diff --git a/src/Minia.cpp b/src/Minia.cpp index 97db68f..3bbed2f 100644 --- 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(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(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 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 index 4e99a76..9957029 160000 --- a/thirdparty/gatb-core +++ b/thirdparty/gatb-core @@ -1 +1 @@ -Subproject commit 4e99a76fa3c7f6697651552791bb91fcf5b378b0 +Subproject commit 9957029ef7e5713a660e719a6bea38d0bf30752d