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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/gatb-core">Debian Med / gatb-core</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/gatb-core/-/commit/7ec79d95a447fb01d785b73d69b4a785519c8aeb">7ec79d95</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2021-02-16T19:31:57+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Addressing new upstream version of minia.
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<h4>3 changed files:</h4>
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#95c7b677e60adebfb850f5e0f348e1dd4e6d52a9">
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+
debian/patches/gatbCoreCompileMinia.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/gatb-core/-/commit/7ec79d95a447fb01d785b73d69b4a785519c8aeb#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">gatb-core (1.4.2+dfsg-7) UNRELEASED; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> * Applied patch from July 2020 (past 1.4.2 release) to allow compilation</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> of minia - just exposing a few variables in the template class.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> Request to tag a new release on https://github.com/GATB/gatb-core/issues/38</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Tue, 16 Feb 2021 17:34:51 +0100</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">gatb-core (1.4.2+dfsg-6) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> * Use int as return of fgetc</span>
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<li id="95c7b677e60adebfb850f5e0f348e1dd4e6d52a9">
<a href="https://salsa.debian.org/med-team/gatb-core/-/commit/7ec79d95a447fb01d785b73d69b4a785519c8aeb#95c7b677e60adebfb850f5e0f348e1dd4e6d52a9"><strong>debian/patches/gatbCoreCompileMinia.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: rchikhi <rayan.chikhi@univ-lille1.fr></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Date: Sun Jun 7 23:17:58 2020 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Upstream commit 7cb8a48cc958f4266c74db57f02e937d583ba9b7</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">diff --git a/gatb-core/src/gatb/debruijn/impl/Graph.cpp b/gatb-core/src/gatb/debruijn/impl/Graph.cpp</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">index fc19c251..a621658f 100644</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/gatb-core/src/gatb/debruijn/impl/Graph.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/gatb-core/src/gatb/debruijn/impl/Graph.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -417,8 +417,12 @@</span> void build_visitor_solid<Node,Edge,GraphDataVariant>::operator() (GraphData<span</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> DEBUG ((cout << "build_visitor : SortingCountAlgorithm END\n"));</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> /** We save the state and kmer size at storage root level. */</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- graph.getGroup().setProperty ("state", Stringify::format("%d", graph._state));</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- graph.getGroup().setProperty ("kmer_size", Stringify::format("%d", graph._kmerSize));</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ graph.getGroup().setProperty ("state", Stringify::format("%d", graph._state));</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ graph.getGroup().setProperty ("kmer_size", Stringify::format("%d", graph._kmerSize));</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ graph.getGroup().setProperty ("nb_solid_kmers", Stringify::format("%d", solidCounts->getNbItems()));</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // also set _nbSolidKmers here, as for example, _kmerSize was set at startup since we knew it already</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ graph._nbSolidKmers = solidCounts->getNbItems();</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="p">@@ -605,6 +609,10 @@</span> void build_visitor_postsolid<Node,Edge,GraphDataVariant>::operator() (GraphData<</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> /** We save the state and kmer size at storage root level. */</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> graph.getGroup().setProperty ("state", Stringify::format("%d", graph._state));</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> graph.getGroup().setProperty ("kmer_size", Stringify::format("%d", graph._kmerSize));</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ graph.getGroup().setProperty ("nb_solid_kmers", Stringify::format("%d", solidCounts->getNbItems()));</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // also set _nbSolidKmers here, as for example, _kmerSize was set at startup since we knew it already</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ graph._nbSolidKmers = solidCounts->getNbItems();</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> /************************************************************/</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> /* Clean up */</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="p">@@ -778,7 +786,8 @@</span> GraphTemplate<Node, Edge, GraphDataVariant_t>::GraphTemplate (const std::string&</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> /** We get some properties. */</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> _state = (GraphTemplate<Node, Edge, GraphDataVariant_t>::StateMask) atol (getGroup().getProperty ("state").c_str());</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- _kmerSize = atol (getGroup().getProperty ("kmer_size").c_str());</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ _kmerSize = atol (getGroup().getProperty ("kmer_size").c_str());</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ _nbSolidKmers= atol (getGroup().getProperty ("nb_solid_kmers").c_str());</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> /** We get library information in the root of the storage. */</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> string xmlString = getGroup().getProperty ("xml");</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="p">@@ -940,8 +949,8 @@</span> GraphTemplate<Node, Edge, GraphDataVariant>::GraphTemplate ()</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> *********************************************************************/</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> template<typename Node, typename Edge, typename GraphDataVariant></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> GraphTemplate<Node, Edge, GraphDataVariant>::GraphTemplate (const GraphTemplate<Node, Edge, GraphDataVariant>& graph)</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- : _storageMode(graph._storageMode), _storage(0),</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- _variant(new GraphDataVariant()), _kmerSize(graph._kmerSize), _info("graph"), _name(graph._name), _state(graph._state)</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ : _storageMode(graph._storageMode), _storage(0), </span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ _variant(new GraphDataVariant()), _kmerSize(graph._kmerSize), _nbSolidKmers(graph._nbSolidKmers), _info("graph"), _name(graph._name), _state(graph._state)</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> setStorage (graph._storage);</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="p">@@ -962,6 +971,7 @@</span> GraphTemplate<Node, Edge, GraphDataVariant>& GraphTemplate<Node, Edge, GraphData</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> if (this != &graph)</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> _kmerSize = graph._kmerSize;</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ _nbSolidKmers = graph._nbSolidKmers;</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> _storageMode = graph._storageMode;</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> _name = graph._name;</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> _info = graph._info;</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/gatb-core/src/gatb/debruijn/impl/Graph.hpp b/gatb-core/src/gatb/debruijn/impl/Graph.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gh" style="color: #999;">index 9728e911..a5b9aed2 100644</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/gatb-core/src/gatb/debruijn/impl/Graph.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/gatb-core/src/gatb/debruijn/impl/Graph.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="p">@@ -1044,6 +1044,9 @@</span> public: // was private: before, but had many compilation errors during the chang</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> /** kmer size of the graph */</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> size_t _kmerSize;</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ /** nb solid kmers in the graph (only populated by GraphUnitigs */</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ size_t _nbSolidKmers;</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> /** Creation information. */</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> tools::misc::impl::Properties _info;</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp b/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gh" style="color: #999;">index 74c16cc9..9eb1e631 100644</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="p">@@ -970,6 +970,7 @@</span> GraphUnitigsTemplate<span>& GraphUnitigsTemplate<span>::operator= (GraphUnitigsT</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> if (this != &graph)</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> BaseGraph::_kmerSize = graph._kmerSize;</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ BaseGraph::_nbSolidKmers = graph._nbSolidKmers;</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> BaseGraph::_storageMode = graph._storageMode;</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> BaseGraph::_name = graph._name;</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> BaseGraph::_info = graph._info;</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="p">@@ -1020,6 +1021,7 @@</span> GraphUnitigsTemplate<span>& GraphUnitigsTemplate<span>::operator= (GraphUnitigsT</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> if (this != &graph)</span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> BaseGraph::_kmerSize = graph._kmerSize;</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ BaseGraph::_nbSolidKmers = graph._nbSolidKmers;</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> BaseGraph::_storageMode = graph._storageMode;</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> BaseGraph::_name = graph._name;</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> BaseGraph::_info = graph._info;</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp b/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gh" style="color: #999;">index f327ce60..dc385b71 100644</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/gatb-core/src/gatb/debruijn/impl/GraphUnitigs.hpp</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="p">@@ -252,7 +252,7 @@</span> public:</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> /**********************************************************************/</span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> /* perform tip removal, bulge removal and EC removal, as in Minia */</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- void simplify(unsigned int nbCores = 1, bool verbose=true);</span></span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ void simplify(unsigned int nbCores = 1, bool verbose=false);</span></span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> /**********************************************************************/</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> /* SIMPLE PATH METHODS */</span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gh" style="color: #999;">diff --git a/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp b/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gh" style="color: #999;">index d75ed56a..4bd0e8c1 100644</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="p">@@ -406,13 +406,13 @@</span> unsigned long Simplifications<GraphType,Node,Edge>::removeTips()</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem> *itNode; </span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> if (_firstNodeIteration )</span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iterator(), buffer, _verbose);</span></span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iterator(), buffer, /*_verbose*/true);</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> if (_verbose)</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> std::cout << "iterating on " << itNode->size() << " nodes on disk" << std::endl;</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> else</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> {</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iteratorCachedNodes(), buffer, _verbose);</span></span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iteratorCachedNodes(), buffer, /*_verbose*/true);</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> if (_verbose)</span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> std::cout << "iterating on " << itNode->size() << " cached nodes" << std::endl;</span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="p">@@ -1307,13 +1307,13 @@</span> unsigned long Simplifications<GraphType,Node,Edge>::removeBulges()</span>
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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem> *itNode; </span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> if (_firstNodeIteration )</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> {</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iterator(), buffer, _verbose);</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iterator(), buffer, /*_verbose*/true);</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> if (_verbose)</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> std::cout << "iterating on " << itNode->size() << " nodes" << std::endl;</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> }</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> else</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> {</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iteratorCachedNodes(), buffer, _verbose);</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iteratorCachedNodes(), buffer, /*_verbose*/true); // always display</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> if (_verbose)</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> std::cout << "iterating on " << itNode->size() << " cached nodes" << std::endl;</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> }</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="p">@@ -1630,13 +1630,13 @@</span> unsigned long Simplifications<GraphType,Node,Edge>::removeErroneousConnections()</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem> *itNode; </span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> if (_firstNodeIteration )</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> {</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iterator(), buffer, _verbose);</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iterator(), buffer, /*_verbose*/true);</span></span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> if (_verbose)</span>
</pre>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> std::cout << "iterating on " << itNode->size() << " nodes on disk" << std::endl;</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> }</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> else</span>
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<td class="diff-line-num new new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> {</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iteratorCachedNodes(), buffer, _verbose);</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ itNode = new ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem>(_graph.GraphType::iteratorCachedNodes(), buffer, /*_verbose*/true);</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> if (_verbose)</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> std::cout << "iterating on " << itNode->size() << " cached nodes" << std::endl;</span>
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<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> }</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/gatb-core/-/commit/7ec79d95a447fb01d785b73d69b4a785519c8aeb#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,3 +8,4 @@ multiarch.patch</td>
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8
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">spelling.patch</span>
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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
9
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">avoid_-msse</span>
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10
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">use-int-as-return-of-fgetc.patch</span>
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<td class="diff-line-num new old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">gatbCoreCompileMinia.patch</span></pre>
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