[med-svn] [Git][med-team/libbpp-seq-omics][master] 3 commits: New upstream version 2.4.1
Julien Y. Dutheil
gitlab at salsa.debian.org
Wed Aug 22 08:03:14 BST 2018
Julien Y. Dutheil pushed to branch master at Debian Med / libbpp-seq-omics
Commits:
f12fcff8 by Julien Y. Dutheil at 2018-08-20T04:40:31Z
New upstream version 2.4.1
- - - - -
50b2d0b4 by Julien Y. Dutheil at 2018-08-20T04:40:32Z
Update upstream source from tag 'upstream/2.4.1'
Update to upstream version '2.4.1'
with Debian dir 61002ea6222bca9396a92fa710e29906f54e11a1
- - - - -
1950286d by Julien Y. Dutheil at 2018-08-20T07:04:55Z
New version 2.4.1.
Ref: #897785
- - - - -
10 changed files:
- CMakeLists.txt
- Doxyfile
- bpp-seq-omics.spec
- debian/changelog
- debian/control
- debian/libbpp-seq-omics3.symbols
- src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp
- src/Bpp/Seq/Io/Maf/MafSequence.cpp
- src/Bpp/Seq/Io/Maf/MafSequence.h
- src/Bpp/Seq/Io/Maf/MafStatistics.cpp
Changes:
=====================================
CMakeLists.txt
=====================================
--- a/CMakeLists.txt
+++ b/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
=====================================
--- a/Doxyfile
+++ b/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
=====================================
--- a/bpp-seq-omics.spec
+++ b/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 at univ-montp2.fr> 2.4.1-1
+- Compatibility update gcc8
* Fri Mar 03 2018 Julien Dutheil <julien.dutheil at univ-montp2.fr> 2.4.0-1
- Increased interface number
- Removed dynamic exceptions declarations.
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,10 @@
+libbpp-seq-omics (2.4.1-1) UNRELEASED; urgency=medium
+
+ * New upstream version.
+ * Addresses: #897785
+
+ -- Julien Dutheil <julien.dutheil at 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
=====================================
--- a/debian/control
+++ b/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.
=====================================
debian/libbpp-seq-omics3.symbols
=====================================
The diff for this file was not included because it is too large.
=====================================
src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp
=====================================
--- a/src/Bpp/Seq/Io/Maf/AlignmentFilterMafIterator.cpp
+++ b/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
=====================================
--- a/src/Bpp/Seq/Io/Maf/MafSequence.cpp
+++ b/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/MafSequence.h
=====================================
--- a/src/Bpp/Seq/Io/Maf/MafSequence.h
+++ b/src/Bpp/Seq/Io/Maf/MafSequence.h
@@ -64,12 +64,12 @@ class MafSequence:
{
private:
bool hasCoordinates_;
- size_t begin_;
+ size_t begin_;
std::string species_;
std::string chromosome_;
char strand_;
- size_t size_;
- size_t srcSize_;
+ size_t size_;
+ size_t srcSize_;
public:
MafSequence(const Alphabet* alphabet = &AlphabetTools::DNA_ALPHABET):
=====================================
src/Bpp/Seq/Io/Maf/MafStatistics.cpp
=====================================
--- a/src/Bpp/Seq/Io/Maf/MafStatistics.cpp
+++ b/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);
}
}
View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq-omics/compare/e477e5f3e48e8bf7abe7dd5c94970f5310883249...1950286d637ac8428abd0d6a220d07869724ac13
--
View it on GitLab: https://salsa.debian.org/med-team/libbpp-seq-omics/compare/e477e5f3e48e8bf7abe7dd5c94970f5310883249...1950286d637ac8428abd0d6a220d07869724ac13
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