[med-svn] [Git][med-team/lambda-align][master] 3 commits: dch -r, add bug refs
Sascha Steinbiss (@satta)
gitlab at salsa.debian.org
Sun Feb 22 22:00:32 GMT 2026
Sascha Steinbiss pushed to branch master at Debian Med / lambda-align
Commits:
7514007a by Sascha Steinbiss at 2026-02-22T22:59:32+01:00
dch -r, add bug refs
- - - - -
50c9f31b by Sascha Steinbiss at 2026-02-22T22:59:49+01:00
add Repository/Repository-Browse metadata
- - - - -
54dc6857 by Sascha Steinbiss at 2026-02-22T22:59:57+01:00
bump copyright year for debian/* files
- - - - -
4 changed files:
- debian/changelog
- debian/copyright
- + debian/patches/namespace.patch
- debian/upstream/metadata
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,16 @@
-lambda-align (1.0.3-9) UNRELEASED; urgency=medium
+lambda-align (1.0.3-9) unstable; urgency=medium
+ [ Enrico Seiler ]
* Team upload.
- * Add SeqAn 2.5.x namespace patch
- * Fix autopkgtest using CMake 4
- * Add version fix patch
+ * Add SeqAn 2.5.x namespace patch.
+ Closes: #1125646
+ * Fix autopkgtest using CMake 4.
+ Closes: #1125595
+ * Add version fix patch.
+
+ [ Sascha Steinbiss ]
+ * Add Repository/Repository-Browse metadata.
+ * Bump copyright year for debian/* files.
-- Enrico Seiler <enrico.seiler.debian at outlook.com> Sun, 22 Feb 2026 19:59:51 +0100
=====================================
debian/copyright
=====================================
@@ -23,7 +23,7 @@ Copyright: © 2013-2016 Hannes Hauswedell
License: BSD-3-clause
Files: debian/*
-Copyright: © 2016 Sascha Steinbiss <satta at debian.org>
+Copyright: © 2016-2026 Sascha Steinbiss <satta at debian.org>
License: GPL-3+
License: GPL-3+
=====================================
debian/patches/namespace.patch
=====================================
@@ -0,0 +1,157 @@
+--- a/src/lambda.cpp
++++ b/src/lambda.cpp
+@@ -33,7 +33,7 @@
+ #include "holders.hpp"
+ #include "lambda.hpp"
+
+-using namespace seqan;
++using namespace seqan2;
+
+ // inline BlastFormatFile
+ // _fileType(LambdaOptions const & options)
+@@ -116,15 +116,15 @@
+ int main(int argc, char const ** argv)
+ {
+ // Parse the command line.
+- seqan::ArgumentParser parser;
++ seqan2::ArgumentParser parser;
+ LambdaOptions options;
+- seqan::ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
++ seqan2::ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
+
+ // If there was an error parsing or built-in argument parser functionality
+ // was triggered then we exit the program. The return code is 1 if there
+ // were errors and 0 if there were none.
+- if (res != seqan::ArgumentParser::PARSE_OK)
+- return res == seqan::ArgumentParser::PARSE_ERROR;
++ if (res != seqan2::ArgumentParser::PARSE_OK)
++ return res == seqan2::ArgumentParser::PARSE_ERROR;
+
+ if (std::string(CMAKE_BUILD_TYPE) != "Release")
+ std::cerr << "WARNING: This binary is not built in release mode and will be much slower than it should be!\n";
+--- a/src/lambda.hpp
++++ b/src/lambda.hpp
+@@ -42,7 +42,7 @@
+ #include "match.hpp"
+ #include "misc.hpp"
+
+-using namespace seqan;
++using namespace seqan2;
+
+ // ============================================================================
+ // Forwards
+--- a/src/lambda_indexer.cpp
++++ b/src/lambda_indexer.cpp
+@@ -30,7 +30,7 @@
+
+ #include "lambda_indexer.hpp"
+
+-using namespace seqan;
++using namespace seqan2;
+
+ // ==========================================================================
+ // Forwards
+@@ -72,15 +72,15 @@
+ int main(int argc, char const ** argv)
+ {
+ // Parse the command line.
+- seqan::ArgumentParser parser;
++ seqan2::ArgumentParser parser;
+ LambdaIndexerOptions options;
+- seqan::ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
++ seqan2::ArgumentParser::ParseResult res = parseCommandLine(options, argc, argv);
+
+ // If there was an error parsing or built-in argument parser functionality
+ // was triggered then we exit the program. The return code is 1 if there
+ // were errors and 0 if there were none.
+- if (res != seqan::ArgumentParser::PARSE_OK)
+- return res == seqan::ArgumentParser::PARSE_ERROR;
++ if (res != seqan2::ArgumentParser::PARSE_OK)
++ return res == seqan2::ArgumentParser::PARSE_ERROR;
+
+ if (std::string(CMAKE_BUILD_TYPE) != "Release")
+ std::cerr << "WARNING: This binary is not built in release mode and will be much slower than it should be!\n";
+--- a/src/lambda_indexer.hpp
++++ b/src/lambda_indexer.hpp
+@@ -37,7 +37,7 @@
+ #include "radix_inplace.h"
+ #include "lambda_indexer_misc.hpp"
+
+-using namespace seqan;
++using namespace seqan2;
+
+ // --------------------------------------------------------------------------
+ // Function loadSubj()
+--- a/src/match.hpp
++++ b/src/match.hpp
+@@ -28,7 +28,7 @@
+
+ #include "options.hpp"
+
+-using namespace seqan;
++using namespace seqan2;
+
+ //-----------------------------------------------------------------------------
+ // Finder
+--- a/src/misc.hpp
++++ b/src/misc.hpp
+@@ -33,7 +33,7 @@
+
+ #include "options.hpp"
+
+-using namespace seqan;
++using namespace seqan2;
+
+ // ============================================================================
+ // Forwards
+@@ -78,8 +78,8 @@
+ inline std::basic_ostream<char> &
+ operator<<(std::basic_ostream<char> & out,
+ const Iter<const String<SimpleType<unsigned char,TAlph>,
+- seqan::Packed<> >,
+- seqan::Packed<> > it)
++ seqan2::Packed<> >,
++ seqan2::Packed<> > it)
+ {
+ out << *it;
+ return out;
+--- a/src/options.hpp
++++ b/src/options.hpp
+@@ -111,7 +111,7 @@
+
+ }
+
+-using namespace seqan;
++using namespace seqan2;
+
+ // Index Specs
+ struct LambdaFMIndexConfig
+--- a/src/output.hpp
++++ b/src/output.hpp
+@@ -25,7 +25,7 @@
+ #include <seqan/blast.h>
+ #include <seqan/bam_io.h>
+
+-using namespace seqan;
++using namespace seqan2;
+
+ template <typename TVoidSpec = void>
+ struct SamBamExtraTags
+@@ -313,7 +313,7 @@
+ } else // SAM or BAM
+ {
+ open(globalHolder.outfileBam, toCString(options.output));
+- auto & context = seqan::context(globalHolder.outfileBam);
++ auto & context = seqan2::context(globalHolder.outfileBam);
+ auto & subjSeqLengths = contigLengths(context);
+ auto & subjIds = contigNames(context);
+
+@@ -407,7 +407,7 @@
+ {
+ // we only write the header records that we actually created ourselves
+ for (unsigned i = 0; i < length(header); ++i)
+- write(globalHolder.outfileBam.iter, header[i], seqan::context(globalHolder.outfileBam), Sam());
++ write(globalHolder.outfileBam.iter, header[i], seqan2::context(globalHolder.outfileBam), Sam());
+ }
+ else
+ {
=====================================
debian/upstream/metadata
=====================================
@@ -1,3 +1,5 @@
+Repository: https://github.com/seqan/lambda
+Repository-Browse: https://github.com/seqan/lambda
Reference:
- Author: Hannes Hauswedell and Jochen Singer and Knut Reinert
Title: "Lambda: the local aligner for massive biological data"
View it on GitLab: https://salsa.debian.org/med-team/lambda-align/-/compare/f32e10d928731fd850ea0748a46c52cfe97d6dde...54dc685787037d77df85d454d85d101957f817b2
--
View it on GitLab: https://salsa.debian.org/med-team/lambda-align/-/compare/f32e10d928731fd850ea0748a46c52cfe97d6dde...54dc685787037d77df85d454d85d101957f817b2
You're receiving this email because of your account on salsa.debian.org.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-med-commit/attachments/20260222/abce6568/attachment-0001.htm>
More information about the debian-med-commit
mailing list