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/bedops-2.4.39+dfsg/applications/bed/bedextract/src/ExtractRows.cpp
Examining data/bedops-2.4.39+dfsg/applications/bed/bedmap/src/Bedmap.cpp
Examining data/bedops-2.4.39+dfsg/applications/bed/bedmap/src/Input.hpp
Examining data/bedops-2.4.39+dfsg/applications/bed/bedmap/src/TDefs.hpp
Examining data/bedops-2.4.39+dfsg/applications/bed/bedops/src/BedPadReader.hpp
Examining data/bedops-2.4.39+dfsg/applications/bed/bedops/src/Bedops.cpp
Examining data/bedops-2.4.39+dfsg/applications/bed/bedops/src/Input.hpp
Examining data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/BedReader.hpp
Examining data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp
Examining data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/Input.hpp
Examining data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/Printers.hpp
Examining data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c
Examining data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.h
Examining data/bedops-2.4.39+dfsg/applications/bed/conversion/src/gprof-helper.c
Examining data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/CheckSort.cpp
Examining data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/Sort.cpp
Examining data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp
Examining data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/Structures.hpp
Examining data/bedops-2.4.39+dfsg/applications/bed/starch/src/starch.c
Examining data/bedops-2.4.39+dfsg/applications/bed/starch/src/starch.h
Examining data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.h
Examining data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c
Examining data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.h
Examining data/bedops-2.4.39+dfsg/applications/bed/starch/src/unstarch.c
Examining data/bedops-2.4.39+dfsg/applications/bed/starch/src/unstarch.h
Examining data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/WindowSweep.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/bed/FindBedRange.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/BedVisitors.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/NumericalVisitors.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/OtherVisitors.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/VisitorFactory.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/Visitors.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/bed/BedBaseVisitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/bed/EchoMapBedVisitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/bed/EchoMapIntersectLengthVisitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/bed/OvrAggregateVisitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/bed/OvrUniqueFractionVisitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/bed/OvrUniqueVisitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/bed/WeightedAverageVisitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/helpers/NamedVisitors.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/helpers/ProcessBedVisitorRow.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/helpers/ProcessVisitorRow.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/numerical/AverageVisitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/numerical/CoeffVariationVisitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/numerical/CountVisitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/numerical/ExtremeVisitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/numerical/IndicatorVisitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/numerical/MedianAbsoluteDeviationVisitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/numerical/MedianVisitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/numerical/RollingKthAverageVisitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/numerical/RollingKthVisitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/numerical/StdevVisitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/numerical/SumVisitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/numerical/TrimmedMeanVisitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/numerical/VarianceVisitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/other/EchoVisitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/other/MultiVisitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/BedCheckIterator.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/BedCompare.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/BedDistances.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/BedTypes.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/data/measurement/NaN.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/data/measurement/SelectMeasureType.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchBase64Coding.h
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchConstants.h
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchFileHelpers.h
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchHelpers.h
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchMetadataHelpers.h
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchSha1Digest.h
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/unstarchHelpers.h
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/suite/BEDOPS.Constants.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/suite/BEDOPS.Version.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/AllocateIterator.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/Assertion.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/BitMonitor.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/ByLine.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/CharPooledMemory.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/CompilerMath.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/Exception.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/FPWrap.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/Factory.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/Formats.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/IteratorPair.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/OrderCompare.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/PooledMemory.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/PrintTypes.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/SingletonType.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/Typify.hpp
Examining data/bedops-2.4.39+dfsg/interfaces/src/algorithm/sweep/WindowSweepImpl.cpp
Examining data/bedops-2.4.39+dfsg/interfaces/src/algorithm/sweep/WindowSweepImpl.specialize.cpp
Examining data/bedops-2.4.39+dfsg/interfaces/src/data/measurement/NaN.cpp
Examining data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchBase64Coding.c
Examining data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchConstants.c
Examining data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c
Examining data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c
Examining data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchSha1Digest.c
Examining data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c
Examining data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchFileHelpers.c
Examining data/bedops-2.4.39+dfsg/interfaces/src/utility/SingletonType.cpp
FINAL RESULTS:
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1065:21: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.dest_line_str, "%s\t%u\t%u\t%s\n", c2b_header_chr_name, c2b_globals.header_line_idx, (c2b_globals.header_line_idx + 1), c2b_globals.src_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1382:17: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(c2b_globals.gtf->element->id, c2b_gtf_field_placeholder);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1456:23: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
*dest_size += sprintf(*dest_line_ptr + *dest_size,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1479:23: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
*dest_size += sprintf(*dest_line_ptr + *dest_size,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1716:17: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.dest_line_str, "%s\t%u\t%u\t%s\n", c2b_header_chr_name, c2b_globals.header_line_idx, (c2b_globals.header_line_idx + 1), c2b_globals.src_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2054:19: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
*dest_size += sprintf(*dest_line_ptr + *dest_size,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2344:17: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.dest_line_str, "%s\t%u\t%u\t%s\n", c2b_header_chr_name, c2b_globals.header_line_idx, (c2b_globals.header_line_idx + 1), c2b_globals.src_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2414:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.dest_line_str, "%s\t%u\t%u\t%s\n", c2b_header_chr_name, c2b_globals.header_line_idx, (c2b_globals.header_line_idx + 1), c2b_globals.src_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3006:19: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
*dest_size += sprintf(*dest_line_ptr + *dest_size,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3303:25: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.dest_line_str, "%s\t%u\t%u\t%s\n", c2b_header_chr_name, c2b_globals.header_line_idx, (c2b_globals.header_line_idx + 1), c2b_globals.src_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3862:23: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
*dest_size += sprintf(*dest_line_ptr + *dest_size,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3895:23: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
*dest_size += sprintf(*dest_line_ptr + *dest_size,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3971:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.dest_line_str, "%s\t%u\t%u\t%s\n", c2b_header_chr_name, c2b_globals.header_line_idx, (c2b_globals.header_line_idx + 1), c2b_globals.src_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4349:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.dest_line_str, "%s\t%u\t%u\t%s\n", c2b_header_chr_name, c2b_globals.header_line_idx, (c2b_globals.header_line_idx + 1), c2b_globals.src_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4693:25: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.sam->element->modified_qname, "%s/%zu", c2b_globals.sam->element->qname, block_idx++);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4733:29: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.sam->element->modified_qname, "%s/%zu", c2b_globals.sam->element->qname, block_idx++);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5108:23: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
*dest_size += sprintf(*dest_line_ptr + *dest_size,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5139:23: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
*dest_size += sprintf(*dest_line_ptr + *dest_size,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5168:23: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
*dest_size += sprintf(*dest_line_ptr + *dest_size,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5242:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.dest_line_str, "%s\t%u\t%u\t%s\n", c2b_header_chr_name, c2b_globals.header_line_idx, (c2b_globals.header_line_idx + 1), c2b_globals.src_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5643:23: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
*dest_size += sprintf(*dest_line_ptr + *dest_size,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5668:23: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
*dest_size += sprintf(*dest_line_ptr + *dest_size,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5714:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.wig->id,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5730:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.wig->id,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5740:17: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.dest_line_str,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5748:17: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.dest_line_str,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5785:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.wig->id,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5795:17: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.dest_line_str,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5803:17: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.dest_line_str,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5839:36: [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.
int variable_step_fields = sscanf(c2b_globals.src_line_str,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5855:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.wig->id,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5867:17: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.dest_line_str,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5875:17: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.dest_line_str,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5911:33: [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.
int fixed_step_fields = sscanf(c2b_globals.src_line_str,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5934:17: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.dest_line_str,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5942:17: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.dest_line_str,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5978:26: [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.
int bed_fields = sscanf(c2b_globals.src_line_str,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6001:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.dest_line_str,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6014:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.dest_line_str,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6065:17: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.dest_line_str,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6078:17: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.dest_line_str,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6125:17: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.dest_line_str,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6138:17: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(c2b_globals.dest_line_str,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6735:21: [4] (shell) execl:
This causes a new program to execute and is difficult to use safely
(CWE-78). try using a library call that implements the same functionality
if available.
execl_ret = execl("/bin/sh", "/bin/sh", "-c", cmd, NULL);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7032:9: [4] (race) access:
This usually indicates a security flaw. If an attacker can change anything
along the path between the call to access() and the file's actual use
(e.g., by moving files), the attacker can exploit the race condition
(CWE-362/CWE-367!). Set up the correct permissions (e.g., using setuid())
and try to open the file directly.
if (access(candidate, X_OK) == 0
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/Sort.cpp:158:29: [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(*tmpPath, argv[i]);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:130:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(tmpl, path);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:140:5: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
strcpy(*fileName, tmpl);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:429:25: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
fields[i] = fscanf(tmpFiles[i], "%s\t%" SCNd64 "\t%" SCNd64 "%[^\n]s\n",
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:483:31: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function.
fields[currMin] = fscanf(tmpFiles[currMin], "%s\t%" SCNd64 "\t%" SCNd64 "%[^\n]s\n",
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:739:21: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
sscanf(tmpArr, "%" SCNd64, &startPos);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:782:21: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
sscanf(tmpArr, "%" SCNd64, &endPos);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1163:21: [4] (format) fprintf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
fprintf(out,
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1206:33: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf(currElem,
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1212:37: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(currElem + strlen(currElem), "\t%s\n", beds->chroms[i]->coords[j].data);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1216:37: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf(nextElem,
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1222:41: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(nextElem + strlen(nextElem), "\t%s\n", beds->chroms[i]->coords[j+1].data);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1232:33: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf(nextElem,
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1238:37: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(nextElem + strlen(nextElem), "\t%s\n", beds->chroms[i]->coords[j+1].data);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:380:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(outFn, "%s.%s.bz2", inChr, outTag);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:393:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(outFn, "%s.%s.gz", inChr, outTag);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:620:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(outFn, "%s.%s.bz2", inChr, outTag);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:633:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(outFn, "%s.%s.gz", inChr, outTag);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1054:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(outTagFn, "%s.%s.bz2", inChr, outTag);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1063:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(outTagFn, "%s.%s.gz", inChr, outTag);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:2433:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(uncomprOutFn, "%s.%s.uncompressed", inChr, outTag);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3517:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(finalOutTagFn, "%s.%s.bz2", inChr, outTag);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3526:13: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(finalOutTagFn, "%s.%s.gz", inChr, outTag);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3885:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(tempOutFn, "%s.%s.uncompressed.%04u", summary->chromosome, outTag, inRecIdx);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3948:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(uncomprOutFn, "%s.%s.uncompressed", summary->chromosome, outTag);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:6753:42: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
static_cast<size_t>( sprintf(extractionBuffer + *t_nExtractionBufferPos,
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:6760:42: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
static_cast<size_t>( sprintf(extractionBuffer + *t_nExtractionBufferPos,
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:6767:30: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
(size_t) sprintf(extractionBuffer + *t_nExtractionBufferPos,
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:6773:30: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
(size_t) sprintf(extractionBuffer + *t_nExtractionBufferPos,
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7097:46: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
static_cast<size_t>( sprintf(extractionBuffer + *t_nExtractionBufferPos,
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7104:46: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
static_cast<size_t>( sprintf(extractionBuffer + *t_nExtractionBufferPos,
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7111:34: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
(size_t) sprintf(extractionBuffer + *t_nExtractionBufferPos,
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7118:34: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
(size_t) sprintf(extractionBuffer + *t_nExtractionBufferPos,
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7515:25: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(retransBuf + *nRetransBuf, "%" PRId64 "\t%s\n", (*retransStart - *retransLastPosition), retransRemainder);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7529:25: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(retransBuf + *nRetransBuf, "%" PRId64 "\t%s\n", *retransStart, retransRemainder);
data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/helpers/ProcessBedVisitorRow.hpp:161:14: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, t->measurement());
data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/helpers/ProcessBedVisitorRow.hpp:167:14: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, t);
data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/helpers/ProcessBedVisitorRow.hpp:198:14: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, t->measurement());
data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/helpers/ProcessBedVisitorRow.hpp:261:14: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, t->measurement());
data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/helpers/ProcessBedVisitorRow.hpp:268:14: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, t);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:68:42: [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).
ChromInfo(const ChromInfo& c) { std::strcpy(chrom_, c.chrom_); }
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:69:47: [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).
explicit ChromInfo(char const* c) { std::strcpy(chrom_, c); }
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:73:49: [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).
inline void chrom(char const* chrom) { std::strcpy(chrom_, chrom); }
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:77:12: [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).
std::strcpy(chrom_, c.chrom_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:91:48: [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).
explicit ChromInfo(char const* chr) { std::strcpy(chrom_, chr); }
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:96:42: [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).
void chrom(char const* chrom) { std::strcpy(chrom_, chrom); }
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:201:12: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, chrom_, start_, end_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:206:12: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, chrom_, start_, end_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:216:26: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
int numScan = std::sscanf(inputLine.c_str(),
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:225:26: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
int numScan = std::fscanf(inputFile,
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:259:14: [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).
{ std::strcpy(fullrest_, c.fullrest_); }
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:271:12: [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).
std::strcpy(fullrest_, c.fullrest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:279:12: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, chrom_, start_, end_, fullrest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:284:12: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, chrom_, start_, end_, fullrest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:296:26: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
int numScan = std::sscanf(inputLine.c_str(),
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:306:26: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
int numScan = std::fscanf(inputFile, format,
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:348:48: [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).
{ *id_ = '\0'; if ( id != nullptr ) std::strcpy(id_, id); }
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:351:27: [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).
{ *id_ = '\0'; std::strcpy(id_, c.id_); }
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:363:19: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
return std::sscanf(inputLine.c_str(), format,
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:371:29: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
int numScanned = std::fscanf(inputFile, format,
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:379:12: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, chrom_, start_, end_, id_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:384:7: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
printf(format, chrom_, start_, end_, id_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:394:77: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
inline void id(char const* id) { *id_ = '\0'; if ( id != nullptr ) std::strcpy(id_, id); }
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:400:12: [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).
std::strcpy(id_, c.id_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:434:15: [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).
std::strcpy(fullrest_, c.fullrest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:448:12: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, chrom_, start_, end_, fullrest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:453:12: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, chrom_, start_, end_, fullrest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:468:29: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
int numScanned = std::sscanf(inputLine.c_str(),
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:485:29: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
int numScanned = std::fscanf(inputFile,
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:500:12: [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).
std::strcpy(fullrest_, c.fullrest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:561:19: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
return std::sscanf(inputLine.c_str(),
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:571:29: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
int numScanned = std::fscanf(inputFile,
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:581:12: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, chrom_, start_, end_, id_, measurement_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:586:12: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, chrom_, start_, end_, id_, measurement_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:631:33: [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).
*fullrest_ = '\0'; std::strcpy(fullrest_, c.fullrest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:646:12: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, chrom_, start_, end_, fullrest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:651:12: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, chrom_, start_, end_, fullrest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:667:35: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
const int numScanned = std::sscanf(inputLine.c_str(),
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:674:35: [4] (format) snprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
const int numWritten = std::snprintf(fullrest_, MAXRESTSIZE+1, f, id_, measurement_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:690:35: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
const int numScanned = std::fscanf(inputFile,
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:699:35: [4] (format) snprintf:
If format strings can be influenced by an attacker, they can be exploited,
and note that sprintf variations do not always \0-terminate (CWE-134). Use
a constant for the format specification.
const int numWritten = std::snprintf(fullrest_, MAXRESTSIZE+1, f, id_, measurement_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:710:12: [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).
std::strcpy(fullrest_, c.fullrest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:71:56: [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).
{ *chrom_ = '\0'; if ( c.chrom_ != NULL ) std::strcpy(chrom_, c.chrom_); }
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:74:49: [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).
{ *chrom_ = '\0'; if ( c != NULL ) std::strcpy(chrom_, c); }
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:83:16: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
std::strcpy(chrom_, chrom);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:95:54: [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).
*chrom_ = '\0'; if ( c.chrom_ != NULL ) std::strcpy(chrom_, c.chrom_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:115:50: [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).
explicit ChromInfo(char const* chr) { std::strcpy(chrom_, chr); }
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:120:44: [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).
void chrom(char const* chrom) { std::strcpy(chrom_, chrom); }
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:225:14: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, chrom_, start_, end_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:230:14: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, chrom_, start_, end_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:237:28: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
int numScan = std::sscanf(inputLine.c_str(),
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:248:28: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
int numScan = std::fscanf(inputFile,
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:287:16: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
std::strcat(rest_, rest);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:292:54: [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).
{ *rest_ = '\0'; if ( c.rest_ != NULL ) std::strcpy(rest_, c.rest_); }
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:310:16: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
std::strcpy(rest_, c.rest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:318:14: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, chrom_, start_, end_, rest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:323:14: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, chrom_, start_, end_, rest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:332:28: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
int numScan = std::sscanf(inputLine.c_str(),
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:339:14: [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).
std::strcpy(rest_, restBuf);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:349:28: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
int numScan = std::fscanf(inputFile, format,
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:357:14: [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).
std::strcpy(rest_, restBuf);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:401:47: [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).
{ *id_ = '\0'; if ( id != NULL ) std::strcpy(id_, id); }
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:404:50: [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).
{ *id_ = '\0'; if ( c.id_ != NULL ) std::strcpy(id_, c.id_); }
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:419:31: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
int numScanned = std::sscanf(inputLine.c_str(), format,
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:436:31: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
int numScanned = std::fscanf(inputFile, format,
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:449:14: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, chrom_, start_, end_, id_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:454:9: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
printf(format, chrom_, start_, end_, id_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:462:45: [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).
*id_ = '\0'; if ( id != NULL ) std::strcpy(id_, id);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:472:48: [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).
*id_ = '\0'; if ( c.id_ != NULL ) std::strcpy(id_, c.id_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:512:40: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if ( c.rest_ != NULL ) std::strcpy(rest_, c.rest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:513:44: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
if ( c.fullrest_ != NULL ) std::strcpy(fullrest_, c.fullrest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:520:16: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
std::strcpy(fullrest_, id);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:525:16: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
std::strcat(rest_, rest);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:526:16: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
std::strcat(fullrest_, rest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:542:14: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, chrom_, start_, end_, id_, rest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:547:14: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, chrom_, start_, end_, id_, rest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:558:31: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
int numScanned = std::sscanf(inputLine.c_str(),
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:567:14: [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).
std::strcpy(rest_, restBuf);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:572:14: [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).
std::strcpy(fullrest_, idBuf);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:573:14: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
std::strcat(fullrest_, restBuf);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:586:31: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
int numScanned = std::fscanf(inputFile,
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:597:14: [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).
std::strcpy(rest_, restBuf);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:602:14: [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).
std::strcpy(fullrest_, idBuf);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:603:14: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
std::strcat(fullrest_, restBuf);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:615:52: [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).
*rest_ = '\0'; if ( c.rest_ != NULL ) std::strcpy(rest_, c.rest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:617:60: [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).
*fullrest_ = '\0'; if ( c.fullrest_ != NULL ) std::strcpy(fullrest_, c.fullrest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:687:31: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
int numScanned = std::sscanf(inputLine.c_str(),
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:702:31: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
int numScanned = std::fscanf(inputFile,
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:715:14: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, chrom_, start_, end_, id_, measurement_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:720:14: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, chrom_, start_, end_, id_, measurement_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:760:54: [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).
*rest_ = '\0'; if ( c.rest_ != NULL ) std::strcpy(rest_, c.rest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:761:62: [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).
*fullrest_ = '\0'; if ( c.fullrest_ != NULL ) std::strcpy(fullrest_, c.fullrest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:771:16: [4] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused).
std::strcpy(fullrest_, id);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:776:16: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
std::strcat(rest_, rest);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:777:16: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
std::strcat(fullrest_, rest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:794:14: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, chrom_, start_, end_, id_, measurement_, rest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:799:14: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, chrom_, start_, end_, id_, measurement_, rest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:810:31: [4] (buffer) sscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
int numScanned = std::sscanf(inputLine.c_str(),
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:820:14: [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).
std::strcpy(rest_, restBuf);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:826:14: [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).
std::strcpy(fullrest_, idBuf);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:829:14: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
std::strcat(fullrest_, restBuf);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:842:31: [4] (buffer) fscanf:
The scanf() family's %s operation, without a limit specification, permits
buffer overflows (CWE-120, CWE-20). Specify a limit to %s, or use a
different input function. If the scanf format is influenceable by an
attacker, it's exploitable.
int numScanned = std::fscanf(inputFile,
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:853:14: [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).
std::strcpy(rest_, restBuf);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:861:14: [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).
std::strcpy(fullrest_, idBuf);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:864:14: [4] (buffer) strcat:
Does not check for buffer overflows when concatenating to destination
[MS-banned] (CWE-120). Consider using strcat_s, strncat, strlcat, or
snprintf (warning: strncat is easily misused).
std::strcat(fullrest_, restBuf);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:876:52: [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).
*rest_ = '\0'; if ( c.rest_ != NULL ) std::strcpy(rest_, c.rest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:878:60: [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).
*fullrest_ = '\0'; if ( c.fullrest_ != NULL ) std::strcpy(fullrest_, c.fullrest_);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:1814:22: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
std::sprintf(out, "%s\t%" PRId64 "\t%" PRId64 "\t%s", _currChr, _currStart, _currStop, _currRemainder);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:1817:22: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
std::sprintf(out, "%s\t%" PRId64 "\t%" PRId64, _currChr, _currStart, _currStop);
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/CharPooledMemory.hpp:213:18: [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).
std::strcpy(_data+nxt->second, c);
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/CharPooledMemory.hpp:239:20: [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).
std::strcpy(_data+f, c);
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/CharPooledMemory.hpp:458:18: [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).
std::strcpy(_data+nxt->second, c);
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/CharPooledMemory.hpp:482:20: [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).
std::strcpy(_data+pos, c);
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/PrintTypes.hpp:50:10: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, t);
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/PrintTypes.hpp:58:10: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, t);
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/PrintTypes.hpp:66:10: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, t);
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/PrintTypes.hpp:74:10: [4] (format) printf:
If format strings can be influenced by an attacker, they can be exploited
(CWE-134). Use a constant for the format specification.
std::printf(format, t);
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/PrintTypes.hpp:82:10: [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.
std::fprintf(out, format, t);
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/PrintTypes.hpp:90:10: [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.
std::fprintf(out, format, t);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c: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(dup, str);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:103:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(*outFn, "%s.gz", inFn);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:171:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(*outFn, "%s.bz2", inFn);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:868:25: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(outFn, "%s.%s", chromosome, tag);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1356:25: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(outFn, "%s.%s", chromosome, tag);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2095:25: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(compressedFn, "%s.%s", prevChromosome, tag);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2365:21: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(compressedFn, "%s.%s", chromosome, tag);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2473:25: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%s", nonCoordLineBuf);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2500:29: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\t%s\n", (start - lastPosition), remainder);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2506:29: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\t%s\n", start, remainder);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2751:21: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\t%s\n", (start - lastPosition), remainder);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2757:21: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\t%s\n", start, remainder);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2824:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(compressedFn, "%s.%s", prevChromosome, tag);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3359:25: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(compressedFn, "%s.%s", prevChromosome, tag);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3628:21: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(compressedFn, "%s.%s", chromosome, tag);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3751:25: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\t%s\n", (start - lastPosition), remainder);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3765:25: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\t%s\n", start, remainder);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4015:21: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\t%s\n", (start - lastPosition), remainder);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4029:21: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\t%s\n", start, remainder);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4113:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(compressedFn, "%s.%s", prevChromosome, tag);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:812:9: [4] (format) sprintf:
Potential format string problem (CWE-134). Make format string constant.
sprintf(recordSize, "%" PRIu64, filenameSize);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2097:5: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(_tag, "pid%d.%s", pid, uts.nodename);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:677:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(out, "%s\n", str);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:679:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(out, "%s\n", str);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:681:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(out, "%s\n", str);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:683:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(out, "%s\n", str);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:685:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(out, "%s\n", str);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:688:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(out, "%s\n", str);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:690:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(out, "%s\n", str);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:692:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(out, "%s\n", str);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:694:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(out, "%s\n", str);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:696:9: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
sprintf(out, "%s\n", str);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2735:25: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
*nLineBuf = sprintf(reinterpret_cast<char *>(lineBuf) + *nLineBufPos, "%" PRId64 "\t%s\n", (*currStart - *lastPosition), *currRemainder);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2737:25: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
*nLineBuf = sprintf((char *)lineBuf + *nLineBufPos, "%" PRId64 "\t%s\n", (*currStart - *lastPosition), *currRemainder);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2757:25: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
*nLineBuf = sprintf(reinterpret_cast<char *>(lineBuf) + *nLineBufPos, "%" PRId64 "\t%s\n", *currStart, *currRemainder);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2759:25: [4] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf.
*nLineBuf = sprintf((char *)lineBuf + *nLineBufPos, "%" PRId64 "\t%s\n", *currStart, *currRemainder);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6772:14: [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.
if ((p = getenv("PATH")) == NULL) {
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7614:22: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
int client_opt = getopt_long(argc,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7779:22: [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.
client_opt = getopt_long(argc,
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/Sort.cpp:239:31: [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.
tmpPath = getenv("TMPDIR");
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starch.c:300:29: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
int starch_client_opt = getopt_long (argc, argv, starch_client_opt_string, starch_client_long_options, &starch_client_long_index);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starch.c:350:29: [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.
starch_client_opt = getopt_long (argc, argv, starch_client_opt_string, starch_client_long_options, &starch_client_long_index);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:275:32: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
int starchcat_client_opt = getopt_long(argc, argv, starchcat_client_opt_string, starchcat_client_long_options, &starchcat_client_long_index);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:316:32: [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.
starchcat_client_opt = getopt_long(argc, argv, starchcat_client_opt_string, starchcat_client_long_options, &starchcat_client_long_index);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:897:22: [3] (buffer) getopt_long:
Some older implementations do not protect against internal buffer overflows
(CWE-120, CWE-20). Check implementation on installation, or limit the size
of all string inputs.
int client_opt = getopt_long(argc,
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:967:22: [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.
client_opt = getopt_long(argc,
data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/numerical/ExtremeVisitor.hpp:49:12: [3] (random) srand:
This function is not sufficiently random for security-related functions
such as key and nonce creation (CWE-327). Use a more secure technique for
acquiring random values.
std::srand(std::time(NULL));
data/bedops-2.4.39+dfsg/applications/bed/bedextract/src/ExtractRows.cpp:120:20: [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).
f1_ = std::fopen(fn.c_str(), "rb");
data/bedops-2.4.39+dfsg/applications/bed/bedextract/src/ExtractRows.cpp:130:20: [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).
f1_ = std::fopen(fn.c_str(), "rb");
data/bedops-2.4.39+dfsg/applications/bed/bedextract/src/ExtractRows.cpp:140:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
f1_ = std::fopen(fn.c_str(), "rb");
data/bedops-2.4.39+dfsg/applications/bed/bedextract/src/ExtractRows.cpp:148:24: [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).
f2_ = std::fopen(argv[argcntr], "rb"), f2Name_ = argv[argcntr];
data/bedops-2.4.39+dfsg/applications/bed/bedops/src/Input.hpp:182:33: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
std::ifstream tmpfile(argv[i]);
data/bedops-2.4.39+dfsg/applications/bed/bedops/src/Input.hpp:183:25: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
if ( !tmpfile ) { // even if an integer, it could name a file input
data/bedops-2.4.39+dfsg/applications/bed/bedops/src/Input.hpp:371:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
subsetPerc_ = atoi(str.c_str());
data/bedops-2.4.39+dfsg/applications/bed/bedops/src/Input.hpp:375:21: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
subsetPerc_ = atoi(l.c_str());
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:186:5: [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 cat2generic_cmd[C2B_MAX_COMMAND_LINE_LENGTH_VALUE];
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:187:5: [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 bed_unsorted2bed_sorted_cmd[C2B_MAX_COMMAND_LINE_LENGTH_VALUE];
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:188:5: [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 bed_sorted2starch_cmd[C2B_MAX_COMMAND_LINE_LENGTH_VALUE];
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:484:5: [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 bam2sam_cmd[C2B_MAX_COMMAND_LINE_LENGTH_VALUE];
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:485:5: [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 bed_unsorted2bed_sorted_cmd[C2B_MAX_COMMAND_LINE_LENGTH_VALUE];
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:486:5: [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 bed_sorted2starch_cmd[C2B_MAX_COMMAND_LINE_LENGTH_VALUE];
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:771:5: [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(cmd,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:774:5: [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(cmd + strlen(c2b_globals.cat->path),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:786:5: [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(cmd,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:789:5: [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(cmd + strlen(c2b_globals.sam->samtools_path),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:798:5: [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 sort_bed_args[C2B_MAX_COMMAND_LINE_LENGTH_VALUE];
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:803:9: [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(sort_bed_args,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:806:9: [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(sort_bed_args + strlen(sort_bed_args),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:812:9: [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(sort_bed_args,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:818:9: [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(sort_bed_args + strlen(sort_bed_args),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:821:9: [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(sort_bed_args + strlen(sort_bed_args),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:826:5: [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(sort_bed_args + strlen(sort_bed_args),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:832:5: [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(cmd,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:835:5: [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(cmd + strlen(c2b_globals.sort->sort_bed_path),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:844:5: [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 starch_args[C2B_MAX_COMMAND_LINE_LENGTH_VALUE];
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:849:9: [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(starch_args,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:855:9: [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(starch_args,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:869:9: [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(starch_args + strlen(starch_args),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:872:9: [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(starch_args + strlen(starch_args),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:875:9: [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(starch_args + strlen(starch_args),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:880:5: [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(starch_args + strlen(starch_args),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:889:5: [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(cmd,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:892:5: [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(cmd + strlen(c2b_globals.starch->path),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1063:21: [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(c2b_globals.src_line_str, src, src_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1066:21: [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(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1098:9: [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(c2b_globals.gtf->element->seqname, src, seqname_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1120:9: [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(c2b_globals.gtf->element->source, src + gtf_field_offsets[0] + 1, source_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1142:9: [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(c2b_globals.gtf->element->feature, src + gtf_field_offsets[1] + 1, feature_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1164:9: [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(c2b_globals.gtf->element->start_str, src + gtf_field_offsets[2] + 1, start_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1188:9: [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(c2b_globals.gtf->element->end_str, src + gtf_field_offsets[3] + 1, end_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1212:9: [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(c2b_globals.gtf->element->score, src + gtf_field_offsets[4] + 1, score_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1234:9: [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(c2b_globals.gtf->element->strand, src + gtf_field_offsets[5] + 1, strand_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1256:9: [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(c2b_globals.gtf->element->frame, src + gtf_field_offsets[6] + 1, frame_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1278:9: [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(c2b_globals.gtf->element->attributes, src + gtf_field_offsets[7] + 1, attributes_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1302:13: [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(c2b_globals.gtf->element->comments, src + gtf_field_offsets[8] + 1, comments_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1317:9: [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(c2b_globals.gtf->element->attributes + strlen(c2b_globals.gtf->element->attributes) - trailing_semicolon_fudge,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1335:5: [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(attributes_copy, c2b_globals.gtf->element->attributes, strlen(c2b_globals.gtf->element->attributes) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1375:17: [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(c2b_globals.gtf->element->id, gtf_id_start + 1, id_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1670:9: [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(c2b_globals.gff->element->header, src, header_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1686:9: [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(c2b_globals.gff->element->non_int_prefix, c2b_globals.gff->element->header, non_int_prefix_size - 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1714:17: [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(c2b_globals.src_line_str, src, src_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1717:17: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1743:9: [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(c2b_globals.gff->element->seqid, src, seqid_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1765:9: [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(c2b_globals.gff->element->source, src + gff_field_offsets[0] + 1, source_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1787:9: [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(c2b_globals.gff->element->type, src + gff_field_offsets[1] + 1, type_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1809:9: [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(c2b_globals.gff->element->start_str, src + gff_field_offsets[2] + 1, start_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1833:9: [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(c2b_globals.gff->element->end_str, src + gff_field_offsets[3] + 1, end_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1857:9: [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(c2b_globals.gff->element->score, src + gff_field_offsets[4] + 1, score_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1879:9: [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(c2b_globals.gff->element->strand, src + gff_field_offsets[5] + 1, strand_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1901:9: [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(c2b_globals.gff->element->phase, src + gff_field_offsets[6] + 1, phase_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1923:9: [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(c2b_globals.gff->element->attributes, src + gff_field_offsets[7] + 1, attributes_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1950:9: [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(c2b_globals.gff->element->attributes + strlen(c2b_globals.gff->element->attributes) - trailing_semicolon_fudge,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1969:5: [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(attributes_copy, c2b_globals.gff->element->attributes, strlen(c2b_globals.gff->element->attributes) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1974:5: [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(c2b_globals.gff->element->id, gff_null_id, strlen(gff_null_id) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1993:17: [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(c2b_globals.gff->element->id, kv_tok + strlen(gff_id_prefix), strlen(kv_tok + strlen(gff_id_prefix)) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2342:17: [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(c2b_globals.src_line_str, src, src_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2345:17: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2381:5: [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(c2b_globals.psl->element->matchesStr, src, matchesStr_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2412:13: [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(c2b_globals.src_line_str, src, src_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2415:13: [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(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2436:5: [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(c2b_globals.psl->element->misMatchesStr, src + psl_field_offsets[0] + 1, misMatchesStr_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2458:5: [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(c2b_globals.psl->element->repMatchesStr, src + psl_field_offsets[1] + 1, repMatchesStr_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2480:5: [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(c2b_globals.psl->element->nCountStr, src + psl_field_offsets[2] + 1, nCountStr_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2502:5: [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(c2b_globals.psl->element->qNumInsertStr, src + psl_field_offsets[3] + 1, qNumInsertStr_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2524:5: [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(c2b_globals.psl->element->qBaseInsertStr, src + psl_field_offsets[4] + 1, qBaseInsertStr_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2546:5: [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(c2b_globals.psl->element->tNumInsertStr, src + psl_field_offsets[5] + 1, tNumInsertStr_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2568:5: [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(c2b_globals.psl->element->tBaseInsertStr, src + psl_field_offsets[6] + 1, tBaseInsertStr_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2590:5: [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(c2b_globals.psl->element->strand, src + psl_field_offsets[7] + 1, strand_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2611:5: [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(c2b_globals.psl->element->qName, src + psl_field_offsets[8] + 1, qName_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2632:5: [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(c2b_globals.psl->element->qSizeStr, src + psl_field_offsets[9] + 1, qSizeStr_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2654:5: [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(c2b_globals.psl->element->qStartStr, src + psl_field_offsets[10] + 1, qStartStr_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2676:5: [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(c2b_globals.psl->element->qEndStr, src + psl_field_offsets[11] + 1, qEndStr_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2698:5: [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(c2b_globals.psl->element->tName, src + psl_field_offsets[12] + 1, tName_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2719:5: [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(c2b_globals.psl->element->tSizeStr, src + psl_field_offsets[13] + 1, tSizeStr_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2741:5: [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(c2b_globals.psl->element->tStartStr, src + psl_field_offsets[14] + 1, tStartStr_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2763:5: [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(c2b_globals.psl->element->tEndStr, src + psl_field_offsets[15] + 1, tEndStr_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2785:5: [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(c2b_globals.psl->element->blockCountStr, src + psl_field_offsets[16] + 1, blockCountStr_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2807:5: [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(c2b_globals.psl->element->blockSizes, src + psl_field_offsets[17] + 1, blockSizes_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2828:5: [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(c2b_globals.psl->element->qStarts, src + psl_field_offsets[18] + 1, qStarts_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2849:5: [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(c2b_globals.psl->element->tStarts, src + psl_field_offsets[19] + 1, tStarts_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2886:5: [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 bs_arr[C2B_MAX_PSL_BLOCK_SIZES_STRING_LENGTH];
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2905:13: [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(bs_arr, s + start_bs_offset, length_bs_offset);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2924:5: [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 ts_arr[C2B_MAX_PSL_T_STARTS_STRING_LENGTH];
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2943:13: [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(ts_arr, s + start_ts_offset, length_ts_offset);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3301:25: [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(c2b_globals.src_line_str, src, src_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3304:25: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
memcpy(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3346:5: [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(c2b_globals.rmsk->element->sw_score, src + sw_score_start, sw_score_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3370:9: [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(c2b_globals.rmsk->element->perc_div, src + perc_div_start, perc_div_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3398:9: [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(c2b_globals.rmsk->element->perc_deleted, src + perc_deleted_start, perc_deleted_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3426:9: [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(c2b_globals.rmsk->element->perc_inserted, src + perc_inserted_start, perc_inserted_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3454:9: [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(c2b_globals.rmsk->element->query_seq, src + query_seq_start, query_seq_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3482:9: [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(c2b_globals.rmsk->element->query_start_str, src + query_start_start, query_start_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3521:9: [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(c2b_globals.rmsk->element->query_end_str, src + query_end_start, query_end_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3561:9: [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(c2b_globals.rmsk->element->bases_past_match, src + bases_past_match_start, bases_past_match_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3589:9: [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(c2b_globals.rmsk->element->strand, src + strand_start, strand_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3592:13: [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(c2b_globals.rmsk->element->strand, c2b_rmsk_strand_complement_replacement, strlen(c2b_rmsk_strand_complement_replacement) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3620:9: [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(c2b_globals.rmsk->element->repeat_name, src + repeat_name_start, repeat_name_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3648:9: [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(c2b_globals.rmsk->element->repeat_class, src + repeat_class_start, repeat_class_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3676:9: [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(c2b_globals.rmsk->element->bases_before_match_comp, src + bases_before_match_comp_start, bases_before_match_comp_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3704:9: [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(c2b_globals.rmsk->element->match_start, src + match_start_start, match_start_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3733:9: [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(c2b_globals.rmsk->element->match_end, src + match_end_start, match_end_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3767:9: [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(c2b_globals.rmsk->element->unique_id, src + unique_id_start, unique_id_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3796:13: [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(c2b_globals.rmsk->element->higher_score_match, src + higher_score_match_start, higher_score_match_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3969:13: [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(c2b_globals.src_line_str, src, src_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3972:13: [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(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4019:5: [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(c2b_globals.sam->element->cigar, src + sam_field_offsets[4] + 1, cigar_size - 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4048:5: [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(c2b_globals.sam->element->flag_str, src + sam_field_offsets[0] + 1, flag_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4074:9: [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(c2b_globals.sam->element->rname, src + sam_field_offsets[1] + 1, rname_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4091:9: [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(c2b_globals.sam->element->rname, c2b_unmapped_read_chr_name, c2b_unmapped_read_chr_name_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4110:5: [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(c2b_globals.sam->element->pos_str, src + sam_field_offsets[2] + 1, pos_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4132:5: [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(c2b_globals.sam->element->qname, src, qname_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4137:5: [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 strand_str[C2B_MAX_STRAND_LENGTH_VALUE] = {0};
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4138:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(strand_str, "%c", (strand_val == 0x10) ? '-' : '+');
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4152:5: [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(c2b_globals.sam->element->strand, strand_str, strand_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4169:5: [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(c2b_globals.sam->element->mapq, src + sam_field_offsets[3] + 1, mapq_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4186:5: [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(c2b_globals.sam->element->rnext, src + sam_field_offsets[5] + 1, rnext_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4203:5: [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(c2b_globals.sam->element->pnext, src + sam_field_offsets[6] + 1, pnext_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4220:5: [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(c2b_globals.sam->element->tlen, src + sam_field_offsets[7] + 1, tlen_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4237:5: [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(c2b_globals.sam->element->seq, src + sam_field_offsets[8] + 1, seq_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4254:5: [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(c2b_globals.sam->element->qual, src + sam_field_offsets[9] + 1, qual_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4275:13: [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(c2b_globals.sam->element->opt + c2b_globals.sam->element->opt_length, src + sam_field_offsets[field_idx - 1] + 1, opt_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4347:13: [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(c2b_globals.src_line_str, src, src_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4350:13: [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(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4397:5: [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(c2b_globals.sam->element->cigar, src + sam_field_offsets[4] + 1, cigar_size - 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4426:5: [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(c2b_globals.sam->element->flag_str, src + sam_field_offsets[0] + 1, flag_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4452:9: [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(c2b_globals.sam->element->rname, src + sam_field_offsets[1] + 1, rname_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4469:9: [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(c2b_globals.sam->element->rname, c2b_unmapped_read_chr_name, c2b_unmapped_read_chr_name_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4488:5: [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(c2b_globals.sam->element->pos_str, src + sam_field_offsets[2] + 1, pos_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4510:5: [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(c2b_globals.sam->element->qname, src, qname_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4515:5: [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 strand_str[C2B_MAX_STRAND_LENGTH_VALUE] = {0};
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4516:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(strand_str, "%c", (strand_val == 0x10) ? '-' : '+');
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4530:5: [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(c2b_globals.sam->element->strand, strand_str, strand_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4547:5: [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(c2b_globals.sam->element->mapq, src + sam_field_offsets[3] + 1, mapq_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4564:5: [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(c2b_globals.sam->element->rnext, src + sam_field_offsets[5] + 1, rnext_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4581:5: [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(c2b_globals.sam->element->pnext, src + sam_field_offsets[6] + 1, pnext_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4598:5: [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(c2b_globals.sam->element->tlen, src + sam_field_offsets[7] + 1, tlen_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4615:5: [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(c2b_globals.sam->element->seq, src + sam_field_offsets[8] + 1, seq_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4632:5: [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(c2b_globals.sam->element->qual, src + sam_field_offsets[9] + 1, qual_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4652:13: [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(c2b_globals.sam->element->opt + c2b_globals.sam->element->opt_length, src + sam_field_offsets[field_idx - 1] + 1, opt_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4777:5: [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 curr_bases_field[C2B_MAX_OPERATION_FIELD_LENGTH_VALUE + 1];
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4803:30: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
curr_bases = atoi(curr_bases_field);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5222:5: [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(c2b_globals.vcf->element->chrom, src, chrom_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5240:9: [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(c2b_globals.src_line_str, src, src_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5243:9: [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(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5266:5: [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(c2b_globals.vcf->element->pos_str, src + vcf_field_offsets[0] + 1, pos_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5287:5: [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(c2b_globals.vcf->element->id, src + vcf_field_offsets[1] + 1, id_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5304:5: [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(c2b_globals.vcf->element->ref, src + vcf_field_offsets[2] + 1, ref_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5321:5: [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(c2b_globals.vcf->element->alt, src + vcf_field_offsets[3] + 1, alt_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5338:5: [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(c2b_globals.vcf->element->qual, src + vcf_field_offsets[4] + 1, qual_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5355:5: [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(c2b_globals.vcf->element->filter, src + vcf_field_offsets[5] + 1, filter_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5372:5: [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(c2b_globals.vcf->element->info, src + vcf_field_offsets[6] + 1, info_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5390:9: [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(c2b_globals.vcf->element->format, src + vcf_field_offsets[7] + 1, format_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5407:9: [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(c2b_globals.vcf->element->samples, src + vcf_field_offsets[8] + 1, samples_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5421:9: [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(alt_alleles_copy, c2b_globals.vcf->element->alt, strlen(c2b_globals.vcf->element->alt) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5424:13: [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(c2b_globals.vcf->element->alt, allele_tok, strlen(allele_tok));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5737:13: [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(c2b_globals.src_line_str, src, src_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5769:13: [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(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5792:13: [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(c2b_globals.src_line_str, src, src_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5824:13: [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(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5837:9: [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(c2b_globals.src_line_str, src, src_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5896:13: [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(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5909:9: [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(c2b_globals.src_line_str, src, src_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5963:13: [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(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5976:9: [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(c2b_globals.src_line_str, src, src_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6041:9: [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(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6048:9: [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(c2b_globals.src_line_str, src, src_size);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6106:13: [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(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6166:13: [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(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6354:9: [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(src_buffer, src_buffer + remainder_offset, remainder_length);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6783:5: [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(path, p, strlen(p) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6793:9: [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(samtools, c2b_samtools, strlen(c2b_samtools) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6802:9: [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(path_samtools, path, strlen(path) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6825:9: [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(sort_bed, c2b_sort_bed, strlen(c2b_sort_bed) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6834:9: [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(path_sort_bed, path, strlen(path) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6857:9: [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(starch, c2b_starch, strlen(c2b_starch) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6866:9: [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(path_starch, path, strlen(path) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6889:9: [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(cat, c2b_cat, strlen(c2b_cat) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6898:9: [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(path_cat, path, strlen(path) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6927:5: [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 candidate[PATH_MAX];
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6950:17: [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(c2b_globals.sam->samtools_path, candidate, strlen(candidate));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6960:17: [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(c2b_globals.sort->sort_bed_path, candidate, strlen(candidate));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6970:17: [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(c2b_globals.starch->path, candidate, strlen(candidate));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6979:17: [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(c2b_globals.cat->path, candidate, strlen(candidate));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7632:17: [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(input_format, optarg, strlen(optarg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7644:17: [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(output_format, optarg, strlen(optarg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7656:17: [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(c2b_globals.sort->max_mem_value, optarg, strlen(optarg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7665:17: [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(c2b_globals.sort->sort_tmpdir_path, optarg, strlen(optarg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7674:17: [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(c2b_globals.starch->note, optarg, strlen(optarg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7683:17: [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(c2b_globals.wig->basename, optarg, strlen(optarg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7798:9: [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(c2b_globals.output_format, c2b_default_output_format, strlen(c2b_default_output_format) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:8007:5: [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(p, src, strlen(src) + 1);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/Sort.cpp:212:11: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
const char *inFiles[MAX_INFILES];
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:73:13: [2] (integer) atoi:
Unless checked, the resulting number can exceed the expected range
(CWE-190). If source untrusted, check both minimum and maximum, even if the
input had no minus sign (large numbers can roll over into negative number;
consider saving to an unsigned value if that is intended).
i = atoi(line);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:80:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* file = fopen("/proc/self/status", "r");
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:82:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[128];
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:98:22: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* file = fopen("/proc/self/status", "r");
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:100:9: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char line[128];
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:126:20: [2] (tmpfile) tmpfile:
Function tmpfile() has a security flaw on some systems (e.g., older System
V systems) (CWE-377).
return tmpfile();
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:131:5: [2] (buffer) strcpy:
Does not check for buffer overflows when copying to destination [MS-banned]
(CWE-120). Consider using snprintf, strcpy_s, or strlcpy (warning: strncpy
easily misused). Risk is low because the source is a constant string.
strcpy(tmpl+strlen(path), "/sb.XXXXXX");
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:132:10: [2] (tmpfile) mkstemp:
Potential for temporary file vulnerability in some circumstances. Some
older Unix-like systems create temp files with permission to write by all
by default, so be sure to set the umask to override this. Also, some older
Unix systems might fail to use O_EXCL when opening the file, so make sure
that O_EXCL is used by the library (CWE-377).
fd = mkstemp(tmpl);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:371:31: [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).
bedFile = fopen(bedFileNames[i], "r");
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:637:31: [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).
bedFile = fopen(bedFileNames[iidx], "r");
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:722:21: [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(tmpArr, cptr, static_cast<size_t>(dptr-cptr));
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:765:21: [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(tmpArr, dptr, static_cast<size_t>(cptr-dptr));
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1231:33: [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(currElem, nextElem, strlen(nextElem)+1);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1243:33: [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(currElem, nextElem, strlen(nextElem)+1);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1283:29: [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(prevElem, currElem, strlen(currElem)+1);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1329:5: [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 chromBuf[CHROM_NAME_LEN + 1];
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/Structures.hpp:89:5: [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 chromName[CHROM_NAME_LEN + 1];
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starch.c:402:22: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
int result = sprintf (avStr, "%d.%d.%d", STARCH_MAJOR_VERSION, STARCH_MINOR_VERSION, STARCH_REVISION_VERSION);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starch.c:432:22: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
int result = sprintf (avStr, "%d.%d.%d", STARCH_MAJOR_VERSION, STARCH_MINOR_VERSION, STARCH_REVISION_VERSION);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:361:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[STARCHCAT_COPY_BUFFER_MAXSIZE];
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:600:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[STARCHCAT_COPY_BUFFER_MAXSIZE];
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1033:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char t_sha1Digest[STARCH2_MD_FOOTER_SHA1_LENGTH] = {0};
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1387:37: [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(retransformBuf + nRetransformBuf, retransformLineBuf, static_cast<size_t>( nRetransformLineBufPos ));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1390:37: [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(retransformBuf + nRetransformBuf, retransformLineBuf, (size_t) nRetransformLineBufPos);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1491:37: [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(retransformBuf, retransformLineBuf, static_cast<size_t>( nRetransformLineBufPos ));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1493:37: [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(retransformBuf, retransformLineBuf, (size_t) nRetransformLineBufPos);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1537:29: [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(bzRemainderBuf, bzReadBuf + lastNewlineOffset + 1, nBzRemainderBuf);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1855:37: [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(retransformBuf + nRetransformBuf, retransformLineBuf, static_cast<size_t>( nRetransformLineBufPos ));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1858:37: [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(retransformBuf + nRetransformBuf, retransformLineBuf, (size_t) nRetransformLineBufPos);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1952:37: [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(retransformBuf, retransformLineBuf, static_cast<size_t>( nRetransformLineBufPos ));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1954:37: [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(retransformBuf, retransformLineBuf, (size_t) nRetransformLineBufPos);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1986:33: [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(zRemainderBuf, zOutBuf + lastNewlineOffset + 1, nZRemainderBuf);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1988:33: [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(zRemainderBuf, zOutBuf + lastNewlineOffset, nZRemainderBuf);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:2572:5: [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 fieldBuf[MAX_DEC_INTEGERS + 1];
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:2849:5: [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 bedLineBuf[TOKENS_MAX_LENGTH + 1] = {0}; /* zeroing the stack array ensures we don't copy extra junk between iterations */
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:2880:5: [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(outLineBuf[recIdx], bedLineBuf, charBufIdx + 1);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:2986:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char r_sha1Digest[STARCH2_MD_FOOTER_SHA1_LENGTH];
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3301:68: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
(const char *) extractedElements[inRecIdx],
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3337:71: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
(const char *) extractedElements[lowestStartElementIdx],
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3433:13: [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(outputRetransformState->r_chromosome, inChr, strlen(inChr) + 1);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3856:5: [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 fieldBuffer[STARCHCAT_FIELD_BUFFER_MAX_LENGTH];
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:5260:19: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
inFile = (char *) argv[idx];
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:5478:22: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
int result = sprintf (avStr, "%d.%d.%d", STARCH_MAJOR_VERSION, STARCH_MINOR_VERSION, STARCH_REVISION_VERSION);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:5518:22: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
int result = sprintf (avStr, "%d.%d.%d", STARCH_MAJOR_VERSION, STARCH_MINOR_VERSION, STARCH_REVISION_VERSION);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:5790:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char sha1Digest[STARCH2_MD_FOOTER_SHA1_LENGTH] = {0};
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:5791:5: [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 footerCumulativeRecordSizeBuffer[STARCH2_MD_FOOTER_CUMULATIVE_RECORD_SIZE_LENGTH + 1] = {0};
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:5792:5: [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 footerRemainderBuffer[STARCH2_MD_FOOTER_REMAINDER_LENGTH + 1] = {0};
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:5793:5: [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 footerBuffer[STARCH2_MD_FOOTER_LENGTH + 1] = {0};
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:6066:51: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
footerCumulativeRecordSizeBufferCharsCopied = sprintf(footerCumulativeRecordSizeBuffer, "%020llu", static_cast<unsigned long long>( *cumulativeOutputSize ));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:6068:51: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
footerCumulativeRecordSizeBufferCharsCopied = sprintf(footerCumulativeRecordSizeBuffer, "%020llu", (unsigned long long) *cumulativeOutputSize);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:6074:5: [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(footerBuffer, footerCumulativeRecordSizeBuffer, strlen(footerCumulativeRecordSizeBuffer));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:6075:5: [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(footerBuffer + STARCH2_MD_FOOTER_CUMULATIVE_RECORD_SIZE_LENGTH, base64EncodedSha1Digest, STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH - 1); /* strip trailing null */
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:6082:5: [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(footerBuffer + STARCH2_MD_FOOTER_CUMULATIVE_RECORD_SIZE_LENGTH + STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH - 1, footerRemainderBuffer, STARCH2_MD_FOOTER_REMAINDER_LENGTH); /* don't forget to offset pointer index by -1 for base64-sha1's null */
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:6685:9: [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(reinterpret_cast<char *>( bzLineBuf ), const_cast<const char *>( bzRemainderBuf ), *nBzRemainderBuf);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:6687:9: [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((char *) bzLineBuf, (const char *) bzRemainderBuf, *nBzRemainderBuf);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7025:13: [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(zLineBuf, *zRemainderBuf, *nZRemainderBuf);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7213:5: [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(*extractedElement, extractionBuffer + previousOffset, size);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7239:5: [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 startStr[MAX_DEC_INTEGERS + 1] = {0};
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7240:5: [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 stopStr[MAX_DEC_INTEGERS + 1] = {0};
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7326:5: [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 startStr[MAX_DEC_INTEGERS + 1] = {0};
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7327:5: [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 stopStr[MAX_DEC_INTEGERS + 1] = {0};
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7410:5: [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(compressionBuffer + compressionBufferLength, extractedElement, extractedElementLength);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7443:5: [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 retransLineBuf[TOKENS_MAX_LENGTH + 1] = {0};
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7500:21: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(retransBuf + *nRetransBuf, "p%" PRId64 "\n", *retransCoordDiff);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7502:29: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
nChar = sprintf(retransBuf + *nRetransBuf, "p%" PRId64 "\n", *retransCoordDiff);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7521:25: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(retransBuf + *nRetransBuf, "%" PRId64 "\n", (*retransStart - *retransLastPosition));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7535:25: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(retransBuf + *nRetransBuf, "%" PRId64 "\n", *retransStart);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7658:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char zBuffer[STARCH_Z_BUFFER_MAX_LENGTH] = {0};
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.h:95:5: [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 t_firstInputToken[UNSTARCH_FIRST_TOKEN_MAX_LENGTH + 1];
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.h:96:5: [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 t_secondInputToken[UNSTARCH_SECOND_TOKEN_MAX_LENGTH + 1];
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.h:97:5: [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 t_currentChromosome[TOKEN_CHR_MAX_LENGTH];
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.h:101:5: [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 t_currentRemainder[UNSTARCH_SECOND_TOKEN_MAX_LENGTH + 1];
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.h:107:5: [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 r_chromosome[TOKEN_CHR_MAX_LENGTH];
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.h:108:5: [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 r_remainder[UNSTARCH_SECOND_TOKEN_MAX_LENGTH + 1];
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:93:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char sha1_digest[STARCH2_MD_FOOTER_SHA1_LENGTH] = {0};
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:94:5: [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 footer_cumulative_record_size_buffer[STARCH2_MD_FOOTER_CUMULATIVE_RECORD_SIZE_LENGTH + 1] = {0};
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:95:5: [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 footer_remainder_buffer[STARCH2_MD_FOOTER_REMAINDER_LENGTH + 1] = {0};
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:96:5: [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 footer_buffer[STARCH2_MD_FOOTER_LENGTH + 1] = {0};
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:127:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(footer_cumulative_record_size_buffer, "%020llu", static_cast<unsigned long long>( starchstrip_globals.cumulative_output_size ));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:134:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(footer_cumulative_record_size_buffer, "%020llu", (unsigned long long) starchstrip_globals.cumulative_output_size);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:137:5: [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(footer_buffer, footer_cumulative_record_size_buffer, strlen(footer_cumulative_record_size_buffer));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:138:5: [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(footer_buffer + STARCH2_MD_FOOTER_CUMULATIVE_RECORD_SIZE_LENGTH, base64_encoded_sha1_digest, STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH - 1); /* strip trailing null */
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:145:5: [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(footer_buffer + STARCH2_MD_FOOTER_CUMULATIVE_RECORD_SIZE_LENGTH + STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH - 1, footer_remainder_buffer, STARCH2_MD_FOOTER_REMAINDER_LENGTH); /* don't forget to offset pointer index by -1 for base64-sha1's null */
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:186:5: [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 byte_buffer[starchstrip_copy_buffer_size];
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:449:21: [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(starchstrip_globals.chromosomes_to_process[chr_to_process_idx], iter->chromosome, strlen(iter->chromosome) + 1);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:531:21: [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(starchstrip_globals.chromosomes_to_process[chr_to_process_idx], iter->chromosome, strlen(iter->chromosome) + 1);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:692:13: [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(starchstrip_globals.chromosomes[chr_idx], starchstrip_globals.chromosomes_str + start, chromosome_str_length);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:705:5: [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(starchstrip_globals.chromosomes[chr_idx], starchstrip_globals.chromosomes_str + start, chromosome_str_length);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:928:17: [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(starchstrip_globals.chromosomes_str, optarg, optarg_length + 1);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:953:17: [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(starchstrip_globals.chromosomes_str, optarg, optarg_length + 1);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:991:5: [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(starchstrip_globals.archive_fn, input_filename, input_filename_length + 1);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/unstarch.c:94:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char mdHashBuffer[STARCH2_MD_FOOTER_SHA1_LENGTH + 1] = {0};
data/bedops-2.4.39+dfsg/applications/bed/starch/src/unstarch.c:1209:22: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
int result = sprintf(avStr, "%d.%d.%d", STARCH_MAJOR_VERSION, STARCH_MINOR_VERSION, STARCH_REVISION_VERSION);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/unstarch.c:1245:22: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
int result = sprintf(avStr, "%d.%d.%d", STARCH_MAJOR_VERSION, STARCH_MINOR_VERSION, STARCH_REVISION_VERSION);
data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/visitors/helpers/ProcessBedVisitorRow.hpp:363:18: [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.
static char formatted[sz+1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:239:5: [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 chr_[Bed::MAXCHROMSIZE+1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:231:5: [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 chr_[Bed::MAXCHROMSIZE+1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:82:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char chrom_[MAXCHROMSIZE+1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:99:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char chrom_[MAXCHROMSIZE+1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:320:5: [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 fullrest_[MAXRESTSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:413:5: [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 id_[MAXIDSIZE+1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:463:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char other[MAXRESTSIZE+1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:480:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char other[MAXRESTSIZE+1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:513:5: [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 fullrest_[MAXRESTSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:661:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char other[MAXRESTSIZE+1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:684:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char other[MAXRESTSIZE+1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:726:5: [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 fullrest_[MAXRESTSIZE+1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/BedCheckIterator.hpp:140:27: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* tmpf = std::fopen(fn_.c_str(), "r");
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/BedCheckIterator_minmem.hpp:138:27: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
FILE* tmpf = std::fopen(fn_.c_str(), "r");
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:123:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char chrom_[MAXCHROMSIZE+1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:233:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char chrBuf[MAXCHROMSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:244:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char chrBuf[MAXCHROMSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:326:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char chrBuf[MAXCHROMSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:328:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char restBuf[MAXRESTSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:343:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char chrBuf[MAXCHROMSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:345:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char restBuf[MAXRESTSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:412:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char chrBuf[MAXCHROMSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:414:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char idBuf[MAXIDSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:429:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char chrBuf[MAXCHROMSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:431:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char idBuf[MAXIDSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:550:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char chrBuf[MAXCHROMSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:552:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char idBuf[MAXIDSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:554:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char restBuf[MAXRESTSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:577:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char chrBuf[MAXCHROMSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:579:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char idBuf[MAXIDSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:581:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char restBuf[MAXRESTSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:681:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char chrBuf[MAXCHROMSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:683:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char idBuf[MAXIDSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:696:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char chrBuf[MAXCHROMSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:698:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char idBuf[MAXIDSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:802:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char chrBuf[MAXCHROMSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:804:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char idBuf[MAXIDSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:806:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char restBuf[MAXRESTSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:833:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char chrBuf[MAXCHROMSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:835:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char idBuf[MAXIDSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:837:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char restBuf[MAXRESTSIZE + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:125:32: [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).
_testFp = std::fopen(_inFn.c_str(), "r");
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:147:17: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char _testMagicBuf[STARCH_TEST_BYTE_COUNT] = {0};
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:475:32: [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).
_testFp = std::fopen(_inFn.c_str(), "r");
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:499:17: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char _tokBuf[STARCH_LEGACY_METADATA_SIZE];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:500:17: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char _recTokBuf[STARCH_LEGACY_METADATA_SIZE];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:630:32: [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).
_testFp = std::fopen(_inFn.c_str(), "r");
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:782:9: [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 t_firstInputToken[UNSTARCH_FIRST_TOKEN_MAX_LENGTH];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:783:9: [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 t_secondInputToken[UNSTARCH_SECOND_TOKEN_MAX_LENGTH];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:1023:25: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
inFp = std::fopen(inFn.c_str(), "rbR");
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:1071:25: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
inFp = std::fopen(inFn.c_str(), "rbR");
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:1105:25: [2] (misc) fopen:
Check when opening files - can an attacker redirect it (via symlinks),
force the opening of special file type (e.g., device files), move things
around to create a race condition, control its ancestors, or change its
contents? (CWE-362).
inFp = std::fopen(inFn.c_str(), "rbR");
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:1517:16: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char out[STARCH_BUFFER_MAX_LENGTH];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchBase64Coding.h:35:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
extern const char kStarchBase64EncodingTable[64];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchSha1Digest.h:141:44: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (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 void STARCH_SHA1_All(const unsigned char *input, size_t inputLength, unsigned char output[20]);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchSha1Digest.h:141:86: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (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 void STARCH_SHA1_All(const unsigned char *input, size_t inputLength, unsigned char output[20]);
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/CharPooledMemory.hpp:264:7: [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 _data[nelements+1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/CharPooledMemory.hpp:503:7: [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 _data[nelements+1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/FPWrap.hpp:41:42: [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_( (file == "-") ? stdin : std::fopen(file.c_str(), mode.c_str()) ), name_(file) {
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/FPWrap.hpp:54:20: [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).
fp_ = std::fopen(file.c_str(), mode.c_str());
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/Formats.hpp:44:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char prec[20];
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/Formats.hpp:46:12: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
std::sprintf(prec, "%%.%de", precision);
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/Formats.hpp:48:12: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
std::sprintf(prec, "%%.%dlf", precision);
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/Formats.hpp:53:12: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static char prec[20];
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/Formats.hpp:55:12: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
std::sprintf(prec, "%%.%dLe", precision);
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/Formats.hpp:57:12: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
std::sprintf(prec, "%%.%dLf", precision);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchBase64Coding.c:42:7: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
const char kStarchBase64EncodingTable[64] = {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchBase64Coding.c:251:5: [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(*output, objResult, *outputLength);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchFileHelpers.c:103:13: [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).
fnPtr = fopen(filename, type);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchFileHelpers.c:180:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char in[STARCH_Z_CHUNK + 1];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchFileHelpers.c:181:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char out[STARCH_Z_CHUNK + 1];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:155:5: [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 bzBuf[STARCH_BZ_BUFFER_MAX_LENGTH];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:272:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[STARCH_BUFFER_MAX_LENGTH];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:511:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[STARCH_BUFFER_MAX_LENGTH];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:727:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[STARCH_BUFFER_MAX_LENGTH];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:739:5: [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 nonCoordLineBuf[STARCH_BUFFER_MAX_LENGTH] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1229:5: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[STARCH_BUFFER_MAX_LENGTH];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1781:33: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
return static_cast<char *>( memcpy (result, s, len) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1783:21: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
return (char *) memcpy (result, s, len);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1901:5: [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 untransformedBuffer[STARCH_BUFFER_MAX_LENGTH];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1902:5: [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 intermediateBuffer[STARCH_BUFFER_MAX_LENGTH];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1903:5: [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 transformedBuffer[STARCH_BUFFER_MAX_LENGTH];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1924:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char sha1Digest[STARCH2_MD_FOOTER_SHA1_LENGTH] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1926:5: [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 zBuffer[STARCH_Z_BUFFER_MAX_LENGTH] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1936:5: [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 footerCumulativeRecordSizeBuffer[STARCH2_MD_FOOTER_CUMULATIVE_RECORD_SIZE_LENGTH + 1] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1937:5: [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 footerRemainderBuffer[STARCH2_MD_FOOTER_REMAINDER_LENGTH] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1938:5: [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 footerBuffer[STARCH2_MD_FOOTER_LENGTH] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1940:5: [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 nonCoordLineBuf[STARCH_BUFFER_MAX_LENGTH] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2496:25: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(intermediateBuffer + strlen(intermediateBuffer), "p%" PRId64 "\n", coordDiff);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2502:29: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\n", (start - lastPosition));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2508:29: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\n", start);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2517:25: [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(transformedBuffer + currentTransformedBufferLength, intermediateBuffer, intermediateBufferLength);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2630:25: [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(transformedBuffer, intermediateBuffer, strlen(intermediateBuffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2747:17: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(intermediateBuffer + strlen(intermediateBuffer), "p%" PRId64 "\n", coordDiff);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2753:21: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\n", (start - lastPosition));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2759:21: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\n", start);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2765:13: [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(transformedBuffer + currentTransformedBufferLength, intermediateBuffer, intermediateBufferLength);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3072:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(footerCumulativeRecordSizeBuffer, "%020llu", static_cast<unsigned long long>( cumulativeRecSize )); /* we cast this size_t to an unsigned long long in order to allow warning-free compilation with an ISO C++ compiler like g++ */
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3074:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(footerCumulativeRecordSizeBuffer, "%020llu", (unsigned long long) cumulativeRecSize); /* we cast this size_t to an unsigned long long in order to allow warning-free compilation with an ISO C++ compiler like g++ */
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3079:5: [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(footerBuffer, footerCumulativeRecordSizeBuffer, strlen(footerCumulativeRecordSizeBuffer));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3080:5: [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(footerBuffer + STARCH2_MD_FOOTER_CUMULATIVE_RECORD_SIZE_LENGTH, base64EncodedSha1Digest, STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH - 1); /* strip trailing null */
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3089:5: [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(footerBuffer + STARCH2_MD_FOOTER_CUMULATIVE_RECORD_SIZE_LENGTH + STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH - 1, footerRemainderBuffer, STARCH2_MD_FOOTER_REMAINDER_LENGTH); /* don't forget to offset pointer index by -1 for base64-sha1's null */
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3165:5: [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 untransformedBuffer[STARCH_BUFFER_MAX_LENGTH + 1] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3166:5: [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 intermediateBuffer[STARCH_BUFFER_MAX_LENGTH + 1] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3167:5: [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 transformedBuffer[STARCH_BUFFER_MAX_LENGTH + 1] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3188:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char sha1Digest[STARCH2_MD_FOOTER_SHA1_LENGTH] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3190:5: [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 zBuffer[STARCH_Z_BUFFER_MAX_LENGTH] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3200:5: [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 footerCumulativeRecordSizeBuffer[STARCH2_MD_FOOTER_CUMULATIVE_RECORD_SIZE_LENGTH + 1] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3201:5: [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 footerRemainderBuffer[STARCH2_MD_FOOTER_REMAINDER_LENGTH] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3202:5: [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 footerBuffer[STARCH2_MD_FOOTER_LENGTH] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3744:21: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(intermediateBuffer + strlen(intermediateBuffer), "p%" PRId64 "\n", coordDiff);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3757:25: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\n", (start - lastPosition));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3771:25: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\n", start);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3785:21: [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(transformedBuffer + currentTransformedBufferLength, intermediateBuffer, intermediateBufferLength);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3872:21: [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(transformedBuffer, intermediateBuffer, strlen(intermediateBuffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4008:17: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(intermediateBuffer + strlen(intermediateBuffer), "p%" PRId64 "\n", coordDiff);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4021:21: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\n", (start - lastPosition));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4035:21: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\n", start);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4047:13: [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(transformedBuffer + currentTransformedBufferLength, intermediateBuffer, intermediateBufferLength);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4372:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(footerCumulativeRecordSizeBuffer, "%020llu", static_cast<unsigned long long>( cumulativeRecSize )); /* size_t cast to unsigned long long to avoid compilation warnings from ISO C++ compiler */
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4374:5: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
sprintf(footerCumulativeRecordSizeBuffer, "%020llu", (unsigned long long) cumulativeRecSize); /* size_t cast to unsigned long long to avoid compilation warnings from ISO C++ compiler */
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4379:5: [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(footerBuffer, footerCumulativeRecordSizeBuffer, strlen(footerCumulativeRecordSizeBuffer));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4380:5: [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(footerBuffer + STARCH2_MD_FOOTER_CUMULATIVE_RECORD_SIZE_LENGTH, base64EncodedSha1Digest, STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH - 1); /* strip trailing null */
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4389:5: [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(footerBuffer + STARCH2_MD_FOOTER_CUMULATIVE_RECORD_SIZE_LENGTH + STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH - 1, footerRemainderBuffer, STARCH2_MD_FOOTER_REMAINDER_LENGTH); /* don't forget to offset pointer index by -1 for base64-sha1's null */
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:996:9: [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(*buf, jsonString, jsonLength);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1005:9: [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(*buf, jsonString, jsonLength);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1037:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char starchRevision2HeaderTestBytes[sizeof(starchRevision2HeaderBytes)] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1038:5: [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 testMagicBuffer[STARCH_TEST_BYTE_COUNT] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1041:5: [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 legacyBuffer[STARCH_LEGACY_METADATA_SIZE] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1140:5: [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 legacyBuffer[STARCH_LEGACY_METADATA_SIZE];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1141:5: [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 testMagicBuffer[STARCH_TEST_BYTE_COUNT] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1142:5: [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 footerBuffer[STARCH2_MD_FOOTER_LENGTH + 1] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1186:5: [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 offsetBuffer[STARCH2_MD_FOOTER_CUMULATIVE_RECORD_SIZE_LENGTH + 1] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1187:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char mdHashBuffer[STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1189:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char testMdHashSha1Buffer[STARCH2_MD_FOOTER_SHA1_LENGTH];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1194:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char starchRevision2HeaderTestBytes[sizeof(starchRevision2HeaderBytes)] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1200:5: [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 legacyBuffer[STARCH_LEGACY_METADATA_SIZE];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1201:5: [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 testMagicBuffer[STARCH_TEST_BYTE_COUNT] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1202:5: [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 footerBuffer[STARCH2_MD_FOOTER_LENGTH + 1] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1246:5: [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 offsetBuffer[STARCH2_MD_FOOTER_CUMULATIVE_RECORD_SIZE_LENGTH + 1] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1247:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char mdHashBuffer[STARCH2_MD_FOOTER_BASE64_ENCODED_SHA1_LENGTH] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1249:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char testMdHashSha1Buffer[STARCH2_MD_FOOTER_SHA1_LENGTH];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1254:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char starchRevision2HeaderTestBytes[sizeof(starchRevision2HeaderBytes)] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2035:24: [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).
chrFnPtr = fopen(iter->filename, "rb");
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2062:24: [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).
chrFnPtr = fopen(iter->filename, "rb");
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2093:5: [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 _tag[STARCH_TAG_MAX_LENGTH];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2176:5: [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 tokBuf[STARCH_LEGACY_METADATA_SIZE];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2177:5: [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 recTokBuf[STARCH_LEGACY_METADATA_SIZE];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchSha1Digest.c:62:23: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
static const unsigned char fillbuf[64] = { 0x80, 0 /* , 0, 0, ... */ };
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchSha1Digest.c:128:3: [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 (&(reinterpret_cast<char *>( ctx->buffer ))[bytes], fillbuf, (size - 2) * 4 - bytes);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchSha1Digest.c:130:3: [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 (&((char *) ctx->buffer)[bytes], fillbuf, (size - 2) * 4 - bytes);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchSha1Digest.c:146:3: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
char buffer[BLOCKSIZE + 72];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchSha1Digest.c:235:9: [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 (&(reinterpret_cast<char *>( ctx->buffer ))[left_over], buffer, add);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchSha1Digest.c:237:9: [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 (&((char *) ctx->buffer)[left_over], buffer, add);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchSha1Digest.c:252:13: [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 (ctx->buffer,
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchSha1Digest.c:256:13: [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 (ctx->buffer,
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchSha1Digest.c:288:37: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
sha1_process_block (memcpy (ctx->buffer, buffer, 64), 64, ctx);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchSha1Digest.c:316:9: [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 (&(reinterpret_cast<char *>( ctx->buffer ))[left_over], buffer, len);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchSha1Digest.c:318:9: [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 (&((char *) ctx->buffer)[left_over], buffer, len);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchSha1Digest.c:325:13: [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 (ctx->buffer, &ctx->buffer[16], left_over);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:75:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char zInBuf[STARCH_Z_CHUNK];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:76:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char zOutBuf[STARCH_Z_CHUNK];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:77:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char zLineBuf[STARCH_Z_CHUNK];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:673:5: [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 out[1024];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1026:5: [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 pTestChars[MAX_DEC_INTEGERS] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1633:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char buffer[UNSTARCH_BUFFER_MAX_LENGTH];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1761:33: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
return static_cast<char *>( memcpy (result, s, len) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1763:21: [2] (buffer) memcpy:
Does not check for buffer overflows when copying to destination (CWE-120).
Make sure destination can always hold the source data.
return (char *) memcpy (result, s, len);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2399:14: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char sha1Digest[STARCH2_MD_FOOTER_SHA1_LENGTH] = {0};
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2495:30: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char zInBuf[STARCH_Z_CHUNK];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2496:30: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char zOutBuf[STARCH_Z_CHUNK];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2497:30: [2] (buffer) char:
Statically-sized arrays can be improperly restricted, leading to potential
overflows or other issues (CWE-119!/CWE-120). Perform bounds checking, use
functions that limit length, or ensure that the size is larger than the
maximum possible length.
unsigned char zLineBuf[STARCH_Z_CHUNK];
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2720:21: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
*nLineBuf = sprintf(reinterpret_cast<char *>(lineBuf) + *nLineBufPos, "p%" PRId64 "\n", coordDiff);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2722:21: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
*nLineBuf = sprintf((char *)lineBuf + *nLineBufPos, "p%" PRId64 "\n", coordDiff);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2742:25: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
*nLineBuf = sprintf(reinterpret_cast<char *>(lineBuf) + *nLineBufPos, "%" PRId64 "\n", *currStart - *lastPosition);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2744:25: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
*nLineBuf = sprintf((char *)lineBuf + *nLineBufPos, "%" PRId64 "\n", *currStart - *lastPosition);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2764:25: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
*nLineBuf = sprintf(reinterpret_cast<char *>(lineBuf) + *nLineBufPos, "%" PRId64 "\n", *currStart);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2766:25: [2] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source has a constant maximum length.
*nLineBuf = sprintf((char *)lineBuf + *nLineBufPos, "%" PRId64 "\n", *currStart);
data/bedops-2.4.39+dfsg/applications/bed/bedextract/src/ExtractRows.cpp:209:41: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ( (c = static_cast<char>(std::fgetc(f))) != EOF ) {
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:298:24: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::list<BedType2*> read;
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:314:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(left);
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:317:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(right);
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:318:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(c);
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:324:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ( !read.empty() ) { // new best left makes all others obsolete
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:325:18: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
remove(read.front());
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:326:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.pop_front();
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:335:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(left);
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:341:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(left);
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:345:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(c);
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:349:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(left);
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:352:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(right);
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:353:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(c);
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:362:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(left);
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:368:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(left);
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:371:13: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(right);
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:379:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(left);
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:382:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(right);
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:388:17: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(left);
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:390:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(c); // may be needed in the future
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:393:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ( !read.empty() ) { // new best left makes all others obsolete
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:394:22: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
remove(read.front());
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:395:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.pop_front();
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:404:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(left);
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:407:15: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(right);
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:417:11: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(left);
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:420:9: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(c);
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:427:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(left);
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:429:7: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.push_back(right);
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:430:21: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
nonRef.PushBack(read);
data/bedops-2.4.39+dfsg/applications/bed/closestfeats/src/ClosestFeature.cpp:431:5: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
read.clear();
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:773:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(c2b_globals.cat->path) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:774:18: [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).
memcpy(cmd + strlen(c2b_globals.cat->path),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:776:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(cat_args) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:777:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
cmd[strlen(c2b_globals.cat->path) + strlen(cat_args)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:777:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
cmd[strlen(c2b_globals.cat->path) + strlen(cat_args)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:788:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(c2b_globals.sam->samtools_path) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:789:18: [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).
memcpy(cmd + strlen(c2b_globals.sam->samtools_path),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:791:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(bam2sam_args) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:792:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
cmd[strlen(c2b_globals.sam->samtools_path) + strlen(bam2sam_args)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:792:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
cmd[strlen(c2b_globals.sam->samtools_path) + strlen(bam2sam_args)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:805:16: [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).
strlen(sort_bed_max_mem_arg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:806:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(sort_bed_args + strlen(sort_bed_args),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:808:16: [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).
strlen(c2b_globals.sort->max_mem_value) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:809:23: [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).
sort_bed_args[strlen(sort_bed_max_mem_arg) + strlen(sort_bed_args)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:809:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sort_bed_args[strlen(sort_bed_max_mem_arg) + strlen(sort_bed_args)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:814:16: [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).
strlen(sort_bed_max_mem_default_arg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:815:23: [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).
sort_bed_args[strlen(sort_bed_max_mem_default_arg)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:818:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(sort_bed_args + strlen(sort_bed_args),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:820:16: [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).
strlen(sort_bed_tmpdir_arg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:821:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(sort_bed_args + strlen(sort_bed_args),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:823:16: [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).
strlen(c2b_globals.sort->sort_tmpdir_path) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:824:23: [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).
sort_bed_args[strlen(sort_bed_args) + strlen(c2b_globals.sort->sort_tmpdir_path)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:824:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sort_bed_args[strlen(sort_bed_args) + strlen(c2b_globals.sort->sort_tmpdir_path)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:826:28: [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).
memcpy(sort_bed_args + strlen(sort_bed_args),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:828:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(sort_bed_stdin) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:829:19: [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).
sort_bed_args[strlen(sort_bed_args) + strlen(sort_bed_stdin)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:829:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sort_bed_args[strlen(sort_bed_args) + strlen(sort_bed_stdin)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:834:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(c2b_globals.sort->sort_bed_path) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:835:18: [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).
memcpy(cmd + strlen(c2b_globals.sort->sort_bed_path),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:837:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(sort_bed_args) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:838:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
cmd[strlen(c2b_globals.sort->sort_bed_path) + strlen(sort_bed_args)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:838:51: [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).
cmd[strlen(c2b_globals.sort->sort_bed_path) + strlen(sort_bed_args)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:851:16: [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).
strlen(starch_bzip2_arg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:852:21: [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).
starch_args[strlen(starch_bzip2_arg)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:857:16: [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).
strlen(starch_gzip_arg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:858:21: [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).
starch_args[strlen(starch_gzip_arg)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:869:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(starch_args + strlen(starch_args),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:871:16: [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).
strlen(starch_note_prefix_arg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:872:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(starch_args + strlen(starch_args),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:874:16: [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).
strlen(c2b_globals.starch->note) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:875:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(starch_args + strlen(starch_args),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:877:16: [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).
strlen(starch_note_suffix_arg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:878:21: [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).
starch_args[strlen(starch_args) + strlen(starch_note_prefix_arg) + strlen(c2b_globals.starch->note) + strlen(starch_note_suffix_arg)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:878:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
starch_args[strlen(starch_args) + strlen(starch_note_prefix_arg) + strlen(c2b_globals.starch->note) + strlen(starch_note_suffix_arg)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:878:76: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
starch_args[strlen(starch_args) + strlen(starch_note_prefix_arg) + strlen(c2b_globals.starch->note) + strlen(starch_note_suffix_arg)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:878:111: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
starch_args[strlen(starch_args) + strlen(starch_note_prefix_arg) + strlen(c2b_globals.starch->note) + strlen(starch_note_suffix_arg)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:880:26: [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).
memcpy(starch_args + strlen(starch_args),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:882:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(starch_stdin_arg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:891:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(c2b_globals.starch->path) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:892:18: [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).
memcpy(cmd + strlen(c2b_globals.starch->path),
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:894:12: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strlen(starch_args) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:895:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
cmd[strlen(c2b_globals.starch->path) + strlen(starch_args)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:895:44: [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).
cmd[strlen(c2b_globals.starch->path) + strlen(starch_args)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1066:75: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1067:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*dest_size += strlen(c2b_globals.dest_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1316:82: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ssize_t trailing_semicolon_fudge = (c2b_globals.gtf->element->attributes[strlen(c2b_globals.gtf->element->attributes) - 1] == ';') ? 1 : 0;
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1317:55: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(c2b_globals.gtf->element->attributes + strlen(c2b_globals.gtf->element->attributes) - trailing_semicolon_fudge,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1319:16: [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).
strlen(c2b_gtf_zero_length_insertion_attribute) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1330:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
attributes_copy = malloc(strlen(c2b_globals.gtf->element->attributes) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1335:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(attributes_copy, c2b_globals.gtf->element->attributes, strlen(c2b_globals.gtf->element->attributes) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1346:44: [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).
gtf_id_start = strchr(kv_tok + strlen(c2b_gtf_gene_id_prefix), c2b_gtf_id_delimiter);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1347:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (gtf_id_start - (kv_tok + strlen(c2b_gtf_gene_id_prefix)) < 0) {
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1353:44: [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).
if (gtf_id_end - (kv_tok + strlen(c2b_gtf_gene_id_prefix)) <= 0) {
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1381:17: [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).
if (strlen(c2b_globals.gtf->element->id) == 0) {
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1451:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(g->seqname) == 0) {
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1455:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(g->comments) == 0) {
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1717:71: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1718:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*dest_size += strlen(c2b_globals.dest_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1936:82: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ssize_t trailing_semicolon_fudge = (c2b_globals.gff->element->attributes[strlen(c2b_globals.gff->element->attributes) - 1] == ';') ? 1 : 0;
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1937:49: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ssize_t new_attributes_size_with_zlia = strlen(c2b_globals.gff->element->attributes) + strlen(c2b_gff_zero_length_insertion_attribute);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1937:96: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ssize_t new_attributes_size_with_zlia = strlen(c2b_globals.gff->element->attributes) + strlen(c2b_gff_zero_length_insertion_attribute);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1950:55: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(c2b_globals.gff->element->attributes + strlen(c2b_globals.gff->element->attributes) - trailing_semicolon_fudge,
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1952:16: [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).
strlen(c2b_gff_zero_length_insertion_attribute) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1964:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
attributes_copy = malloc(strlen(c2b_globals.gff->element->attributes) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1969:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(attributes_copy, c2b_globals.gff->element->attributes, strlen(c2b_globals.gff->element->attributes) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1974:55: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(c2b_globals.gff->element->id, gff_null_id, strlen(gff_null_id) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1975:34: [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).
c2b_globals.gff->element->id[strlen(gff_null_id)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1979:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ssize_t id_size = strlen(id_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1993:63: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(c2b_globals.gff->element->id, kv_tok + strlen(gff_id_prefix), strlen(kv_tok + strlen(gff_id_prefix)) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1993:86: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(c2b_globals.gff->element->id, kv_tok + strlen(gff_id_prefix), strlen(kv_tok + strlen(gff_id_prefix)) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1993:102: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(c2b_globals.gff->element->id, kv_tok + strlen(gff_id_prefix), strlen(kv_tok + strlen(gff_id_prefix)) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1994:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
c2b_globals.gff->element->id[strlen(kv_tok + strlen(gff_id_prefix)) + 1] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:1994:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
c2b_globals.gff->element->id[strlen(kv_tok + strlen(gff_id_prefix)) + 1] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2050:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(g->seqid) == 0) {
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2345:71: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2346:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*dest_size += strlen(c2b_globals.dest_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2415:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:2416:27: [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).
*dest_size += strlen(c2b_globals.dest_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3304:79: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3305:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*dest_size += strlen(c2b_globals.dest_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3592:95: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(c2b_globals.rmsk->element->strand, c2b_rmsk_strand_complement_replacement, strlen(c2b_rmsk_strand_complement_replacement) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3861:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(r->higher_score_match) == 0) {
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3972:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:3973:27: [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).
*dest_size += strlen(c2b_globals.dest_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4078:51: [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).
ssize_t c2b_unmapped_read_chr_name_size = strlen(c2b_unmapped_read_chr_name);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4139:27: [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).
ssize_t strand_size = strlen(strand_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4350:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4351:27: [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).
*dest_size += strlen(c2b_globals.dest_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4456:51: [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).
ssize_t c2b_unmapped_read_chr_name_size = strlen(c2b_unmapped_read_chr_name);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4517:27: [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).
ssize_t strand_size = strlen(strand_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4773:20: [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).
size_t s_len = strlen(s);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:4807:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memset(curr_bases_field, 0, strlen(curr_bases_field));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5243:63: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5244:23: [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).
*dest_size += strlen(c2b_globals.dest_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5411:110: [1] (buffer) strlen:
Does not handle 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 ((!c2b_globals.vcf->do_not_split) && (memchr(c2b_globals.vcf->element->alt, c2b_vcf_alt_allele_delim, strlen(c2b_globals.vcf->element->alt)))) {
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5416:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
alt_alleles_copy = malloc(strlen(c2b_globals.vcf->element->alt) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5421:65: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(alt_alleles_copy, c2b_globals.vcf->element->alt, strlen(c2b_globals.vcf->element->alt) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5424:63: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(c2b_globals.vcf->element->alt, allele_tok, strlen(allele_tok));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5425:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
c2b_globals.vcf->element->alt[strlen(allele_tok)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5427:94: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
c2b_globals.vcf->element->end = c2b_globals.vcf->element->start + ref_size - strlen(c2b_globals.vcf->element->alt) + 1;
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5444:90: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
c2b_globals.vcf->element->end = c2b_globals.vcf->element->start + ref_size - strlen(c2b_globals.vcf->element->alt) + 1;
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5459:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
return ((s[0] == c2b_vcf_id_prefix) && (s[strlen(s)-1] == c2b_vcf_id_suffix)) ? kTrue : kFalse;
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5465:53: [1] (buffer) strlen:
Does not handle 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 ((!c2b_vcf_allele_is_id(alt)) && (((int) strlen(ref) - (int) strlen(alt)) == 0)) ? kTrue : kFalse;
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5465:73: [1] (buffer) strlen:
Does not handle 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 ((!c2b_vcf_allele_is_id(alt)) && (((int) strlen(ref) - (int) strlen(alt)) == 0)) ? kTrue : kFalse;
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5471:53: [1] (buffer) strlen:
Does not handle 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 ((!c2b_vcf_allele_is_id(alt)) && (((int) strlen(ref) - (int) strlen(alt)) < 0)) ? kTrue : kFalse;
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5471:73: [1] (buffer) strlen:
Does not handle 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 ((!c2b_vcf_allele_is_id(alt)) && (((int) strlen(ref) - (int) strlen(alt)) < 0)) ? kTrue : kFalse;
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5477:53: [1] (buffer) strlen:
Does not handle 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 ((!c2b_vcf_allele_is_id(alt)) && (((int) strlen(ref) - (int) strlen(alt)) > 0)) ? kTrue : kFalse;
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5477:73: [1] (buffer) strlen:
Does not handle 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 ((!c2b_vcf_allele_is_id(alt)) && (((int) strlen(ref) - (int) strlen(alt)) > 0)) ? kTrue : kFalse;
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5642:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(v->format) > 0) {
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5769:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5770:27: [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).
*dest_size += strlen(c2b_globals.dest_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5778:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if ((strncmp(src, c2b_wig_track_prefix, strlen(c2b_wig_track_prefix)) == 0) ||
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5779:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
(strncmp(src, c2b_wig_browser_prefix, strlen(c2b_wig_browser_prefix)) == 0)) {
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5824:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5825:27: [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).
*dest_size += strlen(c2b_globals.dest_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5833:57: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(src, c2b_wig_variable_step_prefix, strlen(c2b_wig_variable_step_prefix)) == 0) {
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5860:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(c2b_globals.wig->id) == 0) {
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5896:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5897:27: [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).
*dest_size += strlen(c2b_globals.dest_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5905:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(src, c2b_wig_fixed_step_prefix, strlen(c2b_wig_fixed_step_prefix)) == 0) {
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5921:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(c2b_globals.wig->chr) >= C2B_MAX_CHROMOSOME_LENGTH) {
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5963:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5964:27: [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).
*dest_size += strlen(c2b_globals.dest_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5972:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(src, c2b_wig_chr_prefix, strlen(c2b_wig_chr_prefix)) == 0) {
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:5988:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(c2b_globals.wig->chr) >= C2B_MAX_CHROMOSOME_LENGTH) {
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6041:63: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6042:23: [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).
*dest_size += strlen(c2b_globals.dest_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6106:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6107:27: [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).
*dest_size += strlen(c2b_globals.dest_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6166:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(*dest + *dest_size, c2b_globals.dest_line_str, strlen(c2b_globals.dest_line_str));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6167:27: [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).
*dest_size += strlen(c2b_globals.dest_line_str);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6194:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((bytes_read = read(STDIN_FILENO, buffer, buffer_size)) > 0) {
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6255:30: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((src_bytes_read = read(pipes->out[stage->src][PIPE_READ],
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6398:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((bytes_read = read(pipes->in[stage->src][PIPE_READ], buffer, buffer_size)) > 0) {
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6440:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((bytes_read = read(pipes->out[stage->src][PIPE_READ], buffer, buffer_size)) > 0) {
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6481:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((bytes_read = read(pipes->in[stage->src][PIPE_READ], buffer, buffer_size)) > 0) {
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6520:26: [1] (buffer) read:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((bytes_read = read(pipes->out[stage->src][PIPE_READ], buffer, buffer_size)) > 0) {
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6777:19: [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).
path = malloc(strlen(p) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6783:21: [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).
memcpy(path, p, strlen(p) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6787:27: [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).
samtools = malloc(strlen(c2b_samtools) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6793:40: [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).
memcpy(samtools, c2b_samtools, strlen(c2b_samtools) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6796:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
path_samtools = malloc(strlen(path) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6802:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(path_samtools, path, strlen(path) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6819:27: [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).
sort_bed = malloc(strlen(c2b_sort_bed) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6825:40: [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).
memcpy(sort_bed, c2b_sort_bed, strlen(c2b_sort_bed) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6828:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
path_sort_bed = malloc(strlen(path) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6834:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(path_sort_bed, path, strlen(path) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6851:25: [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).
starch = malloc(strlen(c2b_starch) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6857:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(starch, c2b_starch, strlen(c2b_starch) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6860:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
path_starch = malloc(strlen(path) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6866:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(path_starch, path, strlen(path) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6883:22: [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).
cat = malloc(strlen(c2b_cat) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6889:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(cat, c2b_cat, strlen(c2b_cat) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6892:27: [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).
path_cat = malloc(strlen(path) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6898:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(path_cat, path, strlen(path) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6944:57: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
c2b_globals.sam->samtools_path = malloc(strlen(candidate) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6950:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(c2b_globals.sam->samtools_path, candidate, strlen(candidate));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6951:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
c2b_globals.sam->samtools_path[strlen(candidate)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6954:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
c2b_globals.sort->sort_bed_path = malloc(strlen(candidate) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6960:68: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(c2b_globals.sort->sort_bed_path, candidate, strlen(candidate));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6961:49: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
c2b_globals.sort->sort_bed_path[strlen(candidate)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6964:51: [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).
c2b_globals.starch->path = malloc(strlen(candidate) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6970:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(c2b_globals.starch->path, candidate, strlen(candidate));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6971:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
c2b_globals.starch->path[strlen(candidate)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6974:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
c2b_globals.cat->path = malloc(strlen(candidate) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6979:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(c2b_globals.cat->path, candidate, strlen(candidate));
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:6980:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
c2b_globals.cat->path[strlen(candidate)] = '\0';
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7626:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
input_format = malloc(strlen(optarg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7632:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(input_format, optarg, strlen(optarg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7638:40: [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).
output_format = malloc(strlen(optarg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7644:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(output_format, optarg, strlen(optarg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7650:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
c2b_globals.sort->max_mem_value = malloc(strlen(optarg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7656:65: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(c2b_globals.sort->max_mem_value, optarg, strlen(optarg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7659:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
c2b_globals.sort->sort_tmpdir_path = malloc(strlen(optarg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7665:68: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(c2b_globals.sort->sort_tmpdir_path, optarg, strlen(optarg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7668:51: [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).
c2b_globals.starch->note = malloc(strlen(optarg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7674:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(c2b_globals.starch->note, optarg, strlen(optarg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7677:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
c2b_globals.wig->basename = malloc(strlen(optarg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7683:59: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(c2b_globals.wig->basename, optarg, strlen(optarg) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7792:44: [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).
c2b_globals.output_format = malloc(strlen(c2b_default_output_format) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:7798:70: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(c2b_globals.output_format, c2b_default_output_format, strlen(c2b_default_output_format) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:8001:16: [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).
p = malloc(strlen(src) + 1);
data/bedops-2.4.39+dfsg/applications/bed/conversion/src/convert2bed.c:8007:20: [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).
memcpy(p, src, strlen(src) + 1);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/Sort.cpp:98:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
lng = strlen(argv[i]);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/Sort.cpp:120:45: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(tmp, argv[i], lng);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/Sort.cpp:157:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*tmpPath = static_cast<char*>( malloc(strlen(argv[i])+1) );
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:70:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
int i = static_cast<int>( strlen(line) ); // perhaps better to cast strlen to an int, in order to fulfill parseline contract
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:129:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
tmpl = static_cast<char*>( malloc(1 + strlen(path) + L_tmpnam) );
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:131:17: [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).
strcpy(tmpl+strlen(path), "/sb.XXXXXX");
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:139:44: [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).
*fileName = static_cast<char*>( malloc(strlen(tmpl) + 1) );
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:249:19: [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).
chromBufLen = strlen(chromBuf); // we know >= 1
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:250:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(chrom->chromName, chromBuf, chromBufLen);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:337:26: [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).
dataBufLen = strlen(data);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:350:41: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
chrom->coords[index].data = strncpy(dataPtr, data, dataBufLen + 1);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:859:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(bedLine) > ID_NAME_LEN)
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:937:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if(strlen(bedLine) > ID_NAME_LEN)
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1009:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
totalBytes += (tfile == NULL) ? 0 : (strlen(tfile)+1);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1061:75: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
totalBytes += (tfile == NULL) ? 0 : (strlen(tfile)+1);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1212:56: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(currElem + strlen(currElem), "\t%s\n", beds->chroms[i]->coords[j].data);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1214:37: [1] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source is a constant character.
sprintf(currElem + strlen(currElem), "\n");
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1214:56: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(currElem + strlen(currElem), "\n");
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1222:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(nextElem + strlen(nextElem), "\t%s\n", beds->chroms[i]->coords[j+1].data);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1224:41: [1] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source is a constant character.
sprintf(nextElem + strlen(nextElem), "\n");
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1224:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(nextElem + strlen(nextElem), "\n");
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1231:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(currElem, nextElem, strlen(nextElem)+1);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1238:56: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(nextElem + strlen(nextElem), "\t%s\n", beds->chroms[i]->coords[j+1].data);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1240:37: [1] (buffer) sprintf:
Does not check for buffer overflows (CWE-120). Use sprintf_s, snprintf, or
vsnprintf. Risk is low because the source is a constant character.
sprintf(nextElem + strlen(nextElem), "\n");
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1240:56: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(nextElem + strlen(nextElem), "\n");
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1243:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(currElem, nextElem, strlen(nextElem)+1);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1283:56: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(prevElem, currElem, strlen(currElem)+1);
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1342:27: [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).
chromBufLen = strlen(beds->chroms[i]->chromName); // we know >= 1
data/bedops-2.4.39+dfsg/applications/bed/sort-bed/src/SortDetails.cpp:1343:13: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(chromBuf, beds->chroms[i]->chromName, chromBufLen);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:372:49: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outFn = static_cast<char *>( malloc(strlen(inChr) + strlen(outTag) + 6) ); /* X.Y.bz2\0 */
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:372:65: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outFn = static_cast<char *>( malloc(strlen(inChr) + strlen(outTag) + 6) ); /* X.Y.bz2\0 */
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:374:28: [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).
outFn = malloc(strlen(inChr) + strlen(outTag) + 6); /* X.Y.bz2\0 */
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:374:44: [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).
outFn = malloc(strlen(inChr) + strlen(outTag) + 6); /* X.Y.bz2\0 */
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:385:49: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outFn = static_cast<char *>( malloc(strlen(inChr) + strlen(outTag) + 5) ); /* X.Y.gz\0 */
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:385:65: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outFn = static_cast<char *>( malloc(strlen(inChr) + strlen(outTag) + 5) ); /* X.Y.gz\0 */
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:387:28: [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).
outFn = malloc(strlen(inChr) + strlen(outTag) + 5); /* X.Y.gz\0 */
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:387:44: [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).
outFn = malloc(strlen(inChr) + strlen(outTag) + 5); /* X.Y.gz\0 */
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:430:68: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outSignature = STARCH_strndup(iter->signature, strlen(iter->signature) + 1);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:612:49: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outFn = static_cast<char *>( malloc(strlen(inChr) + strlen(outTag) + 6) ); /* X.Y.bz2\0 */
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:612:65: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outFn = static_cast<char *>( malloc(strlen(inChr) + strlen(outTag) + 6) ); /* X.Y.bz2\0 */
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:614:28: [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).
outFn = malloc(strlen(inChr) + strlen(outTag) + 6); /* X.Y.bz2\0 */
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:614:44: [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).
outFn = malloc(strlen(inChr) + strlen(outTag) + 6); /* X.Y.bz2\0 */
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:625:49: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outFn = static_cast<char *>( malloc(strlen(inChr) + strlen(outTag) + 5) ); /* X.Y.gz\0 */
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:625:65: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outFn = static_cast<char *>( malloc(strlen(inChr) + strlen(outTag) + 5) ); /* X.Y.gz\0 */
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:627:28: [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).
outFn = malloc(strlen(inChr) + strlen(outTag) + 5); /* X.Y.gz\0 */
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:627:44: [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).
outFn = malloc(strlen(inChr) + strlen(outTag) + 5); /* X.Y.gz\0 */
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1050:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outTagFn = static_cast<char *>( malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".bz2")) );
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1050:68: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outTagFn = static_cast<char *>( malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".bz2")) );
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1050:89: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outTagFn = static_cast<char *>( malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".bz2")) );
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1052:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outTagFn = malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".bz2"));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1052:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outTagFn = malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".bz2"));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1052:68: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outTagFn = malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".bz2"));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1059:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outTagFn = static_cast<char *>( malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".gz")) );
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1059:68: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outTagFn = static_cast<char *>( malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".gz")) );
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1059:89: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outTagFn = static_cast<char *>( malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".gz")) );
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1061:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outTagFn = malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".gz"));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1061:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outTagFn = malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".gz"));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:1061:68: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outTagFn = malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".gz"));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:2425:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
uncomprOutFn = static_cast<char *>( malloc(strlen(inChr) + strlen(outTag) + 16) );
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:2425:64: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
uncomprOutFn = static_cast<char *>( malloc(strlen(inChr) + strlen(outTag) + 16) );
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:2427:27: [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).
uncomprOutFn = malloc(strlen(inChr) + strlen(outTag) + 16);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:2427:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
uncomprOutFn = malloc(strlen(inChr) + strlen(outTag) + 16);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:2575:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
for (lineBufIdx = 0; lineBufIdx < strlen(lineBuf); lineBufIdx++) {
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3123:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3123:72: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(transformStates[inRecIdx]->t_currentChromosome, inChr, strlen(inChr) + 1);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3328:80: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
LineLengthType leLineMaxStringLength = static_cast<LineLengthType>(strlen(static_cast<const char *>( extractedElements[lowestStartElementIdx] )) - 1);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3334:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
LineLengthType leLineMaxStringLength = (LineLengthType) strlen(extractedElements[lowestStartElementIdx]) - 1;
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3433:65: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(outputRetransformState->r_chromosome, inChr, strlen(inChr) + 1);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3442:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sha1_process_bytes (retransformedOutputBuffer, strlen(retransformedOutputBuffer), &r_perChromosomeHashCtx);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3513:57: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
finalOutTagFn = static_cast<char *>( malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".bz2")) );
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3513:73: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
finalOutTagFn = static_cast<char *>( malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".bz2")) );
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3513:94: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
finalOutTagFn = static_cast<char *>( malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".bz2")) );
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3515:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
finalOutTagFn = malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".bz2"));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3515:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
finalOutTagFn = malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".bz2"));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3515:73: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
finalOutTagFn = malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".bz2"));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3522:57: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
finalOutTagFn = static_cast<char *>( malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".gz")) );
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3522:73: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
finalOutTagFn = static_cast<char *>( malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".gz")) );
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3522:94: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
finalOutTagFn = static_cast<char *>( malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".gz")) );
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3524:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
finalOutTagFn = malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".gz"));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3524:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
finalOutTagFn = malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".gz"));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3524:73: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
finalOutTagFn = malloc(strlen(inChr) + strlen(outTag) + 3 + strlen(".gz"));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3877:49: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
tempOutFn = static_cast<char *>( malloc(strlen(summary->chromosome) + strlen(outTag) + 20) );
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3877:79: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
tempOutFn = static_cast<char *>( malloc(strlen(summary->chromosome) + strlen(outTag) + 20) );
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3879:28: [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).
tempOutFn = malloc(strlen(summary->chromosome) + strlen(outTag) + 20);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3879:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
tempOutFn = malloc(strlen(summary->chromosome) + strlen(outTag) + 20);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3940:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
uncomprOutFn = static_cast<char *>( malloc(strlen(summary->chromosome) + strlen(outTag) + 16) );
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3940:78: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
uncomprOutFn = static_cast<char *>( malloc(strlen(summary->chromosome) + strlen(outTag) + 16) );
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3942:27: [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).
uncomprOutFn = malloc(strlen(summary->chromosome) + strlen(outTag) + 16);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:3942:57: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
uncomprOutFn = malloc(strlen(summary->chromosome) + strlen(outTag) + 16);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:4001:22: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ( (c = fgetc(tempOutFps[inRecIdx])) ) {
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:4048:67: [1] (buffer) strlen:
Does not handle 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 (bufferIdx = 0U, fieldBufferIdx = 0U; bufferIdx < strlen(lineBuffers[inRecIdx]); bufferIdx++, fieldBufferIdx++) {
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:4140:26: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ( (c = fgetc(tempOutFps[lsiIdx])) ) {
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:4177:26: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ( (c = fgetc(tempOutFps[lowestStopIdx])) ) {
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:5359:49: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
cTime = static_cast<char *>( malloc(strlen(creationTimestamp) + 1) );
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:5361:28: [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).
cTime = malloc(strlen(creationTimestamp) + 1);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:5368:13: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(cTime, creationTimestamp, strlen(creationTimestamp) + 1);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:5368:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(cTime, creationTimestamp, strlen(creationTimestamp) + 1);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:6034:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fwrite(dynamicMdBuffer, 1, strlen(dynamicMdBuffer), stdout);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:6041:13: [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).
strlen(dynamicMdBuffer),
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:6045:13: [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).
strlen(dynamicMdBuffer),
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:6074:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(footerBuffer, footerCumulativeRecordSizeBuffer, strlen(footerCumulativeRecordSizeBuffer));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:6752:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*t_nExtractionBuffer = (strlen(t_currentRemainder) > 0) ?
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:6766:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*t_nExtractionBuffer = (strlen(t_currentRemainder) > 0) ?
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:6789:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(static_cast<char *>( bzRemainderBuf ), reinterpret_cast<const char *>(reinterpret_cast<char *>( bzLineBuf )), bzCharIndex);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:6791:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy((char *) bzRemainderBuf, (const char *) bzLineBuf, bzCharIndex);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7136:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(static_cast<char *>( *zRemainderBuf ), const_cast<const char *>( reinterpret_cast<char *>( zLineBuf ) ), static_cast<size_t>( zCharIndex ) + 1);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7138:5: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy((char *) *zRemainderBuf, (const char *) zLineBuf, (size_t) zCharIndex + 1);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7202:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memset(*extractedElement, 0, strlen(*extractedElement));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7226:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(extractedElement) == 0) {
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7313:9: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(extractedElement) == 0) {
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7407:38: [1] (buffer) strlen:
Does not handle 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 compressionBufferLength = strlen(compressionBuffer);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7408:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t extractedElementLength = strlen(extractedElement);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7428:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ((!retransState->r_chromosome) || (strlen(retransState->r_chromosome) == 0))
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7435:62: [1] (buffer) strlen:
Does not handle 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 nCompBuf = strlen(compBuf);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7468:20: [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).
*nRetransBuf = strlen(retransBuf);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7507:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*nRetransBuf = strlen(retransBuf);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7541:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*nRetransBuf = strlen(retransBuf);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7612:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
nTransformedBuffer = strlen(transformedBuffer);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7666:55: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
zStreamPtr->avail_in = static_cast<unsigned int>( strlen(transformedBuffer) );
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchcat.c:7669:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
zStreamPtr->avail_in = (unsigned int) strlen(transformedBuffer);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:118:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fwrite(md_json_buffer, 1, strlen(md_json_buffer), os);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:122:80: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
STARCH_SHA1_All(reinterpret_cast<const unsigned char *>( md_json_buffer ), strlen(md_json_buffer), sha1_digest);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:129:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
STARCH_SHA1_All((const unsigned char *) md_json_buffer, strlen(md_json_buffer), sha1_digest);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:137:65: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(footer_buffer, footer_cumulative_record_size_buffer, strlen(footer_cumulative_record_size_buffer));
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:441:115: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
starchstrip_globals.chromosomes_to_process[chr_to_process_idx] = static_cast <char*>( malloc( strlen(iter->chromosome) + 1 ) );
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:443:93: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
starchstrip_globals.chromosomes_to_process[chr_to_process_idx] = malloc(strlen(iter->chromosome) + 1);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:449:110: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(starchstrip_globals.chromosomes_to_process[chr_to_process_idx], iter->chromosome, strlen(iter->chromosome) + 1);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:523:115: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
starchstrip_globals.chromosomes_to_process[chr_to_process_idx] = static_cast <char*>( malloc( strlen(iter->chromosome) + 1 ) );
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:525:93: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
starchstrip_globals.chromosomes_to_process[chr_to_process_idx] = malloc(strlen(iter->chromosome) + 1);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:531:110: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(starchstrip_globals.chromosomes_to_process[chr_to_process_idx], iter->chromosome, strlen(iter->chromosome) + 1);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:918:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
optarg_length = strlen(optarg);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:943:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
optarg_length = strlen(optarg);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/starchstrip.c:985:36: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t input_filename_length = strlen(input_filename);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/unstarch.c:320:17: [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).
strlen(jsonString),
data/bedops-2.4.39+dfsg/applications/bed/starch/src/unstarch.c:328:17: [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).
strlen(jsonString),
data/bedops-2.4.39+dfsg/applications/bed/starch/src/unstarch.c:939:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(argv[1]) == 1) {
data/bedops-2.4.39+dfsg/applications/bed/starch/src/unstarch.c:948:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ftr1 = UNSTARCH_strndup(argv[1] + 2, strlen(argv[1]) - 2);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/unstarch.c:976:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(argv[1]) == 1) {
data/bedops-2.4.39+dfsg/applications/bed/starch/src/unstarch.c:982:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(argv[2]) == 1) {
data/bedops-2.4.39+dfsg/applications/bed/starch/src/unstarch.c:996:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ftr1 = UNSTARCH_strndup(argv[1] + 2, strlen(argv[1]) - 2);
data/bedops-2.4.39+dfsg/applications/bed/starch/src/unstarch.c:1006:17: [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).
if (strlen(argv[2]) > 1) {
data/bedops-2.4.39+dfsg/applications/bed/starch/src/unstarch.c:1022:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(argv[1]) == 1) {
data/bedops-2.4.39+dfsg/applications/bed/starch/src/unstarch.c:1028:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(argv[2]) == 1) {
data/bedops-2.4.39+dfsg/applications/bed/starch/src/unstarch.c:1034:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(argv[3]) == 1) {
data/bedops-2.4.39+dfsg/applications/bed/starch/src/unstarch.c:1055:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
ftr2 = UNSTARCH_strndup(argv[2] + 2, strlen(argv[2]) - 2);
data/bedops-2.4.39+dfsg/interfaces/general-headers/algorithm/bed/FindBedRange.hpp:147:39: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
if ( static_cast<char>(std::fgetc(qfile)) != '\n' ) {
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/AllocateIterator_BED_starch.hpp:73:12: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
std::strncpy(chr_, chr.c_str(), sz);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/AllocateIterator_BED_starch_minmem.hpp:67:12: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
std::strncpy(chr_, chr.c_str(), sz);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:228:12: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::fgetc(inputFile); // chomp newline
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:309:12: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::fgetc(inputFile); // chomp newline
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:373:12: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::fgetc(inputFile); // read and discard newline
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:490:12: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::fgetc(inputFile); // Read and discard trailing newline
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:575:12: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::fgetc(inputFile); // Read and discard trailing newline
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed.hpp:695:12: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::fgetc(inputFile); // Read and discard trailing newline
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/BedCompare.hpp:130:19: [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).
return std::strlen(two->full_rest()) != 0;
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/BedCompare.hpp:187:21: [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).
auto n = std::strlen(one->full_rest());
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/BedCompare.hpp:200:21: [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).
auto n = std::strlen(two->full_rest());
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:70:56: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
: chrom_(new char[(c.chrom_ != NULL) ? (std::strlen(c.chrom_) + 1) : 1])
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:73:49: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
: chrom_(new char[(c != NULL) ? (std::strlen(c)+1) : 1])
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:82:34: [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).
chrom_ = new char[std::strlen(chrom) + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:94:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
chrom_ = new char[(c.chrom_ != NULL) ? (std::strlen(c.chrom_) + 1) : 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:251:14: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::fgetc(inputFile); // chomp newline
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:282:79: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
: BaseClass(chrom, start, end), rest_(new char[(rest != NULL) ? (std::strlen(rest)+1) : 1]) {
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:291:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
: BaseClass(c), rest_(new char[(c.rest_ != NULL) ? (std::strlen(c.rest_) + 1) : 1])
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:307:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
rest_ = new char[(c.rest_ != NULL) ? (std::strlen(c.rest_) + 1) : 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:338:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
rest_ = new char[std::strlen(restBuf) + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:352:14: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::fgetc(inputFile); // chomp newline
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:356:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
rest_ = new char[std::strlen(restBuf) + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:400:75: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
: BaseClass(chrom, start, end), id_(new char[(id != NULL) ? (std::strlen(id)+1) : 1])
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:403:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
: BaseClass(c), id_(new char[(c.id_ != NULL) ? (std::strlen(c.id_) + 1) : 1])
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:441:14: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::fgetc(inputFile); // read and discard newline
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:461:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
id_ = new char[(id != NULL) ? (std::strlen(id) + 1) : 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:471:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
id_ = new char[(c.id_ != NULL) ? (std::strlen(c.id_) + 1) : 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:509:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
: BaseClass(c), rest_(new char[(c.rest_ != NULL) ? (std::strlen(c.rest_)+1) : 1]),
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:510:73: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fullrest_(new char[(c.fullrest_ != NULL) ? (std::strlen(c.fullrest_)+1) : 1])
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:516:83: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
: BaseClass(chrom, start, end, id), rest_(new char[(rest != NULL) ? (std::strlen(rest)+1) : 1]),
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:517:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fullrest_(new char[((rest != NULL) ? (std::strlen(rest)+1) : 1) + ((id != NULL) ? (std::strlen(id)+1) : 1)]) {
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:517:103: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fullrest_(new char[((rest != NULL) ? (std::strlen(rest)+1) : 1) + ((id != NULL) ? (std::strlen(id)+1) : 1)]) {
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:566:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
rest_ = new char[std::strlen(restBuf) + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:570:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
std::size_t sz = (std::strlen(restBuf)+1) + (std::strlen(idBuf) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:570:59: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
std::size_t sz = (std::strlen(restBuf)+1) + (std::strlen(idBuf) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:591:14: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::fgetc(inputFile); // Read and discard trailing newline
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:596:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
rest_ = new char[std::strlen(restBuf) + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:598:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
std::size_t sz = (std::strlen(restBuf)+1) + (std::strlen(idBuf) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:598:59: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
std::size_t sz = (std::strlen(restBuf)+1) + (std::strlen(idBuf) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:614:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
rest_ = new char[(c.rest_ != NULL) ? (std::strlen(c.rest_) + 1) : 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:616:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fullrest_ = new char[(c.fullrest_ != NULL) ? (std::strlen(c.fullrest_) + 1) : 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:707:14: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::fgetc(inputFile); // Read and discard trailing newline
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:757:94: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
: BaseClass(c), restOffset_(c.restOffset_), rest_(new char[(c.rest_ != NULL) ? (std::strlen(c.rest_+1)) : 1]),
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:758:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fullrest_(new char[(c.fullrest_ != NULL) ? (std::strlen(c.fullrest_+1)) : 1])
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:766:49: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
rest_(new char[(rest != NULL) ? (std::strlen(rest)+1) : 1]),
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:767:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fullrest_(new char[((rest != NULL) ? (std::strlen(rest)+1) : 1) + ((id != NULL) ? (std::strlen(id)+1) : 1)])
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:767:99: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fullrest_(new char[((rest != NULL) ? (std::strlen(rest)+1) : 1) + ((id != NULL) ? (std::strlen(id)+1) : 1)])
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:819:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
rest_ = new char[std::strlen(restBuf) + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:823:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
std::size_t sz = (std::strlen(restBuf)+1) + (std::strlen(idBuf) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:823:59: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
std::size_t sz = (std::strlen(restBuf)+1) + (std::strlen(idBuf) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:828:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
restOffset_ = std::strlen(idBuf);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:847:14: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
std::fgetc(inputFile); // Read and discard trailing newline
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:852:31: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
rest_ = new char[std::strlen(restBuf) + 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:858:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
std::size_t sz = (std::strlen(restBuf)+1) + (std::strlen(idBuf) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:858:59: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
std::size_t sz = (std::strlen(restBuf)+1) + (std::strlen(idBuf) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:863:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
restOffset_ = std::strlen(idBuf);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:875:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
rest_ = new char[(c.rest_ != NULL) ? (std::strlen(c.rest_) + 1) : 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/bed/Bed_minmem.hpp:877:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fullrest_ = new char[(c.fullrest_ != NULL) ? (std::strlen(c.fullrest_) + 1) : 1];
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:105:38: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
_testByte = std::fgetc(_inFp);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:191:38: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
_testByte = std::fgetc(_inFp);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:244:74: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
*(_mdBuf + _mdOffsetIdx++) = static_cast<char>( std::fgetc(_inFp) );
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:317:30: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
std::strncpy(_archStreamChr, json_string_value(_mdJSONStreamChr), strlen(json_string_value(_mdJSONStreamChr)) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:317:91: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
std::strncpy(_archStreamChr, json_string_value(_mdJSONStreamChr), strlen(json_string_value(_mdJSONStreamChr)) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:324:30: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
std::strncpy(_archStreamFn, json_string_value(_mdJSONStreamFn), strlen(json_string_value(_mdJSONStreamFn)) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:324:89: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
std::strncpy(_archStreamFn, json_string_value(_mdJSONStreamFn), strlen(json_string_value(_mdJSONStreamFn)) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:517:38: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
_buf[_testIdx] = fgetc(_inFp);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:534:131: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
_tokenCheck = STARCH_strnstr(const_cast<const char *>( _token ), STARCH_LEGACY_EXTENSION_BZ2, strlen(_token));
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:536:136: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
_tokenCheck = STARCH_strnstr(const_cast<const char *>( _token ), STARCH_LEGACY_EXTENSION_GZIP, strlen(_token));
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:541:42: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
std::strncpy(_recTokBuf, _token, strlen(_token) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:541:70: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
std::strncpy(_recTokBuf, _token, strlen(_token) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:542:77: [1] (buffer) strlen:
Does not handle 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 (_recTokBufIdx = 0; _recTokBufIdx < strlen(_recTokBuf); _recTokBufIdx++) {
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:548:92: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
_recChromosome = static_cast<char *>( std::malloc(std::strlen(_recTokBuf) + 1) );
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:551:42: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:551:83: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
std::strncpy(_recChromosome, _recTokBuf, std::strlen(_recTokBuf) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:553:90: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
_recFilename = static_cast<char *>( std::malloc(std::strlen(_token) + 1) );
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:556:42: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
std::strncpy(_recFilename, _token, strlen(_token) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:556:72: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
std::strncpy(_recFilename, _token, strlen(_token) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:731:62: [1] (buffer) strlen:
Does not handle 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 (std::strncmp(buf, kStarchBedHeaderTrack, strlen(kStarchBedHeaderTrack)) == 0 ||
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:732:64: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
std::strncmp(buf, kStarchBedHeaderBrowser, strlen(kStarchBedHeaderBrowser)) == 0 ||
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:733:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
std::strncmp(buf, kStarchBedHeaderSAM, strlen(kStarchBedHeaderSAM)) == 0 ||
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:734:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
std::strncmp(buf, kStarchBedHeaderVCF, strlen(kStarchBedHeaderVCF)) == 0 ||
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:735:65: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
std::strncmp(buf, kStarchBedGenericComment, strlen(kStarchBedGenericComment)) == 0);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:885:62: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
currentChromosome = static_cast<char *>( malloc (strlen(_cC) + 1) );
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:887:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(currentChromosome, _cC, strlen(_cC) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:887:49: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(currentChromosome, _cC, strlen(_cC) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:897:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
currentRemainder = static_cast<char *>( malloc (strlen(_remainder) + 1) );
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:899:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(currentRemainder, _remainder, strlen(_remainder) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:899:55: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(currentRemainder, _remainder, strlen(_remainder) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:1913:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:1913:112: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )) + 1);
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:1914:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
zBufOffset = strlen(reinterpret_cast<const char *>( zRemainderBuf ));
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:1952:13: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(reinterpret_cast<const char *>( zLineBuf )) > 0) {
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:1953:17: [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).
if (strlen(reinterpret_cast<const char *>( zLineBuf )) > strlen(reinterpret_cast<const char *>( zRemainderBuf ))) {
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:1953:70: [1] (buffer) strlen:
Does not handle 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(reinterpret_cast<const char *>( zLineBuf )) > strlen(reinterpret_cast<const char *>( zRemainderBuf ))) {
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:1956:71: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
zRemainderBuf = static_cast<char *>( std::malloc(std::strlen(zLineBuf) * 2) ); // resize remainder buffer, if necessary
data/bedops-2.4.39+dfsg/interfaces/general-headers/data/starch/starchApi.hpp:1965:13: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(reinterpret_cast<char *>( zRemainderBuf ), reinterpret_cast<const char *>( zLineBuf ), zBufIdx);
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/CharPooledMemory.hpp:82:21: [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).
if ( std::strlen(val) > Sz )
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/CharPooledMemory.hpp:209:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
std::size_t need = std::strlen(c);
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/CharPooledMemory.hpp:322:21: [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).
if ( std::strlen(val) > Sz )
data/bedops-2.4.39+dfsg/interfaces/general-headers/utility/CharPooledMemory.hpp:455:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
std::size_t sz = std::strlen(c);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchBase64Coding.c:148:24: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t intLength = strlen(objPointer);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:63:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
dup = static_cast<char *>( malloc(strlen(str) + 1) ); /* sizeof(char) = 1, of course */
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:67:22: [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).
dup = malloc(strlen(str) + 1); /* sizeof(char) = 1, of course */
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:95:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*outFn = static_cast<char *>( malloc((strlen(inFn) + 4) * sizeof(**outFn)) ); /* 4 <- ".gz\0" */
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:97:22: [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).
*outFn = malloc((strlen(inFn) + 4) * sizeof(**outFn)); /* 4 <- ".gz\0" */
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:163:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*outFn = static_cast<char *>( malloc((strlen(inFn) + 5) * sizeof(**outFn)) ); /* 5 <- ".bz2\0" */
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:165:22: [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).
*outFn = malloc((strlen(inFn) + 5) * sizeof(**outFn)); /* 5 <- ".bz2\0" */
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:196:17: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = fgetc(inFnPtr)) != EOF) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:288:143: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fprintf(stderr, "\t--- s [%s] buffer [%s], charCnt [%u], strlen(buffer) [%zu], sCnt [%u], strlen(s) [%zu]\n", s, buffer, charCnt, strlen(buffer), sCnt, strlen(s));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:288:165: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fprintf(stderr, "\t--- s [%s] buffer [%s], charCnt [%u], strlen(buffer) [%zu], sCnt [%u], strlen(s) [%zu]\n", s, buffer, charCnt, strlen(buffer), sCnt, strlen(s));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:296:98: [1] (buffer) strlen:
Does not handle 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 (strncmp(reinterpret_cast<const char *>( buffer ), kStarchBedHeaderTrack, strlen(kStarchBedHeaderTrack)) == 0) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:298:79: [1] (buffer) strlen:
Does not handle 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 (strncmp((const char *) buffer, kStarchBedHeaderTrack, strlen(kStarchBedHeaderTrack)) == 0) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:304:105: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(reinterpret_cast<const char *>( buffer ), kStarchBedHeaderBrowser, strlen(kStarchBedHeaderBrowser)) == 0) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:306:86: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp((const char *) buffer, kStarchBedHeaderBrowser, strlen(kStarchBedHeaderBrowser)) == 0) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:312:101: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(reinterpret_cast<const char *>( buffer ), kStarchBedHeaderSAM, strlen(kStarchBedHeaderSAM)) == 0) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:314:82: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp((const char *) buffer, kStarchBedHeaderSAM, strlen(kStarchBedHeaderSAM)) == 0) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:320:101: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(reinterpret_cast<const char *>( buffer ), kStarchBedHeaderVCF, strlen(kStarchBedHeaderVCF)) == 0) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:322:68: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp((const char *) buffer, kStarchBedHeaderVCF, strlen(kStarchBedHeaderVCF)) == 0) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:328:106: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(reinterpret_cast<const char *>( buffer ), kStarchBedGenericComment, strlen(kStarchBedGenericComment)) == 0) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:330:87: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp((const char *) buffer, kStarchBedGenericComment, strlen(kStarchBedGenericComment)) == 0) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:344:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(buffer) > TOKEN_CHR_MAX_LENGTH) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:350:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*chr = static_cast<char *>( malloc((strlen(buffer) + 1) * sizeof(**chr)) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:352:40: [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).
*chr = malloc((strlen(buffer) + 1) * sizeof(**chr));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:359:25: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:359:81: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:361:25: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*chr, (const char *)buffer, strlen(buffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:361:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*chr, (const char *)buffer, strlen(buffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:369:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(s) > TOKENS_HEADER_MAX_LENGTH) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:375:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*chr = static_cast<char *>( malloc((strlen(s) + 1) * sizeof(**chr)) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:377:40: [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).
*chr = malloc((strlen(s) + 1) * sizeof(**chr));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:383:25: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*chr, s, strlen(s) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:383:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*chr, s, strlen(s) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:392:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(buffer) > MAX_DEC_INTEGERS) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:419:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(buffer) > MAX_DEC_INTEGERS) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:453:147: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fprintf(stderr, "\t--- s [%s] buffer [%s], charCnt [%u], strlen(buffer) [%zu], sCnt [%u], strlen(s) [%zu], idIdx [%d]\n", s, buffer, charCnt, strlen(buffer), sCnt, strlen(s), idIdx);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:453:169: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fprintf(stderr, "\t--- s [%s] buffer [%s], charCnt [%u], strlen(buffer) [%zu], sCnt [%u], strlen(s) [%zu], idIdx [%d]\n", s, buffer, charCnt, strlen(buffer), sCnt, strlen(s), idIdx);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:476:51: [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).
*remainder = static_cast<char *>( malloc((strlen(buffer) + 1) * sizeof(**remainder)) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:478:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*remainder = malloc((strlen(buffer) + 1) * sizeof(**remainder));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:485:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:485:71: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:487:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*remainder, (const char *)buffer, strlen(buffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:487:51: [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).
strncpy(*remainder, (const char *)buffer, strlen(buffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:532:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(buffer) > TOKEN_CHR_MAX_LENGTH) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:539:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*chr = static_cast<char *>( malloc((strlen(buffer) + 1) * sizeof(**chr)) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:541:40: [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).
*chr = malloc((strlen(buffer) + 1) * sizeof(**chr));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:543:30: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strlen(buffer) > strlen(*chr)) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:543:47: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strlen(buffer) > strlen(*chr)) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:545:70: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
chrCopy = static_cast<char *>( realloc(*chr, strlen(buffer) * 2) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:547:49: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
chrCopy = realloc(*chr, strlen(buffer) * 2);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:560:21: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:560:77: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*chr, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:562:21: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*chr, (const char *)buffer, strlen(buffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:562:57: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*chr, (const char *)buffer, strlen(buffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:571:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(buffer) > MAX_DEC_INTEGERS) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:598:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(buffer) > MAX_DEC_INTEGERS) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:654:55: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*remainder = static_cast<char *>( malloc((strlen(buffer) + 1) * sizeof(**remainder)) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:656:34: [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).
*remainder = malloc((strlen(buffer) + 1) * sizeof(**remainder));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:658:18: [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).
else if (strlen(buffer) > strlen(*remainder)) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:658:35: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strlen(buffer) > strlen(*remainder)) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:663:70: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
remainderCopy = static_cast<char *>( realloc(*remainder, strlen(buffer) * 2) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:665:49: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
remainderCopy = realloc(*remainder, strlen(buffer) * 2);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:678:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:678:71: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*remainder, reinterpret_cast<const char *>( buffer ), strlen(buffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:680:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*remainder, (const char *)buffer, strlen(buffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:680:51: [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).
strncpy(*remainder, (const char *)buffer, strlen(buffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:749:17: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = fgetc(streamPtr)) != EOF) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:864:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outFn = static_cast<char *>( malloc(strlen(chromosome) + strlen(tag) + 2) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:864:82: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outFn = static_cast<char *>( malloc(strlen(chromosome) + strlen(tag) + 2) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:866:40: [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).
outFn = malloc(strlen(chromosome) + strlen(tag) + 2);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:866:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outFn = malloc(strlen(chromosome) + strlen(tag) + 2);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:922:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
prevChromosome = static_cast<char *>( malloc(strlen(chromosome) + 1) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:923:21: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:923:91: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:929:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
prevChromosome = malloc(strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:930:21: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(prevChromosome, (const char *)chromosome, strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:930:71: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(prevChromosome, (const char *)chromosome, strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:964:21: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:964:92: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:966:21: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
strncat(nonCoordLineBuf, (const char *)chromosome, strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:966:72: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncat(nonCoordLineBuf, (const char *)chromosome, strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:968:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
nonCoordLineBuf[strlen(nonCoordLineBuf)] = '\n';
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:978:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memset(nonCoordLineBuf, 0, strlen(nonCoordLineBuf));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1248:17: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = fgetc(streamPtr)) != EOF) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1352:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outFn = static_cast<char *>( malloc(strlen(chromosome) + strlen(tag) + 2) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1352:82: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outFn = static_cast<char *>( malloc(strlen(chromosome) + strlen(tag) + 2) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1354:40: [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).
outFn = malloc(strlen(chromosome) + strlen(tag) + 2);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1354:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
outFn = malloc(strlen(chromosome) + strlen(tag) + 2);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1410:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
prevChromosome = static_cast<char *>( malloc(strlen(chromosome) + 1) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1411:21: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1411:91: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1417:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
prevChromosome = malloc(strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1418:21: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(prevChromosome, (const char *)chromosome, strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1418:71: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(prevChromosome, (const char *)chromosome, strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:1762:18: [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).
size_t len = strlen(s);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2042:17: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = fgetc(const_cast<FILE *>( inFp ))) != EOF) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2045:17: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = fgetc((FILE *)inFp)) != EOF) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2411:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
prevChromosome = static_cast<char *>( malloc(strlen(chromosome) + 1) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2416:21: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2416:91: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2422:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
prevChromosome = malloc(strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2427:21: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(prevChromosome, (const char *) chromosome, strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2427:72: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(prevChromosome, (const char *) chromosome, strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2464:21: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2464:92: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncat(nonCoordLineBuf, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2466:21: [1] (buffer) strncat:
Easily used incorrectly (e.g., incorrectly computing the correct maximum
size to add) [MS-banned] (CWE-120). Consider strcat_s, strlcat, snprintf,
or automatically resizing strings.
strncat(nonCoordLineBuf, (const char *)chromosome, strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2466:72: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncat(nonCoordLineBuf, (const char *)chromosome, strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2468:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
nonCoordLineBuf[strlen(nonCoordLineBuf)] = '\n';
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2473:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%s", nonCoordLineBuf);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2474:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memset(nonCoordLineBuf, 0, strlen(nonCoordLineBuf));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2496:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(intermediateBuffer + strlen(intermediateBuffer), "p%" PRId64 "\n", coordDiff);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2500:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\t%s\n", (start - lastPosition), remainder);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2502:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\n", (start - lastPosition));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2506:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\t%s\n", start, remainder);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2508:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\n", start);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2510:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
intermediateBufferLength = strlen(intermediateBuffer);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2597:75: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
zStream.avail_in = static_cast<unsigned int>( strlen(intermediateBuffer) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2600:63: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
zStream.avail_in = (unsigned int) strlen(intermediateBuffer);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2630:71: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(transformedBuffer, intermediateBuffer, strlen(intermediateBuffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2631:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
currentTransformedBufferLength = strlen(intermediateBuffer);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2632:55: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memset(intermediateBuffer, 0, strlen(intermediateBuffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2684:64: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pRemainder = STARCH_strndup(remainder, strlen(remainder));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2719:75: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
maxStringLength = (maxStringLength >= static_cast<LineLengthType>(strlen(untransformedBuffer))) ? maxStringLength : static_cast<LineLengthType>(strlen(untransformedBuffer));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2719:153: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
maxStringLength = (maxStringLength >= static_cast<LineLengthType>(strlen(untransformedBuffer))) ? maxStringLength : static_cast<LineLengthType>(strlen(untransformedBuffer));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2721:64: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
maxStringLength = (maxStringLength >= (LineLengthType) strlen(untransformedBuffer)) ? maxStringLength : (LineLengthType) strlen(untransformedBuffer);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2721:130: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
maxStringLength = (maxStringLength >= (LineLengthType) strlen(untransformedBuffer)) ? maxStringLength : (LineLengthType) strlen(untransformedBuffer);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2747:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(intermediateBuffer + strlen(intermediateBuffer), "p%" PRId64 "\n", coordDiff);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2751:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\t%s\n", (start - lastPosition), remainder);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2753:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\n", (start - lastPosition));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2757:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\t%s\n", start, remainder);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2759:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\n", start);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:2761:40: [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).
intermediateBufferLength = strlen(intermediateBuffer);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3033:21: [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).
fwrite(json, 1, strlen(json), stdout);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3041:70: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
STARCH_SHA1_All(reinterpret_cast<const unsigned char *>( json ), strlen(json), sha1Digest);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3043:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
STARCH_SHA1_All((const unsigned char *)json, strlen(json), sha1Digest);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3065:112: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fprintf(stderr, "\tWARNING:\nmdLength: %llu\nmd - [%s]\nsha1 - [%s]\n", static_cast<unsigned long long>( strlen(json) ), json, sha1Digest);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3067:100: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fprintf(stderr, "\tWARNING:\nmdLength: %llu\nmd - [%s]\nsha1 - [%s]\n", (unsigned long long) strlen(json), json, sha1Digest);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3079:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(footerBuffer, footerCumulativeRecordSizeBuffer, strlen(footerCumulativeRecordSizeBuffer));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3303:17: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = fgetc(const_cast<FILE *>( inFp ))) != EOF) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3306:17: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = fgetc((FILE *)inFp)) != EOF) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3682:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
prevChromosome = static_cast<char *>( malloc(strlen(chromosome) + 1) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3688:45: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
prevChromosome = malloc(strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3695:21: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3695:91: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(prevChromosome, reinterpret_cast<const char *>( chromosome ), strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3697:21: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(prevChromosome, (const char *) chromosome, strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3697:72: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(prevChromosome, (const char *) chromosome, strlen(chromosome) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3744:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(intermediateBuffer + strlen(intermediateBuffer), "p%" PRId64 "\n", coordDiff);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3751:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\t%s\n", (start - lastPosition), remainder);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3757:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\n", (start - lastPosition));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3765:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\t%s\n", start, remainder);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3771:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\n", start);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3775:44: [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).
intermediateBufferLength = strlen(intermediateBuffer);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3872:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(transformedBuffer, intermediateBuffer, strlen(intermediateBuffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3873:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
currentTransformedBufferLength = strlen(intermediateBuffer);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3874:51: [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).
memset(intermediateBuffer, 0, strlen(intermediateBuffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3939:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pRemainder = STARCH_strndup(remainder, strlen(remainder));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:3955:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pRemainder = STARCH_strndup(remainder, strlen(remainder));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4008:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(intermediateBuffer + strlen(intermediateBuffer), "p%" PRId64 "\n", coordDiff);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4015:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\t%s\n", (start - lastPosition), remainder);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4021:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\n", (start - lastPosition));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4029:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\t%s\n", start, remainder);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4035:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
sprintf(intermediateBuffer + strlen(intermediateBuffer), "%" PRId64 "\n", start);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4038:40: [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).
intermediateBufferLength = strlen(intermediateBuffer);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4330:21: [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).
fwrite(json, 1, strlen(json), stdout);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4339:74: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
STARCH_SHA1_All(reinterpret_cast<const unsigned char *>( jsonCopy ), strlen(jsonCopy), sha1Digest);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4341:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
STARCH_SHA1_All((const unsigned char *)jsonCopy, strlen(jsonCopy), sha1Digest);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4365:112: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fprintf(stderr, "\tWARNING:\nmdLength: %llu\nmd - [%s]\nsha1 - [%s]\n", static_cast<unsigned long long>( strlen(json) ), json, sha1Digest);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4367:100: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fprintf(stderr, "\tWARNING:\nmdLength: %llu\nmd - [%s]\nsha1 - [%s]\n", (unsigned long long) strlen(json), json, sha1Digest);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchHelpers.c:4379:60: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
memcpy(footerBuffer, footerCumulativeRecordSizeBuffer, strlen(footerCumulativeRecordSizeBuffer));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:83:21: [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).
chrLength = strlen(chr);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:85:20: [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).
fnLength = strlen(fn);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:87:27: [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).
signatureLength = strlen(signature);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:108:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(newMetadata->chromosome, chr, chrLength + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:121:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(newMetadata->filename, fn, fnLength + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:137:13: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(newMetadata->signature, signature, signatureLength + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:306:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iter->filename = static_cast<char *>( malloc(strlen(fn) + 1) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:309:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iter->filename = malloc(strlen(fn) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:311:13: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(iter->filename, fn, strlen(fn) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:311:41: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(iter->filename, fn, strlen(fn) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:326:63: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iter->signature = static_cast<char *>( malloc(strlen(signature) + 1) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:328:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
iter->signature = malloc(strlen(signature) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:330:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(iter->signature, signature, strlen(signature) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:330:53: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(iter->signature, signature, strlen(signature) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:793:61: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
recordFilenameCopy = STARCH_strndup(iter->filename, strlen(iter->filename) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:795:56: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
recordChromosome = STARCH_strndup(recordToken, strlen(recordToken) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:882:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if ((iter->signature) && (strlen(iter->signature) > 0)) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:884:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
recordSignature = STARCH_strndup(iter->signature, strlen(iter->signature) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:988:18: [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).
jsonLength = strlen(jsonString) + 1;
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1073:36: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
currC = static_cast<char>( fgetc(*fp) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1075:24: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
currC = (char) fgetc(*fp);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1303:40: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
currC = static_cast<char>( fgetc(*fp) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1305:28: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
currC = (char) fgetc(*fp);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1411:67: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
*(dynamicBuffer + mdOffsetIndex) = static_cast<char>( fgetc(*fp) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1413:55: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
*(dynamicBuffer + mdOffsetIndex) = (char) fgetc(*fp);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1552:85: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
STARCH_SHA1_All(reinterpret_cast<const unsigned char *>(dynamicBufferCopy), strlen(dynamicBufferCopy), testMdHashSha1Buffer);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1554:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
STARCH_SHA1_All((const unsigned char *)dynamicBufferCopy, strlen(dynamicBufferCopy), testMdHashSha1Buffer);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1658:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*cTime = static_cast<char *>( malloc(strlen(streamCTime) + 1) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1661:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*cTime = malloc(strlen(streamCTime) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1667:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1667:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*cTime, streamCTime, strlen(streamCTime) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1675:53: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*note = static_cast<char *>( malloc(strlen(streamNote) + 1) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1678:32: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*note = malloc(strlen(streamNote) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1684:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*note, streamNote, strlen(streamNote) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1684:44: [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).
strncpy(*note, streamNote, strlen(streamNote) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1940:21: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(streamSig, json_string_value(streamSignature), strlen(json_string_value(streamSignature)) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1940:76: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(streamSig, json_string_value(streamSignature), strlen(json_string_value(streamSignature)) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1952:13: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(streamChr, json_string_value(streamChromosome), strlen(json_string_value(streamChromosome)) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1952:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(streamChr, json_string_value(streamChromosome), strlen(json_string_value(streamChromosome)) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1953:13: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(streamFn, json_string_value(streamFilename), strlen(json_string_value(streamFilename)) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:1953:66: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(streamFn, json_string_value(streamFilename), strlen(json_string_value(streamFilename)) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2033:26: [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).
fwrite(mdHeader, strlen(mdHeader), 1, outPtr);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2040:25: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = fgetc(chrFnPtr)) != EOF) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2060:26: [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).
fwrite(mdHeader, strlen(mdHeader), 1, outPtr);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2067:25: [1] (buffer) fgetc:
Check buffer boundaries if used in a loop including recursive loops
(CWE-120, CWE-20).
while ((c = fgetc(chrFnPtr)) != EOF) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2098:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*tag = STARCH_strndup(_tag, strlen(_tag) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2196:121: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
tokenCheck = STARCH_strnstr(reinterpret_cast<const char *>(token), STARCH_LEGACY_EXTENSION_BZ2, strlen(token));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2198:103: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
tokenCheck = STARCH_strnstr((const char *)token, STARCH_LEGACY_EXTENSION_BZ2, strlen(token));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2202:126: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
tokenCheck = STARCH_strnstr(reinterpret_cast<const char *>(token), STARCH_LEGACY_EXTENSION_GZIP, strlen(token));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2204:108: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
tokenCheck = STARCH_strnstr((const char *)token, STARCH_LEGACY_EXTENSION_GZIP, strlen(token));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2228:25: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(recTokBuf, token, strlen(token) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2228:51: [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).
strncpy(recTokBuf, token, strlen(token) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2229:63: [1] (buffer) strlen:
Does not handle 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 (recTokBufIdx = 0; recTokBufIdx < strlen(recTokBuf); recTokBufIdx++) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2236:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
recChromosome = static_cast<char *>( malloc(strlen(recTokBuf) + 1) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2238:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
recChromosome = malloc(strlen(recTokBuf) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2244:25: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2244:59: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(recChromosome, recTokBuf, strlen(recTokBuf) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2248:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
recFilename = static_cast<char *>( malloc(strlen(token) + 1) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2250:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
recFilename = malloc(strlen(token) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2256:25: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(recFilename, token, strlen(token) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2256:53: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(recFilename, token, strlen(token) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/starchMetadataHelpers.c:2395:18: [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).
size_t len = strlen(needle);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:200:25: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:200:120: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:201:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
zBufOffset = strlen(reinterpret_cast<const char *>( zRemainderBuf ));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:203:25: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy((char *) zLineBuf, (const char *) zRemainderBuf, strlen((const char *) zRemainderBuf));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:203:82: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy((char *) zLineBuf, (const char *) zRemainderBuf, strlen((const char *) zRemainderBuf));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:204:38: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
zBufOffset = strlen((const char *) zRemainderBuf);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:236:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(reinterpret_cast<const char *>( zLineBuf )) > 0) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:238:25: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen((const char *) zLineBuf) > 0) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:242:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(reinterpret_cast<const char *>( zLineBuf )) > strlen(reinterpret_cast<const char *>( zRemainderBuf ))) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:242:82: [1] (buffer) strlen:
Does not handle 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(reinterpret_cast<const char *>( zLineBuf )) > strlen(reinterpret_cast<const char *>( zRemainderBuf ))) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:244:29: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen((const char *) zLineBuf) > strlen((const char *) zRemainderBuf)) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:244:63: [1] (buffer) strlen:
Does not handle 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((const char *) zLineBuf) > strlen((const char *) zRemainderBuf)) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:249:82: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
zRemainderBuf = static_cast<unsigned char *>( malloc(strlen(reinterpret_cast<const char *>( zLineBuf )) * 2) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:251:52: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
zRemainderBuf = malloc(strlen((const char *) zLineBuf) * 2);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:262:25: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(reinterpret_cast<char *>( zRemainderBuf ), reinterpret_cast<const char *>( zLineBuf ), zBufIdx);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:264:25: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy((char *) zRemainderBuf, (const char *) zLineBuf, zBufIdx);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:553:106: [1] (buffer) strlen:
Does not handle 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 (strncmp(reinterpret_cast<const char *>(const_cast<unsigned char *>(str)), kStarchBedHeaderTrack, strlen(kStarchBedHeaderTrack)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:555:113: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(reinterpret_cast<const char *>(const_cast<unsigned char *>(str)), kStarchBedHeaderBrowser, strlen(kStarchBedHeaderBrowser)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:557:109: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(reinterpret_cast<const char *>(const_cast<unsigned char *>(str)), kStarchBedHeaderSAM, strlen(kStarchBedHeaderSAM)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:559:109: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(reinterpret_cast<const char *>(const_cast<unsigned char *>(str)), kStarchBedHeaderVCF, strlen(kStarchBedHeaderVCF)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:561:114: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(reinterpret_cast<const char *>(const_cast<unsigned char *>(str)), kStarchBedGenericComment, strlen(kStarchBedGenericComment)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:564:60: [1] (buffer) strlen:
Does not handle 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 (strncmp((const char *) str, kStarchBedHeaderTrack, strlen(kStarchBedHeaderTrack)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:566:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp((const char *) str, kStarchBedHeaderBrowser, strlen(kStarchBedHeaderBrowser)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:568:63: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp((const char *) str, kStarchBedHeaderSAM, strlen(kStarchBedHeaderSAM)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:570:63: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp((const char *) str, kStarchBedHeaderVCF, strlen(kStarchBedHeaderVCF)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:572:68: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp((const char *) str, kStarchBedGenericComment, strlen(kStarchBedGenericComment)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:613:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pTestChars = static_cast<char *>( malloc(strlen(elemTok1)) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:616:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pTestChars = malloc(strlen(elemTok1));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:618:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(pTestChars, elemTok1 + 1, strlen(elemTok1));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:618:51: [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).
strncpy(pTestChars, elemTok1 + 1, strlen(elemTok1));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:676:106: [1] (buffer) strlen:
Does not handle 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 (strncmp(reinterpret_cast<const char *>(const_cast<unsigned char *>(str)), kStarchBedHeaderTrack, strlen(kStarchBedHeaderTrack)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:678:113: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(reinterpret_cast<const char *>(const_cast<unsigned char *>(str)), kStarchBedHeaderBrowser, strlen(kStarchBedHeaderBrowser)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:680:109: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(reinterpret_cast<const char *>(const_cast<unsigned char *>(str)), kStarchBedHeaderSAM, strlen(kStarchBedHeaderSAM)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:682:109: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(reinterpret_cast<const char *>(const_cast<unsigned char *>(str)), kStarchBedHeaderVCF, strlen(kStarchBedHeaderVCF)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:684:114: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(reinterpret_cast<const char *>(const_cast<unsigned char *>(str)), kStarchBedGenericComment, strlen(kStarchBedGenericComment)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:687:60: [1] (buffer) strlen:
Does not handle 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 (strncmp((const char *) str, kStarchBedHeaderTrack, strlen(kStarchBedHeaderTrack)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:689:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp((const char *) str, kStarchBedHeaderBrowser, strlen(kStarchBedHeaderBrowser)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:691:63: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp((const char *) str, kStarchBedHeaderSAM, strlen(kStarchBedHeaderSAM)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:693:63: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp((const char *) str, kStarchBedHeaderVCF, strlen(kStarchBedHeaderVCF)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:695:68: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp((const char *) str, kStarchBedGenericComment, strlen(kStarchBedGenericComment)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:719:27: [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).
else if ((strlen(chr) + 1) > *currentChrLen) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:723:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*currentChr, chr, strlen(chr) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:723:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*currentChr, chr, strlen(chr) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:732:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*currentRemainder = static_cast<char *>( malloc(strlen(elemTok2) + 1) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:734:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*currentRemainder = malloc(strlen(elemTok2) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:736:44: [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).
*currentRemainderLen = strlen(elemTok2) + 1;
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:738:27: [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).
else if ((strlen(elemTok2) + 1) > *currentRemainderLen) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:740:92: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
currentRemainderCopy = static_cast<char *>( realloc(*currentRemainder, strlen(elemTok2) * 2) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:742:71: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
currentRemainderCopy = realloc(*currentRemainder, strlen(elemTok2) * 2);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:748:55: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
static_cast<uint64_t>(strlen(elemTok2)), static_cast<uint64_t>(*currentRemainderLen));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:750:115: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fprintf(stderr, "ERROR: Ran out of memory while extending remainder token (%zu | %zu)\n", strlen(elemTok2), *currentRemainderLen);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:755:44: [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).
*currentRemainderLen = strlen(elemTok2) * 2;
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:757:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*currentRemainder, elemTok2, strlen(elemTok2) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:757:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*currentRemainder, elemTok2, strlen(elemTok2) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:777:27: [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).
else if ((strlen(chr) + 1) > *currentChrLen) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:781:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*currentChr, chr, strlen(chr) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:781:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*currentChr, chr, strlen(chr) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:794:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*currentRemainder = static_cast<char *>( malloc(strlen(elemTok2) + 1) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:796:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*currentRemainder = malloc(strlen(elemTok2) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:798:44: [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).
*currentRemainderLen = strlen(elemTok2) + 1;
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:800:27: [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).
else if ((strlen(elemTok2) + 1) > *currentRemainderLen) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:802:92: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
currentRemainderCopy = static_cast<char *>( realloc(*currentRemainder, strlen(elemTok2) * 2) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:804:71: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
currentRemainderCopy = realloc(*currentRemainder, strlen(elemTok2) * 2);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:811:44: [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).
*currentRemainderLen = strlen(elemTok2) * 2;
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:813:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*currentRemainder, elemTok2, strlen(elemTok2) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:813:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*currentRemainder, elemTok2, strlen(elemTok2) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:831:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pTestChars = static_cast<char *>( malloc(strlen(elemTok1)) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:834:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pTestChars = malloc(strlen(elemTok1));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:836:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(pTestChars, elemTok1 + 1, strlen(elemTok1));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:836:51: [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).
strncpy(pTestChars, elemTok1 + 1, strlen(elemTok1));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:864:27: [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).
else if ((strlen(chr) + 1) > *currentChrLen) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:868:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*currentChr, chr, strlen(chr) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:868:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*currentChr, chr, strlen(chr) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:904:106: [1] (buffer) strlen:
Does not handle 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 (strncmp(reinterpret_cast<const char *>(const_cast<unsigned char *>(str)), kStarchBedHeaderTrack, strlen(kStarchBedHeaderTrack)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:906:113: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(reinterpret_cast<const char *>(const_cast<unsigned char *>(str)), kStarchBedHeaderBrowser, strlen(kStarchBedHeaderBrowser)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:908:109: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(reinterpret_cast<const char *>(const_cast<unsigned char *>(str)), kStarchBedHeaderSAM, strlen(kStarchBedHeaderSAM)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:910:109: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(reinterpret_cast<const char *>(const_cast<unsigned char *>(str)), kStarchBedHeaderVCF, strlen(kStarchBedHeaderVCF)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:912:114: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(reinterpret_cast<const char *>(const_cast<unsigned char *>(str)), kStarchBedGenericComment, strlen(kStarchBedGenericComment)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:915:60: [1] (buffer) strlen:
Does not handle 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 (strncmp((const char *) str, kStarchBedHeaderTrack, strlen(kStarchBedHeaderTrack)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:917:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp((const char *) str, kStarchBedHeaderBrowser, strlen(kStarchBedHeaderBrowser)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:919:63: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp((const char *) str, kStarchBedHeaderSAM, strlen(kStarchBedHeaderSAM)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:921:63: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp((const char *) str, kStarchBedHeaderVCF, strlen(kStarchBedHeaderVCF)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:923:68: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp((const char *) str, kStarchBedGenericComment, strlen(kStarchBedGenericComment)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:962:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pTestChars = static_cast<char *>( malloc(strlen(elemTok1)) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:965:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pTestChars = malloc(strlen(elemTok1));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:967:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(pTestChars, elemTok1 + 1, strlen(elemTok1));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:967:51: [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).
strncpy(pTestChars, elemTok1 + 1, strlen(elemTok1));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1031:106: [1] (buffer) strlen:
Does not handle 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 (strncmp(reinterpret_cast<const char *>(const_cast<unsigned char *>(str)), kStarchBedHeaderTrack, strlen(kStarchBedHeaderTrack)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1033:113: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(reinterpret_cast<const char *>(const_cast<unsigned char *>(str)), kStarchBedHeaderBrowser, strlen(kStarchBedHeaderBrowser)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1035:109: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(reinterpret_cast<const char *>(const_cast<unsigned char *>(str)), kStarchBedHeaderSAM, strlen(kStarchBedHeaderSAM)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1037:109: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(reinterpret_cast<const char *>(const_cast<unsigned char *>(str)), kStarchBedHeaderVCF, strlen(kStarchBedHeaderVCF)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1039:114: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp(reinterpret_cast<const char *>(const_cast<unsigned char *>(str)), kStarchBedGenericComment, strlen(kStarchBedGenericComment)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1042:60: [1] (buffer) strlen:
Does not handle 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 (strncmp((const char *) str, kStarchBedHeaderTrack, strlen(kStarchBedHeaderTrack)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1044:67: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp((const char *) str, kStarchBedHeaderBrowser, strlen(kStarchBedHeaderBrowser)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1046:63: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp((const char *) str, kStarchBedHeaderSAM, strlen(kStarchBedHeaderSAM)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1048:63: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp((const char *) str, kStarchBedHeaderVCF, strlen(kStarchBedHeaderVCF)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1050:68: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
else if (strncmp((const char *) str, kStarchBedGenericComment, strlen(kStarchBedGenericComment)) == 0)
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1077:27: [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).
else if ((strlen(chr) + 1) > *currentChrLen) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1081:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*currentChr, chr, strlen(chr) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1081:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*currentChr, chr, strlen(chr) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1090:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*currentRemainder = static_cast<char *>( malloc(strlen(elemTok2) + 1) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1092:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*currentRemainder = malloc(strlen(elemTok2) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1094:44: [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).
*currentRemainderLen = strlen(elemTok2) + 1;
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1096:27: [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).
else if ((strlen(elemTok2) + 1) > *currentRemainderLen) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1098:92: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
currentRemainderCopy = static_cast<char *>( realloc(*currentRemainder, strlen(elemTok2) * 2) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1100:71: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
currentRemainderCopy = realloc(*currentRemainder, strlen(elemTok2) * 2);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1107:44: [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).
*currentRemainderLen = strlen(elemTok2) * 2;
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1109:21: [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).
if (strlen(elemTok2) >= *currentRemainderLen) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1117:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*currentRemainder, elemTok2, strlen(elemTok2) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1117:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*currentRemainder, elemTok2, strlen(elemTok2) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1148:26: [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).
else if (strlen(chr) + 1 > *currentChrLen) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1152:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*currentChr, chr, strlen(chr) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1152:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*currentChr, chr, strlen(chr) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1165:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*currentRemainder = static_cast<char *>( malloc(strlen(elemTok2) + 1) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1167:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*currentRemainder = malloc(strlen(elemTok2) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1169:44: [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).
*currentRemainderLen = strlen(elemTok2) + 1;
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1171:27: [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).
else if ((strlen(elemTok2) + 1) > *currentRemainderLen) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1173:92: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
currentRemainderCopy = static_cast<char *>( realloc(*currentRemainder, strlen(elemTok2) * 2) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1175:71: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
currentRemainderCopy = realloc(*currentRemainder, strlen(elemTok2) * 2);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1182:44: [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).
*currentRemainderLen = strlen(elemTok2) * 2;
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1184:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*currentRemainder, elemTok2, strlen(elemTok2) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1184:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*currentRemainder, elemTok2, strlen(elemTok2) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1204:23: [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).
else if ((strlen(chr) + 1) > *currentChrLen) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1208:13: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*currentChr, chr, strlen(chr) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1208:39: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*currentChr, chr, strlen(chr) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1211:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(pTestChars, elemTok1 + 1, strlen(elemTok1));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1211:51: [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).
strncpy(pTestChars, elemTok1 + 1, strlen(elemTok1));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1299:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pTestChars = static_cast<char *>( malloc(strlen(elemTok1)) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1302:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pTestChars = malloc(strlen(elemTok1));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1304:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(pTestChars, elemTok1 + 1, strlen(elemTok1));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1304:51: [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).
strncpy(pTestChars, elemTok1 + 1, strlen(elemTok1));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1455:27: [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).
else if ((strlen(chr) + 1) > *currentChrLen) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1459:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*currentChr, chr, strlen(chr) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1459:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*currentChr, chr, strlen(chr) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1468:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*currentRemainder = static_cast<char *>( malloc(strlen(elemTok2) + 1) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1470:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*currentRemainder = malloc(strlen(elemTok2) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1472:44: [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).
*currentRemainderLen = strlen(elemTok2) + 1;
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1474:27: [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).
else if ((strlen(elemTok2) + 1) > *currentRemainderLen) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1476:92: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
currentRemainderCopy = static_cast<char *>( realloc(*currentRemainder, strlen(elemTok2) * 2) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1478:71: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
currentRemainderCopy = realloc(*currentRemainder, strlen(elemTok2) * 2);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1485:44: [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).
*currentRemainderLen = strlen(elemTok2) * 2;
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1487:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*currentRemainder, elemTok2, strlen(elemTok2) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1487:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*currentRemainder, elemTok2, strlen(elemTok2) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1512:27: [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).
else if ((strlen(chr) + 1) > *currentChrLen) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1516:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*currentChr, chr, strlen(chr) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1516:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*currentChr, chr, strlen(chr) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1529:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*currentRemainder = static_cast<char *>( malloc(strlen(elemTok2) + 1) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1531:48: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
*currentRemainder = malloc(strlen(elemTok2) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1533:44: [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).
*currentRemainderLen = strlen(elemTok2) + 1;
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1535:27: [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).
else if ((strlen(elemTok2) + 1) > *currentRemainderLen) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1537:92: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
currentRemainderCopy = static_cast<char *>( realloc(*currentRemainder, strlen(elemTok2) * 2) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1539:71: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
currentRemainderCopy = realloc(*currentRemainder, strlen(elemTok2) * 2);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1546:44: [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).
*currentRemainderLen = strlen(elemTok2) * 2;
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1548:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*currentRemainder, elemTok2, strlen(elemTok2) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1548:54: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*currentRemainder, elemTok2, strlen(elemTok2) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1566:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pTestChars = static_cast<char *>( malloc(strlen(elemTok1)) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1569:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
pTestChars = malloc(strlen(elemTok1));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1571:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(pTestChars, elemTok1 + 1, strlen(elemTok1));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1571:51: [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).
strncpy(pTestChars, elemTok1 + 1, strlen(elemTok1));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1604:27: [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).
else if ((strlen(chr) + 1) > *currentChrLen) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1608:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(*currentChr, chr, strlen(chr) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1608:43: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(*currentChr, chr, strlen(chr) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1651:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1651:77: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1653:17: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(elemTok1, (const char *) buffer, strlen((const char *) buffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1653:58: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(elemTok1, (const char *) buffer, strlen((const char *) buffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1667:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1667:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(elemTok1, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1669:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(elemTok1, (const char *) buffer, strlen((const char *) buffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1669:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(elemTok1, (const char *) buffer, strlen((const char *) buffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1678:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(elemTok2, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1678:69: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(elemTok2, reinterpret_cast<const char *>( buffer ), strlen(reinterpret_cast<const char *>( buffer )) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1680:9: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(elemTok2, (const char *) buffer, strlen((const char *) buffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1680:50: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(elemTok2, (const char *) buffer, strlen((const char *) buffer) + 1);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1699:18: [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).
size_t len = strlen(needle);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:1741:18: [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).
size_t len = strlen(s);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2241:75: [1] (buffer) strlen:
Does not handle 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 ((strcmp(chr, iter->chromosome) == 0) && (iter->signature) && (strlen(iter->signature) > 0))
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2247:75: [1] (buffer) strlen:
Does not handle 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 ((strcmp(chr, iter->chromosome) == 0) && (iter->signature) && (strlen(iter->signature) > 0))
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2318:55: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
fprintf(stdout, "%s\t%s\n", iter->chromosome, strlen(iter->signature) > 0 ? iter->signature : "NA");
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2471:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t len = strlen(reinterpret_cast<const char *>( bzOutput ));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2473:42: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
size_t len = strlen((const char *)bzOutput);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2559:33: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2559:128: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy(reinterpret_cast<char *>( zLineBuf ), reinterpret_cast<const char *>( zRemainderBuf ), strlen(reinterpret_cast<const char *>( zRemainderBuf )));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2560:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
zBufOffset = strlen(reinterpret_cast<const char *>( zRemainderBuf ));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2564:33: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy((char *) zLineBuf, (const char *) zRemainderBuf, strlen((const char *) zRemainderBuf));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2564:90: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
strncpy((char *) zLineBuf, (const char *) zRemainderBuf, strlen((const char *) zRemainderBuf));
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2565:46: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
zBufOffset = strlen((const char *) zRemainderBuf);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2585:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(reinterpret_cast<const char *>( zLineBuf )) > 0) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2586:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen(reinterpret_cast<const char *>( zLineBuf )) > strlen(reinterpret_cast<const char *>( zRemainderBuf ))) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2586:90: [1] (buffer) strlen:
Does not handle 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(reinterpret_cast<const char *>( zLineBuf )) > strlen(reinterpret_cast<const char *>( zRemainderBuf ))) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2588:95: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
zRemainderBuf = reinterpret_cast<unsigned char *>( malloc(strlen(reinterpret_cast<const char *>( zLineBuf )) * 2) );
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2590:33: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy(reinterpret_cast<char *>( zRemainderBuf ), reinterpret_cast<const char *>( zLineBuf ), zBufIdx);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2594:33: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen((const char *) zLineBuf) > 0) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2595:37: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
if (strlen((const char *) zLineBuf) > strlen((const char *) zRemainderBuf)) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2595:71: [1] (buffer) strlen:
Does not handle 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((const char *) zLineBuf) > strlen((const char *) zRemainderBuf)) {
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2597:78: [1] (buffer) strlen:
Does not handle strings that are not \0-terminated; if given one it may
perform an over-read (it could cause a crash if unprotected) (CWE-126).
zRemainderBuf = (unsigned char *) malloc(strlen((const char *) zLineBuf) * 2);
data/bedops-2.4.39+dfsg/interfaces/src/data/starch/unstarchHelpers.c:2599:33: [1] (buffer) strncpy:
Easily used incorrectly; doesn't always \0-terminate or check for invalid
pointers [MS-banned] (CWE-120).
strncpy((char *) zRemainderBuf, (const char *) zLineBuf, zBufIdx);
ANALYSIS SUMMARY:
Hits = 1627
Lines analyzed = 53838 in approximately 1.86 seconds (28943 lines/second)
Physical Source Lines of Code (SLOC) = 43239
Hits@level = [0] 2112 [1] 898 [2] 478 [3] 11 [4] 240 [5] 0
Hits@level+ = [0+] 3739 [1+] 1627 [2+] 729 [3+] 251 [4+] 240 [5+] 0
Hits/KSLOC@level+ = [0+] 86.4729 [1+] 37.6281 [2+] 16.8598 [3+] 5.80494 [4+] 5.55054 [5+] 0
Dot directories skipped = 1 (--followdotdir overrides)
Minimum risk level = 1
Not every hit is necessarily a security vulnerability.
There may be other security vulnerabilities; review your code!
See 'Secure Programming HOWTO'
(https://dwheeler.com/secure-programs) for more information.