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,[[email protected]],[libmaus2],[https://gitlab.com/german.tischler/libmaus2]) -LIBRARY_VERSION=2:767:0 +AC_INIT(libmaus2,2.0.768,[[email protected]],[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 <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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