fix catching of exceptions by value

Author: notestaff

configure.ac

@@ -5,7 +5,7 @@
 #
 
 AC_PREREQ([2.68])
-AC_INIT([cosi], [2.3.1], [ilya_shl@alum.mit.edu])
+AC_INIT([cosi], [2.3.2rc5], [ilya_shl@alum.mit.edu])
 AC_CONFIG_AUX_DIR([build-aux])
 AC_CONFIG_MACRO_DIR([m4])
 AM_INIT_AUTOMAKE([1.9 tar-pax parallel-tests -Wall])

cosi/condsnp.h

@@ -68,7 +68,7 @@ class CondSnpDef {
 					 pop2cond.insert( make_pair( lexical_cast< popid >( condParts.front() ), util::ValRange<nchroms_t>( condParts.back() ) ) );
 				 }
 			 }
-		 } catch( std::exception& e ) {
+		 } catch( const std::exception& e ) {
 			 std::cerr << "error: " << e.what() << "\n";
 		 }
 

cosi/cositop.cc

@@ -66,7 +66,7 @@ CoSiMain::CoSiMain():
 void CoSiMain::printCompileOptions() {
 	using std::cerr;
 
-	cerr << "cosi coalescent simulator, version 2.3.1\n\n";
+	cerr << "cosi coalescent simulator, version 2.3.2rc5\n\n";
 	cerr << "Compile-time options:\n";
 
 	cerr << "   COSI_SUPPORT_COALAPX (support for approximating the coalescent): " <<

cosi/file.cc

@@ -342,11 +342,11 @@ ParamFileReader::file_get_data (FILE *fileptr, FILE *segfp)
 			}
 			try {
 				try { file_proc_buff(var, buffer, segfp); }
-				catch( const std::ios_base::failure& e ) {
+				catch( const std::ios_base::failure& ) {
 					BOOST_THROW_EXCEPTION( cosi_param_file_error()
 																 << boost::errinfo_errno( errno ) );
 				}
-				catch( std::exception const& e ) {
+				catch( const std::exception& e ) {
 
 					std::cerr << "genMap::readFrom - caught UNKNOWN exception of type " <<
 						 typeid( e ).name() << " demangled " << 

cosi/historical.cc

@@ -864,7 +864,7 @@ HistEvents::EventP HistEvents::parseEvent( const char *buffer ) {
 		else if (  typestr == Event_MSweep::typeStr_standing_variation() ) 
 			event.reset( new Event_MSweep( this, is, Event_MSweep::standing_variation_tag() ) );
 		else chkCond( False, "could not parse event %s", buffer );
-	} catch( ios::failure e ) {
+	} catch( const ios::failure& ) {
 		chkCond( False, "could not parse event %s", buffer );
 	}
 	return event;

cosi/sweep.cc

@@ -93,7 +93,7 @@ void Sweep::sweep_load_traj() {
 			genid gen;
 			freq_t freq;
 			try { f >> gen >> freq; }
-			catch( std::ios::failure fe ) { break; }
+			catch( const std::ios::failure&  ) { break; }
 			//PRINT2( gen, freq );
 			selAlleleFreqTraj.addPt( gen, freq );
 		}

cosi/traj.cc

@@ -25,7 +25,7 @@ TrajFromFile::TrajFromFile( filename_t fname, genid firstGen_, freq_t firstFreq_
 			freq_t a_freq;
 			trajStrm >> a_gen >> a_freq;
 			traj.insert( std::make_pair( a_gen, a_freq ) );
-		} catch( std::ifstream::failure e ) {
+		} catch( const std::ifstream::failure& ) {
 			break;
 		}
 	}