ngs_server 0.1 → 0.2

data/ext/vcftools/cpp/.svn/text-base/vcf_file_diff.cpp.svn-base

@@ -0,0 +1,1282 @@
+/*
+ * vcf_file_merge.cpp
+ *
+ *  Created on: Oct 30, 2009
+ *      Author: Adam Auton
+ *      ($Revision: 230 $)
+ */
+
+#include "vcf_file.h"
+
+void vcf_file::return_site_union(vcf_file &file2, map<pair<string, int>, pair<int, int> > &CHROMPOS_to_filepos_pair)
+{
+	unsigned int s;
+	int POS;
+	string CHROM;
+	string vcf_line;
+	for (s=0; s<N_entries; s++)
+	{
+		if (include_entry[s] == true)
+		{
+			get_vcf_entry(s, vcf_line);
+			vcf_entry e(N_indv, vcf_line);
+			e.parse_basic_entry();
+
+			CHROM = e.get_CHROM();
+			POS = e.get_POS();
+
+			CHROMPOS_to_filepos_pair[make_pair<string,int>(CHROM, POS)] = make_pair<int,int>(s, -1);
+		}
+	}
+	for (s=0; s<file2.N_entries; s++)
+	{
+		if (file2.include_entry[s] == true)
+		{
+			file2.get_vcf_entry(s, vcf_line);
+			vcf_entry e(file2.N_indv, vcf_line);
+			e.parse_basic_entry();
+
+			CHROM = e.get_CHROM();
+			POS = e.get_POS();
+
+			if (CHROMPOS_to_filepos_pair.find(make_pair<string,int>(CHROM, POS)) != CHROMPOS_to_filepos_pair.end())
+			{
+				CHROMPOS_to_filepos_pair[make_pair<string,int>(CHROM, POS)].second = s;
+			}
+			else
+			{
+				CHROMPOS_to_filepos_pair[make_pair<string,int>(CHROM, POS)] = make_pair<int,int>(-1, s);
+			}
+		}
+	}
+}
+
+
+void vcf_file::return_indv_union(vcf_file &file2, map<string, pair< int, int> > &combined_individuals)
+{
+	for (unsigned int ui=0; ui<N_indv; ui++)
+		if (include_indv[ui] == true)
+			combined_individuals[indv[ui]] = make_pair<int,int>(ui, -1);
+
+	for (unsigned int ui=0; ui<file2.N_indv; ui++)
+		if (file2.include_indv[ui] == true)
+		{
+			if (combined_individuals.find(file2.indv[ui]) != combined_individuals.end())
+				combined_individuals[file2.indv[ui]].second = ui;
+			else
+				combined_individuals[file2.indv[ui]] = make_pair<int,int>(-1, ui);
+		}
+}
+
+void vcf_file::output_sites_in_files(const string &output_file_prefix, vcf_file &diff_vcf_file)
+{
+	printLOG("Comparing sites in VCF files...\n");
+	map<pair<string, int>, pair<int, int> > CHROMPOS_to_filepos_pair;
+	map<pair<string, int>, pair<int, int> >::iterator CHROMPOS_to_filepos_pair_it;
+	return_site_union(diff_vcf_file, CHROMPOS_to_filepos_pair);
+
+	string vcf_line;
+	string CHROM;
+	int POS;
+
+	string output_file = output_file_prefix + ".diff.sites_in_files";
+	ofstream sites_in_files(output_file.c_str());
+	sites_in_files << "CHROM\tPOS\tIN_FILE\tREF\tALT1\tALT2" << endl;
+
+	int s1, s2;
+	int N_common_SNPs = 0, N_SNPs_file1_only=0, N_SNPs_file2_only=0;
+	for (CHROMPOS_to_filepos_pair_it=CHROMPOS_to_filepos_pair.begin(); CHROMPOS_to_filepos_pair_it!=CHROMPOS_to_filepos_pair.end(); ++CHROMPOS_to_filepos_pair_it)
+	{
+		s1 = CHROMPOS_to_filepos_pair_it->second.first;
+		s2 = CHROMPOS_to_filepos_pair_it->second.second;
+
+		CHROM = CHROMPOS_to_filepos_pair_it->first.first;
+		POS = CHROMPOS_to_filepos_pair_it->first.second;
+
+		vcf_entry e1(N_indv);
+		vcf_entry e2(diff_vcf_file.N_indv);
+
+		// Read entries from file (if available)
+		if (s1 != -1)
+		{
+			get_vcf_entry(s1, vcf_line);
+			e1.reset(vcf_line);
+		}
+
+		if (s2 != -1)
+		{
+			diff_vcf_file.get_vcf_entry(s2, vcf_line);
+			e2.reset(vcf_line);
+		}
+
+		e1.parse_basic_entry(true);
+		e2.parse_basic_entry(true);
+
+		// Set the reference to the non-missing entry (if available)
+		string REF = e1.get_REF();
+		string REF2 = e2.get_REF();
+		if ((REF == "N") || (REF == "."))
+			REF = REF2;
+		if ((REF2 == "N") || (REF2 == "."))
+			REF2 = REF;
+
+		if ((REF != REF2) && (REF2 != "N") && (REF != "N") && (REF != ".") && (REF2 != "."))
+			warning("Non-matching REF at " + CHROM + ":" + int2str(POS) + " " + REF + "/" + REF2 + ". Diff results may be unreliable.");
+
+		sites_in_files << CHROM << "\t" << POS << "\t";
+		if ((s1 != -1) && (s2 != -1))
+		{
+			N_common_SNPs++;
+			sites_in_files << "B";
+		}
+		else if ((s1 != -1) && (s2 == -1))
+		{
+			N_SNPs_file1_only++;
+			sites_in_files << "1";
+		}
+		else if ((s1 == -1) && (s2 != -1))
+		{
+			N_SNPs_file2_only++;
+			sites_in_files << "2";
+		}
+		else
+			error("SNP in neither file!?");
+
+		sites_in_files << "\t" << REF << "\t" << e1.get_ALT() << "\t" << e2.get_ALT() << endl;
+	}
+
+	sites_in_files.close();
+
+	printLOG("Found " + int2str(N_common_SNPs) + " SNPs common to both files.\n");
+	printLOG("Found " + int2str(N_SNPs_file1_only) + " SNPs only in main file.\n");
+	printLOG("Found " + int2str(N_SNPs_file2_only) + " SNPs only in second file.\n");
+}
+
+void vcf_file::output_indv_in_files(const string &output_file_prefix, vcf_file &diff_vcf_file)
+{
+	printLOG("Comparing individuals in VCF files...\n");
+
+	string output_file = output_file_prefix + ".diff.indv_in_files";
+
+	ofstream out(output_file.c_str());
+	if (!out.is_open())
+		error("Could not open Indv Differences File: " + output_file, 3);
+	out << "INDV\tFILES" << endl;
+
+	// Build a list of individuals contained in each file
+	map<string, pair< int, int> > combined_individuals;
+	map<string, pair< int, int> >::iterator combined_individuals_it;
+	return_indv_union(diff_vcf_file, combined_individuals);
+
+	unsigned int N_combined_indv = combined_individuals.size();
+	unsigned int N[3]={0,0,0};
+	for (combined_individuals_it=combined_individuals.begin(); combined_individuals_it!=combined_individuals.end(); ++combined_individuals_it)
+	{
+		if ((combined_individuals_it->second.first != -1) && (combined_individuals_it->second.second != -1))
+		{
+			N[0]++;
+			out << combined_individuals_it->first << "\tB" << endl;
+		}
+		else if (combined_individuals_it->second.first != -1)
+		{
+			N[1]++;
+			out << combined_individuals_it->first << "\t1" << endl;
+		}
+		else if (combined_individuals_it->second.second != -1)
+		{
+			N[2]++;
+			out << combined_individuals_it->first << "\t2" << endl;
+		}
+		else
+			error("Unhandled case");
+	}
+	out.close();
+
+	printLOG("N_combined_individuals:\t" + int2str(N_combined_indv) + "\n");
+	printLOG("N_individuals_common_to_both_files:\t" + int2str(N[0]) + "\n");
+	printLOG("N_individuals_unique_to_file1:\t" + int2str(N[1]) + "\n");
+	printLOG("N_individuals_unique_to_file2:\t" + int2str(N[2]) + "\n");
+}
+
+void vcf_file::output_discordance_by_indv(const string &output_file_prefix, vcf_file &diff_vcf_file)
+{
+	printLOG("Outputting Discordance By Individual...\n");
+	map<pair<string, int>, pair<int, int> > CHROMPOS_to_filepos_pair;
+	map<pair<string, int>, pair<int, int> >::iterator CHROMPOS_to_filepos_pair_it;
+	return_site_union(diff_vcf_file, CHROMPOS_to_filepos_pair);
+
+	map<string, pair< int, int> > combined_individuals;
+	map<string, pair< int, int> >::iterator combined_individuals_it;
+	return_indv_union(diff_vcf_file, combined_individuals);
+
+	map<string, pair<int, int> > indv_sums;
+
+	string vcf_line, CHROM;
+	int POS;
+	int s1, s2, indv1, indv2;
+
+	for (CHROMPOS_to_filepos_pair_it=CHROMPOS_to_filepos_pair.begin(); CHROMPOS_to_filepos_pair_it != CHROMPOS_to_filepos_pair.end(); ++CHROMPOS_to_filepos_pair_it)
+	{
+		CHROM = CHROMPOS_to_filepos_pair_it->first.first;
+		POS = CHROMPOS_to_filepos_pair_it->first.second;
+
+		s1 = CHROMPOS_to_filepos_pair_it->second.first;
+		s2 = CHROMPOS_to_filepos_pair_it->second.second;
+
+		vcf_entry e1(N_indv);
+		vcf_entry e2(diff_vcf_file.N_indv);
+
+		// Read entries from file (if available)
+		if (s1 != -1)
+		{
+			get_vcf_entry(s1, vcf_line);
+			e1.reset(vcf_line);
+		}
+
+		if (s2 != -1)
+		{
+			diff_vcf_file.get_vcf_entry(s2, vcf_line);
+			e2.reset(vcf_line);
+		}
+
+		e1.parse_basic_entry(true);
+		e2.parse_basic_entry(true);
+
+		// Set the reference to the non-missing entry (if available)
+		string REF = e1.get_REF();
+		string REF2 = e2.get_REF();
+		if (REF == "N")
+			REF = REF2;
+		if (REF2 == "N")
+			REF2 = REF;
+
+		if (REF.size() != REF2.size())
+		{
+			warning("REF sequences at " + CHROM + ":" + int2str(POS) + " are not comparable. Skipping site");
+			continue;
+		}
+
+		if ((REF != REF2) && (REF2 != "N") && (REF != "N"))
+			warning("Non-matching REF " + CHROM + ":" + int2str(POS) + " " + REF + "/" + REF2);
+
+		// Do the alternative alleles match?
+		string ALT, ALT2;
+		ALT = e1.get_ALT();
+		ALT2 = e2.get_ALT();
+
+		bool alleles_match = (ALT == ALT2) && (REF == REF2);
+		e1.parse_full_entry(true);
+		e1.parse_genotype_entries(true);
+
+		e2.parse_full_entry(true);
+		e2.parse_genotype_entries(true);
+
+		pair<string, string> genotype1, genotype2;
+		pair<int,int> geno_ids1, geno_ids2;
+		pair<string, string> missing_genotype(".",".");
+		pair<int, int> missing_id(-1,-1);
+
+		for (combined_individuals_it=combined_individuals.begin(); combined_individuals_it!=combined_individuals.end(); ++combined_individuals_it)
+		{
+			indv1 = combined_individuals_it->second.first;
+			indv2 = combined_individuals_it->second.second;
+
+			if ((indv1 == -1) || (indv2 == -1))
+				continue;	// Individual not found in one of the files
+
+			if (alleles_match)
+			{	// Alleles match, so can compare ids instead of strings
+				e1.get_indv_GENOTYPE_ids(indv1, geno_ids1);
+				e2.get_indv_GENOTYPE_ids(indv2, geno_ids2);
+
+				if ((geno_ids1 != missing_id) && (geno_ids2 != missing_id))
+				{
+					indv_sums[combined_individuals_it->first].first++;
+					if (((geno_ids1.first == geno_ids2.first) && (geno_ids1.second == geno_ids2.second)) ||
+						((geno_ids1.first == geno_ids2.second) && (geno_ids1.second == geno_ids2.first)) )
+					{	// Match
+						// Don't do anything
+					}
+					else
+					{	// Mismatch
+						indv_sums[combined_individuals_it->first].second++;
+					}
+				}
+				else if ((geno_ids1 == missing_id) && (geno_ids2 == missing_id))
+				{	// Both missing
+					// Don't do anything.
+				}
+				else if (geno_ids1 != missing_id)
+				{	// Genotype 1 is not missing, genotype 2 is.
+					// Don't do anything.
+				}
+				else if (geno_ids2 != missing_id)
+				{	// Genotype 2 is not missing, genotype 1 is.
+					// Don't do anything.
+				}
+				else
+					error("Unknown condition");
+			}
+			else
+			{	// Alleles don't match, so need to be more careful and compare strings
+				e1.get_indv_GENOTYPE_strings(indv1, genotype1);
+				e2.get_indv_GENOTYPE_strings(indv2, genotype2);
+
+				if ((genotype1 != missing_genotype) && (genotype2 != missing_genotype))
+				{	// No missing data
+					indv_sums[combined_individuals_it->first].first++;
+					if (((genotype1.first == genotype2.first) && (genotype1.second == genotype2.second)) ||
+						((genotype1.first == genotype2.second) && (genotype1.second == genotype2.first)) )
+					{	// Match
+						// Don't do anything
+					}
+					else
+					{	// Mismatch
+						indv_sums[combined_individuals_it->first].second++;
+					}
+				}
+				else if ((genotype1 == missing_genotype) && (genotype2 == missing_genotype))
+				{	// Both missing
+					// Don't do anything
+				}
+				else if (genotype1 != missing_genotype)
+				{	// Genotype 1 is not missing, genotype 2 is.
+					// Don't do anything
+				}
+				else if (genotype2 != missing_genotype)
+				{	// Genotype 2 is not missing, genotype 1 is.
+					// Don't do anything
+				}
+				else
+					error("Unknown condition");
+			}
+		}
+	}
+
+	string output_file = output_file_prefix + ".diff.indv";
+	ofstream out(output_file.c_str());
+	if (!out.is_open())
+		error("Could not open Sites Differences File: " + output_file, 3);
+	out << "INDV\tN_COMMON_CALLED\tN_DISCORD\tDISCORDANCE" << endl;
+
+	int N, N_discord;
+	double discordance;
+	for (combined_individuals_it=combined_individuals.begin(); combined_individuals_it!=combined_individuals.end(); ++combined_individuals_it)
+	{
+		out << combined_individuals_it->first;
+		N = indv_sums[combined_individuals_it->first].first;
+		N_discord = indv_sums[combined_individuals_it->first].second;
+		discordance = N_discord / double(N);
+		out << "\t" << N << "\t" << N_discord << "\t" << discordance << endl;
+	}
+
+	out.close();
+}
+
+void vcf_file::output_discordance_by_site(const string &output_file_prefix, vcf_file &diff_vcf_file)
+{
+	printLOG("Outputting Discordance By Site...\n");
+	map<pair<string, int>, pair<int, int> > CHROMPOS_to_filepos_pair;
+	map<pair<string, int>, pair<int, int> >::iterator CHROMPOS_to_filepos_pair_it;
+	return_site_union(diff_vcf_file, CHROMPOS_to_filepos_pair);
+
+	map<string, pair< int, int> > combined_individuals;
+	map<string, pair< int, int> >::iterator combined_individuals_it;
+	return_indv_union(diff_vcf_file, combined_individuals);
+
+	string CHROM, vcf_line;
+	int POS;
+	int s1, s2, indv1, indv2;
+
+	string output_file = output_file_prefix + ".diff.sites";
+	ofstream diffsites(output_file.c_str());
+	if (!diffsites.is_open())
+		error("Could not open Sites Differences File: " + output_file, 3);
+	//diffsites << "CHROM\tPOS\tFILES\tMATCHING_ALT\tN_COMMON_CALLED\tN_DISCORD\tDISCORDANCE\tN_FILE1_NONREF_GENOTYPES\tNON_REF_DISCORDANCE" << endl;
+	diffsites << "CHROM\tPOS\tFILES\tMATCHING_ALLELES\tN_COMMON_CALLED\tN_DISCORD\tDISCORDANCE" << endl;
+
+	for (CHROMPOS_to_filepos_pair_it=CHROMPOS_to_filepos_pair.begin(); CHROMPOS_to_filepos_pair_it != CHROMPOS_to_filepos_pair.end(); ++CHROMPOS_to_filepos_pair_it)
+	{
+		CHROM = CHROMPOS_to_filepos_pair_it->first.first;
+		POS = CHROMPOS_to_filepos_pair_it->first.second;
+
+		diffsites << CHROM << "\t" << POS;
+
+		s1 = CHROMPOS_to_filepos_pair_it->second.first;
+		s2 = CHROMPOS_to_filepos_pair_it->second.second;
+
+		vcf_entry e1(N_indv);
+		vcf_entry e2(diff_vcf_file.N_indv);
+
+		bool data_in_both = true;
+		// Read entries from file (if available)
+		if (s1 != -1)
+		{
+			get_vcf_entry(s1, vcf_line);
+			e1.reset(vcf_line);
+		}
+		else
+			data_in_both = false;
+
+		if (s2 != -1)
+		{
+			diff_vcf_file.get_vcf_entry(s2, vcf_line);
+			e2.reset(vcf_line);
+		}
+		else
+			data_in_both = false;
+
+		if (data_in_both)
+			diffsites << "\tB";
+		else if ((s1 != -1) && (s2 == -1))
+			diffsites << "\t1";
+		else if ((s1 == -1) && (s2 != -1))
+			diffsites << "\t2";
+		else
+			error("Unhandled condition");
+
+		e1.parse_basic_entry(true);
+		e2.parse_basic_entry(true);
+
+		// Set the reference to the non-missing entry (if available)
+		string REF = e1.get_REF();
+		string REF2 = e2.get_REF();
+		if (REF == "N")
+			REF = REF2;
+		if (REF2 == "N")
+			REF2 = REF;
+
+		if (REF.size() != REF2.size())
+		{
+			warning("REF sequences at " + CHROM + ":" + int2str(POS) + " are not comparable. Skipping site");
+			continue;
+		}
+
+		if ((REF != REF2) && (REF2 != "N") && (REF != "N"))
+			warning("Non-matching REF " + CHROM + ":" + int2str(POS) + " " + REF + "/" + REF2);
+
+		// Do the alternative alleles match?
+		string ALT, ALT2;
+		ALT = e1.get_ALT();
+		ALT2 = e2.get_ALT();
+
+		bool alleles_match = ((ALT == ALT2) && (REF == REF2));
+		diffsites << "\t" << alleles_match;
+
+		e1.parse_full_entry(true);
+		e1.parse_genotype_entries(true);
+
+		e2.parse_full_entry(true);
+		e2.parse_genotype_entries(true);
+
+		pair<string, string> genotype1, genotype2;
+		pair<int,int> geno_ids1, geno_ids2;
+		pair<string, string> missing_genotype(".",".");
+		pair<int, int> missing_id(-1,-1);
+
+		unsigned int N_common_called=0;	// Number of genotypes called in both files
+		unsigned int N_missing_1=0, N_missing_2=0;
+		unsigned int N_discord=0;
+		unsigned int N_concord_non_missing=0;
+
+		for (combined_individuals_it=combined_individuals.begin(); combined_individuals_it!=combined_individuals.end(); ++combined_individuals_it)
+		{
+			indv1 = combined_individuals_it->second.first;
+			indv2 = combined_individuals_it->second.second;
+
+			if ((indv1 == -1) || (indv2 == -1))
+				continue;	// Individual not found in one of the files
+
+			if (alleles_match)
+			{	// Alleles match, so can compare ids instead of strings
+				e1.get_indv_GENOTYPE_ids(indv1, geno_ids1);
+				e2.get_indv_GENOTYPE_ids(indv2, geno_ids2);
+
+				if ((geno_ids1 != missing_id) && (geno_ids2 != missing_id))
+				{
+					N_common_called++;
+					if (((geno_ids1.first == geno_ids2.first) && (geno_ids1.second == geno_ids2.second)) ||
+						((geno_ids1.first == geno_ids2.second) && (geno_ids1.second == geno_ids2.first)) )
+					{	// Match
+						N_concord_non_missing++;
+					}
+					else
+					{	// Mismatch
+						N_discord++;
+					}
+				}
+				else if ((geno_ids1 == missing_id) && (geno_ids2 == missing_id))
+				{	// Both missing
+					N_missing_1++; N_missing_2++;
+				}
+				else if (geno_ids1 != missing_id)
+				{	// Genotype 1 is not missing, genotype 2 is.
+					N_missing_2++;
+				}
+				else if (geno_ids2 != missing_id)
+				{	// Genotype 2 is not missing, genotype 1 is.
+					N_missing_1++;
+				}
+				else
+					error("Unknown condition");
+			}
+			else
+			{	// Alleles don't match, so need to be more careful and compare strings
+				e1.get_indv_GENOTYPE_strings(indv1, genotype1);
+				e2.get_indv_GENOTYPE_strings(indv2, genotype2);
+
+				if ((genotype1 != missing_genotype) && (genotype2 != missing_genotype))
+				{	// No missing data
+					N_common_called++;
+					if (((genotype1.first == genotype2.first) && (genotype1.second == genotype2.second)) ||
+						((genotype1.first == genotype2.second) && (genotype1.second == genotype2.first)) )
+					{	// Match
+						N_concord_non_missing++;
+					}
+					else
+					{	// Mismatch
+						N_discord++;
+					}
+				}
+				else if ((genotype1 == missing_genotype) && (genotype2 == missing_genotype))
+				{	// Both missing
+					N_missing_1++; N_missing_2++;
+				}
+				else if (genotype1 != missing_genotype)
+				{	// Genotype 1 is not missing, genotype 2 is.
+					N_missing_2++;
+				}
+				else if (genotype2 != missing_genotype)
+				{	// Genotype 2 is not missing, genotype 1 is.
+					N_missing_1++;
+				}
+				else
+					error("Unknown condition");
+			}
+		}
+		double discordance = N_discord / double(N_common_called);
+		diffsites << "\t" << N_common_called << "\t" << N_discord << "\t" << discordance;
+		diffsites << endl;
+	}
+	diffsites.close();
+}
+
+void vcf_file::output_discordance_matrix(const string &output_file_prefix, vcf_file &diff_vcf_file)
+{
+	printLOG("Outputting Discordance Matrix\n\tFor bi-allelic loci, called in both files, with matching alleles only...\n");
+	map<pair<string, int>, pair<int, int> > CHROMPOS_to_filepos_pair;
+	map<pair<string, int>, pair<int, int> >::iterator CHROMPOS_to_filepos_pair_it;
+	return_site_union(diff_vcf_file, CHROMPOS_to_filepos_pair);
+
+	map<string, pair< int, int> > combined_individuals;
+	map<string, pair< int, int> >::iterator combined_individuals_it;
+	return_indv_union(diff_vcf_file, combined_individuals);
+
+	string vcf_line;
+	int s1, s2, indv1, indv2;
+
+	vector<vector<int> > discordance_matrix(4, vector<int>(4, 0));
+
+	for (CHROMPOS_to_filepos_pair_it=CHROMPOS_to_filepos_pair.begin(); CHROMPOS_to_filepos_pair_it != CHROMPOS_to_filepos_pair.end(); ++CHROMPOS_to_filepos_pair_it)
+	{
+		s1 = CHROMPOS_to_filepos_pair_it->second.first;
+		s2 = CHROMPOS_to_filepos_pair_it->second.second;
+
+		vcf_entry e1(N_indv);
+		vcf_entry e2(diff_vcf_file.N_indv);
+
+		// Read entries from file (if available)
+		if (s1 != -1)
+		{
+			get_vcf_entry(s1, vcf_line);
+			e1.reset(vcf_line);
+		}
+
+		if (s2 != -1)
+		{
+			diff_vcf_file.get_vcf_entry(s2, vcf_line);
+			e2.reset(vcf_line);
+		}
+
+		e1.parse_basic_entry(true);
+		e2.parse_basic_entry(true);
+
+		if ((e1.get_N_alleles() != 2) || (e2.get_N_alleles() != 2))
+			continue;
+
+		// Set the reference to the non-missing entry (if available)
+		string REF = e1.get_REF();
+		string REF2 = e2.get_REF();
+		if (REF == "N")
+			REF = REF2;
+		if (REF2 == "N")
+			REF2 = REF;
+
+		if (REF.size() != REF2.size())
+			continue;
+
+		if ((REF != REF2) && (REF2 != "N") && (REF != "N"))
+			continue;
+
+		// Do the alternative alleles match?
+		string ALT, ALT2;
+		ALT = e1.get_ALT();
+		ALT2 = e2.get_ALT();
+
+		bool alleles_match = (ALT == ALT2) && (REF == REF2);
+		if (alleles_match == false)
+			continue;
+
+		e1.parse_full_entry(true);
+		e1.parse_genotype_entries(true);
+
+		e2.parse_full_entry(true);
+		e2.parse_genotype_entries(true);
+
+		pair<int,int> geno_ids1, geno_ids2;
+		int N1, N2;
+
+		for (combined_individuals_it=combined_individuals.begin(); combined_individuals_it!=combined_individuals.end(); ++combined_individuals_it)
+		{
+			indv1 = combined_individuals_it->second.first;
+			indv2 = combined_individuals_it->second.second;
+
+			if ((indv1 == -1) || (indv2 == -1))
+				continue;	// Individual not found in one of the files
+
+			// Alleles match, so can compare ids instead of strings
+			e1.get_indv_GENOTYPE_ids(indv1, geno_ids1);
+			e2.get_indv_GENOTYPE_ids(indv2, geno_ids2);
+
+			if (((geno_ids1.first != -1) && (geno_ids1.second == -1)) ||
+				((geno_ids2.first != -1) && (geno_ids2.second == -1)))
+			{	// Haploid
+				one_off_warning("***Warning: Haploid chromosomes not counted!***");
+				continue;
+			}
+
+			N1 = geno_ids1.first + geno_ids1.second;
+			N2 = geno_ids2.first + geno_ids2.second;
+
+			if ((N1 == -1) || (N1 < -2) || (N1 > 2))
+				error("Unhandled case");
+			if ((N2 == -1) || (N2 < -2) || (N2 > 2))
+				error("Unhandled case");
+
+			if (N1 == -2)
+				N1 = 3;
+
+			if (N2 == -2)
+				N2 = 3;
+
+			discordance_matrix[N1][N2]++;
+		}
+	}
+
+	string output_file = output_file_prefix + ".diff.discordance_matrix";
+	ofstream out(output_file.c_str());
+	if (!out.is_open())
+		error("Could not open Discordance Matrix File: " + output_file, 3);
+
+	out << "-\tN_0/0_file1\tN_0/1_file1\tN_1/1_file1\tN_./._file1" << endl;
+	out << "N_0/0_file2\t" << discordance_matrix[0][0] << "\t" << discordance_matrix[1][0] << "\t" << discordance_matrix[2][0] << "\t" << discordance_matrix[3][0] << endl;
+	out << "N_0/1_file2\t" << discordance_matrix[0][1] << "\t" << discordance_matrix[1][1] << "\t" << discordance_matrix[2][1] << "\t" << discordance_matrix[3][1] << endl;
+	out << "N_1/1_file2\t" << discordance_matrix[0][2] << "\t" << discordance_matrix[1][2] << "\t" << discordance_matrix[2][2] << "\t" << discordance_matrix[3][2] << endl;
+	out << "N_./._file2\t" << discordance_matrix[0][3] << "\t" << discordance_matrix[1][3] << "\t" << discordance_matrix[2][3] << "\t" << discordance_matrix[3][3] << endl;
+	out.close();
+}
+
+void vcf_file::output_switch_error(const string &output_file_prefix, vcf_file &diff_vcf_file)
+{
+	printLOG("Outputting Phase Switch Errors...\n");
+	map<pair<string, int>, pair<int, int> > CHROMPOS_to_filepos_pair;
+	map<pair<string, int>, pair<int, int> >::iterator CHROMPOS_to_filepos_pair_it;
+	return_site_union(diff_vcf_file, CHROMPOS_to_filepos_pair);
+
+	map<string, pair< int, int> > combined_individuals;
+	map<string, pair< int, int> >::iterator combined_individuals_it;
+	return_indv_union(diff_vcf_file, combined_individuals);
+
+	string CHROM, vcf_line;
+	int POS;
+	int s1, s2, indv1, indv2;
+
+	string output_file = output_file_prefix + ".diff.switch";
+	ofstream switcherror(output_file.c_str());
+	if (!switcherror.is_open())
+		error("Could not open Switch Error file: " + output_file, 4);
+	switcherror << "CHROM\tPOS\tINDV" << endl;
+
+	unsigned int N_combined_indv = combined_individuals.size();
+	vector<int> N_phased_het_sites(N_combined_indv, 0);
+	vector<int> N_switch_errors(N_combined_indv, 0);
+
+	pair<string, string> missing_genotype(".",".");
+	vector<pair<string, string> > prev_geno_file1(N_combined_indv, missing_genotype);
+	vector<pair<string, string> > prev_geno_file2(N_combined_indv, missing_genotype);
+	pair<string, string> file1_hap1, file1_hap2, file2_hap1;
+
+	for (CHROMPOS_to_filepos_pair_it=CHROMPOS_to_filepos_pair.begin(); CHROMPOS_to_filepos_pair_it != CHROMPOS_to_filepos_pair.end(); ++CHROMPOS_to_filepos_pair_it)
+	{
+		CHROM = CHROMPOS_to_filepos_pair_it->first.first;
+		POS = CHROMPOS_to_filepos_pair_it->first.second;
+
+		s1 = CHROMPOS_to_filepos_pair_it->second.first;
+		s2 = CHROMPOS_to_filepos_pair_it->second.second;
+
+		vcf_entry e1(N_indv);
+		vcf_entry e2(diff_vcf_file.N_indv);
+
+		// Read entries from file (if available)
+		if (s1 != -1)
+		{
+			get_vcf_entry(s1, vcf_line);
+			e1.reset(vcf_line);
+		}
+
+		if (s2 != -1)
+		{
+			diff_vcf_file.get_vcf_entry(s2, vcf_line);
+			e2.reset(vcf_line);
+		}
+
+		e1.parse_basic_entry(true);
+		e2.parse_basic_entry(true);
+
+		e1.parse_full_entry(true);
+		e1.parse_genotype_entries(true);
+
+		e2.parse_full_entry(true);
+		e2.parse_genotype_entries(true);
+
+		pair<string, string> genotype1, genotype2;
+		pair<string, string> missing_genotype(".",".");
+
+		unsigned int N_common_called=0;	// Number of genotypes called in both files
+		unsigned int indv_count=0;
+
+		// Bug fix applied (#3354189) - July 5th 2011
+		for (combined_individuals_it=combined_individuals.begin();
+				combined_individuals_it!=combined_individuals.end();
+				++combined_individuals_it, indv_count++)
+		{
+			indv1 = combined_individuals_it->second.first;
+			indv2 = combined_individuals_it->second.second;
+
+			if ((indv1 == -1) || (indv2 == -1))
+				continue;	// Individual not found in one of the files
+
+			e1.get_indv_GENOTYPE_strings(indv1, genotype1);
+			e2.get_indv_GENOTYPE_strings(indv2, genotype2);
+
+			if ((genotype1 != missing_genotype) && (genotype2 != missing_genotype))
+			{	// No missing data
+				N_common_called++;
+				if (((genotype1.first == genotype2.first) && (genotype1.second == genotype2.second)) ||
+					((genotype1.first == genotype2.second) && (genotype1.second == genotype2.first)) )
+				{	// Have a matching genotypes in files 1 and 2
+					if (genotype1.first != genotype1.second)
+					{	// It's a heterozgote
+						char phase1, phase2;
+						phase1 = e1.get_indv_PHASE(indv1);
+						phase2 = e2.get_indv_PHASE(indv2);
+						if ((phase1 == '|') && (phase2 == '|'))
+						{	// Calculate Phasing error (switch error)
+							N_phased_het_sites[indv_count]++;
+							file1_hap1 = make_pair<string,string>(prev_geno_file1[indv_count].first, genotype1.first);
+							file1_hap2 = make_pair<string,string>(prev_geno_file1[indv_count].second, genotype1.second);
+							file2_hap1 = make_pair<string,string>(prev_geno_file2[indv_count].first, genotype2.first);
+
+							if ((file2_hap1 != file1_hap1) && (file2_hap1 != file1_hap2))
+							{	// Must be a switch error
+								string indv_id;
+								N_switch_errors[indv_count]++;
+								if (indv1 != -1)
+									indv_id = indv[indv1];
+								else
+									indv_id = diff_vcf_file.indv[indv2];
+								switcherror << CHROM << "\t" << POS << "\t" << indv_id << endl;
+							}
+							prev_geno_file1[indv_count] = genotype1;
+							prev_geno_file2[indv_count] = genotype2;
+						}
+					}
+				}
+			}
+		}
+	}
+	switcherror.close();
+
+	output_file = output_file_prefix + ".diff.indv.switch";
+	ofstream idiscord(output_file.c_str());
+	if (!idiscord.is_open())
+		error("Could not open Individual Discordance File: " + output_file, 3);
+
+	idiscord << "INDV\tN_COMMON_PHASED_HET\tN_SWITCH\tSWITCH" << endl;
+	unsigned int indv_count=0;
+	double switch_error;
+	string indv_id;
+	for (combined_individuals_it=combined_individuals.begin(); combined_individuals_it!=combined_individuals.end(); ++combined_individuals_it)
+	{
+		indv1 = combined_individuals_it->second.first;
+		indv2 = combined_individuals_it->second.second;
+
+		if (indv1 != -1)
+			indv_id = indv[indv1];
+		else
+			indv_id = diff_vcf_file.indv[indv2];
+
+		if (N_phased_het_sites[indv_count] > 0)
+			switch_error = double(N_switch_errors[indv_count]) / N_phased_het_sites[indv_count];
+		else
+			switch_error = 0;
+		idiscord << indv_id << "\t" << N_phased_het_sites[indv_count] << "\t" << N_switch_errors[indv_count] << "\t" << switch_error << endl;
+
+		indv_count++;
+	}
+	idiscord.close();
+}
+
+/*
+void vcf_file::output_concensus_statistics(const string &output_file_prefix, vcf_file &diff_vcf_file)
+{
+	printLOG("Outputting Consensus Statistics... \n");
+	unsigned int ui;
+
+	string output_file;
+	string vcf_line;
+
+	// Build a list of individuals contained in each file
+	map<string, pair< int, int> > combined_individuals;
+	map<string, pair< int, int> >::iterator combined_individuals_it;
+	for (ui=0; ui<N_indv; ui++)
+		if (include_indv[ui] == true)
+			combined_individuals[indv[ui]] = make_pair<int,int>(ui, -1);
+
+	for (ui=0; ui<diff_vcf_file.N_indv; ui++)
+		if (diff_vcf_file.include_indv[ui] == true)
+		{
+			if (combined_individuals.find(diff_vcf_file.indv[ui]) != combined_individuals.end())
+				combined_individuals[diff_vcf_file.indv[ui]].second = ui;
+			else
+				combined_individuals[diff_vcf_file.indv[ui]] = make_pair<int,int>(-1, ui);
+		}
+
+	unsigned int N_combined_indv = combined_individuals.size();
+	unsigned int N[3]={0,0,0};
+	for (combined_individuals_it=combined_individuals.begin(); combined_individuals_it!=combined_individuals.end(); ++combined_individuals_it)
+	{
+		if ((combined_individuals_it->second.first != -1) && (combined_individuals_it->second.second != -1))
+			N[0]++;
+		else if (combined_individuals_it->second.first != -1)
+			N[1]++;
+		else
+			N[2]++;
+	}
+
+	vector<int> indv_N_discord(N_combined_indv, 0);
+	vector<int> indv_N_called_sites(N_combined_indv, 0);
+
+	printLOG("N_combined_individuals:\t" + int2str(N_combined_indv) + "\n");
+	printLOG("N_individuals_common_to_both_files:\t" + int2str(N[0]) + "\n");
+	printLOG("N_individuals_unique_to_file1:\t" + int2str(N[1]) + "\n");
+	printLOG("N_individuals_unique_to_file2:\t" + int2str(N[2]) + "\n");
+
+	// Build a table of included entries in both files
+	map<pair<string, int>, pair<int, int> > CHROMPOS_to_filepos_pair;
+	map<pair<string, int>, pair<int, int> >::iterator CHROMPOS_to_filepos_pair_it;
+	string CHROM;
+	int POS;
+	return_site_union(diff_vcf_file, CHROMPOS_to_filepos_pair);
+
+	output_file = output_file_prefix + ".diff.sites_in_files";
+	ofstream sites_in_files(output_file.c_str());
+	sites_in_files << "CHROM\tPOS\tIN_FILE" << endl;
+
+	int s1, s2;
+	int N_common_SNPs = 0, N_SNPs_file1_only=0, N_SNPs_file2_only=0;
+	for (CHROMPOS_to_filepos_pair_it=CHROMPOS_to_filepos_pair.begin(); CHROMPOS_to_filepos_pair_it!=CHROMPOS_to_filepos_pair.end(); ++CHROMPOS_to_filepos_pair_it)
+	{
+		s1 = CHROMPOS_to_filepos_pair_it->second.first;
+		s2 = CHROMPOS_to_filepos_pair_it->second.second;
+
+		sites_in_files << CHROMPOS_to_filepos_pair_it->first.first << "\t" << CHROMPOS_to_filepos_pair_it->first.second << "\t";
+		if ((s1 != -1) && (s2 != -1))
+		{
+			N_common_SNPs++;
+			sites_in_files << "B" << endl;
+		}
+		else if ((s1 != -1) && (s2 == -1))
+		{
+			N_SNPs_file1_only++;
+			sites_in_files << "1" << endl;
+		}
+		else if ((s1 == -1) && (s2 != -1))
+		{
+			N_SNPs_file2_only++;
+			sites_in_files << "2" << endl;
+		}
+		else
+			error("SNP in neither file!?");
+	}
+
+	sites_in_files.close();
+
+	printLOG("Found " + int2str(N_common_SNPs) + " SNPs common to both files.\n");
+	printLOG("Found " + int2str(N_SNPs_file1_only) + " SNPs only in main file.\n");
+	printLOG("Found " + int2str(N_SNPs_file2_only) + " SNPs only in second file.\n");
+
+	output_file = output_file_prefix + ".diff.sites";
+	ofstream diffsites(output_file.c_str());
+	if (!diffsites.is_open())
+		error("Could not open Sites Differences File: " + output_file, 3);
+	diffsites << "CHROM\tPOS\tFILES\tMATCHING_ALT\tN_COMMON_CALLED\tN_DISCORD\tDISCORDANCE\tN_FILE1_NONREF_GENOTYPES\tNON_REF_DISCORDANCE" << endl;
+
+	output_file = output_file_prefix + ".diff.switch";
+	ofstream switcherror(output_file.c_str());
+	if (!switcherror.is_open())
+		error("Could not open Switch Error file: " + output_file, 4);
+	switcherror << "CHROM\tPOS\tINDV" << endl;
+
+	// Now try and merge the entries.
+	unsigned int N_common_genotypes = 0;
+	unsigned int N_common_discordant_genotypes = 0;
+	unsigned int N_sites_with_mismatching_ALT = 0;
+	unsigned int N_non_ref_genotypes = 0;
+	unsigned int N_discordant_non_ref_genotypes = 0;
+
+	pair<string, string> genotype1, genotype2;
+	pair<int,int> geno_ids1, geno_ids2;
+	pair<string, string> missing_genotype(".",".");
+	pair<int, int> missing_HQUAL(0,0);
+
+	pair<int, int> homo_ref(0, 0);
+	vector<pair<string, string> > prev_geno_file1(N_combined_indv, missing_genotype);
+	vector<pair<string, string> > prev_geno_file2(N_combined_indv, missing_genotype);
+	pair<string, string> file1_hap1, file1_hap2, file2_hap1;
+
+	vector<int> N_phased_het_sites(N_combined_indv, 0);
+	vector<int> N_switch_errors(N_combined_indv, 0);
+	vector<pair<int,int> > indv_depth_at_common_sites(N_combined_indv, make_pair(0,0));
+	vector<pair<int,int> > indv_count_at_common_sites(N_combined_indv, make_pair(0,0));
+
+	vector<vector<int> > genotype_concord_matrix(4, vector<int>(4, 0));
+
+	for (CHROMPOS_to_filepos_pair_it=CHROMPOS_to_filepos_pair.begin(); CHROMPOS_to_filepos_pair_it != CHROMPOS_to_filepos_pair.end(); ++CHROMPOS_to_filepos_pair_it)
+	{
+		CHROM = CHROMPOS_to_filepos_pair_it->first.first;
+		POS = CHROMPOS_to_filepos_pair_it->first.second;
+
+		s1 = CHROMPOS_to_filepos_pair_it->second.first;
+		s2 = CHROMPOS_to_filepos_pair_it->second.second;
+
+		vcf_entry e1(N_indv);
+		vcf_entry e2(diff_vcf_file.N_indv);
+
+		bool data_in_both = true;
+		// Read entries from file (if available)
+		if (s1 != -1)
+		{
+			get_vcf_entry(s1, vcf_line);
+			e1.reset(vcf_line);
+		}
+		else
+			data_in_both = false;
+
+		if (s2 != -1)
+		{
+			diff_vcf_file.get_vcf_entry(s2, vcf_line);
+			e2.reset(vcf_line);
+		}
+		else
+			data_in_both = false;
+
+		e1.parse_basic_entry(true, true, true);
+		e2.parse_basic_entry(true, true, true);
+
+		// Set the reference to the non-missing entry (if available)
+		string REF = e1.get_REF();
+		string REF2 = e2.get_REF();
+		if (REF == "N")
+			REF = REF2;
+		if (REF2 == "N")
+			REF2 = REF;
+
+		if (REF.size() != REF2.size())
+		{
+			warning("REF sequences at " + CHROM + ":" + int2str(POS) + " are not comparable. Skipping site");
+			continue;
+		}
+
+		if ((REF != REF2) && (REF2 != "N") && (REF != "N"))
+			warning("Non-matching REF " + CHROM + ":" + int2str(POS) + " " + REF + "/" + REF2);
+
+		// Do the alternative alleles match?
+		set<string> ALT1, ALT2;
+		for (ui=0; ui<(e1.get_N_alleles()-1); ui++)
+			ALT1.insert(e1.get_ALT_allele(ui));
+
+		for (ui=0; ui<(e2.get_N_alleles()-1); ui++)
+			ALT2.insert(e2.get_ALT_allele(ui));
+
+		bool matching_ALT=true;
+		if ((data_in_both) && (ALT1 != ALT2) && (ALT1.size() > 0) && (ALT2.size() > 0))
+		{
+			N_sites_with_mismatching_ALT++;
+			matching_ALT = false;
+		}
+
+		if (data_in_both)
+		{
+			diffsites << CHROM << "\t" << POS << "\t";
+			diffsites << "B\t" << matching_ALT << "\t";
+		}
+		else
+		{
+			continue;
+		}
+
+		if (s1 != -1)
+		{
+			e1.parse_full_entry(true);
+			e1.parse_genotype_entries(true, true, true, true, true);
+		}
+
+		if (s2 != -1)
+		{
+			e2.parse_full_entry(true);
+			e2.parse_genotype_entries(true, true, true, true, true);
+		}
+
+		// Now merge the genotypes.
+		unsigned int indv_count=0;
+		int indv1, indv2;
+		unsigned int N_discordant_site_counter=0;
+		unsigned int N_indvs_with_data=0;
+		unsigned int site_N_non_ref_genotypes=0;
+		unsigned int site_N_discordant_non_ref_genotypes = 0;
+		int depth;
+		for (combined_individuals_it=combined_individuals.begin(); combined_individuals_it!=combined_individuals.end(); ++combined_individuals_it)
+		{
+			indv1 = combined_individuals_it->second.first;
+			indv2 = combined_individuals_it->second.second;
+
+			if ((indv1 == -1) && (indv2 == -1))
+			{	// Genotype is completely missing... should never happen
+				error("Missing genotype!?", 83);
+			}
+			else if ((indv1 == -1) && (indv2 != -1))
+			{	// Data is missing from first file, so just use second file.
+
+			}
+			else if ((indv1 != -1) && (indv2 == -1))
+			{	// Data is missing from second file, so just use first file.
+
+			}
+			else
+			{	// Data from both files, so figure out what to do
+				bool non_ref_genotype = false;
+				if (data_in_both)
+				{
+					e1.get_indv_GENOTYPE_strings(indv1, genotype1);
+					e2.get_indv_GENOTYPE_strings(indv2, genotype2);
+					e1.get_indv_GENOTYPE_ids(indv1, geno_ids1);
+					e2.get_indv_GENOTYPE_ids(indv2, geno_ids2);
+
+					N_common_genotypes++;
+					N_indvs_with_data++;
+
+					if (geno_ids1 != homo_ref)
+					{	// First file is not a hom ref
+						N_non_ref_genotypes++;
+						site_N_non_ref_genotypes++;
+						non_ref_genotype = true;
+					}
+
+					depth = e1.get_indv_DEPTH(indv1);
+					if (depth >= 0)
+					{
+						indv_depth_at_common_sites[indv_count].first += depth;
+						indv_count_at_common_sites[indv_count].first++;
+					}
+					depth = e2.get_indv_DEPTH(indv2);
+					if (depth >= 0)
+					{
+						indv_depth_at_common_sites[indv_count].second += depth;
+						indv_count_at_common_sites[indv_count].second++;
+					}
+				}
+
+				if ((genotype1 == missing_genotype) && (genotype2 == missing_genotype))
+				{
+					genotype_concord_matrix[3][3]++;
+				}
+
+				if ((genotype1 == missing_genotype) && (genotype2 != missing_genotype))
+				{	// Missing data, Favour second file
+					if (matching_ALT && (ALT2.size() <= 1))
+					{
+						unsigned int idx2 = geno_ids2.first + geno_ids2.second;
+						genotype_concord_matrix[3][idx2]++;
+					}
+				}
+
+				if ((genotype2 == missing_genotype) && (genotype1 != missing_genotype))
+				{	// Favour first file
+					if (matching_ALT && (ALT1.size() <= 1))
+					{
+						unsigned int idx1 = geno_ids1.first + geno_ids1.second;
+						genotype_concord_matrix[idx1][3]++;
+					}
+				}
+
+				if ((genotype1 != missing_genotype) && (genotype2 != missing_genotype))
+				{
+					if (data_in_both)
+					{
+						if (matching_ALT && (ALT1.size() <= 1) && (ALT2.size() <= 1))
+						{
+							unsigned int idx1 = geno_ids1.first + geno_ids1.second;
+							unsigned int idx2 = geno_ids2.first + geno_ids2.second;
+							genotype_concord_matrix[idx1][idx2]++;
+						}
+
+						indv_N_called_sites[indv_count]++;
+						if (!vcf_entry::genotypes_equal(genotype1, genotype2))
+						{
+							N_common_discordant_genotypes++;
+							N_discordant_site_counter++;
+							indv_N_discord[indv_count]++;
+
+							if (non_ref_genotype)
+							{
+								N_discordant_non_ref_genotypes++;
+								site_N_discordant_non_ref_genotypes++;
+							}
+						}
+						else
+						{	// Have a matching genotype in files 1 and 2
+							if (geno_ids1.first != geno_ids1.second)
+							{	// It's a heterozgote
+								char phase1, phase2;
+								phase1 = e1.get_indv_PHASE(indv1);
+								phase2 = e2.get_indv_PHASE(indv2);
+								if ((phase1 == '|') && (phase2 == '|'))
+								{	// Calculate Phasing error (switch error)
+									N_phased_het_sites[indv_count]++;
+									file1_hap1 = make_pair<string,string>(prev_geno_file1[indv_count].first, genotype1.first);
+									file1_hap2 = make_pair<string,string>(prev_geno_file1[indv_count].second, genotype1.second);
+									file2_hap1 = make_pair<string,string>(prev_geno_file2[indv_count].first, genotype2.first);
+
+									if ((file2_hap1 != file1_hap1) && (file2_hap1 != file1_hap2))
+									{	// Must be a switch error
+										string indv_id;
+										N_switch_errors[indv_count]++;
+										if (indv1 != -1)
+											indv_id = indv[indv1];
+										else
+											indv_id = diff_vcf_file.indv[indv2];
+										switcherror << CHROM << "\t" << POS << "\t" << indv_id << endl;
+									}
+									prev_geno_file1[indv_count] = genotype1;
+									prev_geno_file2[indv_count] = genotype2;
+								}
+							}
+						}
+					}
+				}
+			}
+
+			indv_count++;
+		}
+		double discordance = 0.0;
+		if (N_indvs_with_data > 0)
+			discordance = double(N_discordant_site_counter) / N_indvs_with_data;
+		double non_ref_discordance = 0.0;
+		if (site_N_non_ref_genotypes > 0)
+			non_ref_discordance = double(site_N_discordant_non_ref_genotypes) / site_N_non_ref_genotypes;
+		diffsites << N_indvs_with_data << "\t" << N_discordant_site_counter << "\t" << discordance;
+		diffsites << "\t" << site_N_non_ref_genotypes << "\t" << non_ref_discordance;
+		diffsites << endl;
+	}
+
+	output_file = output_file_prefix + ".diff.4x4";
+	ofstream four_by_four(output_file.c_str());
+	if (!four_by_four.is_open())
+		error("Could not open 3x3 File: " + output_file, 3);
+
+	four_by_four << "-\tN00_file1\tN01_file1\tN11_file1\tN.._file1" << endl;
+
+	four_by_four << "N00_file2\t" << genotype_concord_matrix[0][0] << "\t" << genotype_concord_matrix[1][0] << "\t" << genotype_concord_matrix[2][0] << "\t" << genotype_concord_matrix[3][0] << endl;
+	four_by_four << "N01_file2\t" << genotype_concord_matrix[0][1] << "\t" << genotype_concord_matrix[1][1] << "\t" << genotype_concord_matrix[2][1] << "\t" << genotype_concord_matrix[3][1] << endl;
+	four_by_four << "N11_file2\t" << genotype_concord_matrix[0][2] << "\t" << genotype_concord_matrix[1][2] << "\t" << genotype_concord_matrix[2][2] << "\t" << genotype_concord_matrix[3][2] << endl;
+	four_by_four << "N.._file2\t" << genotype_concord_matrix[0][3] << "\t" << genotype_concord_matrix[1][3] << "\t" << genotype_concord_matrix[2][3] << "\t" << genotype_concord_matrix[3][3] << endl;
+	four_by_four.close();
+
+
+	output_file = output_file_prefix + ".diff.indv.discord";
+	ofstream idiscord(output_file.c_str());
+	if (!idiscord.is_open())
+		error("Could not open Individual Discordance File: " + output_file, 3);
+
+	idiscord << "INDV\tMEAN_DP_1\tMEAN_DP_2\tN_COMMON_CALLED\tN_DISCORD\tDISCORD\tN_COMMON_PHASED_HET\tN_SWITCH\tSWITCH" << endl;
+	unsigned int indv_count=0;
+	double discordance, switch_error;
+	int indv1, indv2;
+	string indv_id;
+	for (combined_individuals_it=combined_individuals.begin(); combined_individuals_it!=combined_individuals.end(); ++combined_individuals_it)
+	{
+		indv1 = combined_individuals_it->second.first;
+		indv2 = combined_individuals_it->second.second;
+
+		if (indv1 != -1)
+			indv_id = indv[indv1];
+		else
+			indv_id = diff_vcf_file.indv[indv2];
+
+		if (indv_N_called_sites[indv_count] > 0)
+			discordance = double(indv_N_discord[indv_count]) / indv_N_called_sites[indv_count];
+		else
+			discordance = 0.0;
+		idiscord << indv_id;
+
+		double mean_depth1 = 0, mean_depth2=0;
+		if (indv_count_at_common_sites[indv_count].first > 0)
+		{
+			mean_depth1 = double(indv_depth_at_common_sites[indv_count].first) / indv_count_at_common_sites[indv_count].first;
+		}
+
+		if (indv_count_at_common_sites[indv_count].second > 0)
+		{
+			mean_depth2 = double(indv_depth_at_common_sites[indv_count].second) / indv_count_at_common_sites[indv_count].second;
+		}
+		idiscord << "\t" << mean_depth1 << "\t" << mean_depth2;
+
+		idiscord << "\t" << indv_N_called_sites[indv_count] << "\t" << indv_N_discord[indv_count] << "\t" << discordance;
+		if (N_phased_het_sites[indv_count] > 0)
+			switch_error = double(N_switch_errors[indv_count]) / N_phased_het_sites[indv_count];
+		else
+			switch_error = 0;
+		idiscord << "\t" << N_phased_het_sites[indv_count] << "\t" << N_switch_errors[indv_count] << "\t" << switch_error << endl;
+
+		indv_count++;
+	}
+	idiscord.close();
+
+	printLOG("Found " + int2str(N_sites_with_mismatching_ALT) + " sites with mismatching ALT alleles.\n");
+
+	printLOG("Found " + int2str(N_non_ref_genotypes) + " non-reference genotypes called in both files.\n");
+	printLOG("Found " + int2str(N_discordant_non_ref_genotypes) + " discordant non-reference genotypes.\n");
+	double concordance = 1.0 - (double(N_discordant_non_ref_genotypes)) / N_non_ref_genotypes;
+	printLOG("Concordance rate: " + dbl2str_fixed(concordance * 100,2) + "%\n");
+
+	printLOG("Found " + int2str(N_common_genotypes) + " genotypes called in both files.\n");
+	printLOG("Found " + int2str(N_common_discordant_genotypes) + " discordant genotypes.\n");
+	concordance = 1.0 - (double(N_common_discordant_genotypes)) / N_common_genotypes;
+	printLOG("Overall Concordance rate: " + dbl2str_fixed(concordance * 100,2) + "%\n");
+
+	diffsites.close();
+	switcherror.close();
+	printLOG("Done\n");
+}
+*/