[med-svn] [Git][med-team/libmaus2][master] 4 commits: routine-update: New upstream version

[Étienne Mollier]

Étienne Mollier pushed to branch master at Debian Med / libmaus2


Commits:
121bd0a2 by Étienne Mollier at 2021-01-02T21:34:11+01:00
routine-update: New upstream version

- - - - -
06204815 by Étienne Mollier at 2021-01-02T21:34:25+01:00
New upstream version 2.0.768+dfsg
- - - - -
556a6573 by Étienne Mollier at 2021-01-02T21:34:30+01:00
Update upstream source from tag 'upstream/2.0.768+dfsg'

Update to upstream version '2.0.768+dfsg'
with Debian dir 197dec2ea0ea16d1c59f66633527ef06d750f88d
- - - - -
d1126b1f by Étienne Mollier at 2021-01-02T21:51:06+01:00
routine-update: Ready to upload to unstable

- - - - -


6 changed files:

- configure.ac
- debian/changelog
- src/libmaus2/bambam/BamNumericalIndexGenerator.hpp
- src/libmaus2/lcs/AlignmentTraceContainer.hpp
- src/libmaus2/protein/Align.hpp
- src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp


Changes:

=====================================
configure.ac
=====================================
@@ -1,5 +1,5 @@
-AC_INIT(libmaus2,2.0.767,[germant at miltenyibiotec.de],[libmaus2],[https://gitlab.com/german.tischler/libmaus2])
-LIBRARY_VERSION=2:767:0
+AC_INIT(libmaus2,2.0.768,[germant at miltenyibiotec.de],[libmaus2],[https://gitlab.com/german.tischler/libmaus2])
+LIBRARY_VERSION=2:768:0
 AC_MSG_NOTICE([Configuring for source in directory ${srcdir}])
 AC_CANONICAL_SYSTEM
 AC_CANONICAL_HOST


=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+libmaus2 (2.0.768+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+
+ -- Étienne Mollier <etienne.mollier at mailoo.org>  Sat, 02 Jan 2021 21:34:35 +0100
+
 libmaus2 (2.0.767+dfsg-1) unstable; urgency=medium
 
   * Add spelling-error-in-header.patch to fix spelling-error-in-binary affecting


=====================================
src/libmaus2/bambam/BamNumericalIndexGenerator.hpp
=====================================
@@ -204,7 +204,7 @@ namespace libmaus2
 			{
 				std::string const tmpfn = indexfn + ".tmp";
 				libmaus2::aio::InputStreamInstance::unique_ptr_type ISI(new libmaus2::aio::InputStreamInstance(indexfn));
-				libmaus2::aio::OutputStreamInstance::unique_ptr_type OSI(new libmaus2::aio::OutputStreamInstance(indexfn));
+				libmaus2::aio::OutputStreamInstance::unique_ptr_type OSI(new libmaus2::aio::OutputStreamInstance(tmpfn));
 
 				// copy header
 				libmaus2::util::NumberSerialisation::serialiseNumber(*OSI,libmaus2::util::NumberSerialisation::deserialiseNumber(*ISI));


=====================================
src/libmaus2/lcs/AlignmentTraceContainer.hpp
=====================================
@@ -1924,6 +1924,27 @@ namespace libmaus2
 				return suffixPositive(ta,te,match_score,mismatch_score,ins_score,del_score);
 			}
 
+			void push(step_type const & step)
+			{
+				if ( te == trace.end() )
+				{
+					std::size_t const curtracelen = getTraceLength();
+					std::size_t const one = 1;
+					std::size_t const newsize = std::max(2*curtracelen,one);
+
+					::libmaus2::autoarray::AutoArray<step_type> ntrace(newsize,false);
+
+					std::copy(ta,te,ntrace.begin());
+
+					trace = ntrace;
+					ta = trace.begin();
+					te = trace.begin()+curtracelen;
+					assert ( te != trace.end() );
+				}
+
+				assert ( te != trace.end() );
+				*(te++) = step;
+			}
 
 			void push(AlignmentTraceContainer const & O)
 			{


=====================================
src/libmaus2/protein/Align.hpp
=====================================
@@ -20,6 +20,7 @@
 
 #include <libmaus2/protein/Blosum62.hpp>
 #include <libmaus2/autoarray/AutoArray.hpp>
+#include <libmaus2/util/NumberSerialisation.hpp>
 
 namespace libmaus2
 {


=====================================
src/libmaus2/suffixsort/bwtb3m/BwtMergeSortTemplate.hpp
=====================================
@@ -4928,7 +4928,7 @@ namespace libmaus2
 
 						assert ( astr.str() == bstr.str() );
 
-						if ( options.verbose >= 5 )
+						if ( options.verbose >= 5 && logstr )
 							*logstr << "[V] checked serialisation" << std::endl;
 					}
 
@@ -4982,7 +4982,7 @@ namespace libmaus2
 
 						assert ( astr.str() == bstr.str() );
 
-						// if ( options.verbose >= 5 )
+						if ( options.verbose >= 5 && logstr )
 							*logstr << "[V] checked serialisation after block sorting" << std::endl;
 					}
 
@@ -5022,7 +5022,7 @@ namespace libmaus2
 
 						assert ( astr.str() == bstr.str() );
 
-						// if ( options.verbose >= 5 )
+						if ( options.verbose >= 5 && logstr )
 							*logstr << "[V] checked serialisation after filling gap request objects" << std::endl;
 					}
 



View it on GitLab: https://salsa.debian.org/med-team/libmaus2/-/compare/1290dd831b58532ea9eae44df28ad8ab955a59c7...d1126b1fddc17cebf2dbedf8618db3eaab0b2edc

-- 
View it on GitLab: https://salsa.debian.org/med-team/libmaus2/-/compare/1290dd831b58532ea9eae44df28ad8ab955a59c7...d1126b1fddc17cebf2dbedf8618db3eaab0b2edc
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