void GetNext(vcf_file &vfile, uint entry_index, vcf_entry &entry)
{
Assert (entry_index < vfile.N_entries);
string line;
vfile.get_vcf_entry(entry_index, line);
entry.reset(line);
// For the locus
bool PARSE_ALT=true;
bool PARSE_FILTER=true;
bool PARSE_INFO=true;
entry.parse_basic_entry(PARSE_ALT, PARSE_FILTER, PARSE_INFO);
// For the individuals
bool PARSE_FORMAT=true;
entry.parse_full_entry(PARSE_FORMAT);
}
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::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_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_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_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_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();
}
