Commit f12fcff8 authored by Julien Y. Dutheil's avatar Julien Y. Dutheil
Browse files

New upstream version 2.4.1

parent f1ead48d

CMakeLists.txt

+2 −2
Original line number Diff line number Diff line
@@ -95,10 +95,10 @@ ENDIF(NO_DEP_CHECK) 
# Packager

SET(CPACK_PACKAGE_NAME "libbpp-seq-omics")

SET(CPACK_PACKAGE_VENDOR "Bio++ Development Team")

SET(CPACK_PACKAGE_VERSION "2.4.0")

SET(CPACK_PACKAGE_VERSION "2.4.1")

SET(CPACK_PACKAGE_VERSION_MAJOR "2")

SET(CPACK_PACKAGE_VERSION_MINOR "4")

SET(CPACK_PACKAGE_VERSION_PATCH "0")

SET(CPACK_PACKAGE_VERSION_PATCH "1")

SET(CPACK_PACKAGE_DESCRIPTION_SUMMARY "The Bio++ Sequence-Omics library")

SET(CPACK_RESOURCE_FILE_LICENSE "${CMAKE_SOURCE_DIR}/COPYING.txt")

SET(CPACK_RESOURCE_FILE_AUTHORS "${CMAKE_SOURCE_DIR}/AUTHORS.txt")

Doxyfile

+1 −1
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@@ -38,7 +38,7 @@ PROJECT_NAME = bpp-seq-omics 
# could be handy for archiving the generated documentation or if some version

# control system is used.



PROJECT_NUMBER         = 2.4.0

PROJECT_NUMBER         = 2.4.1



# Using the PROJECT_BRIEF tag one can provide an optional one line description

# for a project that appears at the top of each page and should give viewer a

bpp-seq-omics.spec

+3 −1
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@@ -3,7 +3,7 @@ 
URL: https://github.com/BioPP/bpp-seq-omics



Name: bpp-seq-omics

Version: 2.4.0

Version: 2.4.1

Release: 1%{?dist}

License: CECILL-2.0

Vendor: The Bio++ Project
@@ -84,6 +84,8 @@ rm -rf $RPM_BUILD_ROOT 
%{_prefix}/include/*



%changelog

* Wed Aug 15 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.1-1

- Compatibility update gcc8

* Fri Mar 03 2018 Julien Dutheil <julien.dutheil@univ-montp2.fr> 2.4.0-1

- Increased interface number

- Removed dynamic exceptions declarations.

src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp

+4 −2
Original line number Diff line number Diff line
@@ -60,6 +60,8 @@ MafBlock* AlignmentFilterMafIterator::analyseCurrentBlock_() 
      int unk = AlphabetTools::DNA_ALPHABET.getUnknownCharacterCode();

      size_t nr;

      size_t nc = static_cast<size_t>(block->getNumberOfSites());

      if (nc < windowSize_)

        throw Exception("AlignmentFilterMafIterator::analyseCurrentBlock_. Block is smaller than window size: " + TextTools::toString(nc));



      vector< vector<int> > aln;

      if (missingAsGap_) {
@@ -94,8 +96,6 @@ MafBlock* AlignmentFilterMafIterator::analyseCurrentBlock_() 
      window_.clear();

      //Init window:

      size_t i;

      if (nc < windowSize_)

        throw Exception("AlignmentFilterMafIterator::analyseCurrentBlock_. Block is smaller than window size: " + TextTools::toString(nc));

      for (i = 0; i < windowSize_; ++i) {

        for (size_t j = 0; j < nr; ++j) {

          col[j] = aln[j][i];
@@ -284,6 +284,8 @@ MafBlock* AlignmentFilter2MafIterator::analyseCurrentBlock_() 
      int unk = AlphabetTools::DNA_ALPHABET.getUnknownCharacterCode();

      size_t nr;

      size_t nc = static_cast<size_t>(block->getNumberOfSites());

      if (nc < windowSize_)

        throw Exception("AlignmentFilter2MafIterator::analyseCurrentBlock_. Block is smaller than window size: " + TextTools::toString(nc));



      vector< vector<int> > aln;

      if (missingAsGap_) {

src/Bpp/Seq/Io/Maf/MafSequence.cpp

+1 −1
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@@ -50,7 +50,7 @@ MafSequence* MafSequence::subSequence(size_t startAt, size_t length) const 
  string subseq = toString().substr(startAt, length);

  size_t begin = begin_;

  if (hasCoordinates_) {

    for (unsigned int i = 0; i < startAt; ++i) {

    for (size_t i = 0; i < startAt; ++i) {

      if (! getAlphabet()->isGap(operator[](i))) begin++;

    }

  }