[med-svn] [Git][med-team/gatb-core][master] Addressing new upstream version of minia.
Steffen Möller
gitlab at salsa.debian.org
Tue Feb 16 18:32:25 GMT 2021
Steffen Möller pushed to branch master at Debian Med / gatb-core
Commits:
7ec79d95 by Steffen Moeller at 2021-02-16T19:31:57+01:00
Addressing new upstream version of minia.
- - - - -
3 changed files:
- debian/changelog
- + debian/patches/gatbCoreCompileMinia.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+gatb-core (1.4.2+dfsg-7) UNRELEASED; urgency=medium
+
+ * Team upload.
+
+ * Applied patch from July 2020 (past 1.4.2 release) to allow compilation
+ of minia - just exposing a few variables in the template class.
+
+ Request to tag a new release on https://github.com/GATB/gatb-core/issues/38
+
+ -- Steffen Moeller <moeller at debian.org> Tue, 16 Feb 2021 17:34:51 +0100
+
gatb-core (1.4.2+dfsg-6) unstable; urgency=medium
* Use int as return of fgetc
=====================================
debian/patches/gatbCoreCompileMinia.patch
=====================================
@@ -0,0 +1,162 @@
+Author: rchikhi <rayan.chikhi at univ-lille1.fr>
+Date: Sun Jun 7 23:17:58 2020 +0200
+Description: Upstream commit 7cb8a48cc958f4266c74db57f02e937d583ba9b7
+
+diff --git a/gatb-core/src/gatb/debruijn/impl/Graph.cpp b/gatb-core/src/gatb/debruijn/impl/Graph.cpp
+index fc19c251..a621658f 100644
+--- a/gatb-core/src/gatb/debruijn/impl/Graph.cpp
++++ b/gatb-core/src/gatb/debruijn/impl/Graph.cpp
+@@ -417,8 +417,12 @@ void build_visitor_solid<Node,Edge,GraphDataVariant>::operator() (GraphData<span
+ DEBUG ((cout << "build_visitor : SortingCountAlgorithm END\n"));
+
+ /** We save the state and kmer size at storage root level. */
+- graph.getGroup().setProperty ("state", Stringify::format("%d", graph._state));
+- graph.getGroup().setProperty ("kmer_size", Stringify::format("%d", graph._kmerSize));
++ graph.getGroup().setProperty ("state", Stringify::format("%d", graph._state));
++ graph.getGroup().setProperty ("kmer_size", Stringify::format("%d", graph._kmerSize));
++ graph.getGroup().setProperty ("nb_solid_kmers", Stringify::format("%d", solidCounts->getNbItems()));
++
++ // also set _nbSolidKmers here, as for example, _kmerSize was set at startup since we knew it already
++ graph._nbSolidKmers = solidCounts->getNbItems();
+ }
+
+
+@@ -605,6 +609,10 @@ void build_visitor_postsolid<Node,Edge,GraphDataVariant>::operator() (GraphData<
+ /** We save the state and kmer size at storage root level. */
+ graph.getGroup().setProperty ("state", Stringify::format("%d", graph._state));
+ graph.getGroup().setProperty ("kmer_size", Stringify::format("%d", graph._kmerSize));
++ graph.getGroup().setProperty ("nb_solid_kmers", Stringify::format("%d", solidCounts->getNbItems()));
++
++ // also set _nbSolidKmers here, as for example, _kmerSize was set at startup since we knew it already
++ graph._nbSolidKmers = solidCounts->getNbItems();
+
+ /************************************************************/
+ /* Clean up */
+@@ -778,7 +786,8 @@ GraphTemplate<Node, Edge, GraphDataVariant_t>::GraphTemplate (const std::string&
+
+ /** We get some properties. */
+ _state = (GraphTemplate<Node, Edge, GraphDataVariant_t>::StateMask) atol (getGroup().getProperty ("state").c_str());
+- _kmerSize = atol (getGroup().getProperty ("kmer_size").c_str());
++ _kmerSize = atol (getGroup().getProperty ("kmer_size").c_str());
++ _nbSolidKmers= atol (getGroup().getProperty ("nb_solid_kmers").c_str());
+
+ /** We get library information in the root of the storage. */
+ string xmlString = getGroup().getProperty ("xml");
+@@ -940,8 +949,8 @@ GraphTemplate<Node, Edge, GraphDataVariant>::GraphTemplate ()
+ *********************************************************************/
+ template<typename Node, typename Edge, typename GraphDataVariant>
+ GraphTemplate<Node, Edge, GraphDataVariant>::GraphTemplate (const GraphTemplate<Node, Edge, GraphDataVariant>& graph)
+- : _storageMode(graph._storageMode), _storage(0),
+- _variant(new GraphDataVariant()), _kmerSize(graph._kmerSize), _info("graph"), _name(graph._name), _state(graph._state)
++ : _storageMode(graph._storageMode), _storage(0),
++ _variant(new GraphDataVariant()), _kmerSize(graph._kmerSize), _nbSolidKmers(graph._nbSolidKmers), _info("graph"), _name(graph._name), _state(graph._state)
+ {
+ setStorage (graph._storage);
+
+@@ -962,6 +971,7 @@ GraphTemplate<Node, Edge, GraphDataVariant>& GraphTemplate<Node, Edge, GraphData
+ if (this != &graph)
+ {
+ _kmerSize = graph._kmerSize;
++ _nbSolidKmers = graph._nbSolidKmers;
+ _storageMode = graph._storageMode;
+ _name = graph._name;
+ _info = graph._info;
+diff --git a/gatb-core/src/gatb/debruijn/impl/Graph.hpp b/gatb-core/src/gatb/debruijn/impl/Graph.hpp
+index 9728e911..a5b9aed2 100644
+--- a/gatb-core/src/gatb/debruijn/impl/Graph.hpp
++++ b/gatb-core/src/gatb/debruijn/impl/Graph.hpp
+@@ -1044,6 +1044,9 @@ public: // was private: before, but had many compilation errors during the chang
+
+ /** kmer size of the graph */
+ size_t _kmerSize;
++
++ /** nb solid kmers in the graph (only populated by GraphUnitigs */
++ size_t _nbSolidKmers;
+
+ /** Creation information. */
+ tools::misc::impl::Properties _info;
+diff --git a/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp b/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp
+index 74c16cc9..9eb1e631 100644
+--- a/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp
++++ b/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp
+@@ -970,6 +970,7 @@ GraphUnitigsTemplate<span>& GraphUnitigsTemplate<span>::operator= (GraphUnitigsT
+ if (this != &graph)
+ {
+ BaseGraph::_kmerSize = graph._kmerSize;
++ BaseGraph::_nbSolidKmers = graph._nbSolidKmers;
+ BaseGraph::_storageMode = graph._storageMode;
+ BaseGraph::_name = graph._name;
+ BaseGraph::_info = graph._info;
+@@ -1020,6 +1021,7 @@ GraphUnitigsTemplate<span>& GraphUnitigsTemplate<span>::operator= (GraphUnitigsT
+ if (this != &graph)
+ {
+ BaseGraph::_kmerSize = graph._kmerSize;
++ BaseGraph::_nbSolidKmers = graph._nbSolidKmers;
+ BaseGraph::_storageMode = graph._storageMode;
+ BaseGraph::_name = graph._name;
+ BaseGraph::_info = graph._info;
+diff --git a/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp b/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp
+index f327ce60..dc385b71 100644
+--- a/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp
++++ b/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp
+@@ -252,7 +252,7 @@ public:
+ /**********************************************************************/
+
+ /* perform tip removal, bulge removal and EC removal, as in Minia */
+- void simplify(unsigned int nbCores = 1, bool verbose=true);
++ void simplify(unsigned int nbCores = 1, bool verbose=false);
+
+ /**********************************************************************/
+ /* SIMPLE PATH METHODS */
+diff --git a/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp b/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp
+index d75ed56a..4bd0e8c1 100644
+--- a/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp
++++ b/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp
+@@ -406,13 +406,13 @@ unsigned long Simplifications<GraphType,Node,Edge>::removeTips()
+ ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem> *itNode;
+ if (_firstNodeIteration )
+ {
+- itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iterator(), buffer, _verbose);
++ itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iterator(), buffer, /*_verbose*/true);
+ if (_verbose)
+ std::cout << "iterating on " << itNode->size() << " nodes on disk" << std::endl;
+ }
+ else
+ {
+- itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iteratorCachedNodes(), buffer, _verbose);
++ itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iteratorCachedNodes(), buffer, /*_verbose*/true);
+ if (_verbose)
+ std::cout << "iterating on " << itNode->size() << " cached nodes" << std::endl;
+ }
+@@ -1307,13 +1307,13 @@ unsigned long Simplifications<GraphType,Node,Edge>::removeBulges()
+ ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem> *itNode;
+ if (_firstNodeIteration )
+ {
+- itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iterator(), buffer, _verbose);
++ itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iterator(), buffer, /*_verbose*/true);
+ if (_verbose)
+ std::cout << "iterating on " << itNode->size() << " nodes" << std::endl;
+ }
+ else
+ {
+- itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iteratorCachedNodes(), buffer, _verbose);
++ itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iteratorCachedNodes(), buffer, /*_verbose*/true); // always display
+ if (_verbose)
+ std::cout << "iterating on " << itNode->size() << " cached nodes" << std::endl;
+ }
+@@ -1630,13 +1630,13 @@ unsigned long Simplifications<GraphType,Node,Edge>::removeErroneousConnections()
+ ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem> *itNode;
+ if (_firstNodeIteration )
+ {
+- itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iterator(), buffer, _verbose);
++ itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iterator(), buffer, /*_verbose*/true);
+ if (_verbose)
+ std::cout << "iterating on " << itNode->size() << " nodes on disk" << std::endl;
+ }
+ else
+ {
+- itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iteratorCachedNodes(), buffer, _verbose);
++ itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iteratorCachedNodes(), buffer, /*_verbose*/true);
+ if (_verbose)
+ std::cout << "iterating on " << itNode->size() << " cached nodes" << std::endl;
+ }
=====================================
debian/patches/series
=====================================
@@ -8,3 +8,4 @@ multiarch.patch
spelling.patch
avoid_-msse
use-int-as-return-of-fgetc.patch
+gatbCoreCompileMinia.patch
View it on GitLab: https://salsa.debian.org/med-team/gatb-core/-/commit/7ec79d95a447fb01d785b73d69b4a785519c8aeb
--
View it on GitLab: https://salsa.debian.org/med-team/gatb-core/-/commit/7ec79d95a447fb01d785b73d69b4a785519c8aeb
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