CMakeLists.txt

@@ -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

@@ -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

@@ -3,7 +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.

debian/changelog

+libbpp-seq-omics (2.4.1-1) UNRELEASED; urgency=medium
+
+  * New upstream version.
+  * Addresses: #897785 
+
+ -- Julien Dutheil <julien.dutheil@univ-montp2.fr>  Mon, 20 Aug 2018 08:48:12 +0200
+
 libbpp-seq-omics (2.4.0-2) unstable; urgency=medium
 
   [ Julien Dutheil ]

debian/control

@@ -7,7 +7,7 @@ Priority: optional
 Build-Depends: debhelper (>= 11~),
                cmake,
                d-shlibs (>= 0.82),
-               libbpp-seq-dev (>= 2.4.0)
+               libbpp-seq-dev (>= 2.4.1)
 Standards-Version: 4.1.3
 Vcs-Browser: https://salsa.debian.org/med-team/libbpp-seq-omics
 Vcs-Git: https://salsa.debian.org/med-team/libbpp-seq-omics.git
@@ -18,7 +18,7 @@ Architecture: any
 Section: libdevel
 Depends: libbpp-seq-omics3 (= ${binary:Version}),
          ${misc:Depends},
-         libbpp-seq-dev (>= 2.4.0)
+         libbpp-seq-dev (>= 2.4.1)
 Description: Bio++ Sequence library: genomics components (development files)
  Bio++ is a set of C++ libraries for Bioinformatics, including sequence
  analysis, phylogenetics, molecular evolution and population genetics.

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

@@ -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

@@ -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++;
     }
   }

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

@@ -509,7 +509,7 @@ void SequenceDiversityMafStatistics::compute(const MafBlock& block)
   double e1 = c1 / a1;
   double e2 = c2 / (a1 * a1 + a2);
   
-  //Compute pairwise heterozigocity:
+  //Compute pairwise heterozigosity:
   double pi = 0;
   for (size_t i = 0; i < n - 1; ++i) {
     for (size_t j = i + 1; j < n; ++j) {
@@ -517,7 +517,7 @@ void SequenceDiversityMafStatistics::compute(const MafBlock& block)
           alignment2->getSequence(i),
           alignment2->getSequence(j),
           true,
-          SiteContainerTools::SIMILARITY_ALL,
+          SiteContainerTools::SIMILARITY_NOGAP,
           false);
     }
   }