void Formatter::format(double lambda, char new_separator, int& n_total, int& n_filtered) throw (FormatterException) {
Descriptor* descriptor = NULL;
char* line = NULL;
int line_length = 0;
unsigned int line_number = 2;
char* token = NULL;
char data_separator = '\0';
const char* output_prefix = NULL;
const char* file_name = NULL;
char* o_gwafile_name = NULL;
vector<double>* snp_hq = NULL;
double maf_filter_value = -numeric_limits<double>::infinity();
double oevar_imp_filter_value = -numeric_limits<double>::infinity();
bool maf_filter = false;
bool oevar_imp_filter = false;
Column* column = NULL;
ofstream ofile_stream;
double d_value = 0.0;
n_total = 0;
n_filtered = 0;
if (gwafile == NULL) {
return;
}
try {
descriptor = gwafile->get_descriptor();
output_prefix = descriptor->get_property(Descriptor::PREFIX);
file_name = descriptor->get_name();
snp_hq = descriptor->get_threshold(Descriptor::SNP_HQ);
data_separator = gwafile->get_data_separator();
auxiliary::transform_file_name(&o_gwafile_name, output_prefix, file_name, NULL, true);
if (o_gwafile_name == NULL) {
throw FormatterException("Formatter", "format( double , char , int& , int& )", __LINE__, 10);
}
if (((maf_filter_value = snp_hq->at(0)) > 0) && (maf_column_pos >= 0)){
maf_filter = true;
}
if (((oevar_imp_filter_value = snp_hq->at(1)) > 0) && (oevar_imp_column_pos >= 0)) {
oevar_imp_filter = true;
}
for (columns_it = input_columns.begin(); columns_it != input_columns.end(); columns_it++) {
output_columns.push_back(*columns_it);
}
if (!isnan(lambda)) {
if (stderr_column != NULL) {
column = new CorrectedStandardErrorColumn(stderr_column, lambda);
column->set_header("%s_gc", stderr_column->get_header());
column->set_order(descriptor->get_column_order(column->get_header(), gwafile->is_case_sensitive()));
output_columns.push_back(column);
}
if (pvalue_column != NULL) {
column = new CorrectedPvalueColumn(pvalue_column, lambda);
column->set_header("%s_gc", pvalue_column->get_header());
column->set_order(descriptor->get_column_order(column->get_header(), gwafile->is_case_sensitive()));
output_columns.push_back(column);
}
}
if ((oevar_imp_column != NULL) && (n_total_column != NULL)) {
column = new EffectiveSampleSizeColumn(n_total_column, oevar_imp_column);
column->set_header("%s_effective", n_total_column->get_header());
column->set_order(descriptor->get_column_order(column->get_header(), gwafile->is_case_sensitive()));
output_columns.push_back(column);
}
if (gwafile->is_order_on()) {
if (descriptor->get_reordered_columns_number() > 0) {
stable_sort(output_columns.begin(), output_columns.end(), compare_columns);
} else {
stable_sort(output_columns.begin(), output_columns.end(), compare_columns_by_name);
}
}
ofile_stream.exceptions(ios_base::failbit | ios_base::badbit);
ofile_stream.precision(numeric_limits<double>::digits10);
try {
ofile_stream.open(o_gwafile_name);
} catch (ofstream::failure &e) {
throw FormatterException("Formatter", "format( double , char , int& , int& )", __LINE__, 11, o_gwafile_name);
}
try {
columns_it = output_columns.begin();
if (columns_it != output_columns.end()) {
ofile_stream << (*columns_it)->get_header();
while (++columns_it != output_columns.end()) {
ofile_stream << new_separator << (*columns_it)->get_header();
}
ofile_stream << endl;
}
if (maf_filter) {
if (oevar_imp_filter) {
// all filters
while ((line_length = reader.read_line()) > 0) {
line = *reader.line;
// for (columns_it = input_columns.begin(); columns_it != input_columns.end(); (*columns_it)->char_value = auxiliary::strtok(&line, data_separator), columns_it++);
for (columns_it = input_columns.begin(); columns_it != input_columns.end(); ++columns_it) {
token = auxiliary::strtok(&line, data_separator);
if (token == NULL) {
(*columns_it)->char_value = "";
} else {
auxiliary::trim(&token);
(*columns_it)->char_value = token;
}
// auxiliary::trim(&token);
// (*columns_it)->char_value = token;
}
d_value = maf_column->get_numeric_value();
d_value = d_value > 0.5 ? 1.0 - d_value : d_value;
if (auxiliary::fcmp(d_value, maf_filter_value, EPSILON) == 1) {
d_value = oevar_imp_column->get_numeric_value();
if (auxiliary::fcmp(d_value, oevar_imp_filter_value, EPSILON) == 1) {
columns_it = output_columns.begin();
if (columns_it != output_columns.end()) {
(*columns_it)->out(ofile_stream);
while (++columns_it != output_columns.end()) {
ofile_stream << new_separator;
(*columns_it)->out(ofile_stream);
}
ofile_stream << endl;
}
n_filtered += 1;
}
}
line_number += 1;
}
} else {
// only maf filter
while ((line_length = reader.read_line()) > 0) {
line = *reader.line;
// for (columns_it = input_columns.begin(); columns_it != input_columns.end(); (*columns_it)->char_value = auxiliary::strtok(&line, data_separator), columns_it++);
for (columns_it = input_columns.begin(); columns_it != input_columns.end(); ++columns_it) {
token = auxiliary::strtok(&line, data_separator);
if (token == NULL) {
(*columns_it)->char_value = "";
} else {
auxiliary::trim(&token);
(*columns_it)->char_value = token;
}
// auxiliary::trim(&token);
// (*columns_it)->char_value = token;
}
d_value = maf_column->get_numeric_value();
d_value = d_value > 0.5 ? 1.0 - d_value : d_value;
if (auxiliary::fcmp(d_value, maf_filter_value, EPSILON) == 1) {
columns_it = output_columns.begin();
if (columns_it != output_columns.end()) {
(*columns_it)->out(ofile_stream);
while (++columns_it != output_columns.end()) {
ofile_stream << new_separator;
(*columns_it)->out(ofile_stream);
}
ofile_stream << endl;
}
n_filtered += 1;
}
line_number += 1;
}
}
} else if (oevar_imp_filter) {
// only oevar_imp filter
while ((line_length = reader.read_line()) > 0) {
line = *reader.line;
// for (columns_it = input_columns.begin(); columns_it != input_columns.end(); (*columns_it)->char_value = auxiliary::strtok(&line, data_separator), columns_it++);
for (columns_it = input_columns.begin(); columns_it != input_columns.end(); ++columns_it) {
token = auxiliary::strtok(&line, data_separator);
if (token == NULL) {
(*columns_it)->char_value = "";
} else {
auxiliary::trim(&token);
(*columns_it)->char_value = token;
}
// auxiliary::trim(&token);
// (*columns_it)->char_value = token;
}
d_value = oevar_imp_column->get_numeric_value();
if (auxiliary::fcmp(d_value, oevar_imp_filter_value, EPSILON) == 1) {
columns_it = output_columns.begin();
if (columns_it != output_columns.end()) {
(*columns_it)->out(ofile_stream);
while (++columns_it != output_columns.end()) {
ofile_stream << new_separator;
(*columns_it)->out(ofile_stream);
}
ofile_stream << endl;
}
n_filtered += 1;
}
line_number += 1;
}
} else {
// no filters
while ((line_length = reader.read_line()) > 0) {
line = *reader.line;
// for (columns_it = input_columns.begin(); columns_it != input_columns.end(); (*columns_it)->char_value = auxiliary::strtok(&line, data_separator), columns_it++);
for (columns_it = input_columns.begin(); columns_it != input_columns.end(); ++columns_it) {
token = auxiliary::strtok(&line, data_separator);
if (token == NULL) {
(*columns_it)->char_value = "";
} else {
auxiliary::trim(&token);
(*columns_it)->char_value = token;
}
// auxiliary::trim(&token);
// (*columns_it)->char_value = token;
}
columns_it = output_columns.begin();
if (columns_it != output_columns.end()) {
(*columns_it)->out(ofile_stream);
while (++columns_it != output_columns.end()) {
ofile_stream << new_separator;
(*columns_it)->out(ofile_stream);
}
ofile_stream << endl;
}
n_filtered += 1;
line_number += 1;
}
}
} catch (ofstream::failure &e) {
throw FormatterException("Formatter", "format( double , char , int& , int& )", __LINE__, 13, o_gwafile_name);
}
try {
ofile_stream.close();
} catch (ofstream::failure &e) {
throw FormatterException("Formatter", "format( double , char , int& , int& )", __LINE__, 12, o_gwafile_name);
}
n_total = line_number - 2;
if (line_length == 0) {
throw FormatterException("Formatter", "format( double , char , int& , int& )", __LINE__, 7, line_number, gwafile->get_descriptor()->get_name());
}
} catch (DescriptorException &e) {
FormatterException new_e(e);
e.add_message("Formatter", "format( double , char , int& , int& )", __LINE__, 14, gwafile->get_descriptor()->get_name());
throw new_e;
} catch (ColumnException &e) {
FormatterException new_e(e);
e.add_message("Formatter", "format( double , char , int& , int& )", __LINE__, 14, gwafile->get_descriptor()->get_name());
throw new_e;
} catch (FormatterException &e) {
e.add_message("Formatter", "format( double , char , int& , int& )", __LINE__, 14, gwafile->get_descriptor()->get_name());
throw;
}
}
void Formatter::process_header() throw (FormatterException) {
Descriptor* descriptor = NULL;
char header_separator = '\0';
char* header = NULL;
char* token = NULL;
int column_position = 0;
const char* column_name = NULL;
const char* new_column_name = NULL;
Column* column = NULL;
if (gwafile == NULL) {
return;
}
try {
if (reader.read_line() <= 0) {
throw FormatterException("Formatter", "process_header()", __LINE__, 5, gwafile->get_descriptor()->get_name());
}
descriptor = gwafile->get_descriptor();
header_separator = gwafile->get_header_separator();
header = *reader.line;
token = auxiliary::strtok(&header, header_separator);
while (token != NULL) {
column = new Column();
new_column_name = descriptor->get_renamed_column(token);
if (new_column_name == NULL) {
new_column_name = token;
}
column_name = descriptor->get_default_column(new_column_name, gwafile->is_case_sensitive());
if (column_name != NULL) {
if (strcmp(column_name, Descriptor::MARKER) == 0) {
} else if (strcmp(column_name, Descriptor::CHR) == 0) {
} else if (strcmp(column_name, Descriptor::POSITION) == 0) {
} else if (strcmp(column_name, Descriptor::ALLELE1) == 0) {
} else if (strcmp(column_name, Descriptor::ALLELE2) == 0) {
} else if (strcmp(column_name, Descriptor::STRAND) == 0) {
} else if (strcmp(column_name, Descriptor::EFFECT) == 0) {
} else if (strcmp(column_name, Descriptor::STDERR) == 0) {
stderr_column = column;
} else if (strcmp(column_name, Descriptor::PVALUE) == 0) {
pvalue_column = column;
pvalue_column_pos = column_position;
} else if (strcmp(column_name, Descriptor::FREQLABEL) == 0) {
maf_column = column;
maf_column_pos = column_position;
} else if (strcmp(column_name, Descriptor::HWE_PVAL) == 0) {
} else if (strcmp(column_name, Descriptor::CALLRATE) == 0) {
} else if (strcmp(column_name, Descriptor::N_TOTAL) == 0) {
n_total_column = column;
} else if (strcmp(column_name, Descriptor::IMPUTED) == 0) {
} else if (strcmp(column_name, Descriptor::USED_FOR_IMP) == 0) {
} else if (strcmp(column_name, Descriptor::OEVAR_IMP) == 0) {
oevar_imp_column = column;
oevar_imp_column_pos = column_position;
} else if (strcmp(column_name, Descriptor::AVPOSTPROB) == 0) {
}
}
column->set_header(new_column_name);
column->set_order(descriptor->get_column_order(new_column_name, gwafile->is_case_sensitive()));
input_columns.push_back(column);
token = auxiliary::strtok(&header, header_separator);
column_position += 1;
}
} catch (ReaderException &e) {
FormatterException new_e(e);
new_e.add_message("Formatter", "process_header()", __LINE__, 6, gwafile->get_descriptor()->get_name());
throw new_e;
} catch (DescriptorException &e) {
FormatterException new_e(e);
new_e.add_message("Formatter", "process_header()", __LINE__, 6, gwafile->get_descriptor()->get_name());
throw new_e;
}
}