update gatb-core for verbosity fixes

GATB · Dec 10, 2024 · 15c3a01 · 15c3a01
1 parent 88c8430
commit 15c3a01
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Showing 2 changed files with 8 additions and 4 deletions.
diff --git a/src/Minia.cpp b/src/Minia.cpp
@@ -153,8 +153,10 @@ struct MiniaFunctor  {  void operator ()  (Parameter parameter)
 
     // link contigs
     uint nb_threads = 1;  // doesn't matter because for now link_tigs is single-threaded
-    bool verbose = true;
-    link_tigs<span>(output, minia.k, nb_threads, minia.nbContigs, verbose, false);
+    int verbose = 1;
+    if (minia.getInput()->get(STR_VERBOSE))
+        verbose = minia.getInput()->getInt(STR_VERBOSE);
+    link_tigs<span>(output, minia.k, nb_threads, minia.nbContigs, verbose > 0, false);
 
     /** We gather some statistics. */
     minia.getInfo()->add (1, minia.getTimeInfo().getProperties("time"));
@@ -246,7 +248,9 @@ string Minia::assemble (/*const, removed because Simplifications isn't const any
     /** We get an iterator over all nodes . */
     ProgressGraphIteratorTemplate<Node,ProgressTimerAndSystem> itNode (graph.Graph_type::iterator(), progressFormat0);
 
-    bool verbose = getParser()->saw("-verbose");
+    int verbose = 1;
+    if (getInput()->get(STR_VERBOSE))
+        verbose = getInput()->getInt(STR_VERBOSE);
 
     // if we want unitigs, then don't simplify the graph; else do it
     if (simplifyGraph)

diff --git a/thirdparty/gatb-core b/thirdparty/gatb-core
+0 −1		gatb-core/src/gatb/bcalm2/logging.cpp
+52 −36		gatb-core/src/gatb/debruijn/impl/Simplifications.cpp
+2 −2		gatb-core/src/gatb/debruijn/impl/Simplifications.hpp
+2 −2		gatb-core/src/gatb/debruijn/impl/UnitigsConstructionAlgorithm.cpp