[med-svn] [Git][med-team/libmaus2][upstream] New upstream version 2.0.813+ds
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Jan 1 19:52:40 GMT 2023
Étienne Mollier pushed to branch upstream at Debian Med / libmaus2
Commits:
cee4cd3e by Étienne Mollier at 2023-01-01T17:57:51+01:00
New upstream version 2.0.813+ds
- - - - -
8 changed files:
- ChangeLog
- config.h.in
- configure.ac
- src/libmaus2/fastx/RefPathTokenVector.hpp
- src/libmaus2/gtf/ExonSubInfo.hpp
- src/libmaus2/util/DirectoryStructure.hpp
- src/libmaus2/util/MemUsage.cpp
- src/libmaus2/util/OutputFileNameTools.cpp
Changes:
=====================================
ChangeLog
=====================================
@@ -1,3 +1,10 @@
+libmaus2 (2.0.813-1) unstable; urgency=medium
+
+ * Add range checks in DirectoryStructure
+ * Add missing includes required for gcc13
+
+ -- German Tischler-Höhle <germant at miltenyibiotec.de> Sat, 10 Dec 2022 18:30:06 +0100
+
libmaus2 (2.0.812-1) unstable; urgency=medium
* Add BamAlignmentTagOnlyComparator class
=====================================
config.h.in
=====================================
@@ -12,12 +12,12 @@
/* Define to 1 if you have the <inttypes.h> header file. */
#undef HAVE_INTTYPES_H
-/* Define to 1 if you have the <memory.h> header file. */
-#undef HAVE_MEMORY_H
-
/* Define to 1 if you have the <stdint.h> header file. */
#undef HAVE_STDINT_H
+/* Define to 1 if you have the <stdio.h> header file. */
+#undef HAVE_STDIO_H
+
/* Define to 1 if you have the <stdlib.h> header file. */
#undef HAVE_STDLIB_H
@@ -63,7 +63,9 @@
/* The size of `unsigned long', as computed by sizeof. */
#undef SIZEOF_UNSIGNED_LONG
-/* Define to 1 if you have the ANSI C header files. */
+/* Define to 1 if all of the C90 standard headers exist (not just the ones
+ required in a freestanding environment). This macro is provided for
+ backward compatibility; new code need not use it. */
#undef STDC_HEADERS
/* Version number of package */
@@ -81,11 +83,6 @@
# endif
#endif
-/* Enable large inode numbers on Mac OS X 10.5. */
-#ifndef _DARWIN_USE_64_BIT_INODE
-# define _DARWIN_USE_64_BIT_INODE 1
-#endif
-
/* Number of bits in a file offset, on hosts where this is settable. */
#undef _FILE_OFFSET_BITS
=====================================
configure.ac
=====================================
@@ -1,5 +1,5 @@
-AC_INIT(libmaus2,2.0.812,[germant at miltenyibiotec.de],[libmaus2],[https://gitlab.com/german.tischler/libmaus2])
-LIBRARY_VERSION=2:812:0
+AC_INIT(libmaus2,2.0.813,[germant at miltenyibiotec.de],[libmaus2],[https://gitlab.com/german.tischler/libmaus2])
+LIBRARY_VERSION=2:813:0
AC_MSG_NOTICE([Configuring for source in directory ${srcdir}])
AC_CANONICAL_SYSTEM
AC_CANONICAL_HOST
=====================================
src/libmaus2/fastx/RefPathTokenVector.hpp
=====================================
@@ -19,6 +19,7 @@
#if ! defined(LIBMAUS2_FASTX_REFPATHTOKENVECTOR_HPP)
#define LIBMAUS2_FASTX_REFPATHTOKENVECTOR_HPP
+#include <cstdint>
#include <libmaus2/fastx/RefPathToken.hpp>
#include <vector>
#include <limits>
=====================================
src/libmaus2/gtf/ExonSubInfo.hpp
=====================================
@@ -18,6 +18,7 @@
#if ! defined(LIBMAUS2_GTF_EXONSUBINFO_HPP)
#define LIBMAUS2_GTF_EXONSUBINFO_HPP
+#include <cstdint>
#include <ostream>
namespace libmaus2
=====================================
src/libmaus2/util/DirectoryStructure.hpp
=====================================
@@ -105,6 +105,13 @@ namespace libmaus2
std::vector<uint64_t> getVector(uint64_t const i) const
{
+ if ( ! (i<n) ) {
+ libmaus2::exception::LibMausException lme;
+ lme.getStream() << "[E] libmaus2::util::DirectoryStructure::getVector: i=" << i << " is out of range for n=" << n << std::endl;
+ lme.finish();
+ throw lme;
+ }
+
std::vector<uint64_t> V;
uint64_t z = i;
@@ -130,6 +137,13 @@ namespace libmaus2
**/
std::string operator[](uint64_t const i) const
{
+ if ( ! (i<n) ) {
+ libmaus2::exception::LibMausException lme;
+ lme.getStream() << "[E] libmaus2::util::DirectoryStructure::operator[]: i=" << i << " is out of range for n=" << n << std::endl;
+ lme.finish();
+ throw lme;
+ }
+
std::vector<uint64_t> V = getVector(i);
DirectoryEntry DS(prefix,V);
@@ -146,6 +160,13 @@ namespace libmaus2
**/
std::string getDirectoryFor(uint64_t const i) const
{
+ if ( ! (i<n) ) {
+ libmaus2::exception::LibMausException lme;
+ lme.getStream() << "[E] libmaus2::util::DirectoryStructure::getDirectoryFor: i=" << i << " is out of range for n=" << n << std::endl;
+ lme.finish();
+ throw lme;
+ }
+
std::vector<uint64_t> V = getVector(i);
DirectoryEntry DS(prefix,V);
=====================================
src/libmaus2/util/MemUsage.cpp
=====================================
@@ -16,7 +16,7 @@
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>..
*/
-
+#include <cstdint>
#include <libmaus2/util/MemUsage.hpp>
#include <libmaus2/util/MemoryStatistics.hpp>
#include <libmaus2/posix/PosixFunctions.hpp>
=====================================
src/libmaus2/util/OutputFileNameTools.cpp
=====================================
@@ -17,6 +17,7 @@
along with this program. If not, see <http://www.gnu.org/licenses/>..
*/
+#include <cstdint>
#include <libmaus2/util/OutputFileNameTools.hpp>
std::string libmaus2::util::OutputFileNameTools::lcp(std::string const & a, std::string const & b)
View it on GitLab: https://salsa.debian.org/med-team/libmaus2/-/commit/cee4cd3e08512b76c90bc0b0c1f459471ec512a0
--
View it on GitLab: https://salsa.debian.org/med-team/libmaus2/-/commit/cee4cd3e08512b76c90bc0b0c1f459471ec512a0
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