Silent mode

include/KMC_wrapper.hh

@@ -5,4 +5,4 @@
 using namespace std;
 
 // Only works for alphabet {a,c,g,t,A,C,G,T}
-void KMC_wrapper(int64_t k, int64_t ram_gigas, int64_t n_threads, string fastafile, string tempdir, string database_filename_prefix, bool only_canonical_kmers);
+void KMC_wrapper(int64_t k, int64_t ram_gigas, int64_t n_threads, string fastafile, string tempdir, string database_filename_prefix, bool only_canonical_kmers, bool silent);

include/Themisto.hh

@@ -237,7 +237,7 @@ public:
 
         write_log("Building KMC database", LogLevel::MAJOR);
         string KMC_db_path_prefix = get_temp_file_manager().create_filename("KMC-");
-        KMC_wrapper(k+1, max(1LL, memory_bytes / (1LL << 30)), n_threads, fastafile, get_temp_file_manager().get_dir(), KMC_db_path_prefix, revcomps);
+        KMC_wrapper(k+1, max(1LL, memory_bytes / (1LL << 30)), n_threads, fastafile, get_temp_file_manager().get_dir(), KMC_db_path_prefix, revcomps, get_log_level() == LogLevel::OFF);
         write_log("Building KMC database finished", LogLevel::MAJOR);
         Kmer_stream_from_KMC_DB edgemer_stream(KMC_db_path_prefix, revcomps);
         BOSS_builder<BOSS<sdsl::bit_vector>, Kmer_stream_from_KMC_DB> builder;

include/globals.hh

@@ -41,6 +41,7 @@ long long cur_time_millis();
 double seconds_since_program_start();
 string getTimeString();
 void set_log_level(LogLevel level);
+LogLevel get_log_level();
 void write_log(string message, LogLevel level);
 map<string,vector<string> > parse_args(int argc, char** argv);
 string figure_out_file_format(string filename);

include/libwheeler/BOSS_tests.hh

@@ -154,7 +154,7 @@ void test_construction(BOSS_TestCase& tcase, bool reverse_complements){
     for(string S : tcase.reads) out << ">\n" << S << "\n";
     out.flush();
     string KMC_db_path_prefix = get_temp_file_manager().create_filename("KMC");
-    KMC_wrapper(tcase.k+1, 1, 2, fastafile, get_temp_file_manager().get_dir(), KMC_db_path_prefix, reverse_complements);
+    KMC_wrapper(tcase.k+1, 1, 2, fastafile, get_temp_file_manager().get_dir(), KMC_db_path_prefix, reverse_complements, get_log_level() == LogLevel::OFF);
     Kmer_stream_from_KMC_DB kmer_stream(KMC_db_path_prefix, reverse_complements);
     BOSS_builder<boss_t, Kmer_stream_from_KMC_DB> bb;
     boss_t boss_KMC = bb.build(kmer_stream, 1e9, 2);

src/KMC_wrapper.cpp

@@ -479,12 +479,12 @@ void call_kmc(int argc, _TCHAR* argv[])
 }
 
 // Only works for alphabet {a,c,g,t,A,C,G,T}
-void KMC_wrapper(int64_t k, int64_t ram_gigas, int64_t n_threads, string fastafile, string tempdir, string database_filename_prefix, bool only_canonical_kmers){
+void KMC_wrapper(int64_t k, int64_t ram_gigas, int64_t n_threads, string fastafile, string tempdir, string database_filename_prefix, bool only_canonical_kmers, bool silent){
 
 	// Check that the alphabet is {a,c,g,t,A,C,G,T} (otherwise k-mers would be dropped silently)
 	throwing_ifstream fasta_input(fastafile);
 	string line;
-	cerr << "Validating input alphabet" << endl;
+	if(!silent) cerr << "Validating input alphabet" << endl;
 	while(getline(fasta_input.stream, line)){
 		if(line.size() > 0 && line[0] != '>'){
 			for(char c : line){
@@ -511,13 +511,22 @@ void KMC_wrapper(int64_t k, int64_t ram_gigas, int64_t n_threads, string fastafi
 	if(!only_canonical_kmers){
 		argv.insert(argv.begin()+1, "-b");
 	}
+	if(silent){
+		std::stringstream buffer; // Redirect stderr here
+		std::streambuf* old = std::cerr.rdbuf(buffer.rdbuf());
 
-	cerr << "Calling KMC with: ";
-	for(string S : argv) cerr << S << " ";
-	cerr << endl;
-
-	Argv A(argv);
-    call_kmc(argv.size(), A.array);
+		Argv A(argv);
+		call_kmc(argv.size(), A.array);
+
+		std::cerr.rdbuf(old); // Restore cerr
+	}
 
+	else{ // Not silent
+		cerr << "Calling KMC with: ";
+		for(string S : argv) cerr << S << " ";
+		cerr << endl;
+		Argv A(argv);
+		call_kmc(argv.size(), A.array);
+	}
 }
 

src/globals.cpp

@@ -26,6 +26,9 @@ static LogLevel loglevel = MAJOR;
 void set_log_level(LogLevel level){
     loglevel = level;
 }
+LogLevel get_log_level(){
+    return loglevel;
+}
 
 static std::mutex write_log_mutex;
 void write_log(string message, LogLevel level){