fix some CI build issues

Author: bhaller

core/haplosome.cpp

@@ -1298,7 +1298,7 @@ EidosValue_SP Haplosome::ExecuteMethod_sumOfMutationsOfType(EidosGlobalStringID
 }
 
 // print the sample represented by haplosomes, using SLiM's own format
-void Haplosome::PrintHaplosomes_SLiM(std::ostream &p_out, std::vector<Haplosome *> &p_haplosomes, const Chromosome &p_chromosome)
+void Haplosome::PrintHaplosomes_SLiM(std::ostream &p_out, std::vector<Haplosome *> &p_haplosomes)
 {
 	Mutation *mut_block_ptr = gSLiM_Mutation_Block;
 	slim_popsize_t sample_size = (slim_popsize_t)p_haplosomes.size();
@@ -3104,7 +3104,7 @@ EidosValue_SP Haplosome_Class::ExecuteMethod_outputX(EidosGlobalStringID p_metho
 
 		// Call out to print the actual sample
 		if (p_method_id == gID_output)
-			Haplosome::PrintHaplosomes_SLiM(output_stream, haplosomes, *chromosome);
+			Haplosome::PrintHaplosomes_SLiM(output_stream, haplosomes);
 		else if (p_method_id == gID_outputMS)
 			Haplosome::PrintHaplosomes_MS(output_stream, haplosomes, *chromosome, filter_monomorphic);
 		else if (p_method_id == gID_outputVCF)
@@ -3139,7 +3139,7 @@ EidosValue_SP Haplosome_Class::ExecuteMethod_outputX(EidosGlobalStringID p_metho
 
 					outfile << " " << outfile_path << std::endl;
 
-					Haplosome::PrintHaplosomes_SLiM(outfile, haplosomes, *chromosome);
+					Haplosome::PrintHaplosomes_SLiM(outfile, haplosomes);
 					break;
 				case gID_outputMS:
 					Haplosome::PrintHaplosomes_MS(outfile, haplosomes, *chromosome, filter_monomorphic);

core/haplosome.h

@@ -401,7 +401,7 @@ class Haplosome : public EidosObject
 	void record_derived_states(Species *p_species) const;
 
 	// print the sample represented by haplosomes, using SLiM's own format
-	static void PrintHaplosomes_SLiM(std::ostream &p_out, std::vector<Haplosome *> &p_haplosomes, const Chromosome &p_chromosome);
+	static void PrintHaplosomes_SLiM(std::ostream &p_out, std::vector<Haplosome *> &p_haplosomes);
 
 	// print the sample represented by haplosomes, using "ms" format
 	static void PrintHaplosomes_MS(std::ostream &p_out, std::vector<Haplosome *> &p_haplosomes, const Chromosome &p_chromosome, bool p_filter_monomorphic);

core/population.cpp

@@ -8395,7 +8395,7 @@ void Population::PrintSample_SLiM(std::ostream &p_out, Subpopulation &p_subpop,
 	}
 
 	// print the sample using Haplosome's static member function
-	Haplosome::PrintHaplosomes_SLiM(p_out, sample, p_chromosome);
+	Haplosome::PrintHaplosomes_SLiM(p_out, sample);
 }
 
 // print sample of p_sample_size haplosomes from subpopulation p_subpop_id, using "ms" format

core/species.cpp

@@ -1413,7 +1413,7 @@ slim_tick_t Species::_InitializePopulationFromTextFile(const char *p_file, Eidos
 			int haplosome_index = first_haplosome_index + is_individual_index_repeat;
 			Haplosome &haplosome = *(ind->haplosomes_[haplosome_index]);
 
-			if (haplosome.chromosome_index_ != chromosome->index_)
+			if (haplosome.chromosome_index_ != chromosome->Index())
 				EIDOS_TERMINATION << "ERROR (Species::_InitializePopulationFromTextFile): (internal error) haplosome does not belong to the focal chromosome." << EidosTerminate();
 
 			if (iss >> sub)