void Annotator::open_regions_file() throw (AnnotatorException) {
if (gwafile == NULL) {
return;
}
try {
close_regions_file();
regions_file = gwafile->get_descriptor()->get_property(Descriptor::REGIONS_FILE);
if (regions_file == NULL) {
return;
}
regions_reader.set_file_name(regions_file);
regions_reader.open();
} catch (ReaderException& e) {
AnnotatorException new_e(e);
new_e.add_message("Annotator", "open_regions_file()", __LINE__, 3, (regions_file != NULL) ? regions_file : "NULL");
throw new_e;
} catch (DescriptorException& e) {
AnnotatorException new_e(e);
new_e.add_message("Annotator", "open_regions_file()", __LINE__, 3, (regions_file != NULL) ? regions_file : "NULL");
throw new_e;
} catch (AnnotatorException& e) {
e.add_message("Annotator", "open_regions_file()", __LINE__, 3, (regions_file != NULL) ? regions_file : "NULL");
throw;
}
}
void Annotator::open_gwafile(GwaFile* gwafile) throw (AnnotatorException) {
if (gwafile == NULL) {
throw AnnotatorException("Annotator", "open_gwafile( GwaFile* )", __LINE__, 0, "gwafile");
}
try {
close_gwafile();
if (gwafile->get_descriptor()->get_property(Descriptor::MAP_FILE) != NULL) {
has_map = true;
} else {
has_map = false;
}
this->gwafile = gwafile;
reader.set_file_name(gwafile->get_descriptor()->get_full_path());
reader.open();
} catch (DescriptorException& e) {
AnnotatorException new_e(e);
new_e.add_message("Annotator", "open_gwafile( GwaFile* )", __LINE__, 3, gwafile->get_descriptor()->get_full_path());
throw new_e;
} catch (ReaderException& e) {
AnnotatorException new_e(e);
new_e.add_message("Annotator", "open_gwafile( GwaFile* )", __LINE__, 3, gwafile->get_descriptor()->get_full_path());
throw new_e;
} catch (AnnotatorException& e) {
e.add_message("Annotator", "open_gwafile( GwaFile* )", __LINE__, 3, gwafile->get_descriptor()->get_full_path());
throw;
}
}
void Formatter::close_gwafile() throw (FormatterException) {
try {
reader.close();
} catch (ReaderException &e) {
FormatterException new_e(e);
new_e.add_message("Formatter", "close_gwafile()", __LINE__, 4, gwafile != NULL ? gwafile->get_descriptor()->get_full_path() : "NULL");
throw new_e;
}
gwafile = NULL;
input_columns.clear();
for (columns_it = output_columns.begin(); columns_it != output_columns.end(); columns_it++) {
delete *columns_it;
}
output_columns.clear();
maf_column = NULL;
pvalue_column = NULL;
stderr_column = NULL;
n_total_column = NULL;
oevar_imp_column = NULL;
pvalue_column_pos = numeric_limits<int>::min();
maf_column_pos = numeric_limits<int>::min();
oevar_imp_column_pos = numeric_limits<int>::min();
}
/**
* \brief Get the scene elements of the component.
* \param e (out) The scene elements.
*/
void bear::gui::static_text::display
( std::list<visual::scene_element>& e ) const
{
visual::scene_writing new_e
(left() + m_margin.x, bottom() + m_margin.y, m_writing);
new_e.get_rendering_attributes().combine(m_text_rendering_attributes);
e.push_back( new_e );
} // static_text::display()
// Apply transformations of the form
//
// (ite c (+ k1 a) (+ k2 a)) --> (+ (ite c k1 k2) a)
// (ite c (* k1 a) (* k2 a)) --> (* (ite c k1 k2) a)
//
// These transformations are useful for bit-vector problems, since
// they will minimize the number of adders/multipliers/etc
br_status push_ite(func_decl * f, unsigned num, expr * const * args, expr_ref & result) {
if (!m().is_ite(f))
return BR_FAILED;
expr * c = args[0];
expr * t = args[1];
expr * e = args[2];
func_decl * f_prime = 0;
expr_ref new_t(m()), new_e(m()), common(m());
bool first;
TRACE("push_ite", tout << "unifying:\n" << mk_ismt2_pp(t, m()) << "\n" << mk_ismt2_pp(e, m()) << "\n";);
void Annotator::close_regions_file() throw (AnnotatorException) {
try {
regions_reader.close();
} catch (ReaderException &e) {
AnnotatorException new_e(e);
new_e.add_message("Annotator", "close_regions_file()", __LINE__, 4, (regions_file != NULL) ? regions_file : "NULL");
throw new_e;
}
regions_file = NULL;
}
void Annotator::close_gwafile() throw (AnnotatorException) {
try {
reader.close();
} catch (ReaderException &e) {
AnnotatorException new_e(e);
new_e.add_message("Annotator", "close_gwafile()", __LINE__, 4, (gwafile != NULL) ? gwafile->get_descriptor()->get_full_path() : "NULL");
throw new_e;
}
regions_indices_it = regions_indices.begin();
while (regions_indices_it != regions_indices.end()) {
free(regions_indices_it->first);
delete regions_indices_it->second;
regions_indices_it++;
}
regions_indices.clear();
if (map_index != NULL) {
for (unsigned int i = 0u; i < map_index_size; ++i) {
free(map_index[i].name);
map_index[i].name = NULL;
}
free(map_index);
map_index = NULL;
}
if (map_chromosomes != NULL) {
for (unsigned int i = 0u; i < map_index_size; ++i) {
free(map_chromosomes[i]);
map_chromosomes[i] = NULL;
}
free(map_chromosomes);
map_chromosomes = NULL;
}
if (map_positions != NULL) {
free(map_positions);
map_positions = NULL;
}
map_index_size = 0u;
current_map_heap_size = 0u;
if (header_backup != NULL) {
free(header_backup);
header_backup = NULL;
}
gwafile = NULL;
has_map = false;
}
void MetaNumeric::finalize() throw (MetaException) {
if (n <= 0) {
numeric = false;
free(data);
data = NULL;
return;
}
if (numeric) {
mean = auxiliary::stats_mean(data, n);
sd = auxiliary::stats_sd(data, n, mean);
skew = auxiliary::stats_skewness(data, n, mean, sd);
kurtosis = auxiliary::stats_kurtosis(data, n, mean, sd);
qsort(data, n, sizeof(double), dblcmp);
median = auxiliary::stats_median_from_sorted_data(data, n);
for (unsigned int j = 0; j < 9; j++) {
quantiles[j][1] = auxiliary::stats_quantile_from_sorted_data(data, n, quantiles[j][0]);
}
min = data[0];
max = data[n - 1];
try {
if (create_histogram) {
histogram = Histogram::create(actual_name, data, n, 1000);
if (histogram != NULL) {
histogram->set_title(get_description());
}
}
if (create_boxplot) {
boxplot = Boxplot::create(actual_name, data, n, median);
if (boxplot != NULL) {
boxplot->set_quantiles(quantiles[0][1], quantiles[3][1], quantiles[4][1], quantiles[5][1], quantiles[8][1]);
boxplot->set_title(get_description());
}
}
} catch (PlotException &e) {
MetaException new_e(e);
new_e.add_message("MetaNumeric", "finalize()", __LINE__, 4, actual_name != NULL ? actual_name : "NULL");
throw new_e;
}
}
free(data);
data = NULL;
}
void Formatter::open_gwafile(GwaFile* gwafile) throw (FormatterException) {
if (gwafile == NULL) {
throw FormatterException("Formatter", "open_gwafile( GwaFile* )", __LINE__, 0, "gwafile");
}
try {
close_gwafile();
this->gwafile = gwafile;
reader.set_file_name(gwafile->get_descriptor()->get_full_path());
reader.open();
} catch (ReaderException& e) {
FormatterException new_e(e);
new_e.add_message("Formatter", "open_gwafile( GwaFile* )", __LINE__, 3, gwafile->get_descriptor()->get_full_path());
throw new_e;
} catch (FormatterException& e) {
e.add_message("Formatter", "open_gwafile( GwaFile* )", __LINE__, 3, gwafile->get_descriptor()->get_full_path());
throw;
}
}
void Annotator::process_map_file_data() throw (AnnotatorException) {
Descriptor* descriptor = NULL;
char* line = NULL;
int line_length = 0;
unsigned int line_number = 2u;
char data_separator = '\0';
char* token = NULL;
char* end_ptr = NULL;
int column_position = 0;
const char* map_marker_column = NULL;
const char* map_chr_column = NULL;
const char* map_position_column = NULL;
char* map_marker_token = NULL;
char* map_chr_token = NULL;
char* map_position_token = NULL;
marker_index* map_index_new = NULL;
char** map_chromosomes_new = NULL;
int* map_positions_new = NULL;
if ((gwafile == NULL) || (map_file == NULL)) {
return;
}
try {
descriptor = gwafile->get_descriptor();
data_separator = gwafile->get_regions_file_data_separator();
map_marker_column = descriptor->get_property(Descriptor::MAP_MARKER);
map_chr_column = descriptor->get_property(Descriptor::MAP_CHR);
map_position_column = descriptor->get_property(Descriptor::MAP_POSITION);
current_map_heap_size = MAP_HEAP_SIZE;
map_index = (marker_index*)malloc(current_map_heap_size * sizeof(marker_index));
if (map_index == NULL) {
throw AnnotatorException("Annotator", "process_map_file_data()", __LINE__, 2, (current_map_heap_size * sizeof(marker_index)));
}
map_chromosomes = (char**)malloc(current_map_heap_size * sizeof(char*));
if (map_chromosomes == NULL) {
throw AnnotatorException("Annotator", "process_map_file_data()", __LINE__, 2, (current_map_heap_size * sizeof(char*)));
}
map_positions = (int*)malloc(current_map_heap_size * sizeof(int));
if (map_positions == NULL) {
throw AnnotatorException("Annotator", "process_map_file_data()", __LINE__, 2, (current_map_heap_size * sizeof(int)));
}
while ((line_length = map_reader.read_line()) > 0) {
line = *map_reader.line;
column_position = 0;
map_marker_token = NULL;
map_chr_token = NULL;
map_position_token = NULL;
token = auxiliary::strtok(&line, data_separator);
while (token != NULL) {
if (column_position == map_marker_column_pos) {
map_marker_token = token;
} else if (column_position == map_chr_column_pos) {
map_chr_token = token;
} else if (column_position == map_position_column_pos) {
map_position_token = token;
}
token = auxiliary::strtok(&line, data_separator);
++column_position;
}
if (column_position < map_file_total_columns) {
throw AnnotatorException("Annotator", "process_map_file_data()", __LINE__, 8, line_number, map_file, column_position, map_file_total_columns);
} else if (column_position > map_file_total_columns) {
throw AnnotatorException("Annotator", "process_map_file_data()", __LINE__, 9, line_number, map_file, column_position, map_file_total_columns);
}
if ((auxiliary::strcmp_ignore_case(map_marker_token, "NA") != 0) &&
(auxiliary::strcmp_ignore_case(map_chr_token, "NA") != 0) &&
(auxiliary::strcmp_ignore_case(map_position_token, "NA") != 0)) {
if (map_index_size >= current_map_heap_size) {
current_map_heap_size += MAP_HEAP_INCREMENT;
map_index_new = (marker_index*)realloc(map_index, current_map_heap_size * sizeof(marker_index));
if (map_index_new == NULL) {
throw AnnotatorException("Annotator", "process_map_file_data()", __LINE__, 22);
}
map_index = map_index_new;
map_index_new = NULL;
map_chromosomes_new = (char**)realloc(map_chromosomes, current_map_heap_size * sizeof(char*));
if (map_chromosomes_new == NULL) {
throw AnnotatorException("Annotator", "process_map_file_data()", __LINE__, 22);
}
map_chromosomes = map_chromosomes_new;
map_chromosomes_new = NULL;
map_positions_new = (int*)realloc(map_positions, current_map_heap_size * sizeof(int));
if (map_positions_new == NULL) {
throw AnnotatorException("Annotator", "process_map_file_data()", __LINE__, 22);
}
map_positions = map_positions_new;
map_positions_new = NULL;
}
map_index[map_index_size].name = (char*)malloc((strlen(map_marker_token) + 1u) * sizeof(char));
if (map_index[map_index_size].name == NULL) {
throw AnnotatorException("Annotator", "process_map_file_data()", __LINE__, 2, ((strlen(map_marker_token) + 1u) * sizeof(char)));
}
strcpy(map_index[map_index_size].name, map_marker_token);
map_index[map_index_size].index = map_index_size;
map_chromosomes[map_index_size] = (char*)malloc((strlen(map_chr_token) + 1u) * sizeof(char));
if (map_chromosomes[map_index_size] == NULL) {
throw AnnotatorException("Annotator", "process_map_file_data()", __LINE__, 2, ((strlen(map_chr_token) + 1u) * sizeof(char)));
}
strcpy(map_chromosomes[map_index_size], map_chr_token);
map_positions[map_index_size] = (int)strtol(map_position_token, &end_ptr, 10);
if (*end_ptr != '\0') {
throw AnnotatorException("Annotator", "process_map_file_data()", __LINE__, 10, map_position_token, map_position_column, line_number);
}
if (map_positions[map_index_size] < 0) {
throw AnnotatorException("Annotator", "process_map_file_data()", __LINE__, 11, map_position_column, map_positions[map_index_size], line_number);
}
++map_index_size;
}
++line_number;
}
if (line_length == 0) {
throw AnnotatorException("Annotator", "process_map_file_data()", __LINE__, 13, line_number, map_file);
}
qsort(map_index, map_index_size, sizeof(marker_index), qsort_marker_index_cmp);
} catch (ReaderException &e) {
AnnotatorException new_e(e);
new_e.add_message("Annotator", "process_map_file_data()", __LINE__, 14, map_file);
throw new_e;
} catch (DescriptorException &e) {
AnnotatorException new_e(e);
new_e.add_message("Annotator", "process_map_file_data()", __LINE__, 14, map_file);
throw new_e;
} catch (AnnotatorException &e) {
e.add_message("Annotator", "process_map_file_data()", __LINE__, 14, map_file);
throw;
}
}
void Annotator::process_regions_file_data() throw (AnnotatorException) {
Descriptor* descriptor = NULL;
char* line = NULL;
int line_length = 0;
unsigned int line_number = 2u;
char data_separator = '\0';
char* token = NULL;
char* end_ptr = NULL;
int column_position = 0;
const char* region_name_column = NULL;
const char* region_chr_column = NULL;
const char* region_start_column = NULL;
const char* region_end_column = NULL;
char* region_name_token = NULL;
char* region_chr_token = NULL;
char* region_start_token = NULL;
char* region_end_token = NULL;
char* region_name = NULL;
char* region_chr = NULL;
int region_start = 0;
int region_end = 0;
IntervalTree<char*>* regions_index = NULL;
if ((gwafile == NULL) || (regions_file == NULL)) {
return;
}
try {
descriptor = gwafile->get_descriptor();
data_separator = gwafile->get_regions_file_data_separator();
region_name_column = descriptor->get_property(Descriptor::REGION_NAME);
region_chr_column = descriptor->get_property(Descriptor::REGION_CHR);
region_start_column = descriptor->get_property(Descriptor::REGION_START);
region_end_column = descriptor->get_property(Descriptor::REGION_END);
while ((line_length = regions_reader.read_line()) > 0) {
line = *regions_reader.line;
column_position = 0;
region_name_token = NULL;
region_chr_token = NULL;
region_start_token = NULL;
region_end_token = NULL;
token = auxiliary::strtok(&line, data_separator);
while (token != NULL) {
if (column_position == region_name_column_pos) {
region_name_token = token;
} else if (column_position == region_chr_column_pos) {
region_chr_token = token;
} else if (column_position == region_start_column_pos) {
region_start_token = token;
} else if (column_position == region_end_column_pos) {
region_end_token = token;
}
token = auxiliary::strtok(&line, data_separator);
++column_position;
}
if (column_position < regions_file_total_columns) {
throw AnnotatorException("Annotator", "process_regions_file_data()", __LINE__, 8, line_number, regions_file, column_position, regions_file_total_columns);
} else if (column_position > regions_file_total_columns) {
throw AnnotatorException("Annotator", "process_regions_file_data()", __LINE__, 9, line_number, regions_file, column_position, regions_file_total_columns);
}
region_name = (char*)malloc((strlen(region_name_token) + 1u) * sizeof(char));
if (region_name == NULL) {
throw AnnotatorException("Annotator", "process_regions_file_data()", __LINE__, 2, ((strlen(region_name_token) + 1u) * sizeof(char)));
}
strcpy(region_name, region_name_token);
region_start = (int)strtol(region_start_token, &end_ptr, 10);
if (*end_ptr != '\0') {
throw AnnotatorException("Annotator", "process_regions_file_data()", __LINE__, 10, region_start_token, region_start_column, line_number);
}
if (region_start < 0) {
throw AnnotatorException("Annotator", "process_regions_file_data()", __LINE__, 11, region_start_column, region_start, line_number);
}
region_end = (int)strtol(region_end_token, &end_ptr, 10);
if (*end_ptr != '\0') {
throw AnnotatorException("Annotator", "process_regions_file_data()", __LINE__, 10, region_end_token, region_end_column, line_number);
}
if (region_end < 0) {
throw AnnotatorException("Annotator", "process_regions_file_data()", __LINE__, 11, region_end_column, region_end, line_number);
}
if (region_start > region_end) {
throw AnnotatorException("Annotator", "process_regions_file_data()", __LINE__, 12, region_start_column, region_start, region_end, region_end_column, line_number);
}
regions_indices_it = regions_indices.find(region_chr_token);
if (regions_indices_it == regions_indices.end()) {
regions_index = new IntervalTree<char*>();
region_chr = (char*)malloc((strlen(region_chr_token) + 1u) * sizeof(char));
if (region_chr == NULL) {
throw AnnotatorException("Annotator", "process_regions_file_data()", __LINE__, 2, ((strlen(region_chr_token) + 1u) * sizeof(char)));
}
strcpy(region_chr, region_chr_token);
regions_indices.insert(pair<char*, IntervalTree<char*>* >(region_chr, regions_index));
} else {
regions_index = regions_indices_it->second;
}
regions_index->add(region_start, region_end, region_name);
++line_number;
}
if (line_length == 0) {
throw AnnotatorException("Annotator", "process_regions_file_data()", __LINE__, 13, line_number, regions_file);
}
} catch (ReaderException &e) {
AnnotatorException new_e(e);
new_e.add_message("Annotator", "process_regions_file_data()", __LINE__, 14, regions_file);
throw new_e;
} catch (DescriptorException &e) {
AnnotatorException new_e(e);
new_e.add_message("Annotator", "process_regions_file_data()", __LINE__, 14, regions_file);
throw new_e;
} catch (AnnotatorException &e) {
e.add_message("Annotator", "process_regions_file_data()", __LINE__, 14, regions_file);
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;
}
}
void Annotator::process_regions_file_header() throw (AnnotatorException) {
Descriptor* descriptor = NULL;
char header_separator = '\0';
char* header = NULL;
char* token = NULL;
int column_position = 0;
const char* region_name_column = NULL;
const char* region_chr_column = NULL;
const char* region_start_column = NULL;
const char* region_end_column = NULL;
if ((gwafile == NULL) || (regions_file == NULL)) {
return;
}
try {
descriptor = gwafile->get_descriptor();
header_separator = gwafile->get_regions_file_header_separator();
if (regions_reader.read_line() <= 0) {
throw AnnotatorException("Annotator", "process_regions_file_header()", __LINE__, 5, 1, regions_file);
}
header = *regions_reader.line;
region_name_column = descriptor->get_property(Descriptor::REGION_NAME);
region_chr_column = descriptor->get_property(Descriptor::REGION_CHR);
region_start_column = descriptor->get_property(Descriptor::REGION_START);
region_end_column = descriptor->get_property(Descriptor::REGION_END);
regions_file_total_columns = numeric_limits<int>::min();
region_name_column_pos = numeric_limits<int>::min();
region_chr_column_pos = numeric_limits<int>::min();
region_start_column_pos = numeric_limits<int>::min();
region_end_column_pos = numeric_limits<int>::min();
token = auxiliary::strtok(&header, header_separator);
if (gwafile->is_case_sensitive()) {
while (token != NULL) {
if (strcmp(token, region_name_column) == 0) {
region_name_column_pos = column_position;
} else if (strcmp(token, region_chr_column) == 0) {
region_chr_column_pos = column_position;
} else if (strcmp(token, region_start_column) == 0) {
region_start_column_pos = column_position;
} else if (strcmp(token, region_end_column) == 0) {
region_end_column_pos = column_position;
}
token = auxiliary::strtok(&header, header_separator);
++column_position;
}
} else {
while (token != NULL) {
if (auxiliary::strcmp_ignore_case(token, region_name_column) == 0) {
region_name_column_pos = column_position;
} else if (auxiliary::strcmp_ignore_case(token, region_chr_column) == 0) {
region_chr_column_pos = column_position;
} else if (auxiliary::strcmp_ignore_case(token, region_start_column) == 0) {
region_start_column_pos = column_position;
} else if (auxiliary::strcmp_ignore_case(token, region_end_column) == 0) {
region_end_column_pos = column_position;
}
token = auxiliary::strtok(&header, header_separator);
++column_position;
}
}
regions_file_total_columns = column_position;
if (region_name_column_pos < 0) {
throw AnnotatorException("Annotator", "process_regions_file_header()", __LINE__, 7, (region_name_column != NULL) ? region_name_column : "NULL", regions_file);
}
if (region_chr_column_pos < 0) {
throw AnnotatorException("Annotator", "process_regions_file_header()", __LINE__, 7, (region_chr_column != NULL) ? region_chr_column : "NULL", regions_file);
}
if (region_start_column_pos < 0) {
throw AnnotatorException("Annotator", "process_regions_file_header()", __LINE__, 7, (region_start_column != NULL) ? region_start_column : "NULL", regions_file);
}
if (region_end_column_pos < 0) {
throw AnnotatorException("Annotator", "process_regions_file_header()", __LINE__, 7, (region_end_column != NULL) ? region_end_column : "NULL", regions_file);
}
} catch (ReaderException &e) {
AnnotatorException new_e(e);
new_e.add_message("Annotator", "process_regions_file_header()", __LINE__, 6, regions_file);
throw new_e;
} catch (DescriptorException &e) {
AnnotatorException new_e(e);
new_e.add_message("Annotator", "process_regions_file_header()", __LINE__, 6, regions_file);
throw new_e;
}
}
double Formatter::calculate_lambda(int& n_total, int& n_filtered) throw (FormatterException) {
Descriptor* descriptor = NULL;
char* line = NULL;
int line_length = 0;
unsigned int line_number = 2;
char data_separator = '\0';
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;
char* token = NULL;
char* pvalue_token = NULL;
char* maf_token = NULL;
char* oevar_imp_token = NULL;
int column_position = 0;
char* end_ptr = NULL;
double d_value = 0.0;
int n = 0;
double* data = NULL;
double* new_data = NULL;
int current_heap_size = HEAP_SIZE;
double lambda = numeric_limits<double>::quiet_NaN();
n_total = 0;
n_filtered = 0;
if ((gwafile == NULL) || (pvalue_column_pos < 0)) {
return lambda;
}
try {
descriptor = gwafile->get_descriptor();
snp_hq = descriptor->get_threshold(Descriptor::SNP_HQ);
data_separator = gwafile->get_data_separator();
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;
}
data = (double*)malloc(HEAP_SIZE * sizeof(double));
if (data == NULL) {
throw FormatterException("Formatter", "double calculate_lambda( int& , int& )", __LINE__, 2, HEAP_SIZE * sizeof(double));
}
if (maf_filter) {
if (oevar_imp_filter) {
// all filters
while ((line_length = reader.read_line()) > 0) {
line = *reader.line;
column_position = 0;
pvalue_token = NULL;
maf_token = NULL;
oevar_imp_token = NULL;
token = auxiliary::strtok(&line, data_separator);
while (token != NULL) {
if (column_position == pvalue_column_pos) {
auxiliary::trim(&token);
pvalue_token = token;
} else if (column_position == maf_column_pos) {
auxiliary::trim(&token);
maf_token = token;
} else if (column_position == oevar_imp_column_pos) {
auxiliary::trim(&token);
oevar_imp_token = token;
}
token = auxiliary::strtok(&line, data_separator);
column_position += 1;
}
if (pvalue_token == NULL) {
throw FormatterException("Formatter", "double calculate_lambda( int& , int& )", __LINE__, 8, pvalue_column->get_header(), line_number, gwafile->get_descriptor()->get_name());
}
if (maf_token == NULL) {
throw FormatterException("Formatter", "double calculate_lambda( int& , int& )", __LINE__, 8, maf_column->get_header(), line_number, gwafile->get_descriptor()->get_name());
}
if (oevar_imp_token == NULL) {
throw FormatterException("Formatter", "double calculate_lambda( int& , int& )", __LINE__, 8, oevar_imp_column->get_header(), line_number, gwafile->get_descriptor()->get_name());
}
d_value = R_strtod(maf_token, &end_ptr);
if ((*end_ptr != '\0') || (isnan(d_value))) {
line_number += 1;
continue;
}
d_value = d_value > 0.5 ? 1.0 - d_value : d_value;
if (auxiliary::fcmp(d_value, maf_filter_value, EPSILON) == 1) {
d_value = R_strtod(oevar_imp_token, &end_ptr);
if ((*end_ptr != '\0') || (isnan(d_value))) {
line_number += 1;
continue;
}
if (auxiliary::fcmp(d_value, oevar_imp_filter_value, EPSILON) == 1) {
d_value = R_strtod(pvalue_token, &end_ptr);
if ((*end_ptr != '\0') || (isnan(d_value))) {
line_number += 1;
continue;
}
n += 1;
if (n > current_heap_size) {
current_heap_size += HEAP_INCREMENT;
new_data = (double*)realloc(data, current_heap_size * sizeof(double));
if (new_data == NULL) {
free(data);
data = NULL;
throw FormatterException("Formatter", "double calculate_lambda( int& , int& )", __LINE__, 2, current_heap_size * sizeof(double));
}
data = new_data;
}
data[n - 1] = d_value;
}
}
line_number += 1;
}
} else {
// only maf filter
while ((line_length = reader.read_line()) > 0) {
line = *reader.line;
column_position = 0;
pvalue_token = NULL;
maf_token = NULL;
token = auxiliary::strtok(&line, data_separator);
while (token != NULL) {
if (column_position == pvalue_column_pos) {
auxiliary::trim(&token);
pvalue_token = token;
} else if (column_position == maf_column_pos) {
auxiliary::trim(&token);
maf_token = token;
}
token = auxiliary::strtok(&line, data_separator);
column_position += 1;
}
if (pvalue_token == NULL) {
throw FormatterException("Formatter", "double calculate_lambda( int& , int& )", __LINE__, 8, pvalue_column->get_header(), line_number, gwafile->get_descriptor()->get_name());
}
if (maf_token == NULL) {
throw FormatterException("Formatter", "double calculate_lambda( int& , int& )", __LINE__, 8, maf_column->get_header(), line_number, gwafile->get_descriptor()->get_name());
}
d_value = R_strtod(maf_token, &end_ptr);
if ((*end_ptr != '\0') || (isnan(d_value))) {
line_number += 1;
continue;
}
d_value = d_value > 0.5 ? 1.0 - d_value : d_value;
if (auxiliary::fcmp(d_value, maf_filter_value, EPSILON) == 1) {
d_value = R_strtod(pvalue_token, &end_ptr);
if ((*end_ptr != '\0') || (isnan(d_value))) {
line_number += 1;
continue;
}
n += 1;
if (n > current_heap_size) {
current_heap_size += HEAP_INCREMENT;
new_data = (double*)realloc(data, current_heap_size * sizeof(double));
if (new_data == NULL) {
free(data);
data = NULL;
throw FormatterException("Formatter", "double calculate_lambda( int& , int& )", __LINE__, 2, current_heap_size * sizeof(double));
}
data = new_data;
}
data[n - 1] = d_value;
}
line_number += 1;
}
}
} else if (oevar_imp_filter) {
// only oevar_imp_filter
while ((line_length = reader.read_line()) > 0) {
line = *reader.line;
column_position = 0;
pvalue_token = NULL;
oevar_imp_token = NULL;
token = auxiliary::strtok(&line, data_separator);
while (token != NULL) {
if (column_position == pvalue_column_pos) {
auxiliary::trim(&token);
pvalue_token = token;
} else if (column_position == oevar_imp_column_pos) {
auxiliary::trim(&token);
oevar_imp_token = token;
}
token = auxiliary::strtok(&line, data_separator);
column_position += 1;
}
if (pvalue_token == NULL) {
throw FormatterException("Formatter", "double calculate_lambda( int& , int& )", __LINE__, 8, pvalue_column->get_header(), line_number, gwafile->get_descriptor()->get_name());
}
if (oevar_imp_token == NULL) {
throw FormatterException("Formatter", "double calculate_lambda( int& , int& )", __LINE__, 8, oevar_imp_column->get_header(), line_number, gwafile->get_descriptor()->get_name());
}
d_value = R_strtod(oevar_imp_token, &end_ptr);
if ((*end_ptr != '\0') || (isnan(d_value))) {
line_number += 1;
continue;
}
if (auxiliary::fcmp(d_value, oevar_imp_filter_value, EPSILON) == 1) {
d_value = R_strtod(pvalue_token, &end_ptr);
if ((*end_ptr != '\0') || (isnan(d_value))) {
line_number += 1;
continue;
}
n += 1;
if (n > current_heap_size) {
current_heap_size += HEAP_INCREMENT;
new_data = (double*)realloc(data, current_heap_size * sizeof(double));
if (new_data == NULL) {
free(data);
data = NULL;
throw FormatterException("Formatter", "double calculate_lambda( int& , int& )", __LINE__, 2, current_heap_size * sizeof(double));
}
data = new_data;
}
data[n - 1] = d_value;
}
line_number += 1;
}
} else {
// no filters
while ((line_length = reader.read_line()) > 0) {
line = *reader.line;
column_position = 0;
pvalue_token = NULL;
token = auxiliary::strtok(&line, data_separator);
while (token != NULL) {
if (column_position == pvalue_column_pos) {
auxiliary::trim(&token);
pvalue_token = token;
break;
}
token = auxiliary::strtok(&line, data_separator);
column_position += 1;
}
if (pvalue_token == NULL) {
throw FormatterException("Formatter", "double calculate_lambda( int& , int& )", __LINE__, 8, pvalue_column->get_header(), line_number, gwafile->get_descriptor()->get_name());
}
d_value = R_strtod(pvalue_token, &end_ptr);
if ((*end_ptr != '\0') || (isnan(d_value))) {
line_number += 1;
continue;
}
n += 1;
if (n > current_heap_size) {
current_heap_size += HEAP_INCREMENT;
new_data = (double*)realloc(data, current_heap_size * sizeof(double));
if (new_data == NULL) {
free(data);
data = NULL;
throw FormatterException("Formatter", "double calculate_lambda( int& , int& )", __LINE__, 2, current_heap_size * sizeof(double));
}
data = new_data;
}
data[n - 1] = d_value;
line_number += 1;
}
}
n_filtered = n;
n_total = line_number - 2;
if (line_length == 0) {
throw FormatterException("Formatter", "double calculate_lambda( int& , int& )", __LINE__, 7, line_number, gwafile->get_descriptor()->get_name());
}
reader.reset();
if (reader.read_line() <= 0) {
throw FormatterException("Formatter", "double calculate_lambda( int& , int& )", __LINE__, 5, line_number, gwafile->get_descriptor()->get_name());
}
} catch (DescriptorException &e) {
FormatterException new_e(e);
new_e.add_message("Formatter", "double calculate_lambda( int& , int& )", __LINE__, 9, gwafile->get_descriptor()->get_name());
throw new_e;
} catch (ReaderException &e) {
FormatterException new_e(e);
new_e.add_message("Formatter", "double calculate_lambda( int& , int& )", __LINE__, 9, gwafile->get_descriptor()->get_name());
throw new_e;
} catch (FormatterException &e) {
e.add_message("Formatter", "double calculate_lambda( int& , int& )", __LINE__, 9, gwafile->get_descriptor()->get_name());
throw;
}
if (n > 0) {
for (int i = 0; i < n; i++) {
data[i] = pow(Rf_qnorm5(0.5 * data[i], 0.0, 1.0, 0, 0), 2.0);
}
qsort(data, n, sizeof(double), auxiliary::dblcmp);
lambda = auxiliary::stats_median_from_sorted_data(data, n) / Rf_qchisq(0.5, 1.0, 0, 0);
}
free(data);
data = NULL;
return lambda;
}
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 Annotator::annotate_with_map() throw (AnnotatorException) {
Descriptor* descriptor = NULL;
ofstream ofile_stream;
const char* output_prefix = NULL;
const char* file_name = NULL;
char* output_file_name = NULL;
char* line = NULL;
int line_length = 0;
unsigned int line_number = 2u;
char* line_backup = NULL;
char header_separator = '\0';
char data_separator = '\0';
char region_separator = '\0';
bool regions_append = false;
char* token = NULL;
int column_position = 0;
const char* column_name = NULL;
marker_index key_marker_index;
marker_index* found_marker_index = NULL;
unsigned int found_marker_index_pos = 0u;
unsigned int index = 0u;
char* chr = NULL;
int position = 0;
vector<double>* deviation = NULL;
int deviation_value = 0;
IntervalTree<char*>* genes_index = NULL;
IntervalTree<char*> genes_index_subset;
map<int, vector<char*>*> annotated_genes;
map<int, vector<char*>*>::iterator annotated_genes_it;
if (gwafile == NULL) {
return;
}
try {
descriptor = gwafile->get_descriptor();
output_prefix = descriptor->get_property(Descriptor::PREFIX);
file_name = descriptor->get_name();
header_separator = gwafile->get_header_separator();
data_separator = gwafile->get_data_separator();
deviation = descriptor->get_threshold(Descriptor::REGIONS_DEVIATION);
regions_append = gwafile->is_regions_append_on();
auxiliary::transform_file_name(&output_file_name, output_prefix, file_name, NULL, true);
if (output_file_name == NULL) {
throw AnnotatorException("Annotator", "annotate_with_map()", __LINE__, 16);
}
if (regions_append) {
line_backup = (char*)malloc(reader.get_buffer_size() * sizeof(char));
if (line_backup == NULL) {
throw AnnotatorException("Annotator", "annotate_with_map()", __LINE__, 2, (reader.get_buffer_size() * sizeof(char)));
}
}
if (data_separator == ',') {
region_separator = ';';
} else {
region_separator = ',';
}
ofile_stream.exceptions(ios_base::failbit | ios_base::badbit);
try {
ofile_stream.open(output_file_name);
} catch (ofstream::failure &e) {
throw AnnotatorException("Annotator", "annotate_with_map()", __LINE__, 17, output_file_name);
}
try {
if (regions_append) {
ofile_stream << header_backup;
ofile_stream << header_separator;
ofile_stream << ((column_name = descriptor->get_property(Descriptor::MAP_CHR)) != NULL ? column_name : Descriptor::MAP_CHR);
ofile_stream << header_separator;
ofile_stream << ((column_name = descriptor->get_property(Descriptor::MAP_POSITION)) != NULL ? column_name : Descriptor::MAP_POSITION);
} else {
ofile_stream << ((column_name = descriptor->get_column(Descriptor::MARKER)) != NULL ? column_name : Descriptor::MARKER);
ofile_stream << header_separator;
ofile_stream << ((column_name = descriptor->get_property(Descriptor::MAP_CHR)) != NULL ? column_name : Descriptor::MAP_CHR);
ofile_stream << header_separator;
ofile_stream << ((column_name = descriptor->get_property(Descriptor::MAP_POSITION)) != NULL ? column_name : Descriptor::MAP_POSITION);
}
for (unsigned int i = 0u; i < deviation->size(); ++i) {
deviation_value = (int)deviation->at(i);
if (deviation_value != 0) {
ofile_stream << header_separator << "+/-" << deviation_value;
} else {
ofile_stream << header_separator << "IN";
}
}
ofile_stream << endl;
while ((line_length = reader.read_line()) > 0) {
line = *reader.line;
if (regions_append) {
strcpy(line_backup, line);
}
column_position = 0;
key_marker_index.name = NULL;
token = auxiliary::strtok(&line, data_separator);
while (token != NULL) {
if (column_position == marker_column_pos) {
key_marker_index.name = token;
}
token = auxiliary::strtok(&line, data_separator);
++column_position;
}
if (column_position < total_columns) {
throw AnnotatorException("Annotator", "annotate_with_map()", __LINE__, 8, line_number, gwafile->get_descriptor()->get_name(), column_position, total_columns);
} else if (column_position > total_columns) {
throw AnnotatorException("Annotator", "annotate_with_map()", __LINE__, 9, line_number, gwafile->get_descriptor()->get_name(), column_position, total_columns);
}
found_marker_index = (marker_index*)bsearch(&key_marker_index, map_index, map_index_size, sizeof(marker_index), qsort_marker_index_cmp);
if (found_marker_index == NULL) {
if (regions_append) {
ofile_stream << line_backup << data_separator << "NA" << data_separator << "NA";
} else {
ofile_stream << key_marker_index.name << data_separator << "NA" << data_separator << "NA";
}
for (unsigned int i = 0u; i < deviation->size(); ++i) {
ofile_stream << data_separator << "NA";
}
ofile_stream << endl;
} else {
found_marker_index_pos = found_marker_index - map_index;
while ((found_marker_index_pos < map_index_size) && (auxiliary::strcmp_ignore_case(key_marker_index.name, map_index[found_marker_index_pos].name) == 0)) {
index = map_index[found_marker_index_pos].index;
chr = map_chromosomes[index];
position = map_positions[index];
if (regions_append) {
ofile_stream << line_backup << data_separator << chr << data_separator << position;
} else {
ofile_stream << key_marker_index.name << data_separator << chr << data_separator << position;
}
regions_indices_it = regions_indices.find(chr);
if (regions_indices_it != regions_indices.end()) {
genes_index = regions_indices_it->second;
deviation_value = (int)deviation->back();
genes_index->get_intersecting_intervals(position - deviation_value, position + deviation_value, deviation_value, genes_index_subset);
for (int i = deviation->size() - 2; i >= 0; --i) {
deviation_value = (int)deviation->at(i);
genes_index_subset.mark_intersecting_intervals(position - deviation_value, position + deviation_value, deviation_value);
}
genes_index_subset.get_marked_values(annotated_genes);
if (annotated_genes.size() > 0) {
for (unsigned int i = 0u; i < deviation->size(); ++i) {
ofile_stream << data_separator;
annotated_genes_it = annotated_genes.find(((int)deviation->at(i)));
if (annotated_genes_it != annotated_genes.end()) {
write_char_vector(ofile_stream, annotated_genes_it->second, region_separator);
} else {
ofile_stream << "NA";
}
}
ofile_stream << endl;
} else {
for (unsigned int i = 0u; i < deviation->size(); ++i) {
ofile_stream << data_separator << "NA";
}
ofile_stream << endl;
}
annotated_genes_it = annotated_genes.begin();
while(annotated_genes_it != annotated_genes.end()) {
delete annotated_genes_it->second;
annotated_genes_it++;
}
annotated_genes.clear();
genes_index_subset.clear();
} else {
for (unsigned int i = 0u; i < deviation->size(); ++i) {
ofile_stream << data_separator << "NA";
}
ofile_stream << endl;
}
++found_marker_index_pos;
}
}
++line_number;
}
} catch (ofstream::failure &e) {
throw AnnotatorException("Annotator", "annotate_with_map()", __LINE__, 19, output_file_name);
}
try {
ofile_stream.close();
} catch (ofstream::failure &e) {
throw AnnotatorException("Annotator", "annotate_with_map()", __LINE__, 18, output_file_name);
}
if (line_backup != NULL) {
free(line_backup);
line_backup = NULL;
}
if (line_length == 0) {
throw AnnotatorException("Annotator", "annotate_with_map()", __LINE__, 13, line_number, gwafile->get_descriptor()->get_name());
}
} catch (DescriptorException &e) {
AnnotatorException new_e(e);
new_e.add_message("Annotator", "annotate_with_map()", __LINE__, 14, gwafile->get_descriptor()->get_name());
throw new_e;
} catch (ReaderException &e) {
AnnotatorException new_e(e);
new_e.add_message("Annotator", "annotate_with_map()", __LINE__, 14, gwafile->get_descriptor()->get_name());
throw new_e;
} catch (AnnotatorException &e) {
e.add_message("Annotator", "annotate_with_map()", __LINE__, 14, gwafile->get_descriptor()->get_name());
throw;
}
}
void Annotator::annotate_without_map() throw (AnnotatorException) {
Descriptor* descriptor = NULL;
ofstream ofile_stream;
const char* output_prefix = NULL;
const char* file_name = NULL;
char* output_file_name = NULL;
char* line = NULL;
int line_length = 0;
unsigned int line_number = 2u;
char header_separator = '\0';
char data_separator = '\0';
char region_separator = '\0';
bool regions_append = false;
char* token = NULL;
char* end_ptr = NULL;
int column_position = 0;
const char* column_name = NULL;
char* marker_token = NULL;
char* chr_token = NULL;
char* position_token = NULL;
int position = 0;
vector<double>* deviation = NULL;
int deviation_value = 0;
IntervalTree<char*>* genes_index = NULL;
IntervalTree<char*> genes_index_subset;
map<int, vector<char*>*> annotated_genes;
map<int, vector<char*>*>::iterator annotated_genes_it;
if (gwafile == NULL) {
return;
}
try {
descriptor = gwafile->get_descriptor();
output_prefix = descriptor->get_property(Descriptor::PREFIX);
file_name = descriptor->get_name();
header_separator = gwafile->get_header_separator();
data_separator = gwafile->get_data_separator();
deviation = descriptor->get_threshold(Descriptor::REGIONS_DEVIATION);
regions_append = gwafile->is_regions_append_on();
auxiliary::transform_file_name(&output_file_name, output_prefix, file_name, NULL, true);
if (output_file_name == NULL) {
throw AnnotatorException("Annotator", "annotate_without_map()", __LINE__, 16);
}
if (data_separator == ',') {
region_separator = ';';
} else {
region_separator = ',';
}
ofile_stream.exceptions(ios_base::failbit | ios_base::badbit);
try {
ofile_stream.open(output_file_name);
} catch (ofstream::failure &e) {
throw AnnotatorException("Annotator", "annotate_without_map()", __LINE__, 17, output_file_name);
}
try {
if (regions_append) {
ofile_stream << header_backup;
} else {
ofile_stream << ((column_name = descriptor->get_column(Descriptor::MARKER)) != NULL ? column_name : Descriptor::MARKER);
ofile_stream << header_separator;
ofile_stream << ((column_name = descriptor->get_column(Descriptor::CHR)) != NULL ? column_name : Descriptor::CHR);
ofile_stream << header_separator;
ofile_stream << ((column_name = descriptor->get_column(Descriptor::POSITION)) != NULL ? column_name : Descriptor::POSITION);
}
for (unsigned int i = 0u; i < deviation->size(); ++i) {
deviation_value = (int)deviation->at(i);
if (deviation_value != 0) {
ofile_stream << header_separator << "+/-" << deviation_value;
} else {
ofile_stream << header_separator << "IN";
}
}
ofile_stream << endl;
while ((line_length = reader.read_line()) > 0) {
line = *reader.line;
if (regions_append) {
ofile_stream << line;
}
column_position = 0;
marker_token = NULL;
chr_token = NULL;
position_token = NULL;
token = auxiliary::strtok(&line, data_separator);
while (token != NULL) {
if (column_position == marker_column_pos) {
marker_token = token;
} else if (column_position == chr_column_pos) {
chr_token = token;
} else if (column_position == position_column_pos) {
position_token = token;
}
token = auxiliary::strtok(&line, data_separator);
++column_position;
}
if (column_position < total_columns) {
throw AnnotatorException("Annotator", "annotate_without_map()", __LINE__, 8, line_number, gwafile->get_descriptor()->get_name(), column_position, total_columns);
} else if (column_position > total_columns) {
throw AnnotatorException("Annotator", "annotate_without_map()", __LINE__, 9, line_number, gwafile->get_descriptor()->get_name(), column_position, total_columns);
}
position = (int)strtol(position_token, &end_ptr, 10);
if (*end_ptr != '\0') {
throw AnnotatorException("Annotator", "annotate_without_map()", __LINE__, 10, position_token, ((column_name = descriptor->get_column(Descriptor::POSITION)) != NULL) ? column_name : Descriptor::POSITION, line_number);
}
if (position < 0) {
throw AnnotatorException("Annotator", "annotate_without_map()", __LINE__, 11, ((column_name = descriptor->get_column(Descriptor::POSITION)) != NULL) ? column_name : Descriptor::POSITION, position, line_number);
}
if (!regions_append) {
ofile_stream << marker_token << data_separator << chr_token << data_separator << position_token;
}
regions_indices_it = regions_indices.find(chr_token);
if (regions_indices_it != regions_indices.end()) {
genes_index = regions_indices_it->second;
deviation_value = (int)deviation->back();
genes_index->get_intersecting_intervals(position - deviation_value, position + deviation_value, deviation_value, genes_index_subset);
for (int i = deviation->size() - 2; i >= 0; --i) {
deviation_value = (int)deviation->at(i);
genes_index_subset.mark_intersecting_intervals(position - deviation_value, position + deviation_value, deviation_value);
}
genes_index_subset.get_marked_values(annotated_genes);
if (annotated_genes.size() > 0) {
for (unsigned int i = 0u; i < deviation->size(); ++i) {
ofile_stream << data_separator;
annotated_genes_it = annotated_genes.find(((int)deviation->at(i)));
if (annotated_genes_it != annotated_genes.end()) {
write_char_vector(ofile_stream, annotated_genes_it->second, region_separator);
} else {
ofile_stream << "NA";
}
}
ofile_stream << endl;
} else {
for (unsigned int i = 0u; i < deviation->size(); ++i) {
ofile_stream << data_separator << "NA";
}
ofile_stream << endl;
}
annotated_genes_it = annotated_genes.begin();
while(annotated_genes_it != annotated_genes.end()) {
delete annotated_genes_it->second;
annotated_genes_it++;
}
annotated_genes.clear();
genes_index_subset.clear();
} else {
for (unsigned int i = 0u; i < deviation->size(); ++i) {
ofile_stream << data_separator << "NA";
}
ofile_stream << endl;
}
++line_number;
}
} catch (ofstream::failure &e) {
throw AnnotatorException("Annotator", "annotate_without_map()", __LINE__, 19, output_file_name);
}
try {
ofile_stream.close();
} catch (ofstream::failure &e) {
throw AnnotatorException("Annotator", "annotate_without_map()", __LINE__, 18, output_file_name);
}
if (line_length == 0) {
throw AnnotatorException("Annotator", "annotate_without_map()", __LINE__, 13, line_number, gwafile->get_descriptor()->get_name());
}
} catch (DescriptorException &e) {
AnnotatorException new_e(e);
new_e.add_message("Annotator", "annotate_without_map()", __LINE__, 14, gwafile->get_descriptor()->get_name());
throw new_e;
} catch (ReaderException &e) {
AnnotatorException new_e(e);
new_e.add_message("Annotator", "annotate_without_map()", __LINE__, 14, gwafile->get_descriptor()->get_name());
throw new_e;
} catch (AnnotatorException &e) {
e.add_message("Annotator", "annotate_without_map()", __LINE__, 14, gwafile->get_descriptor()->get_name());
throw;
}
}
void Annotator::process_header_with_map() throw (AnnotatorException) {
Descriptor* descriptor = NULL;
char header_separator = '\0';
char* header = NULL;
char* token = NULL;
int column_position = 0;
const char* column_name = NULL;
bool regions_append = false;
if (gwafile == NULL) {
return;
}
try {
descriptor = gwafile->get_descriptor();
header_separator = gwafile->get_header_separator();
regions_append = gwafile->is_regions_append_on();
if (reader.read_line() <= 0) {
throw AnnotatorException("Annotator", "process_header_with_map()", __LINE__, 5, 1, gwafile->get_descriptor()->get_name());
}
header = *reader.line;
if (regions_append) {
header_backup = (char*)malloc((strlen(header) + 1u) * sizeof(char));
if (header_backup == NULL) {
throw AnnotatorException("Annotator", "process_header_with_map()", __LINE__, 2, ((strlen(header) + 1u) * sizeof(char)));
}
strcpy(header_backup, header);
}
total_columns = numeric_limits<int>::min();
marker_column_pos = numeric_limits<int>::min();
token = auxiliary::strtok(&header, header_separator);
while (token != NULL) {
column_name = descriptor->get_default_column(token, gwafile->is_case_sensitive());
if (column_name != NULL) {
if (strcmp(column_name, Descriptor::MARKER) == 0) {
marker_column_pos = column_position;
}
}
token = auxiliary::strtok(&header, header_separator);
++column_position;
}
total_columns = column_position;
if (marker_column_pos < 0) {
throw AnnotatorException("Annotator", "process_header_with_map()", __LINE__, 7, ((column_name = descriptor->get_column(Descriptor::MARKER)) != NULL) ? column_name : Descriptor::MARKER, gwafile->get_descriptor()->get_name());
}
} catch (ReaderException &e) {
AnnotatorException new_e(e);
new_e.add_message("Annotator", "process_header_with_map()", __LINE__, 6, gwafile->get_descriptor()->get_name());
throw new_e;
} catch (DescriptorException &e) {
AnnotatorException new_e(e);
new_e.add_message("Annotator", "process_header_with_map()", __LINE__, 6, gwafile->get_descriptor()->get_name());
throw new_e;
}
}
void Annotator::process_map_file_header() throw (AnnotatorException) {
Descriptor* descriptor = NULL;
char header_separator = '\0';
char* header = NULL;
char* token = NULL;
int column_position = 0;
const char* map_marker_column = NULL;
const char* map_chr_column = NULL;
const char* map_position_column = NULL;
if ((gwafile == NULL) || (map_file == NULL)) {
return;
}
try {
descriptor = gwafile->get_descriptor();
header_separator = gwafile->get_regions_file_header_separator();
if (map_reader.read_line() <= 0) {
throw AnnotatorException("Annotator", "process_map_file_header()", __LINE__, 5, 1, map_file);
}
header = *map_reader.line;
map_marker_column = descriptor->get_property(Descriptor::MAP_MARKER);
map_chr_column = descriptor->get_property(Descriptor::MAP_CHR);
map_position_column = descriptor->get_property(Descriptor::MAP_POSITION);
map_file_total_columns = numeric_limits<int>::min();
map_marker_column_pos = numeric_limits<int>::min();
map_chr_column_pos = numeric_limits<int>::min();
map_position_column_pos = numeric_limits<int>::min();
token = auxiliary::strtok(&header, header_separator);
if (gwafile->is_case_sensitive()) {
while (token != NULL) {
if (strcmp(token, map_marker_column) == 0) {
map_marker_column_pos = column_position;
} else if (strcmp(token, map_chr_column) == 0) {
map_chr_column_pos = column_position;
} else if (strcmp(token, map_position_column) == 0) {
map_position_column_pos = column_position;
}
token = auxiliary::strtok(&header, header_separator);
++column_position;
}
} else {
while (token != NULL) {
if (auxiliary::strcmp_ignore_case(token, map_marker_column) == 0) {
map_marker_column_pos = column_position;
} else if (auxiliary::strcmp_ignore_case(token, map_chr_column) == 0) {
map_chr_column_pos = column_position;
} else if (auxiliary::strcmp_ignore_case(token, map_position_column) == 0) {
map_position_column_pos = column_position;
}
token = auxiliary::strtok(&header, header_separator);
++column_position;
}
}
map_file_total_columns = column_position;
if (map_marker_column_pos < 0) {
throw AnnotatorException("Annotator", "process_map_file_header()", __LINE__, 7, (map_marker_column != NULL) ? map_marker_column : "NULL", map_file);
}
if (map_chr_column_pos < 0) {
throw AnnotatorException("Annotator", "process_map_file_header()", __LINE__, 7, (map_chr_column != NULL) ? map_chr_column : "NULL", map_file);
}
if (map_position_column_pos < 0) {
throw AnnotatorException("Annotator", "process_map_file_header()", __LINE__, 7, (map_position_column != NULL) ? map_position_column : "NULL", map_file);
}
} catch (ReaderException &e) {
AnnotatorException new_e(e);
new_e.add_message("Annotator", "process_map_file_header()", __LINE__, 6, map_file);
throw new_e;
} catch (DescriptorException &e) {
AnnotatorException new_e(e);
new_e.add_message("Annotator", "process_map_file_header()", __LINE__, 6, map_file);
throw new_e;
}
}
