ngs_server 0.1 → 0.2

data/ext/vcftools/cpp/vcf_file_format_convert.cpp

@@ -0,0 +1,1138 @@
+/*
+ * vcf_file_output.cpp
+ *
+ *  Created on: Aug 28, 2009
+ *      Author: Adam Auton
+ *      ($Revision: 249 $)
+ */
+#include "vcf_file.h"
+/*
+void vcf_file::output_as_plink(const string &output_file_prefix)
+{
+	// Output as PLINK formatted PED/MAP files.
+	if (has_genotypes == false)
+		error("Require Genotypes in VCF file in order to output as PLINK.");
+
+	printLOG("Writing PLINK PED file ... ");
+	string ped_file = output_file_prefix + ".ped";
+	string map_file = output_file_prefix + ".map";
+
+	ofstream PED(ped_file.c_str());
+	if (!PED.is_open()) error("Could not open output file: " + ped_file, 12);
+
+	vector<string> alleles;
+	char phase;
+	pair<int, int> genotype;
+	string vcf_line;
+	vcf_entry e(N_indv);
+	for (unsigned int ui=0; ui<N_indv; ui++)
+	{
+		if (include_indv[ui] == false)
+			continue;
+		PED << indv[ui] << "\t" << indv[ui] << "\t" << 0 << "\t" << 0 << "\t" << 0 << "\t" << 0;
+
+		for (unsigned int s=0; s<N_entries; s++)
+		{
+			if (include_entry[s] == false)
+				continue;
+
+			get_vcf_entry(s, vcf_line);
+			e.reset(vcf_line);
+			e.parse_basic_entry(true);
+
+			if (e.get_N_alleles() <= 2)	// Only output sites with one alternative allele
+			{
+				e.get_alleles_vector(alleles);
+				genotype = make_pair(-1,-1);
+				phase = '/';
+				if (include_genotype[s][ui] == true)
+				{
+					e.parse_genotype_entry(ui, true);
+					e.get_indv_GENOTYPE_ids(ui, genotype);
+					phase = e.get_indv_PHASE(ui);
+				}
+
+				if (genotype.first == -1)
+					PED << "\t0";
+				else
+					PED << "\t" << alleles[genotype.first];
+
+				if (genotype.second == -1)
+				{
+					if (phase == '/')
+						PED << "\t0";
+					else if (genotype.first != -1)
+						PED << "\t" << alleles[genotype.first];	// Male X-chr, Y-chr etc
+					else
+						PED << "\t0";
+				}
+				else
+					PED << "\t" << alleles[genotype.second];
+			}
+		}
+		PED << endl;
+	}
+
+	PED.close();
+
+	printLOG("Writing PLINK MAP file ... ");
+	ofstream MAP(map_file.c_str());
+	if (!MAP.is_open()) error("Could not open output file: " + map_file, 12);
+	for (unsigned int s=0; s<N_entries; s++)
+	{
+		if (include_entry[s] == false)
+			continue;
+
+		get_vcf_entry(s, vcf_line);
+		e.reset(vcf_line);
+		e.parse_basic_entry(true);
+		if (e.get_N_alleles() <= 2)	// Only output sites with one alternative allele
+		{
+			if (e.get_ID() == ".")
+				MAP << e.get_CHROM() << "\t" << e.get_POS() << "\t0\t" << e.get_POS() << endl;
+			else
+				MAP << e.get_CHROM() << "\t" << e.get_ID() << "\t0\t" << e.get_POS() << endl;
+		}
+	}
+
+	MAP.close();
+	printLOG("Done.\n");
+}
+*/
+
+void vcf_file::output_as_plink(const string &output_file_prefix)
+{
+	// Output as PLINK formatted PED/MAP files.
+	if (has_genotypes == false)
+		error("Require Genotypes in VCF file in order to output as PLINK.");
+
+	printLOG("Writing PLINK PED file ... \n");
+	string ped_file = output_file_prefix + ".ped";
+	string map_file = output_file_prefix + ".map";
+
+	vector<ofstream *> tmp_files(N_indv);
+	vector<string> tmp_filenames(N_indv);
+	for (unsigned int ui=0; ui<N_indv; ui++)
+	{
+		if (include_indv[ui] == false)
+			continue;
+		string filename(tmpnam(NULL));
+		ofstream *tmp_file = new ofstream(filename.c_str());
+		if (!tmp_file->good())
+			error("\n\nCould not open temporary file.\n\n"
+					"Most likely this is because the system is not allowing me to open enough temporary files.\n"
+					"Try using ulimit -n <int> to increase the number of allowed open files.\n"
+					"Alternatively, try the --plink-tped command.", 12);
+		(*tmp_file) << indv[ui] << "\t" << indv[ui] << "\t" << 0 << "\t" << 0 << "\t" << 0 << "\t" << 0;
+		tmp_files[ui] = tmp_file;
+		tmp_filenames[ui] = filename;
+	}
+
+	vector<string> alleles;
+	char phase;
+	pair<int, int> genotype;
+	string vcf_line;
+	vcf_entry e(N_indv);
+	ofstream *tmp_file;
+	for (unsigned int s=0; s<N_entries; s++)
+	{
+		if (include_entry[s] == false)
+			continue;
+
+		get_vcf_entry(s, vcf_line);
+		e.reset(vcf_line);
+		e.parse_basic_entry(true);
+
+		if (e.get_N_alleles() > 2)
+		{
+			one_off_warning("\tPLINK: Only outputting biallelic loci.");
+			continue;
+		}
+
+		e.get_alleles_vector(alleles);
+
+		for (unsigned int ui=0; ui<N_indv; ui++)
+		{
+			if (include_indv[ui] == false)
+				continue;
+
+			tmp_file = tmp_files[ui];
+
+			genotype = make_pair(-1,-1);
+			phase = '/';
+			if (include_genotype[s][ui] == true)
+			{
+				e.parse_genotype_entry(ui, true);
+				e.get_indv_GENOTYPE_ids(ui, genotype);
+				phase = e.get_indv_PHASE(ui);
+			}
+
+			if (genotype.first == -1)
+				(*tmp_file) << "\t0";
+			else
+				(*tmp_file) << "\t" << alleles[genotype.first];
+
+			if (genotype.second == -1)
+			{
+				if (phase == '/')
+					(*tmp_file) << "\t0";
+				else if (genotype.first != -1)
+					(*tmp_file) << "\t" << alleles[genotype.first];	// Male X-chr, Y-chr etc
+				else
+					(*tmp_file) << "\t0";
+			}
+			else
+				(*tmp_file) << "\t" << alleles[genotype.second];
+		}
+	}
+
+	ofstream PED(ped_file.c_str());
+	if (!PED.is_open()) error("Could not open output file: " + ped_file, 12);
+	string tmp_line;
+	for (unsigned int ui=0; ui<N_indv; ui++)
+	{
+		if (include_indv[ui] == false)
+			continue;
+
+		ofstream *tmp_file = tmp_files[ui];
+		(*tmp_file) << endl;
+		tmp_file->close();
+
+		ifstream read_file(tmp_filenames[ui].c_str());
+		if (!read_file.good())
+			error("\n\nCould not open temporary file.\n\n"
+					"Most likely this is because the system is not allowing me to open enough temporary files.\n"
+					"Try using ulimit -n <int> to increase the number of allowed open files.\n"
+					"Alternatively, try the --plink-tped command.", 12);
+		getline(read_file, tmp_line);
+		PED << tmp_line << endl;
+		read_file.close();
+		remove(tmp_filenames[ui].c_str());
+	}
+	PED.close();
+
+	printLOG("Writing PLINK MAP file ... ");
+	ofstream MAP(map_file.c_str());
+	if (!MAP.is_open()) error("Could not open output file: " + map_file, 12);
+	int POS; string ID;
+	for (unsigned int s=0; s<N_entries; s++)
+	{
+		if (include_entry[s] == false)
+			continue;
+
+		get_vcf_entry(s, vcf_line);
+		e.reset(vcf_line);
+		e.parse_basic_entry(true);
+		if (e.get_N_alleles() > 2)
+			continue;
+		POS = e.get_POS();
+		ID = e.get_ID();
+		if (ID == ".")
+			MAP << e.get_CHROM() << "\t" << POS << "\t0\t" << POS << endl;
+		else
+			MAP << e.get_CHROM() << "\t" << ID << "\t0\t" << POS << endl;
+	}
+
+	MAP.close();
+	printLOG("Done.\n");
+}
+
+// Output as Plink Transposed file
+void vcf_file::output_as_plink_tped(const string &output_file_prefix)
+{
+	// Output as PLINK formatted PED/MAP files.
+	if (has_genotypes == false)
+		error("Require Genotypes in VCF file in order to output as PLINK TPED.");
+
+	printLOG("Writing PLINK TPED file ... ");
+	string tped_file = output_file_prefix + ".tped";
+	string tfam_file = output_file_prefix + ".tfam";
+
+	ofstream TPED(tped_file.c_str());
+	if (!TPED.is_open()) error("Could not open output file: " + tped_file, 12);
+
+	vector<string> alleles;
+	char phase;
+	pair<int, int> genotype;
+	string vcf_line;
+	vcf_entry e(N_indv);
+	for (unsigned int s=0; s<N_entries; s++)
+	{
+		if (include_entry[s] == false)
+			continue;
+
+		get_vcf_entry(s, vcf_line);
+		e.reset(vcf_line);
+		e.parse_basic_entry(true);
+
+		if (e.get_N_alleles() > 2)	// Only output sites with at most one alternative allele
+		{
+			one_off_warning("\tPLINK-TPED: Only outputting biallelic loci.");
+			continue;
+		}
+
+		if (e.get_ID() == ".")
+			TPED << e.get_CHROM() << "\t" << e.get_POS() << "\t0\t" << e.get_POS();
+		else
+			TPED << e.get_CHROM() << "\t" << e.get_ID() << "\t0\t" << e.get_POS();
+
+		e.get_alleles_vector(alleles);
+
+		for (unsigned int ui=0; ui<N_indv; ui++)
+		{
+			if (include_indv[ui] == false)
+				continue;
+
+			genotype = make_pair(-1,-1);
+			phase = '/';
+			if (include_genotype[s][ui] == true)
+			{
+				e.parse_genotype_entry(ui, true);
+				e.get_indv_GENOTYPE_ids(ui, genotype);
+				phase = e.get_indv_PHASE(ui);
+			}
+
+			if (genotype.first == -1)
+				TPED << "\t0";
+			else
+				TPED << "\t" << alleles[genotype.first];
+
+			if (genotype.second == -1)
+			{
+				if (phase == '/')
+					TPED << "\t0";
+				else if (genotype.first != -1)
+					TPED << "\t" << alleles[genotype.first];	// Male X-chr, Y-chr etc
+				else
+					TPED << "\t0";
+			}
+			else
+				TPED << "\t" << alleles[genotype.second];
+		}
+		TPED << endl;
+	}
+
+	TPED.close();
+
+	printLOG("Writing PLINK TFAM file ... ");
+	ofstream TFAM(tfam_file.c_str());
+	if (!TFAM.is_open()) error("Could not open output file: " + tfam_file, 12);
+	for (unsigned int ui=0; ui<N_indv; ui++)
+	{
+		if (include_indv[ui] == false)
+			continue;
+		TFAM << indv[ui] << "\t" << indv[ui] << "\t" << 0 << "\t" << 0 << "\t" << 0 << "\t" << 0 << endl;
+	}
+
+	TFAM.close();
+	printLOG("Done.\n");
+}
+
+/*
+// Output as a simple 0/1/2 matrix
+void vcf_file::output_as_012_matrix(const string &output_file_prefix)
+{
+	if (has_genotypes == false)
+		error("Require Genotypes in VCF file in order to output as 0/1/2 matrix.");
+
+	printLOG("Writing 012 matrix file ... ");
+	string ped_file = output_file_prefix + ".012";
+	string map_file = output_file_prefix + ".012.pos";
+	string fam_file = output_file_prefix + ".012.indv";
+
+	ofstream PED(ped_file.c_str());
+	if (!PED.is_open()) error("Could not open output file: " + ped_file, 12);
+	string allele1, allele2;
+
+	ofstream FAM(fam_file.c_str());
+	if (!FAM.is_open()) error("Could not open output file: " + fam_file, 12);
+
+	pair<int, int> genotype;
+	string vcf_line;
+	vcf_entry e(N_indv);
+	for (unsigned int ui=0; ui<N_indv; ui++)
+	{
+		if (include_indv[ui] == false)
+			continue;
+		FAM << indv[ui] << endl;
+		PED << ui;
+		//uk = 2*ui;
+		for (unsigned int s=0; s<N_entries; s++)
+		{
+			if (include_entry[s] == false)
+				continue;
+
+			get_vcf_entry(s, vcf_line);
+			e.reset(vcf_line);
+			e.parse_basic_entry(true);
+
+			if (e.get_N_alleles() <= 2)	// Only output sites with one alternative allele
+			{
+				genotype = make_pair(-1,-1);
+				if (include_genotype[s][ui] == true)
+				{
+					e.parse_genotype_entry(ui, true);
+					e.get_indv_GENOTYPE_ids(ui, genotype);
+				}
+
+				if ((genotype.first == -1) && (genotype.second == -1))
+					PED << "\t-1";	// Missing data
+				else if ((genotype.first == 0) && (genotype.second == 0))
+					PED << "\t0";	// No copies of the alternative allele
+				else
+				{
+					if ((genotype.first == 1) && (genotype.second == 1))
+						PED << "\t2";	// Two copies of the alternative allele
+					else
+						PED << "\t1";	// Must be one copy of the alternative allele.
+				}
+			}
+		}
+		PED << endl;
+	}
+
+	FAM.close();
+	PED.close();
+
+	ofstream MAP(map_file.c_str());
+	if (!MAP.is_open()) error("Could not open output file: " + map_file, 12);
+	for (unsigned int s=0; s<N_entries; s++)
+	{
+		if (include_entry[s] == false)
+			continue;
+
+		get_vcf_entry(s, vcf_line);
+		e.reset(vcf_line);
+		e.parse_basic_entry(true);
+		if (e.get_N_alleles() <= 2)	// Only output sites with one alternative allele
+		{
+			MAP << e.get_CHROM() << "\t" << e.get_POS() << endl;
+		}
+	}
+
+	MAP.close();
+	printLOG("Done.\n");
+}
+*/
+
+void vcf_file::output_as_012_matrix(const string &output_file_prefix)
+{
+	// Output as PLINK formatted PED/MAP files.
+	if (has_genotypes == false)
+		error("Require Genotypes in VCF file in order to output as 0/1/2 matrix.");
+
+	printLOG("Writing 012 matrix file ... ");
+	string ped_file = output_file_prefix + ".012";
+	string map_file = output_file_prefix + ".012.pos";
+	string fam_file = output_file_prefix + ".012.indv";
+
+	ofstream FAM(fam_file.c_str());
+	if (!FAM.is_open()) error("Could not open output file: " + fam_file, 12);
+
+	vector<ofstream *> tmp_files(N_indv);
+	vector<string> tmp_filenames(N_indv);
+	for (unsigned int ui=0; ui<N_indv; ui++)
+	{
+		if (include_indv[ui] == false)
+			continue;
+		FAM << indv[ui] << endl;
+		string filename(tmpnam(NULL));
+		ofstream *tmp_file = new ofstream(filename.c_str());
+		if (!tmp_file->good())
+			error("\n\nCould not open temporary file.\n\n"
+			"Most likely this is because the system is not allowing me to open enough temporary files.\n"
+			"Try using ulimit -n <int> to increase the number of allowed open files.\n", 12);
+		(*tmp_file) << ui;
+		tmp_files[ui] = tmp_file;
+		tmp_filenames[ui] = filename;
+	}
+
+	FAM.close();
+
+	vector<string> alleles;
+	char phase;
+	pair<int, int> genotype;
+	string vcf_line;
+	vcf_entry e(N_indv);
+	ofstream *tmp_file;
+	for (unsigned int s=0; s<N_entries; s++)
+	{
+		if (include_entry[s] == false)
+			continue;
+
+		get_vcf_entry(s, vcf_line);
+		e.reset(vcf_line);
+		e.parse_basic_entry(true);
+
+		if (e.get_N_alleles() > 2)
+		{
+			one_off_warning("\t012: Only outputting biallelic loci.");
+			continue;
+		}
+
+		e.get_alleles_vector(alleles);
+
+		for (unsigned int ui=0; ui<N_indv; ui++)
+		{
+			if (include_indv[ui] == false)
+				continue;
+
+			tmp_file = tmp_files[ui];
+
+			genotype = make_pair(-1,-1);
+			phase = '/';
+			if (include_genotype[s][ui] == true)
+			{
+				e.parse_genotype_entry(ui, true);
+				e.get_indv_GENOTYPE_ids(ui, genotype);
+				phase = e.get_indv_PHASE(ui);
+			}
+
+			if ((genotype.first == -1) && (genotype.second == -1))
+				(*tmp_file) << "\t-1";	// Missing data
+			else if ((genotype.first == 0) && (genotype.second == 0))
+				(*tmp_file) << "\t0";	// No copies of the alternative allele
+			else
+			{
+				if ((genotype.first == 1) && (genotype.second == 1))
+					(*tmp_file) << "\t2";	// Two copies of the alternative allele
+				else
+					(*tmp_file) << "\t1";	// Must be one copy of the alternative allele.
+			}
+		}
+	}
+
+	ofstream PED(ped_file.c_str());
+	if (!PED.is_open()) error("Could not open output file: " + ped_file, 12);
+	string tmp_line;
+	for (unsigned int ui=0; ui<N_indv; ui++)
+	{
+		if (include_indv[ui] == false)
+			continue;
+
+		ofstream *tmp_file = tmp_files[ui];
+		(*tmp_file) << endl;
+		tmp_file->close();
+
+		ifstream read_file(tmp_filenames[ui].c_str());
+		if (!read_file.good())
+			error("\n\nCould not open temporary file.\n\n"
+			"Most likely this is because the system is not allowing me to open enough temporary files.\n"
+			"Try using ulimit -n <int> to increase the number of allowed open files.\n", 12);
+		getline(read_file, tmp_line);
+		PED << tmp_line << endl;
+		read_file.close();
+		remove(tmp_filenames[ui].c_str());
+	}
+	PED.close();
+
+	printLOG("Writing 012 positions file ... ");
+	ofstream MAP(map_file.c_str());
+	if (!MAP.is_open()) error("Could not open output file: " + map_file, 12);
+	for (unsigned int s=0; s<N_entries; s++)
+	{
+		if (include_entry[s] == false)
+			continue;
+
+		get_vcf_entry(s, vcf_line);
+		e.reset(vcf_line);
+		e.parse_basic_entry(true);
+		if (e.get_N_alleles() <= 2)	// Only output sites with one alternative allele
+		{
+			MAP << e.get_CHROM() << "\t" << e.get_POS() << endl;
+		}
+	}
+
+	MAP.close();
+	printLOG("Done.\n");
+}
+
+// Output as IMPUTE format
+void vcf_file::output_as_IMPUTE(const string &output_file_prefix)
+{
+	if (has_genotypes == false)
+		error("Require Genotypes in VCF file in order to output IMPUTE format.");
+
+	printLOG("Outputting in IMPUTE format (bi-allelic, completely phased SNPs only)\n");
+	unsigned int s, ui;
+	string legend_file = output_file_prefix + ".impute.legend";
+	string haplotype_file = output_file_prefix + ".impute.hap";
+	string indv_file = output_file_prefix + ".impute.hap.indv";
+	ofstream legend(legend_file.c_str());
+	if (!legend.is_open())
+		error("Could not open IMPUTE Legend Output File: " + legend_file, 2);
+	legend << "ID pos allele0 allele1" << endl;
+
+	ofstream hap(haplotype_file.c_str());
+	if (!hap.is_open())
+		error("Could not open IMPUTE Haplotype Output File: " + haplotype_file, 2);
+
+	ofstream indv_out(indv_file.c_str());
+	if (!indv_out.is_open())
+		error("Could not open IMPUTE Individual Output File: " + indv_file, 2);
+
+	for (ui=0; ui<N_indv; ui++)
+	{
+		if (include_indv[ui] == false)
+			continue;
+		indv_out << indv[ui] << endl;
+	}
+	indv_out.close();
+
+	pair<int, int> alleles;
+	string vcf_line;
+	vcf_entry e(N_indv);
+	for (s=0; s<N_entries; s++)
+	{
+		if (include_entry[s] == false)
+			continue;
+
+		get_vcf_entry(s, vcf_line);
+		e.reset(vcf_line);
+		e.parse_basic_entry(true);
+
+		if (e.get_N_alleles() > 2)
+		{
+			one_off_warning("\tIMPUTE: Only outputting biallelic loci.");
+			continue;
+		}
+
+		// Exclude entries with missing data and/or unphased
+		bool missing = false;
+		for (ui=0; ui<N_indv; ui++)
+		{
+			if (include_indv[ui] == false)
+				continue;
+
+			if (include_genotype[s][ui] == false)
+			{
+				missing = true;
+				break;
+			}
+
+			e.parse_genotype_entry(ui, true);
+			e.get_indv_GENOTYPE_ids(ui, alleles);
+			if ((alleles.first == -1) || (alleles.second == -1))
+			{
+				missing = true;
+				break;
+			}
+
+			if (e.get_indv_PHASE(ui) != '|')
+			{
+				missing = true;
+				break;
+			}
+		}
+		if (missing == true)
+			continue;
+
+		if (e.get_ID() == ".")
+		{
+			legend << e.get_CHROM() << "-" << e.get_POS() << " " << e.get_POS() << " " << e.get_REF() << " " << e.get_ALT_allele(0) << endl;
+		}
+		else
+			legend << e.get_ID() << " " << e.get_POS() << " " << e.get_REF() << " " << e.get_ALT_allele(0) << endl;
+
+		bool first = true;
+		for (ui=0; ui<N_indv; ui++)
+		{
+			if (include_indv[ui] == false)
+				continue;
+
+			e.parse_genotype_entry(ui, true);
+			e.get_indv_GENOTYPE_ids(ui, alleles);
+			if (first == true)
+			{
+				hap << alleles.first << " " << alleles.second;
+				first = false;
+			}
+			else
+				hap << " " << alleles.first << " " << alleles.second;
+		}
+		hap << endl;
+	}
+
+	hap.close();
+	legend.close();
+}
+
+void vcf_file::output_LDhat_locs_file(const string &output_file_prefix, const string &chr, unsigned int &n_sites_out)
+{
+	string locs_file = output_file_prefix + ".ldhat.locs";
+	ofstream locs(locs_file.c_str());
+	if (!locs.is_open())
+		error("Could not open LDhat locs Output File: " + locs_file, 2);
+
+	int max_pos = -1;
+	unsigned int n_sites=0;
+
+	vcf_entry e(N_indv);
+	string vcf_line;
+	string chrom;
+	for (unsigned int s=0; s<N_entries; s++)
+	{
+		if (include_entry[s] == false)
+			continue;
+
+		get_vcf_entry(s, vcf_line);
+		e.reset(vcf_line);
+		e.parse_basic_entry(true);
+
+		if (e.get_N_alleles() != 2)
+		{
+			continue;
+		}
+
+		e.get_CHROM(chrom);
+		if (chrom != chr)
+			error("Mismatching chromosome in LDhat loci", 13);
+
+		max_pos = max(e.get_POS(), max_pos);
+		n_sites++;
+	}
+
+	locs << n_sites;
+	locs.setf(ios::fixed,ios::floatfield);
+	locs.precision(4);
+	locs << "\t" << max_pos / 1000.0 << "\tL" << endl;
+	for (unsigned int s=0; s<N_entries; s++)
+	{
+		if (include_entry[s] == false)
+			continue;
+
+		get_vcf_entry(s, vcf_line);
+		e.reset(vcf_line);
+		e.parse_basic_entry(true);
+
+		if (e.get_N_alleles() != 2)
+		{
+			one_off_warning("\tLDhat: Only outputting biallelic loci.");
+			continue;
+		}
+
+		locs << e.get_POS() / 1000.0 << endl;
+	}
+	locs.close();
+
+	n_sites_out = n_sites;
+}
+
+void vcf_file::output_as_LDhat_phased(const string &output_file_prefix, const string &chr)
+{
+	if (has_genotypes == false)
+		error("Require Genotypes in VCF file in order to output LDhat format.");
+
+	printLOG("Outputting in phased LDhat format\n");
+	if (chr == "")
+		error("Require chromosome for LDhat output", 10);
+
+	unsigned int n_sites;
+	output_LDhat_locs_file(output_file_prefix, chr, n_sites);
+
+	string sites_file = output_file_prefix + ".ldhat.sites";
+	ofstream sites(sites_file.c_str());
+	if (!sites.is_open())
+		error("Could not open LDhat sites Output File: " + sites_file, 2);
+
+	unsigned int n_indv = N_kept_individuals();
+	pair<int, int> alleles;
+
+	sites << n_indv*2 << "\t" << n_sites << "\t1" << endl;	// Note - this is incorrect for the X-chr.
+
+	vector<ofstream *> tmp_files(2*N_indv);
+	vector<string> tmp_filenames(2*N_indv);
+	for (unsigned int ui=0; ui<N_indv; ui++)
+	{
+		if (include_indv[ui] == false)
+			continue;
+		string filename(tmpnam(NULL));
+		ofstream *tmp_file = new ofstream(filename.c_str());
+		if (!tmp_file->good())
+			error("Could not open temp file.\n", 12);
+		tmp_files[2*ui] = tmp_file;
+		tmp_filenames[2*ui] = filename;
+
+		string filename2(tmpnam(NULL));
+		ofstream *tmp_file2 = new ofstream(filename2.c_str());
+		if (!tmp_file2->good())
+			error("\n\nCould not open temporary file.\n\n"
+				"Most likely this is because the system is not allowing me to open enough temporary files.\n"
+				"Try using ulimit -n <int> to increase the number of allowed open files.\n", 12);
+		tmp_files[2*ui+1] = tmp_file2;
+		tmp_filenames[2*ui+1] = filename2;
+	}
+
+	string vcf_line;
+	vcf_entry e(N_indv);
+	ofstream *tmp_file;
+
+	for (unsigned int s=0; s<N_entries; s++)
+	{
+		if (include_entry[s] == false)
+			continue;
+
+		get_vcf_entry(s, vcf_line);
+		e.reset(vcf_line);
+		e.parse_basic_entry(true);
+
+		if (e.get_N_alleles() != 2)
+		{
+			one_off_warning("\tLDhat: Only outputting biallelic loci.");
+			continue;
+		}
+
+		for (unsigned int ui=0; ui<N_indv; ui++)
+		{
+			if (include_indv[ui] == false)
+				continue;
+
+			e.parse_genotype_entry(ui, true);
+			e.get_indv_GENOTYPE_ids(ui, alleles);
+
+			for (unsigned int k=0; k<2; k++)
+			{
+				tmp_file = tmp_files[(2*ui)+k];
+
+				int geno;
+				if (k == 0)
+					geno = alleles.first;
+				else
+					geno = alleles.second;
+
+				if ((geno != -1) && (include_genotype[s][ui]==true))
+					(*tmp_file) << geno;
+				else
+					(*tmp_file) << "?";
+			}
+		}
+	}
+
+	string tmp_line;
+	for (unsigned int ui=0; ui<N_indv; ui++)
+	{
+		if (include_indv[ui] == false)
+			continue;
+
+		for (unsigned int k=0; k<2; k++)
+		{
+			ofstream *tmp_file = tmp_files[2*ui+k];
+			(*tmp_file) << endl;
+			tmp_file->close();
+
+			ifstream read_file(tmp_filenames[2*ui+k].c_str());
+			if (!read_file.good())
+				error("\n\nCould not open temporary file.\n\n"
+				"Most likely this is because the system is not allowing me to open enough temporary files.\n"
+				"Try using ulimit -n <int> to increase the number of allowed open files.\n", 12);
+			getline(read_file, tmp_line);
+			sites << ">" << indv[ui] << "-" << k << endl;
+			sites << tmp_line << endl;
+			read_file.close();
+			remove(tmp_filenames[2*ui+k].c_str());
+		}
+	}
+
+	sites.close();
+}
+
+void vcf_file::output_as_LDhat_unphased(const string &output_file_prefix, const string &chr)
+{
+	if (has_genotypes == false)
+		error("Require Genotypes in VCF file in order to output LDhat format.");
+
+	printLOG("Outputting in unphased LDhat format\n");
+	if (chr == "")
+		error("Require chromosome for LDhat output", 10);
+
+	unsigned int n_sites;
+	output_LDhat_locs_file(output_file_prefix, chr, n_sites);
+
+	string sites_file = output_file_prefix + ".ldhat.sites";
+	ofstream sites(sites_file.c_str());
+	if (!sites.is_open())
+		error("Could not open LDhat sites Output File: " + sites_file, 2);
+
+	unsigned int n_indv = N_kept_individuals();
+	pair<int, int> alleles;
+
+	sites << n_indv << "\t" << n_sites << "\t2" << endl;
+
+	vector<ofstream *> tmp_files(N_indv);
+	vector<string> tmp_filenames(N_indv);
+	for (unsigned int ui=0; ui<N_indv; ui++)
+	{
+		if (include_indv[ui] == false)
+			continue;
+		string filename(tmpnam(NULL));
+		ofstream *tmp_file = new ofstream(filename.c_str());
+		if (!tmp_file->good())
+			error("\n\nCould not open temporary file.\n\n"
+					"Most likely this is because the system is not allowing me to open enough temporary files.\n"
+					"Try using ulimit -n <int> to increase the number of allowed open files.\n", 12);
+		tmp_files[ui] = tmp_file;
+		tmp_filenames[ui] = filename;
+	}
+
+	string vcf_line;
+	vcf_entry e(N_indv);
+	ofstream *tmp_file;
+	for (unsigned int s=0; s<N_entries; s++)
+	{
+		if (include_entry[s] == false)
+			continue;
+
+		get_vcf_entry(s, vcf_line);
+		e.reset(vcf_line);
+		e.parse_basic_entry(true);
+
+		if (e.get_N_alleles() != 2)
+		{
+			one_off_warning("\tLDhat: Only outputting biallelic loci.");
+			continue;
+		}
+
+		for (unsigned int ui=0; ui<N_indv; ui++)
+		{
+			if (include_indv[ui] == false)
+				continue;
+
+			tmp_file = tmp_files[ui];
+
+			if (include_genotype[s][ui] == false)
+				(*tmp_file) << "?";
+			else
+			{
+				e.parse_genotype_entry(ui, true);
+				e.get_indv_GENOTYPE_ids(ui, alleles);
+
+				switch (alleles.first)
+				{
+				case -1:
+					(*tmp_file) << "?"; break;
+				case 0:
+					if (alleles.second == 0)
+						(*tmp_file) << 0;
+					else if (alleles.second == 1)
+						(*tmp_file) << 2;
+					else if ((alleles.second == -1) && (e.get_indv_PHASE(ui) == '|'))
+						(*tmp_file) << 0;	// Haploid case
+					else
+						(*tmp_file) << '?';
+					break;
+				case 1:
+					if (alleles.second == 0)
+						(*tmp_file) << 2;
+					else if (alleles.second == 1)
+						(*tmp_file) << 1;
+					else if ((alleles.second == -1) && (e.get_indv_PHASE(ui) == '|'))
+						(*tmp_file) << 1;	// Haploid case
+					else
+						(*tmp_file) << '?';
+					break;
+				default:
+					(*tmp_file) << '?';
+				}
+			}
+		}
+	}
+
+	string tmp_line;
+	for (unsigned int ui=0; ui<N_indv; ui++)
+	{
+		if (include_indv[ui] == false)
+			continue;
+
+		ofstream *tmp_file = tmp_files[ui];
+		(*tmp_file) << endl;
+		tmp_file->close();
+
+		ifstream read_file(tmp_filenames[ui].c_str());
+		if (!read_file.good())
+			error("\n\nCould not open temporary file.\n\n"
+				"Most likely this is because the system is not allowing me to open enough temporary files.\n"
+				"Try using ulimit -n <int> to increase the number of allowed open files.\n", 12);
+		getline(read_file, tmp_line);
+		sites << ">" << indv[ui] << endl;
+		sites << tmp_line << endl;
+		read_file.close();
+		remove(tmp_filenames[ui].c_str());
+	}
+
+	sites.close();
+}
+
+// Output INFO fields in tab-delimited format
+void vcf_file::output_INFO_for_each_site(const string &output_file_prefix, const vector<string> &INFO_to_extract)
+{
+	if (INFO_to_extract.size() == 0)
+		return;
+
+	printLOG("Outputting INFO for each site\n");
+	string output = output_file_prefix + ".INFO";
+	ofstream out(output.c_str());
+	if (!out.is_open())
+		error("Could not open INFO Output File: " + output, 3);
+
+	out << "CHROM\tPOS\tREF\tALT";
+	for (unsigned int ui=0; ui<INFO_to_extract.size(); ui++)
+		out << "\t" << INFO_to_extract[ui];
+	out << endl;
+
+	string vcf_line;
+	vcf_entry e(N_indv);
+	for (unsigned int s=0; s<N_entries; s++)
+	{
+		if (include_entry[s] == false)
+			continue;
+
+		get_vcf_entry(s, vcf_line);
+		e.reset(vcf_line);
+		e.parse_basic_entry(true, false, true);
+
+		out << e.get_CHROM() << "\t" << e.get_POS() << "\t" << e.get_REF() << "\t" << e.get_ALT();
+
+		for (unsigned int ui=0; ui<INFO_to_extract.size(); ui++)
+		{
+			out << "\t" << e.get_INFO_value(INFO_to_extract[ui]);
+		}
+		out << endl;
+	}
+
+	out.close();
+}
+
+
+// Output FORMAT information in tab-delimited format.
+void vcf_file::output_FORMAT_information(const string &output_file_prefix, const string &FORMAT_id)
+{
+	if (FORMAT_id == "")
+		return;
+
+	if (has_genotypes == false)
+		error("Require Genotypes in VCF file in order to output FORMAT information.");
+
+	printLOG("Outputting FORMAT information for " + FORMAT_id + "\n");
+	string output = output_file_prefix + "." + FORMAT_id + ".FORMAT";
+	ofstream out(output.c_str());
+	if (!out.is_open())
+		error("Could not open FORMAT Output File: " + output, 7);
+
+	out << "CHROM\tPOS";
+	for (unsigned int ui=0; ui<N_indv; ui++)
+	{
+		if (include_indv[ui] == true)
+			out << "\t" << indv[ui];
+	}
+	out << endl;
+
+	string vcf_line, FORMAT_out;
+	vcf_entry e(N_indv);
+	for (unsigned int s=0; s<N_entries; s++)
+	{
+		if (include_entry[s] == false)
+			continue;
+
+		get_vcf_entry(s, vcf_line);
+		e.reset(vcf_line);
+		e.parse_basic_entry();
+		e.parse_full_entry(true);
+
+		if (e.FORMAT_id_exists(FORMAT_id) == false)
+			continue;
+
+		out << e.get_CHROM() << "\t" << e.get_POS();
+
+		for (unsigned int ui=0; ui<N_indv; ui++)
+		{
+			if (include_indv[ui] == false)
+				continue;
+
+			e.read_indv_generic_entry(ui, FORMAT_id, FORMAT_out);
+			out << "\t" << FORMAT_out;
+		}
+		out << endl;
+	}
+	out.close();
+}
+
+// Output genotype likelihoods from GL FORMAT tag, ready for input into BEAGLE
+// using the Genotype likelihoods file format.
+void vcf_file::output_BEAGLE_genotype_likelihoods(const string &output_file_prefix)
+{
+	if (has_genotypes == false)
+		error("Require Genotypes in VCF file in order to output BEAGLE genotype likelihoods.");
+
+	printLOG("Outputting in BEAGLE Genotype Likelihood format (bi-allelic SNPs with GL tags only)\n");
+
+	string output = output_file_prefix + ".BEAGLE.GL";
+	ofstream out(output.c_str());
+	if (!out.is_open())
+		error("Could not open BEAGLE GL Output File: " + output, 3);
+	out << "marker\talleleA\talleleB";
+	for (unsigned int ui=0; ui<N_indv; ui++)
+	{
+		if (include_indv[ui] == true)
+			out << "\t" << indv[ui] << "\t" << indv[ui] << "\t" << indv[ui];
+	}
+	out << endl;
+
+	string vcf_line, GL_entry, tmp_string;
+	vcf_entry e(N_indv);
+	double lk1, lk2, lk3;
+	bool found_GL=false;
+	istringstream ss;
+
+	for (unsigned int s=0; s<N_entries; s++)
+	{
+		if (include_entry[s] == false)
+			continue;
+
+		get_vcf_entry(s, vcf_line);
+		e.reset(vcf_line);
+		e.parse_basic_entry(true);
+
+		if (e.get_N_alleles() != 2)
+		{
+			one_off_warning("\tBEAGLE: Only outputting biallelic loci.");
+			continue;
+		}
+
+		e.parse_full_entry(true);
+
+		if (e.FORMAT_id_exists("GL") == false)
+			continue;
+		found_GL = true;
+
+		out << e.get_CHROM() << ":" << e.get_POS() << "\t" << e.get_REF() << "\t" << e.get_ALT();
+
+		for (unsigned int ui=0; ui<N_indv; ui++)
+		{
+			if (include_indv[ui] == false)
+				continue;
+
+			if (include_genotype[s][ui] == true)
+			{
+				e.read_indv_generic_entry(ui, "GL", GL_entry);
+				ss.clear();
+				ss.str(GL_entry);
+				getline(ss, tmp_string, ',');
+				lk1 = atof(tmp_string.c_str());
+				getline(ss, tmp_string, ',');
+				lk2 = atof(tmp_string.c_str());
+				getline(ss, tmp_string);
+				lk3 = atof(tmp_string.c_str());
+				out << "\t" << pow(10,lk1) << "\t" << pow(10,lk2) << "\t" << pow(10,lk3);
+			}
+			else
+			{
+				out << "\t1\t1\t1";	// Mark as unknown
+			}
+		}
+		out << endl;
+	}
+
+	if (found_GL == false)
+		error("Require GL FORMAT tags in VCF file to output BEAGLE input.");
+}
+