be thrown in low-memory
situations. Use InitializeCriticalSectionAndSpinCount instead.
EnterCriticalSection(&mWaitersCountLock);
data/hisat2-2.2.1/tinythread.h:168:7: [3] (misc) InitializeCriticalSection:
Exceptions can be thrown in low-memory situations. Use
InitializeCriticalSectionAndSpinCount instead.
InitializeCriticalSection(&mHandle);
data/hisat2-2.2.1/tinythread.h:191:7: [3] (misc) EnterCriticalSection:
On some versions of Windows, exceptions can be thrown in low-memory
situations. Use InitializeCriticalSectionAndSpinCount instead.
EnterCriticalSection(&mHandle);
data/hisat2-2.2.1/tinythread.h:257:7: [3] (misc) InitializeCriticalSection:
Exceptions can be thrown in low-memory situations. Use
InitializeCriticalSectionAndSpinCount instead.
InitializeCriticalSection(&mHandle);
data/hisat2-2.2.1/tinythread.h:283:7: [3] (misc) EnterCriticalSection:
On some versions of Windows, exceptions can be thrown in low-memory
situations. Use InitializeCriticalSectionAndSpinCount instead.
EnterCriticalSection(&mHandle);
data/hisat2-2.2.1/tinythread.h:424:7: [3] (misc) EnterCriticalSection:
On some versions of Windows, exceptions can be thrown in low-memory
situations. Use InitializeCriticalSectionAndSpinCount instead.
EnterCriticalSection(&mWaitersCountLock);
data/hisat2-2.2.1/aligner_cache.cpp:116:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buf[5];
data/hisat2-2.2.1/aligner_result.cpp:906:3: [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 buf[128];
data/hisat2-2.2.1/aligner_result.cpp:936:2: [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 buf[128];
data/hisat2-2.2.1/aligner_result.cpp:1355:3: [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 buf1[1024];
data/hisat2-2.2.1/aligner_result.cpp:1361:3: [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 buf2[1024];
data/hisat2-2.2.1/aligner_result.cpp:1367:3: [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 buf3[1024];
data/hisat2-2.2.1/aligner_result.cpp:1373:3: [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 buf4[1024];
data/hisat2-2.2.1/aligner_result.cpp:1413:3: [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 buf1[1024];
data/hisat2-2.2.1/aligner_result.cpp:1419:3: [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 buf2[1024];
data/hisat2-2.2.1/aligner_result.cpp:1425:3: [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 buf3[1024];
data/hisat2-2.2.1/aligner_result.cpp:1431:3: [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 buf4[1024];
data/hisat2-2.2.1/aligner_result.cpp:1577:3: [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 buf1[1024];
data/hisat2-2.2.1/aligner_result.cpp:1583:3: [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 buf2[1024];
data/hisat2-2.2.1/aligner_result.cpp:1589:3: [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 buf3[1024];
data/hisat2-2.2.1/aligner_result.cpp:1595:3: [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 buf4[1024];
data/hisat2-2.2.1/aligner_result.cpp:1640:3: [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 buf1[1024];
data/hisat2-2.2.1/aligner_result.cpp:1646:3: [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 buf2[1024];
data/hisat2-2.2.1/aligner_result.cpp:1652:3: [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 buf3[1024];
data/hisat2-2.2.1/aligner_result.cpp:1658:3: [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 buf4[1024];
data/hisat2-2.2.1/aligner_result.cpp:1706:3: [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 buf1[1024];
data/hisat2-2.2.1/aligner_result.cpp:1712:3: [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 buf2[1024];
data/hisat2-2.2.1/aligner_result.cpp:1760:3: [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 buf1[1024];
data/hisat2-2.2.1/aligner_result.cpp:1766:3: [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 buf2[1024];
data/hisat2-2.2.1/aligner_result.cpp:1814:3: [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 buf1[1024];
data/hisat2-2.2.1/aligner_result.cpp:1820:3: [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 buf2[1024];
data/hisat2-2.2.1/aligner_result.cpp:1868:3: [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 buf1[1024];
data/hisat2-2.2.1/aligner_result.cpp:1874:3: [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 buf2[1024];
data/hisat2-2.2.1/aligner_result.cpp:1922:3: [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 buf1[1024];
data/hisat2-2.2.1/aligner_result.cpp:1928:3: [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 buf2[1024];
data/hisat2-2.2.1/aligner_result.cpp:1976:3: [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 buf1[1024];
data/hisat2-2.2.1/aligner_result.cpp:1982:3: [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 buf2[1024];
data/hisat2-2.2.1/aligner_result.cpp:2030:3: [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 buf1[1024];
data/hisat2-2.2.1/aligner_result.cpp:2036:3: [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 buf2[1024];
data/hisat2-2.2.1/aligner_result.cpp:2066:3: [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 buf[1024];
data/hisat2-2.2.1/aligner_result.cpp:2089:3: [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 buf[1024];
data/hisat2-2.2.1/aligner_swsse_ee_i16.cpp:731:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dst, vbuf_r, sizeof(__m128i) * wordspercol);
data/hisat2-2.2.1/aligner_swsse_ee_i16.cpp:739:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dst, vbuf_r, sizeof(__m128i) * wordspercol);
data/hisat2-2.2.1/aligner_swsse_ee_u8.cpp:729:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dst, vbuf_r, sizeof(__m128i) * wordspercol);
data/hisat2-2.2.1/aligner_swsse_ee_u8.cpp:737:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dst, vbuf_r, sizeof(__m128i) * wordspercol);
data/hisat2-2.2.1/aligner_swsse_loc_i16.cpp:826:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dst, vbuf_r, sizeof(__m128i) * wordspercol);
data/hisat2-2.2.1/aligner_swsse_loc_i16.cpp:834:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dst, vbuf_r, sizeof(__m128i) * wordspercol);
data/hisat2-2.2.1/aligner_swsse_loc_u8.cpp:828:6: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dst, vbuf_r, sizeof(__m128i) * wordspercol);
data/hisat2-2.2.1/aligner_swsse_loc_u8.cpp:836:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(dst, vbuf_r, sizeof(__m128i) * wordspercol);
data/hisat2-2.2.1/aln_sink.h:2952:2: [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 buf[1024];
data/hisat2-2.2.1/aln_sink.h:3043:2: [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 buf[1024];
data/hisat2-2.2.1/aln_sink.h:3044:2: [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 mapqInps[1024];
data/hisat2-2.2.1/alphabet.cpp:403:1: [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 mask2iupac[16] = {
data/hisat2-2.2.1/alphabet.h:68:8: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
extern char mask2iupac[16];
data/hisat2-2.2.1/bit_packed_array.cpp:65:25: [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.
fp.write((const char *)blocks_[i], block_size_);
data/hisat2-2.2.1/bit_packed_array.cpp:126:18: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
fp.read((char *)blocks_[i], block_size_);
data/hisat2-2.2.1/diff_sample.h:785:21: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(sOrig, sPrimeArr, OFF_SIZE * sPrimeSz);
data/hisat2-2.2.1/ds.h:663:8: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
std::memcpy(list_ + cur_, l, bytes);
data/hisat2-2.2.1/ds.h:1784:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(list_, o.list_, cur_ * sizeof(T));
data/hisat2-2.2.1/ds.h:2501:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(list_, o.list_, cur_ * sizeof(std::pair<K, V>));
data/hisat2-2.2.1/filebuf.h:411:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(buf, _lastn_buf, _lastn_cur);
data/hisat2-2.2.1/filebuf.h:450:2: [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 _lastn_buf[LASTN_BUF_SZ]; // buffer of the last N chars dispensed
data/hisat2-2.2.1/filebuf.h:463:10: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
out_ = fopen(in, "wb");
data/hisat2-2.2.1/filebuf.h:516:2: [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 buf_[BUF_SZ]; // (large) input buffer
data/hisat2-2.2.1/filebuf.h:534:10: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
out_ = fopen(out.c_str(), binary ? "wb" : "w");
data/hisat2-2.2.1/filebuf.h:550:10: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
out_ = fopen(out, binary ? "wb" : "w");
data/hisat2-2.2.1/filebuf.h:574:10: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
out_ = fopen(out, binary ? "wb" : "w");
data/hisat2-2.2.1/filebuf.h:603:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&buf_[cur_], s.data(), slen);
data/hisat2-2.2.1/filebuf.h:608:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&buf_[cur_], s.data(), slen);
data/hisat2-2.2.1/filebuf.h:626:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&buf_[cur_], s.toZBuf(), slen);
data/hisat2-2.2.1/filebuf.h:631:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&buf_[cur_], s.toZBuf(), slen);
data/hisat2-2.2.1/filebuf.h:647:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&buf_[cur_], s, len);
data/hisat2-2.2.1/filebuf.h:652:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&buf_[cur_], s, len);
data/hisat2-2.2.1/filebuf.h:714:2: [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 buf_[BUF_SZ]; // (large) input buffer
data/hisat2-2.2.1/gfm.cpp:51:8: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
in.open((str + ".1." + gfm_ext).c_str(), ios_base::in | ios::binary);
data/hisat2-2.2.1/gfm.cpp:58:16: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
in.open((str + ".1." + gfm_ext).c_str(), ios_base::in | ios::binary);
data/hisat2-2.2.1/gfm.h:315:4: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
f.open(name, std::ios_base::binary | std::ios_base::in);
data/hisat2-2.2.1/gfm.h:2805:9: [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 extra[256] = {0,};
data/hisat2-2.2.1/gfm.h:4437:8: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
in.open((instr + ".1." + gfm_ext).c_str(), ios_base::in | ios::binary);
data/hisat2-2.2.1/gfm.h:4949:13: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(((char*)_gfm.get()) + side - sideSz, (const char *)gfmSide.ptr(), sideSz);
data/hisat2-2.2.1/gfm.h:4990:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(_fchr.get(), fchr, sizeof(index_t) * 5);
data/hisat2-2.2.1/gfm.h:5847:20: [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((_in1 = fopen(_in1Str.c_str(), "rb")) == NULL) {
data/hisat2-2.2.1/gfm.h:5853:24: [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((_in2 = fopen(_in2Str.c_str(), "rb")) == NULL) {
data/hisat2-2.2.1/gfm.h:6549:8: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
in.open((instr + ".1." + gfm_ext).c_str(), ios_base::in | ios::binary);
data/hisat2-2.2.1/gfm.h:6566:8: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
in.open((instr + ".1." + gfm_ext).c_str(), ios_base::in | ios::binary);
data/hisat2-2.2.1/hgfm.h:585:13: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(((char*)this->_gfm.get()) + side - sideSz, (const char *)gfmSide.ptr(), sideSz);
data/hisat2-2.2.1/hgfm.h:622:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(this->_fchr.get(), fchr, sizeof(index_t) * 5);
data/hisat2-2.2.1/hgfm.h:2486:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if((_in5 = fopen(_in5Str.c_str(), "rb")) == NULL) {
data/hisat2-2.2.1/hgfm.h:2492:15: [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((_in6 = fopen(_in6Str.c_str(), "rb")) == NULL) {
data/hisat2-2.2.1/hi_aligner.h:3847:20: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if(open) score -= sc.readGapOpen();
data/hisat2-2.2.1/hi_aligner.h:3859:20: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if(open) score -= sc.refGapOpen();
data/hisat2-2.2.1/hisat2.cpp:2186:3: [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 buf[1024];
data/hisat2-2.2.1/hisat2_build.cpp:481:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *f = fopen(infiles[i].c_str(), "r");
data/hisat2-2.2.1/hisat2_build_main.cpp:47:6: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
in.open(file);
data/hisat2-2.2.1/hisat2_build_main.cpp:48:3: [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 buf[4096];
data/hisat2-2.2.1/hisat2_main.cpp:46:6: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
in.open(file);
data/hisat2-2.2.1/hisat2_main.cpp:47:3: [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 buf[4096];
data/hisat2-2.2.1/hisat2_repeat.cpp:530:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *f = fopen(infiles[i].c_str(), "r");
data/hisat2-2.2.1/hisat2_repeat_main.cpp:47:6: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
in.open(file);
data/hisat2-2.2.1/hisat2_repeat_main.cpp:48:3: [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 buf[4096];
data/hisat2-2.2.1/hisat2lib/ht2_init.cpp:168:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&handle->options, options, sizeof(struct ht2_options));
data/hisat2-2.2.1/hisat2lib/ht2_init.cpp:170:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(&handle->options, &ht2_default_options, sizeof(struct ht2_options));
data/hisat2-2.2.1/hisat2lib/ht2_init.cpp:200:5: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(options, &ht2_default_options, sizeof(ht2_default_options));
data/hisat2-2.2.1/hisat_bp.cpp:1852:3: [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 buf[1024];
data/hisat2-2.2.1/li_hla/alignments.hpp:20:2: [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[1024] ;
data/hisat2-2.2.1/li_hla/defs.h:13:1: [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 nucToNum[26] = { 0, -1, 1, -1, -1, -1, 2,
data/hisat2-2.2.1/li_hla/defs.h:18:1: [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 numToNuc[26] = {'A', 'C', 'G', 'T'} ;
data/hisat2-2.2.1/li_hla/main.cpp:83:2: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[10100] ;
data/hisat2-2.2.1/li_hla/main.cpp:114:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen( buffer, "r" ) ;
data/hisat2-2.2.1/li_hla/main.cpp:126:20: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
info.position = atoi( fields[3].c_str() ) ;
data/hisat2-2.2.1/li_hla/main.cpp:127:18: [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).
info.length = atoi( fields[4].c_str() ) ;
data/hisat2-2.2.1/li_hla/main.cpp:131:20: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
info.position = atoi( fields[3].c_str() ) ;
data/hisat2-2.2.1/li_hla/main.cpp:136:20: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
info.position = atoi( fields[3].c_str() ) ; // notice that the snp file is 0-based index.
data/hisat2-2.2.1/li_hla/main.cpp:163:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen( buffer, "r" ) ;
data/hisat2-2.2.1/li_hla/main.cpp:206:7: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
fp = fopen( buffer, "r" ) ;
data/hisat2-2.2.1/multikey_qsort.h:657:9: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(sOrig, s, OFF_SIZE * slen);
data/hisat2-2.2.1/multikey_qsort.h:1088:27: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if(cnts[1] > 0) { memcpy(&s[cur], bkts[0], cnts[1] << (OFF_SIZE/4 + 1)); cur += cnts[1]; }
data/hisat2-2.2.1/multikey_qsort.h:1089:27: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if(cnts[2] > 0) { memcpy(&s[cur], bkts[1], cnts[2] << (OFF_SIZE/4 + 1)); cur += cnts[2]; }
data/hisat2-2.2.1/multikey_qsort.h:1090:27: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if(cnts[3] > 0) { memcpy(&s[cur], bkts[2], cnts[3] << (OFF_SIZE/4 + 1)); cur += cnts[3]; }
data/hisat2-2.2.1/multikey_qsort.h:1091:27: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
if(cnts[4] > 0) { memcpy(&s[cur], bkts[3], cnts[4] << (OFF_SIZE/4 + 1)); }
data/hisat2-2.2.1/pat.cpp:674:7: [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 buf[2048];
data/hisat2-2.2.1/pat.cpp:839:3: [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 cbuf[20];
data/hisat2-2.2.1/pat.cpp:1000:3: [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 buf[4096];
data/hisat2-2.2.1/pat.cpp:1008:26: [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).
char c = intToPhred33(atoi(qualToks_[j].c_str()), solQuals_);
data/hisat2-2.2.1/pat.cpp:1147:3: [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 cbuf[20];
data/hisat2-2.2.1/pat.cpp:1375:3: [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 cbuf[20];
data/hisat2-2.2.1/pat.cpp:1456:3: [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 buf[4096];
data/hisat2-2.2.1/pat.cpp:1461:27: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
char c = intToPhred33(atoi(qualToks_[j].c_str()), solQuals_);
data/hisat2-2.2.1/pat.cpp:1737:24: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
void SRAPatternSource::open() {
data/hisat2-2.2.1/pat.h:773:3: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open(); // open first file in the list
data/hisat2-2.2.1/pat.h:800:5: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open();
data/hisat2-2.2.1/pat.h:832:5: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open();
data/hisat2-2.2.1/pat.h:854:3: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open();
data/hisat2-2.2.1/pat.h:883:7: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
void open() {
data/hisat2-2.2.1/pat.h:890:20: [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).
} else if((in = fopen(infiles_[filecur_].c_str(), "rb")) == NULL) {
data/hisat2-2.2.1/pat.h:1297:6: [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 cbuf[20];
data/hisat2-2.2.1/pat.h:1346:2: [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 buf_[1024]; /// read buffer
data/hisat2-2.2.1/pat.h:1578:3: [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 cbuf[20];
data/hisat2-2.2.1/pat.h:1658:9: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open(); // open first file in the list
data/hisat2-2.2.1/pat.h:1683:17: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open();
data/hisat2-2.2.1/pat.h:1715:17: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open();
data/hisat2-2.2.1/pat.h:1737:9: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
open();
data/hisat2-2.2.1/pat.h:1769:10: [2] (misc) open:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
void open();
data/hisat2-2.2.1/read_qseq.cpp:62:3: [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 cbuf[20];
data/hisat2-2.2.1/read_qseq.cpp:151:3: [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 buf[4096];
data/hisat2-2.2.1/read_qseq.cpp:156:27: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
char c = intToPhred33(atoi(qualToks_[j].c_str()), solQuals_);
data/hisat2-2.2.1/reference.cpp:55:11: [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).
if((f3 = fopen(s3.c_str(), "rb")) == NULL) {
data/hisat2-2.2.1/reference.cpp:63:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if((f4 = fopen(s4.c_str(), "rb")) == NULL) {
data/hisat2-2.2.1/reference.cpp:196:17: [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).
FILE *ftmp = fopen(s4.c_str(), "rb");
data/hisat2-2.2.1/reference.cpp:231:15: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE *f4 = fopen(s4.c_str(), "rb");
data/hisat2-2.2.1/rfm.h:972:14: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
if((_in1 = fopen(_in1Str.c_str(), "rb")) == NULL) {
data/hisat2-2.2.1/rfm.h:978:15: [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((_in2 = fopen(_in2Str.c_str(), "rb")) == NULL) {
data/hisat2-2.2.1/sam.h:480:5: [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 buf[1024];
data/hisat2-2.2.1/sam.h:540:5: [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 buf[1024];
data/hisat2-2.2.1/sam.h:1061:5: [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 buf[1024];
data/hisat2-2.2.1/sequence_io.h:43:13: [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).
FILE *in = fopen(sstr_to_cstr(infile), "r");
data/hisat2-2.2.1/sequence_io.h:80:13: [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).
FILE *in = fopen(sstr_to_cstr(infile), "r");
data/hisat2-2.2.1/sstring.h:71:38: [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.
static inline size_t sstr_len(const char s[N]) {
data/hisat2-2.2.1/sstring.h:688:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(cs_, b, sz * sizeof(T));
data/hisat2-2.2.1/sstring.h:699:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(cs_, b.c_str(), sz * sizeof(T));
data/hisat2-2.2.1/sstring.h:1165:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(cs_, b, sizeof(uint32_t)*nwords());
data/hisat2-2.2.1/sstring.h:1843:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(cs_, b, sz * sizeof(T));
data/hisat2-2.2.1/sstring.h:2012:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(cs_ + len_, b, sz * sizeof(T));
data/hisat2-2.2.1/sstring.h:2101:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(tmp, cs_, sizeof(T)*len_);
data/hisat2-2.2.1/sstring.h:2105:4: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(ptmp, printcs_, sizeof(char)*len_);
data/hisat2-2.2.1/sstring.h:2306:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(cs_, b, sz * sizeof(T));
data/hisat2-2.2.1/sstring.h:2474:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(cs_ + len_, b, sz * sizeof(T));
data/hisat2-2.2.1/sstring.h:2545:2: [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 printcs_[S+1]; // +1 so that we have the option of dropping in a terminating "\0"
data/hisat2-2.2.1/sstring.h:2673:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(this->cs_, b, sz);
data/hisat2-2.2.1/sstring.h:2985:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(this->cs_, b, sz);
data/hisat2-2.2.1/sstring.h:3252:3: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(this->cs_, b, sz);
data/hisat2-2.2.1/aligner_metrics.h:194:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void nextRead(const BTDnaString& read) {
data/hisat2-2.2.1/aligner_metrics.h:208:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const size_t len = read.length();
data/hisat2-2.2.1/aligner_metrics.h:210:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if((int)read[i] == 4) curNumNs_++;
data/hisat2-2.2.1/aligner_seed.cpp:89:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const Read& read,
data/hisat2-2.2.1/aligner_seed.cpp:101:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if((int)read.length() < seedlen) {
data/hisat2-2.2.1/aligner_seed.cpp:103:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
seedlen = (int)read.length();
data/hisat2-2.2.1/aligner_seed.cpp:190:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.cons[i].instantiate(read.length());
data/hisat2-2.2.1/aligner_seed.cpp:193:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
is.overall.instantiate(read.length());
data/hisat2-2.2.1/aligner_seed.h:373:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const Read& read,
data/hisat2-2.2.1/aligner_seed.h:638:28: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void nextRead(const Read& read) {
data/hisat2-2.2.1/aligner_seed.h:639:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read_ = &read;
data/hisat2-2.2.1/aligner_seed.h:684:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const Read& read,
data/hisat2-2.2.1/aligner_seed.h:709:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read_ = &read;
data/hisat2-2.2.1/aligner_seed.h:935:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const Read& read() const { return *read_; }
data/hisat2-2.2.1/aligner_seed.h:1408:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const Read& read, // input read
data/hisat2-2.2.1/aligner_seed.h:1423:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const Read& read, // read to align
data/hisat2-2.2.1/aligner_seed.h:1439:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const Read& read, // read to align
data/hisat2-2.2.1/aligner_seed.h:1467:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const Read& read, // read to align
data/hisat2-2.2.1/aligner_seed.h:1484:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const Read& read, // read to align
data/hisat2-2.2.1/aligner_seed.h:1612:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const Read& read, // input read
data/hisat2-2.2.1/aligner_seed.h:1621:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if((int)read.length() < seedlen) seedlen = (int)read.length();
data/hisat2-2.2.1/aligner_seed.h:1621:50: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if((int)read.length() < seedlen) seedlen = (int)read.length();
data/hisat2-2.2.1/aligner_seed.h:1627:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
seq.set(read.patFw.windowGetDna(i, fw, read.color, depth, len), i);
data/hisat2-2.2.1/aligner_seed.h:1627:42: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
seq.set(read.patFw.windowGetDna(i, fw, read.color, depth, len), i);
data/hisat2-2.2.1/aligner_seed.h:1628:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
qual.set(read.qual.windowGet(i, fw, depth, len), i);
data/hisat2-2.2.1/aligner_seed.h:1642:28: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const Read& read, // read to align
data/hisat2-2.2.1/aligner_seed.h:1651:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
assert_gt(read.length(), 0);
data/hisat2-2.2.1/aligner_seed.h:1662:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if((int)read.length() - (int)off > len) {
data/hisat2-2.2.1/aligner_seed.h:1663:19: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
nseeds += ((int)read.length() - (int)off - len) / per;
data/hisat2-2.2.1/aligner_seed.h:1671:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
sr.reset(read, offIdx2off_, nseeds);
data/hisat2-2.2.1/aligner_seed.h:1688:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read,
data/hisat2-2.2.1/aligner_seed.h:1691:43: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::min<int>((int)seedlen, (int)read.length()),
data/hisat2-2.2.1/aligner_seed.h:1702:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read,
data/hisat2-2.2.1/aligner_seed.h:1739:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const Read& read, // read to align
data/hisat2-2.2.1/aligner_seed.h:1753:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read_ = &read;
data/hisat2-2.2.1/aligner_seed.h:1881:33: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const Read& read, // read to align
data/hisat2-2.2.1/aligner_seed.h:1895:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const size_t len = read.length();
data/hisat2-2.2.1/aligner_seed.h:1901:33: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BTDnaString& seq = fw ? read.patFw : read.patRc;
data/hisat2-2.2.1/aligner_seed.h:1901:46: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BTDnaString& seq = fw ? read.patFw : read.patRc;
data/hisat2-2.2.1/aligner_seed.h:2011:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const Read& read, // read to align
data/hisat2-2.2.1/aligner_seed.h:2023:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const size_t len = read.length();
data/hisat2-2.2.1/aligner_seed.h:2025:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
size_t ns = read.ns();
data/hisat2-2.2.1/aligner_seed.h:2071:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(fw ? (ebwtfw ? read.patFw : read.patFwRev) :
data/hisat2-2.2.1/aligner_seed.h:2071:33: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(fw ? (ebwtfw ? read.patFw : read.patFwRev) :
data/hisat2-2.2.1/aligner_seed.h:2072:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(ebwtfw ? read.patRc : read.patRcRev));
data/hisat2-2.2.1/aligner_seed.h:2072:28: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(ebwtfw ? read.patRc : read.patRcRev));
data/hisat2-2.2.1/aligner_seed.h:2075:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(fw ? (ebwtfw ? read.qual : read.qualRev) :
data/hisat2-2.2.1/aligner_seed.h:2075:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(fw ? (ebwtfw ? read.qual : read.qualRev) :
data/hisat2-2.2.1/aligner_seed.h:2076:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(ebwtfw ? read.qualRev : read.qual));
data/hisat2-2.2.1/aligner_seed.h:2076:30: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
(ebwtfw ? read.qualRev : read.qual));
data/hisat2-2.2.1/aligner_seed.h:2304:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
Edit::toRef(fw ? read.patFw : read.patRc, edits_, rf);
data/hisat2-2.2.1/aligner_seed.h:2304:39: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
Edit::toRef(fw ? read.patFw : read.patRc, edits_, rf);
data/hisat2-2.2.1/aligner_seed2.h:3370:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for(size_t i = 0; i < read.length(); i++) {
data/hisat2-2.2.1/aligner_seed2.h:3371:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(i < trimLf || i >= read.length() - trimRg) {
data/hisat2-2.2.1/aligner_seed2.h:3372:42: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(os != NULL) { *os << (char)tolower(read.toChar(i)); }
data/hisat2-2.2.1/aligner_seed2.h:3381:38: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
assert_eq((int)edits[eidx].qchr, read.toChar(i));
data/hisat2-2.2.1/aligner_seed2.h:3382:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(os != NULL) { *os << read.toChar(i); }
data/hisat2-2.2.1/aligner_seed2.h:3386:38: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
assert_eq((int)edits[eidx].qchr, read.toChar(i));
data/hisat2-2.2.1/aligner_seed2.h:3393:28: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(os != NULL) { *os << read.toChar(i); }
data/hisat2-2.2.1/aligner_seed2.h:3402:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for(size_t i = 0; i < read.length(); i++) {
data/hisat2-2.2.1/aligner_seed2.h:3403:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(i < trimLf || i >= read.length() - trimRg) {
data/hisat2-2.2.1/aligner_seed2.h:3429:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for(size_t i = 0; i < read.length(); i++) {
data/hisat2-2.2.1/aligner_seed2.h:3430:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(i < trimLf || i >= read.length() - trimRg) {
data/hisat2-2.2.1/aligner_seed2.h:3451:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
rf.append(read[i]);
data/hisat2-2.2.1/aligner_seed2.h:3452:28: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(os != NULL) { *os << read.toChar(i); }
data/hisat2-2.2.1/aligner_seed2.h:3992:16: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int rdc = q.getc(off5p, fw);
data/hisat2-2.2.1/aligner_seed2.h:4094:15: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int rdc = q.getc(off5p, fw);
data/hisat2-2.2.1/aligner_sw.cpp:1205:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BTDnaString& read,
data/hisat2-2.2.1/aligner_sw.cpp:1219:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
assert_eq(read.length(), qual.length());
data/hisat2-2.2.1/aligner_sw.cpp:1220:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
size_t nrow = read.length();
data/hisat2-2.2.1/aligner_sw.cpp:1227:40: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int readGaps = sc.maxReadGaps(minsc, read.length());
data/hisat2-2.2.1/aligner_sw.cpp:1228:38: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int refGaps = sc.maxRefGaps(minsc, read.length());
data/hisat2-2.2.1/aligner_sw.cpp:1236:44: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
size_t nceil = (size_t)sc.nCeil.f((double)read.length());
data/hisat2-2.2.1/aligner_sw.cpp:1288:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
readrc = read;
data/hisat2-2.2.1/aligner_sw.cpp:1291:3: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read, // read sequence
data/hisat2-2.2.1/aligner_sw.cpp:1296:3: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.length(), // offset of last char (exclusive) in 'read' to consider
data/hisat2-2.2.1/aligner_sw.cpp:1323:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const char *read,
data/hisat2-2.2.1/aligner_sw.cpp:1335:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
btread.install(read, true);
data/hisat2-2.2.1/aligner_sw.cpp:1368:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const char *read,
data/hisat2-2.2.1/aligner_sw.cpp:1382:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
btread.install(read, true);
data/hisat2-2.2.1/aligner_sw.cpp:1420:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const char *read,
data/hisat2-2.2.1/aligner_sw.cpp:1435:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
btread.install(read, true);
data/hisat2-2.2.1/aligner_sw.cpp:3156:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
BTDnaString read;
data/hisat2-2.2.1/aligner_sw.cpp:3159:2: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.installChars(argv[optind]);
data/hisat2-2.2.1/aligner_sw.cpp:3162:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
assert_eq(read.length(), qual.length());
data/hisat2-2.2.1/aligner_sw.cpp:3191:3: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.length(),
data/hisat2-2.2.1/aligner_sw.cpp:3195:3: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.length(),
data/hisat2-2.2.1/aligner_sw.cpp:3202:3: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read,
data/hisat2-2.2.1/aligner_sw_driver.h:1014:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const Read& read, // read
data/hisat2-2.2.1/aligner_sw_driver.h:1033:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const int matei = (read.mate <= 1 ? 0 : 1);
data/hisat2-2.2.1/aligner_sw_driver.h:1100:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read,
data/hisat2-2.2.1/alt.h:82:10: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
bool mismatch() const { return type == ALT_SNP_SGL; }
data/hisat2-2.2.1/alt.h:197:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool read(ifstream& f_in, bool bigEndian) {
data/hisat2-2.2.1/alt.h:239:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool read(ifstream& f_in, bool bigEndian) {
data/hisat2-2.2.1/bit_packed_array.cpp:82:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
#define read_fp(x) fp.read((char *)&(x), sizeof((x)))
data/hisat2-2.2.1/bit_packed_array.cpp:126:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
fp.read((char *)blocks_[i], block_size_);
data/hisat2-2.2.1/edit.cpp:119:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BTDnaString& read,
data/hisat2-2.2.1/edit.cpp:122:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
printQAlign(os, "", read, edits);
data/hisat2-2.2.1/edit.cpp:131:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BTDnaString& read,
data/hisat2-2.2.1/edit.cpp:134:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
printQAlignNoCheck(os, "", read, edits);
data/hisat2-2.2.1/edit.cpp:144:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BTDnaString& read,
data/hisat2-2.2.1/edit.cpp:150:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for(size_t i = 0; i < read.length(); i++) {
data/hisat2-2.2.1/edit.cpp:157:38: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
assert_eq((int)edits[eidx].qchr, read.toChar(i));
data/hisat2-2.2.1/edit.cpp:158:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
os << read.toChar(i);
data/hisat2-2.2.1/edit.cpp:162:38: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
assert_eq((int)edits[eidx].qchr, read.toChar(i));
data/hisat2-2.2.1/edit.cpp:167:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(!del && !mm) os << read.toChar(i);
data/hisat2-2.2.1/edit.cpp:173:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for(size_t i = 0; i < read.length(); i++) {
data/hisat2-2.2.1/edit.cpp:194:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for(size_t i = 0; i < read.length(); i++) {
data/hisat2-2.2.1/edit.cpp:209:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(!del && !mm) os << read.toChar(i);
data/hisat2-2.2.1/edit.cpp:221:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BTDnaString& read,
data/hisat2-2.2.1/edit.cpp:227:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for(size_t i = 0; i < read.length(); i++) {
data/hisat2-2.2.1/edit.cpp:234:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
os << read.toChar(i);
data/hisat2-2.2.1/edit.cpp:241:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(!del && !mm) os << read.toChar(i);
data/hisat2-2.2.1/edit.cpp:247:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for(size_t i = 0; i < read.length(); i++) {
data/hisat2-2.2.1/edit.cpp:267:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for(size_t i = 0; i < read.length(); i++) {
data/hisat2-2.2.1/edit.cpp:281:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(!del && !mm) os << read.toChar(i);
data/hisat2-2.2.1/edit.cpp:302:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BTDnaString& read,
data/hisat2-2.2.1/edit.cpp:312:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const size_t rdlen = read.length();
data/hisat2-2.2.1/edit.cpp:315:28: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
assert(Edit::repOk(edits, read, fw, trim5, trim3));
data/hisat2-2.2.1/edit.cpp:317:47: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
invertPoss(const_cast<EList<Edit>&>(edits), read.length()-trimBeg-trimEnd, false);
data/hisat2-2.2.1/edit.cpp:320:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ASSERT_ONLY(int c = read[i]);
data/hisat2-2.2.1/edit.cpp:347:16: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ref.append(read[i]);
data/hisat2-2.2.1/edit.cpp:361:47: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
invertPoss(const_cast<EList<Edit>&>(edits), read.length()-trimBeg-trimEnd, false);
data/hisat2-2.2.1/edit.h:300:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BTDnaString& read,
data/hisat2-2.2.1/edit.h:314:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BTDnaString& read,
data/hisat2-2.2.1/edit.h:326:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BTDnaString& read,
data/hisat2-2.2.1/edit.h:336:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BTDnaString& read,
data/hisat2-2.2.1/edit.h:348:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BTDnaString& read,
data/hisat2-2.2.1/filebuf.h:193:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
_inf->read((char*)_buf, BUF_SZ);
data/hisat2-2.2.1/filebuf.h:196:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
_ins->read((char*)_buf, BUF_SZ);
data/hisat2-2.2.1/filebuf.h:662:17: [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).
writeChars(s, strlen(s));
data/hisat2-2.2.1/gbwt_graph.h:78:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool read(ifstream& f_in, bool bigEndian) {
data/hisat2-2.2.1/gbwt_graph.h:109:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool read(ifstream& f_in, bool bigEndian) {
data/hisat2-2.2.1/gbwt_graph.h:170:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void read(const string& fname, bool bigEndian) {
data/hisat2-2.2.1/gbwt_graph.h:179:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
nodes[i].read(rg_file, bigEndian);
data/hisat2-2.2.1/gbwt_graph.h:184:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
edges[i].read(rg_file, bigEndian);
data/hisat2-2.2.1/gbwt_graph.h:556:34: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
nodes.back().read(rg_in_file, bigEndian);
data/hisat2-2.2.1/gbwt_graph.h:561:34: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
edges.back().read(rg_in_file, bigEndian);
data/hisat2-2.2.1/gbwt_graph.h:1811:14: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
base.read(rf_fname, bigEndian);
data/hisat2-2.2.1/gfm.h:753:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
alts.back().read(in7, this->toBe());
data/hisat2-2.2.1/gfm.h:786:39: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
haplotypes.back().read(in7, this->toBe());
data/hisat2-2.2.1/gfm.h:847:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
repeatdb->read(in7, this->toBe(), _repeatIncluded);
data/hisat2-2.2.1/gfm.h:860:43: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
_repeat_kmertables.back().read(in7, this->toBe());
data/hisat2-2.2.1/gfm.h:4408:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(&c, 1);
data/hisat2-2.2.1/gfm.h:6520:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read(&c, 1);
data/hisat2-2.2.1/hgfm.h:2271:36: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
if(alt.mismatch()) {
data/hisat2-2.2.1/hi_aligner.h:4278:54: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BTDnaString& seq = (fwi == 0 ? read.patFw : read.patRc);
data/hisat2-2.2.1/hi_aligner.h:4278:67: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BTDnaString& seq = (fwi == 0 ? read.patFw : read.patRc);
data/hisat2-2.2.1/hi_aligner.h:4901:51: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const Read& read, // read to align
data/hisat2-2.2.1/hi_aligner.h:4919:52: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const Read& read, // read to align
data/hisat2-2.2.1/hi_aligner.h:4939:61: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const Read& read, // read to align
data/hisat2-2.2.1/hi_aligner.h:6363:85: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const Read& read, // read to align
data/hisat2-2.2.1/hi_aligner.h:6381:31: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const index_t len = (index_t)read.length();
data/hisat2-2.2.1/hi_aligner.h:6382:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BTDnaString& seq = fw ? read.patFw : read.patRc;
data/hisat2-2.2.1/hi_aligner.h:6382:48: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BTDnaString& seq = fw ? read.patFw : read.patRc;
data/hisat2-2.2.1/hi_aligner.h:6608:84: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const Read& read, // read to align
data/hisat2-2.2.1/hi_aligner.h:6628:31: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const index_t len = (index_t)read.length();
data/hisat2-2.2.1/hi_aligner.h:6631:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BTDnaString& seq = fw ? read.patFw : read.patRc;
data/hisat2-2.2.1/hi_aligner.h:6631:48: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BTDnaString& seq = fw ? read.patFw : read.patRc;
data/hisat2-2.2.1/hi_aligner.h:6753:93: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const Read& read, // read to align
data/hisat2-2.2.1/hi_aligner.h:6776:43: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const local_index_t len = (local_index_t)read.length();
data/hisat2-2.2.1/hi_aligner.h:6779:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BTDnaString& seq = fw ? read.patFw : read.patRc;
data/hisat2-2.2.1/hi_aligner.h:6779:48: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const BTDnaString& seq = fw ? read.patFw : read.patRc;
data/hisat2-2.2.1/hisat2.cpp:784:17: [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).
size_t solen = strlen(short_options);
data/hisat2-2.2.1/hisat2.cpp:1080:20: [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).
s.replace(found, strlen("%LOCAL%"), localAlign ? "-local" : "");
data/hisat2-2.2.1/hisat2.cpp:1410:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(arg == NULL || strlen(arg) == 0) {
data/hisat2-2.2.1/hisat2.cpp:1462:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(arg) > 0) {
data/hisat2-2.2.1/hisat2.cpp:4096:33: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read); // read?
data/hisat2-2.2.1/hisat2.cpp:4097:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ssdb->read(gfm, altdb->alts());
data/hisat2-2.2.1/hisat2.cpp:4101:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ssdb->read(ssdb_file,
data/hisat2-2.2.1/hisat2.cpp:4109:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ssdb->read(ssdb_file,
data/hisat2-2.2.1/hisat2.cpp:4349:5: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
getchar();
data/hisat2-2.2.1/hisat2lib/ht2_index.cpp:60:28: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
result_buf_size += strlen(hp->gfm->_refnames[i].c_str()) + 1;
data/hisat2-2.2.1/hisat2lib/ht2_index.cpp:72:23: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t rlen = strlen(hp->gfm->_refnames[i].c_str());
data/hisat2-2.2.1/hisat_bp.cpp:668:17: [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).
size_t solen = strlen(short_options);
data/hisat2-2.2.1/hisat_bp.cpp:925:20: [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).
s.replace(found, strlen("%LOCAL%"), localAlign ? "-local" : "");
data/hisat2-2.2.1/hisat_bp.cpp:1251:22: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(arg == NULL || strlen(arg) == 0) {
data/hisat2-2.2.1/hisat_bp.cpp:1300:7: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(arg) > 0) {
data/hisat2-2.2.1/hisat_bp.cpp:3641:33: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read); // read?
data/hisat2-2.2.1/hisat_bp.cpp:3646:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ssdb->read(ssdb_file, false); // known splice sites
data/hisat2-2.2.1/hisat_bp.cpp:3653:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
ssdb->read(ssdb_file, true); // novel splice sites
data/hisat2-2.2.1/hisat_bp.cpp:3864:5: [1] (buffer) getchar:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
getchar();
data/hisat2-2.2.1/li_hla/main.cpp:132:18: [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).
info.length = strlen( fields[4].c_str() ) ;
data/hisat2-2.2.1/li_hla/main.cpp:187:14: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len = strlen( buffer ) ;
data/hisat2-2.2.1/ls.cpp:37:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for(size_t i = 0; i < strlen(t); i++) {
data/hisat2-2.2.1/ls.cpp:59:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for(size_t i = 0; i < strlen(t); i++) {
data/hisat2-2.2.1/ls.cpp:87:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for(size_t i = 0; i < strlen(t); i++) {
data/hisat2-2.2.1/ls.cpp:105:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for(size_t i = 0; i < strlen(t); i++) {
data/hisat2-2.2.1/ls.cpp:123:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for(size_t i = 0; i < strlen(t); i++) {
data/hisat2-2.2.1/msvcc/codeStubs/getopt.c:251:51: [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 (!defined __STDC__ || !__STDC__) && !defined strlen
data/hisat2-2.2.1/msvcc/codeStubs/getopt.c:254:12: [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).
extern int strlen (const char *);
data/hisat2-2.2.1/msvcc/codeStubs/getopt.c:450:44: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int len = nonoption_flags_max_len = strlen (orig_str);
data/hisat2-2.2.1/msvcc/codeStubs/getopt.c:667:21: [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).
== (unsigned int) strlen (p->name))
data/hisat2-2.2.1/msvcc/codeStubs/getopt.c:691:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
nextchar += strlen (nextchar);
data/hisat2-2.2.1/msvcc/codeStubs/getopt.c:722:21: [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).
nextchar += strlen (nextchar);
data/hisat2-2.2.1/msvcc/codeStubs/getopt.c:739:17: [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).
nextchar += strlen (nextchar);
data/hisat2-2.2.1/msvcc/codeStubs/getopt.c:744:16: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
nextchar += strlen (nextchar);
data/hisat2-2.2.1/msvcc/codeStubs/getopt.c:855:51: [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 ((unsigned int) (nameend - nextchar) == strlen (p->name))
data/hisat2-2.2.1/msvcc/codeStubs/getopt.c:878:18: [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).
nextchar += strlen (nextchar);
data/hisat2-2.2.1/msvcc/codeStubs/getopt.c:898:19: [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).
nextchar += strlen (nextchar);
data/hisat2-2.2.1/msvcc/codeStubs/getopt.c:912:19: [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).
nextchar += strlen (nextchar);
data/hisat2-2.2.1/msvcc/codeStubs/getopt.c:916:18: [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).
nextchar += strlen (nextchar);
data/hisat2-2.2.1/pat.cpp:725:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool FastaPatternSource::read(
data/hisat2-2.2.1/pat.cpp:852:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool FastqPatternSource::read(
data/hisat2-2.2.1/pat.cpp:1159:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool TabbedPatternSource::read(
data/hisat2-2.2.1/pat.h:796:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
do { read(r, rdid, endid, success, done); }
data/hisat2-2.2.1/pat.h:862:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
virtual bool read(
data/hisat2-2.2.1/pat.h:967:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
virtual bool read(
data/hisat2-2.2.1/pat.h:1042:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
virtual bool read(
data/hisat2-2.2.1/pat.h:1179:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
virtual bool read(
data/hisat2-2.2.1/pat.h:1233:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
virtual bool read(
data/hisat2-2.2.1/pat.h:1426:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
virtual bool read(
data/hisat2-2.2.1/pat.h:1493:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
virtual bool read(
data/hisat2-2.2.1/pat.h:1679:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
do { read(r, rdid, endid, success, done); }
data/hisat2-2.2.1/pat.h:1743:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
virtual bool read(
data/hisat2-2.2.1/read.h:298:6: [1] (buffer) getc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
int getc(TReadOff off5p, bool fw) const {
data/hisat2-2.2.1/read_qseq.cpp:202:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool QseqPatternSource::read(
data/hisat2-2.2.1/ref_read.h:91:11: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
first = fgetc(in) ? true : false;
data/hisat2-2.2.1/repeat.h:95:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool read(ifstream& f_in, bool bigEndian) {
data/hisat2-2.2.1/repeat.h:158:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool read(ifstream& f_in, bool bigEndian) {
data/hisat2-2.2.1/repeat.h:165:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
alleles[i].read(f_in, bigEndian);
data/hisat2-2.2.1/repeat.h:248:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void read(ifstream& f_in, bool bigEndian, const EList<uint8_t>& includeRepeat) {
data/hisat2-2.2.1/repeat.h:265:41: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
_repeats[repeat_size+j].read(f_in, bigEndian);
data/hisat2-2.2.1/repeat_builder.cpp:206:54: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
string toMDZ(const EList<Edit>& edits, const string& read)
data/hisat2-2.2.1/repeat_builder.cpp:212:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
btread.install(read.c_str(), true);
data/hisat2-2.2.1/repeat_builder.cpp:223:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
string read;
data/hisat2-2.2.1/repeat_builder.cpp:229:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(ref[ref_pos]);
data/hisat2-2.2.1/repeat_builder.cpp:237:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(edits[i].qchr);
data/hisat2-2.2.1/repeat_builder.cpp:241:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(edits[i].qchr);
data/hisat2-2.2.1/repeat_builder.cpp:251:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(ref[ref_pos]);
data/hisat2-2.2.1/repeat_builder.cpp:254:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
return read;
data/hisat2-2.2.1/repeat_builder.cpp:2907:48: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const string& read,
data/hisat2-2.2.1/repeat_builder.cpp:2917:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(read[i] == pad[i]) {
data/hisat2-2.2.1/repeat_builder.cpp:2927:12: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(read[i] == pad[pad_start + i]) {
data/hisat2-2.2.1/repeat_builder.cpp:2935:46: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const string &read,
data/hisat2-2.2.1/repeat_builder.cpp:2956:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
for(size_t i = 0; i < read.length(); i++) {
data/hisat2-2.2.1/repeat_builder.cpp:2962:25: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
cerr << "READ: " << read << endl;
data/hisat2-2.2.1/repeat_builder.cpp:2966:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
btread.install(read.c_str(), true);
data/hisat2-2.2.1/repeat_builder.cpp:3061:29: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
cerr << "READ: " << read << endl;
data/hisat2-2.2.1/repeat_builder.cpp:3968:64: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const string& read,
data/hisat2-2.2.1/repeat_builder.cpp:3978:35: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
swaligner_.makePadString(ref, read, pad, 5);
data/hisat2-2.2.1/repeat_builder.cpp:3981:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
string read2 = pad + read;
data/hisat2-2.2.1/repeat_builder.cpp:3996:27: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
size_t right = left + read.length();
data/hisat2-2.2.1/repeat_builder.cpp:4007:42: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
max_matchlen = getMaxMatchLen(edits, read.length());
data/hisat2-2.2.1/repeat_builder.cpp:4013:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
btread.install(read.c_str(), true);
data/hisat2-2.2.1/repeat_builder.cpp:4711:23: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
#define read_fp(x) fp.read((char *)&(x), sizeof((x)))
data/hisat2-2.2.1/repeat_builder.h:735:36: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const string &read,
data/hisat2-2.2.1/repeat_builder.h:740:38: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const string& read,
data/hisat2-2.2.1/repeat_builder.h:890:47: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
const string& read,
data/hisat2-2.2.1/repeat_kmer.h:461:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool read(ifstream& f_in, bool bigEndian) {
data/hisat2-2.2.1/rfm.h:781:24: [1] (buffer) mismatch:
Function does not check the second iterator for over-read conditions
(CWE-126). This function is often discouraged by most C++ coding standards
in favor of its safer alternatives provided since C++14. Consider using a
form of this function that checks the second iterator before potentially
overflowing it.
if(alt.mismatch()) {
data/hisat2-2.2.1/splice_site.cpp:128:33: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool read) :
data/hisat2-2.2.1/splice_site.cpp:131:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
_read(read),
data/hisat2-2.2.1/splice_site.cpp:653:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void SpliceSiteDB::read(const GFM<TIndexOffU>& gfm, const EList<ALT<TIndexOffU> >& alts)
data/hisat2-2.2.1/splice_site.cpp:727:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void SpliceSiteDB::read(ifstream& in, bool known)
data/hisat2-2.2.1/splice_site.h:547:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool read() const { return _read; }
data/hisat2-2.2.1/splice_site.h:556:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void read(const GFM<TIndexOffU>& gfm, const EList<ALT<TIndexOffU> >& alts);
data/hisat2-2.2.1/splice_site.h:557:10: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void read(ifstream& in, bool known = false);
data/hisat2-2.2.1/splice_site_new.cpp:125:33: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool read) :
data/hisat2-2.2.1/splice_site_new.cpp:129:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
_read(read),
data/hisat2-2.2.1/splice_site_new.cpp:559:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void SpliceSiteDB::read(ifstream& in, bool novel)
data/hisat2-2.2.1/splice_site_new.cpp:627:33: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
bool read) :
data/hisat2-2.2.1/splice_site_new.cpp:631:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
_read(read),
data/hisat2-2.2.1/splice_site_new.cpp:1043:20: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
void SpliceSiteDB::read(ifstream& in, bool novel)
data/hisat2-2.2.1/sstring.h:72:10: [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).
return strlen(s);
data/hisat2-2.2.1/sstring.h:80:10: [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).
return strlen(s);
data/hisat2-2.2.1/sstring.h:88:10: [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).
return strlen((const char *)s);
data/hisat2-2.2.1/sstring.h:563:14: [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).
install(b, strlen(b));
data/hisat2-2.2.1/sstring.h:706:14: [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).
install(b, strlen(b));
data/hisat2-2.2.1/sstring.h:849:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ASSERT_ONLY(size_t xformElts = strlen(xform));
data/hisat2-2.2.1/sstring.h:983:22: [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).
installColors(b, strlen(b));
data/hisat2-2.2.1/sstring.h:985:21: [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).
installChars(b, strlen(b));
data/hisat2-2.2.1/sstring.h:988:15: [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).
install(b, strlen(b));
data/hisat2-2.2.1/sstring.h:1234:14: [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).
install(b, strlen(b));
data/hisat2-2.2.1/sstring.h:1241:19: [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).
installChars(b, strlen(b));
data/hisat2-2.2.1/sstring.h:1248:20: [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).
installColors(b, strlen(b));
data/hisat2-2.2.1/sstring.h:1298:21: [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).
installReverse(b, strlen(b));
data/hisat2-2.2.1/sstring.h:1330:26: [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).
installReverseChars(b, strlen(b));
data/hisat2-2.2.1/sstring.h:1362:27: [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).
installReverseColors(b, strlen(b));
data/hisat2-2.2.1/sstring.h:1704:14: [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).
install(b, strlen(b));
data/hisat2-2.2.1/sstring.h:1851:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
void install(const T* b) { install(b, strlen(b)); }
data/hisat2-2.2.1/sstring.h:2020:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
append(b, strlen(b));
data/hisat2-2.2.1/sstring.h:2043:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ASSERT_ONLY(size_t xformElts = strlen(xform));
data/hisat2-2.2.1/sstring.h:2175:14: [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).
install(b, strlen(b));
data/hisat2-2.2.1/sstring.h:2313:40: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
void install(const T* b) { install(b, strlen(b)); }
data/hisat2-2.2.1/sstring.h:2482:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
append(b, strlen(b));
data/hisat2-2.2.1/sstring.h:2523:34: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ASSERT_ONLY(size_t xformElts = strlen(xform));
data/hisat2-2.2.1/sstring.h:2608:22: [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).
installColors(b, strlen(b));
data/hisat2-2.2.1/sstring.h:2610:21: [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).
installChars(b, strlen(b));
data/hisat2-2.2.1/sstring.h:2613:15: [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).
install(b, strlen(b));
data/hisat2-2.2.1/sstring.h:2971:22: [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).
installColors(b, strlen(b));
data/hisat2-2.2.1/sstring.h:2973:21: [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).
installChars(b, strlen(b));
data/hisat2-2.2.1/sstring.h:2976:15: [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).
install(b, strlen(b));
data/hisat2-2.2.1/sstring.h:3184:20: [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).
installChars(b, strlen(b));
data/hisat2-2.2.1/sstring.h:3186:15: [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).
install(b, strlen(b));
data/hisat2-2.2.1/tinythread.h:704:5: [1] (obsolete) usleep:
This C routine is considered obsolete (as opposed to the shell command by
the same name). The interaction of this function with SIGALRM and other
timer functions such as sleep(), alarm(), setitimer(), and nanosleep() is
unspecified (CWE-676). Use nanosleep(2) or setitimer(2) instead.
usleep(int(double(aTime.count()) * (1000000.0 * _Period::_as_double()) + 0.5));
data/hisat2-2.2.1/word_io.h:115:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read((char *)&x, 4);
data/hisat2-2.2.1/word_io.h:131:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(read(in, (void *)&x, 4) != 4) {
data/hisat2-2.2.1/word_io.h:165:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read((char *)&x, 4);
data/hisat2-2.2.1/word_io.h:181:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(read(in, (void *)&x, 4) != 4) {
data/hisat2-2.2.1/word_io.h:215:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read((char *)&x, 2);
data/hisat2-2.2.1/word_io.h:231:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(read(in, (void *)&x, 2) != 2) {
data/hisat2-2.2.1/word_io.h:265:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read((char *)&x, 2);
data/hisat2-2.2.1/word_io.h:281:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(read(in, (void *)&x, 2) != 2) {
data/hisat2-2.2.1/word_io.h:313:8: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read((char *)&x, 1);
data/hisat2-2.2.1/word_io.h:331:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
in.read((char *)&x, sizeof(index_t));
data/hisat2-2.2.1/word_io.h:348:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if(read(in, (void *)&x, sizeof(index_t)) != sizeof(index_t)) {
ANALYSIS SUMMARY:
Hits = 518
Lines analyzed = 129708 in approximately 4.54 seconds (28576 lines/second)
Physical Source Lines of Code (SLOC) = 98569
Hits@level = [0] 54 [1] 307 [2] 165 [3] 36 [4] 8 [5] 2
Hits@level+ = [0+] 572 [1+] 518 [2+] 211 [3+] 46 [4+] 10 [5+] 2
Hits/KSLOC@level+ = [0+] 5.80304 [1+] 5.2552 [2+] 2.14063 [3+] 0.466678 [4+] 0.101452 [5+] 0.0202904
Dot directories skipped = 1 (--followdotdir overrides)
Minimum risk level = 1
Not every hit is necessarily a security vulnerability.
There may be other security vulnerabilities; review your code!
See 'Secure Programming HOWTO'
(https://dwheeler.com/secure-programs) for more information.