@@ -1,322 +1,323 @@

-#include <Rcpp.h>

-using namespace Rcpp;

-

-#include <cstdlib>

-#include <sstream>

-#include <iostream>

-#include <fstream>

-#include <map>

-#include <vector>

-#include <string>

-#include <cmath>

-#include <cstdlib>

-#include <boost/algorithm/string.hpp>

-#include <boost/assign.hpp>

-#include "data_types.h"

-

-using namespace std;

-using namespace boost;

-

-//

-// bins (or features) annotation format

-//

-//1. file of bins (features) annotation: "biomarkers.all_bins"

-//Each line is a bin (or feature). All columns are delimited by TAB. There is one header line.

-//Column 1: marker_index, 1-based index. Those bins that are not markers, are indexed as 0.

-//Column 2: chr

-//Column 3: start coordinate of read (1-base)

-//Column 4: end coordinate of read (1-base). The range of the bin is [start, end)

-//Column 5: marker_type. "I" is Marker_type_I, "II" is Marker_type_II, "-" is the complementary bin, only facilitating the searching.

-//

-// The following is an example file

-//

-//marker_index    chr     start   end     marker_type

-//0       chr1    1       855266  -

-//1       chr1    855266  855766  II

-//0       chr1    855766  969796  -

-//2       chr1    969796  970296  II

-//0       chr1    970296  1099044 -

-//3       chr1    1099044 1099544 II

-//0       chr1    1099544 1109315 -

-//4       chr1    1109315 1109815 II

-//

-void read_bins_annot_file(string input_bins_annot_file, Bins_end_coord & bins_end_coord,

-	Bins_index & bins_index, Bins_info & bins_info, bool has_header_line=true)

-{

-	ifstream fin;

-	fin.open(input_bins_annot_file.c_str());

-	if (fin.fail()){

-	  Rcpp::Rcerr << "Error: Unable to open " << input_bins_annot_file << " in read_bins_annot_file()" << endl;

-	  // exit(EXIT_FAILURE);

-  }

-	string line;

-	if (has_header_line)

-		// skip the first header line

-		getline(fin, line);

-	unsigned long i=0;

-	string old_chr;

-	while (!fin.eof()) {

-		getline(fin, line);

-		if (line.empty()) {

-			// this is the last line of the file

-			break;

-		}

-		//cout << line << endl;

-

-		vector<string> strs1;

-		split(strs1, line, is_any_of("\t"));

-		int bin_index = atoi(strs1[0].c_str());

-		string chr = strs1[1];

-		//int start_coord = atoi(strs1[2].c_str()); // start coordinate

-		int end_coord = atoi(strs1[3].c_str()); // end coordinate

-		if (i==0) {

-			// this is the first bin of all the genome, so we initialize old_chr

-			old_chr = chr;

-		}

-		if (chr.compare(old_chr)!=0) {

-			// This is the 1st bin of the new chromosome

-			old_chr = chr;

-			bins_end_coord.insert(make_pair(chr, vector<unsigned int>()));

-			bins_index.insert(make_pair(chr, vector<int >()));

-			bins_info.insert(make_pair(chr, vector<string >()));

-		}

-		vector<unsigned int> & coords = bins_end_coord[chr];

-		coords.push_back( end_coord );

-		vector<int> & indexes = bins_index[chr];

-		indexes.push_back( bin_index );

-		vector<string> & infos = bins_info[chr];

-		infos.push_back( line );

-		i++;

-	}

-	Rcpp::Rcerr << "#bins=" << i << endl;

-}

-

-int get_num_of_non_void_bins(Bins_index & bins_index, vector<int> & returned_markers_index)

-{

-	int num_of_non_void_bins = 0;

-	Bins_index::iterator it;

-	for (it=bins_index.begin(); it!=bins_index.end(); ++it) {

-		vector<int> & bins_of_chr = it->second;

-		for (int i=0; i<bins_of_chr.size(); i++)

-			if (bins_of_chr[i] > 0) {

-				num_of_non_void_bins++;

-				returned_markers_index.push_back( bins_of_chr[i] );

-			}

-	}

-	return num_of_non_void_bins;

-}

-

-// We find out the index of the bin with the range [bin_start_coord, bin_end_coord), where both "bin_start_coord" and "bin_end_coord" are 0-base.

-// Returned bin_internal_index is 0-base. If not found, return -1

-int find_exact_bin(Bins_end_coord & bins_end_coord, string chr, unsigned int bin_start_coord, unsigned int bin_end_coord) {

-	int bin_internal_index=-1;

-	vector<unsigned int> & coords_bins_of_chr = bins_end_coord[chr]; // a vector of end coordinates (1-base) of this chr.

-	vector<unsigned int>::iterator bin_it = find( coords_bins_of_chr.begin(), coords_bins_of_chr.end(), bin_end_coord);

-	if (bin_it!=coords_bins_of_chr.end()) {

-		// found

-		bin_internal_index = bin_it-coords_bins_of_chr.begin();

-	}

-	return bin_internal_index;

-}

-

-// We find out the index of the bin with the range [bin_start_coord, bin_end_coord), where the input paramter "position" (1-base) falls into this bin.

-// Returned bin_internal_index is 0-base. If not found, return -1

-int find_bin_of_position(Bins_end_coord & bins_end_coord, string chr, unsigned int position) {

-	int bin_internal_index=-1;

-	if ( bins_end_coord.find(chr) == bins_end_coord.end() ) {

-		// chr name is not found in binning system

-		bin_internal_index = -1;

-	} else {

-		vector<unsigned int> & coords_bins_of_chr = bins_end_coord[chr]; // a vector of end coordinates (1-base) of this chr.

-		vector<unsigned int>::iterator bin_it = lower_bound( coords_bins_of_chr.begin(), coords_bins_of_chr.end(), position);

-		if (position==*bin_it) bin_it++;

-		bin_internal_index = bin_it - coords_bins_of_chr.begin(); // bin_internal_index is 0-base

-		if (bin_internal_index==coords_bins_of_chr.size()) {

-			//cerr << "position(1-base): " << position << " doesn't exist in " << chr << endl;

-			bin_internal_index=-1;

-		}

-	}

-	return bin_internal_index;

-}

-

-// Each bin is in the range [ bins_end_coord[i-1], bins_end_coord[i] )

-// Given a query region, we want to know which bin has overlap with this query region. If there is overlap,

-// return (1) bin index, and (2) the overlap length

-// ongoing devevloping

-int find_overlap_bin(Bins_end_coord & bins_end_coord, string query_region_chr, unsigned int query_region_start_coord,

-	unsigned int query_region_end_coord, int & overlap_length)

-{

-	int bin_internal_index = -1;

-	overlap_length = -1;

-	if ( bins_end_coord.find(query_region_chr) != bins_end_coord.end() ) {

-		// chr name is found in binning system

-		bin_internal_index = find_bin_of_position(bins_end_coord, query_region_chr, query_region_start_coord);

-		if (bin_internal_index != -1) {

-			unsigned int bin_end_coord = bins_end_coord[query_region_chr][bin_internal_index];

-			if ( query_region_end_coord > bin_end_coord )

-				overlap_length = bin_end_coord - query_region_start_coord + 1;

-			else

-				overlap_length = query_region_end_coord - query_region_start_coord + 1;

-		}

-	}

-	return bin_internal_index;

-}

-

-void print_uint_vec( ostream& os, vector<unsigned int>& v, int len )

-{

-	int i;

-	if (len>v.size() || len==0) len=v.size();

-	if (len==0 || v.size()==0) {

-		os << "[" << "]";

-	} else {

-		os << "[";

-		for (i=0; i<len-1; i++)

-			os << v[i] << ",";

-		os << v[i] << "]";

-	}

-}

-

-void print_bins( ostream& os, Bins_end_coord & bins_end_coord, Bins_index & bins_index, Bins_info & bins_info) {

-	Bins_end_coord::iterator it;

-	for (it=bins_end_coord.begin(); it!=bins_end_coord.end(); ++it) {

-		string chr = it->first;

-		vector<unsigned int> coords=it->second;

-		vector<int> indexes=bins_index[chr];

-		vector<string> infos=bins_info[chr];

-		int n_bins = coords.size();

-		for (int i=0; i<n_bins; i++) {

-			os << indexes[i] << "\t" << chr << "\t" << coords[i] << "\t'" << infos[i] << "'"  << endl;

-		}

-	}

-}

-

-/*

-void print_bins_fullinfo( Bins_FullInfo & bins_fullinfo ) {

-	Bins_FullInfo::iterator: it;

-	for (it=bins.begin(); it!=bins.end(); ++it) {

-		cout << it.first << "\t";

-		print_int_vec(cout, it.second, it.second.size());

-		cout << endl;

-	}

-}

-*/

-

-// Bins2Values: a map of bin_index -> a vector of values. bin_index is always 1-base

-void create_Bins2Values(int num_bins, int num_of_values, double init_value, Bins2Values & bins2values)

-{

-	for (int bin_index=1; bin_index<=num_bins; bin_index++) {

-		vector<double> values;

-		for (int i=0; i<num_of_values; i++)

-			values.push_back( init_value );

-		bins2values[bin_index] = values;

-	}

-}

-

-// Bins2Values: a map of marker_index -> a vector of values.

-void create_Bins2Values(vector<int> markers_index, int num_of_values, double init_value, Bins2Values & bins2values)

-{

-	int num_bins = markers_index.size();

-	for (int ibin=0; ibin<num_bins; ibin++) {

-		vector<double> values;

-		for (int i=0; i<num_of_values; i++)

-			values.push_back( init_value );

-		bins2values[markers_index[ibin]] = values;

-	}

-}

-

-void print_Bins2Values(Bins2Values & bins2values)

-{

-	// cout.precision(15);

-	Bins2Values::iterator it;

-	for (it=bins2values.begin(); it!=bins2values.end(); ++it) {

-		vector<double> & values = it->second;

-	  Rcpp::Rcout << it->first;

-		for (int i=0; i<values.size(); i++)

-		  Rcpp::Rcout << "\t" << values[i];

-		Rcpp::Rcout << endl;

-	}

-}

-

-void print_Bins2UnsignedIntegers(Bins2UnsignedIntegers& bins2values)

-{

-	Bins2UnsignedIntegers::iterator it;

-	for (it=bins2values.begin(); it!=bins2values.end(); ++it) {

-		vector<unsigned int> & values = it->second;

-	  Rcpp::Rcout << it->first;

-		for (int i=0; i<(int)values.size(); i++)

-		  Rcpp::Rcout << "\t" << values[i];

-		Rcpp::Rcout << endl;

-	}

-}

-

-// when optional_write==TRUE, we assume there are two values associated with each bin

-void write_Bins2Values(Bins2Values & bins2values, vector<string> & columns_names,

-	string output_file, bool optional_write)

-{

-	ofstream out;

-	out.open(output_file.c_str());

-	if (out.fail()){

-	  Rcpp::Rcerr << "Error: Unable to write " << output_file << " in write_Bins2Value()" << endl;

-	  // exit(EXIT_FAILURE);

-	}

-	int i;

-	for (i=0; i<columns_names.size()-1; i++)

-		out << columns_names[i] << "\t";

-	out << columns_names[i] << endl;

-

-	out.precision(15);

-	Bins2Values::iterator it;

-	for (it=bins2values.begin(); it!=bins2values.end(); ++it) {

-		vector<double> & values = it->second;

-		out << it->first;

-		if (optional_write) {

-			// assume there are at least two values associated with each bin

-			// for example, when we have three associated values, they can be

-			// (1) methylation_count

-			// (2) unmethylation_count

-			// (3) number of reads

-			double n = values[0] + values[1];

-			double v;

-			if (n==0) v=0;

-			else v=values[0]/n;

-			out << "\t" << v << "\t" << n;

-		}

-		for (i=0; i<values.size(); i++)

-			out << "\t" << values[i];

-		out << endl;

-	}

-	out.close();

-}

-

-// Bins2Value: a map of bin_index -> a value. bin_index is always 1-base

-void create_Bins2Value(int num_bins, double init_value, Bins2Value & bins2value)

-{

-	for (int bin_index=1; bin_index<=num_bins; bin_index++)

-		bins2value[bin_index] = init_value;

-}

-

-ostream& operator<<(ostream& out, Bins2Value& bins2value) {

-	out << "bin_index" << "\t" << "value" << endl;

-	out.precision(15);

-	Bins2Value::iterator it;

-	for (it=bins2value.begin(); it!=bins2value.end(); ++it)

-		out << it->first << "\t" << it->second << endl;

-	return(out);

-}

-

-void write_Bins2Value(Bins2Value & bins2value, string output_file)

-{

-	ofstream out;

-	out.open(output_file.c_str());

-	if (out.fail()){

-	  Rcpp::Rcerr << "Error: Unable to write " << output_file << " in write_Bins2Value()" << endl;

-	  // exit(EXIT_FAILURE);

-	}

-	out << "bin_index" << "\t" << "value" << endl;

-	out.precision(15);

-	Bins2Value::iterator it;

-	for (it=bins2value.begin(); it!=bins2value.end(); ++it)

-		out << it->first << "\t" << it->second << endl;

-	out.close();

-}

-

+// [[Rcpp::depends(BH)]]

+#include <Rcpp.h>

+using namespace Rcpp;

+

+#include <cstdlib>

+#include <sstream>

+#include <iostream>

+#include <fstream>

+#include <map>

+#include <vector>

+#include <string>

+#include <cmath>

+#include <cstdlib>

+#include <boost/algorithm/string.hpp>

+#include <boost/assign.hpp>

+#include "data_types.h"

+

+using namespace std;

+using namespace boost;

+

+//

+// bins (or features) annotation format

+//

+//1. file of bins (features) annotation: "biomarkers.all_bins"

+//Each line is a bin (or feature). All columns are delimited by TAB. There is one header line.

+//Column 1: marker_index, 1-based index. Those bins that are not markers, are indexed as 0.

+//Column 2: chr

+//Column 3: start coordinate of read (1-base)

+//Column 4: end coordinate of read (1-base). The range of the bin is [start, end)

+//Column 5: marker_type. "I" is Marker_type_I, "II" is Marker_type_II, "-" is the complementary bin, only facilitating the searching.

+//

+// The following is an example file

+//

+//marker_index    chr     start   end     marker_type

+//0       chr1    1       855266  -

+//1       chr1    855266  855766  II

+//0       chr1    855766  969796  -

+//2       chr1    969796  970296  II

+//0       chr1    970296  1099044 -

+//3       chr1    1099044 1099544 II

+//0       chr1    1099544 1109315 -

+//4       chr1    1109315 1109815 II

+//

+void read_bins_annot_file(string input_bins_annot_file, Bins_end_coord & bins_end_coord,

+	Bins_index & bins_index, Bins_info & bins_info, bool has_header_line=true)

+{

+	ifstream fin;

+	fin.open(input_bins_annot_file.c_str());

+	if (fin.fail()){

+	  Rcpp::Rcerr << "Error: Unable to open " << input_bins_annot_file << " in read_bins_annot_file()" << endl;

+	  // exit(EXIT_FAILURE);

+  }

+	string line;

+	if (has_header_line)

+		// skip the first header line

+		getline(fin, line);

+	unsigned long i=0;

+	string old_chr;

+	while (!fin.eof()) {

+		getline(fin, line);

+		if (line.empty()) {

+			// this is the last line of the file

+			break;

+		}

+		//cout << line << endl;

+

+		vector<string> strs1;

+		split(strs1, line, is_any_of("\t"));

+		int bin_index = atoi(strs1[0].c_str());

+		string chr = strs1[1];

+		//int start_coord = atoi(strs1[2].c_str()); // start coordinate

+		int end_coord = atoi(strs1[3].c_str()); // end coordinate

+		if (i==0) {

+			// this is the first bin of all the genome, so we initialize old_chr

+			old_chr = chr;

+		}

+		if (chr.compare(old_chr)!=0) {

+			// This is the 1st bin of the new chromosome

+			old_chr = chr;

+			bins_end_coord.insert(make_pair(chr, vector<unsigned int>()));

+			bins_index.insert(make_pair(chr, vector<int >()));

+			bins_info.insert(make_pair(chr, vector<string >()));

+		}

+		vector<unsigned int> & coords = bins_end_coord[chr];

+		coords.push_back( end_coord );

+		vector<int> & indexes = bins_index[chr];

+		indexes.push_back( bin_index );

+		vector<string> & infos = bins_info[chr];

+		infos.push_back( line );

+		i++;

+	}

+	Rcpp::Rcerr << "#bins=" << i << endl;

+}

+

+int get_num_of_non_void_bins(Bins_index & bins_index, vector<int> & returned_markers_index)

+{

+	int num_of_non_void_bins = 0;

+	Bins_index::iterator it;

+	for (it=bins_index.begin(); it!=bins_index.end(); ++it) {

+		vector<int> & bins_of_chr = it->second;

+		for (int i=0; i<bins_of_chr.size(); i++)

+			if (bins_of_chr[i] > 0) {

+				num_of_non_void_bins++;

+				returned_markers_index.push_back( bins_of_chr[i] );

+			}

+	}

+	return num_of_non_void_bins;

+}

+

+// We find out the index of the bin with the range [bin_start_coord, bin_end_coord), where both "bin_start_coord" and "bin_end_coord" are 0-base.

+// Returned bin_internal_index is 0-base. If not found, return -1

+int find_exact_bin(Bins_end_coord & bins_end_coord, string chr, unsigned int bin_start_coord, unsigned int bin_end_coord) {

+	int bin_internal_index=-1;

+	vector<unsigned int> & coords_bins_of_chr = bins_end_coord[chr]; // a vector of end coordinates (1-base) of this chr.

+	vector<unsigned int>::iterator bin_it = find( coords_bins_of_chr.begin(), coords_bins_of_chr.end(), bin_end_coord);

+	if (bin_it!=coords_bins_of_chr.end()) {

+		// found

+		bin_internal_index = bin_it-coords_bins_of_chr.begin();

+	}

+	return bin_internal_index;

+}

+

+// We find out the index of the bin with the range [bin_start_coord, bin_end_coord), where the input paramter "position" (1-base) falls into this bin.

+// Returned bin_internal_index is 0-base. If not found, return -1

+int find_bin_of_position(Bins_end_coord & bins_end_coord, string chr, unsigned int position) {

+	int bin_internal_index=-1;

+	if ( bins_end_coord.find(chr) == bins_end_coord.end() ) {

+		// chr name is not found in binning system

+		bin_internal_index = -1;

+	} else {

+		vector<unsigned int> & coords_bins_of_chr = bins_end_coord[chr]; // a vector of end coordinates (1-base) of this chr.

+		vector<unsigned int>::iterator bin_it = lower_bound( coords_bins_of_chr.begin(), coords_bins_of_chr.end(), position);

+		if (position==*bin_it) bin_it++;

+		bin_internal_index = bin_it - coords_bins_of_chr.begin(); // bin_internal_index is 0-base

+		if (bin_internal_index==coords_bins_of_chr.size()) {

+			//cerr << "position(1-base): " << position << " doesn't exist in " << chr << endl;

+			bin_internal_index=-1;

+		}

+	}

+	return bin_internal_index;

+}

+

+// Each bin is in the range [ bins_end_coord[i-1], bins_end_coord[i] )

+// Given a query region, we want to know which bin has overlap with this query region. If there is overlap,

+// return (1) bin index, and (2) the overlap length

+// ongoing devevloping

+int find_overlap_bin(Bins_end_coord & bins_end_coord, string query_region_chr, unsigned int query_region_start_coord,

+	unsigned int query_region_end_coord, int & overlap_length)

+{

+	int bin_internal_index = -1;

+	overlap_length = -1;

+	if ( bins_end_coord.find(query_region_chr) != bins_end_coord.end() ) {

+		// chr name is found in binning system

+		bin_internal_index = find_bin_of_position(bins_end_coord, query_region_chr, query_region_start_coord);

+		if (bin_internal_index != -1) {

+			unsigned int bin_end_coord = bins_end_coord[query_region_chr][bin_internal_index];

+			if ( query_region_end_coord > bin_end_coord )

+				overlap_length = bin_end_coord - query_region_start_coord + 1;

+			else

+				overlap_length = query_region_end_coord - query_region_start_coord + 1;

+		}

+	}

+	return bin_internal_index;

+}

+

+void print_uint_vec( ostream& os, vector<unsigned int>& v, int len )

+{

+	int i;

+	if (len>v.size() || len==0) len=v.size();

+	if (len==0 || v.size()==0) {

+		os << "[" << "]";

+	} else {

+		os << "[";

+		for (i=0; i<len-1; i++)

+			os << v[i] << ",";

+		os << v[i] << "]";

+	}

+}

+

+void print_bins( ostream& os, Bins_end_coord & bins_end_coord, Bins_index & bins_index, Bins_info & bins_info) {

+	Bins_end_coord::iterator it;

+	for (it=bins_end_coord.begin(); it!=bins_end_coord.end(); ++it) {

+		string chr = it->first;

+		vector<unsigned int> coords=it->second;

+		vector<int> indexes=bins_index[chr];

+		vector<string> infos=bins_info[chr];

+		int n_bins = coords.size();

+		for (int i=0; i<n_bins; i++) {

+			os << indexes[i] << "\t" << chr << "\t" << coords[i] << "\t'" << infos[i] << "'"  << endl;

+		}

+	}

+}

+

+/*

+void print_bins_fullinfo( Bins_FullInfo & bins_fullinfo ) {

+	Bins_FullInfo::iterator: it;

+	for (it=bins.begin(); it!=bins.end(); ++it) {

+		cout << it.first << "\t";

+		print_int_vec(cout, it.second, it.second.size());

+		cout << endl;

+	}

+}

+*/

+

+// Bins2Values: a map of bin_index -> a vector of values. bin_index is always 1-base

+void create_Bins2Values(int num_bins, int num_of_values, double init_value, Bins2Values & bins2values)

+{

+	for (int bin_index=1; bin_index<=num_bins; bin_index++) {

+		vector<double> values;

+		for (int i=0; i<num_of_values; i++)

+			values.push_back( init_value );

+		bins2values[bin_index] = values;

+	}

+}

+

+// Bins2Values: a map of marker_index -> a vector of values.

+void create_Bins2Values(vector<int> markers_index, int num_of_values, double init_value, Bins2Values & bins2values)

+{

+	int num_bins = markers_index.size();

+	for (int ibin=0; ibin<num_bins; ibin++) {

+		vector<double> values;

+		for (int i=0; i<num_of_values; i++)

+			values.push_back( init_value );

+		bins2values[markers_index[ibin]] = values;

+	}

+}

+

+void print_Bins2Values(Bins2Values & bins2values)

+{

+	// cout.precision(15);

+	Bins2Values::iterator it;

+	for (it=bins2values.begin(); it!=bins2values.end(); ++it) {

+		vector<double> & values = it->second;

+	  Rcpp::Rcout << it->first;

+		for (int i=0; i<values.size(); i++)

+		  Rcpp::Rcout << "\t" << values[i];

+		Rcpp::Rcout << endl;

+	}

+}

+

+void print_Bins2UnsignedIntegers(Bins2UnsignedIntegers& bins2values)

+{

+	Bins2UnsignedIntegers::iterator it;

+	for (it=bins2values.begin(); it!=bins2values.end(); ++it) {

+		vector<unsigned int> & values = it->second;

+	  Rcpp::Rcout << it->first;

+		for (int i=0; i<(int)values.size(); i++)

+		  Rcpp::Rcout << "\t" << values[i];

+		Rcpp::Rcout << endl;

+	}

+}

+

+// when optional_write==TRUE, we assume there are two values associated with each bin

+void write_Bins2Values(Bins2Values & bins2values, vector<string> & columns_names,

+	string output_file, bool optional_write)

+{

+	ofstream out;

+	out.open(output_file.c_str());

+	if (out.fail()){

+	  Rcpp::Rcerr << "Error: Unable to write " << output_file << " in write_Bins2Value()" << endl;

+	  // exit(EXIT_FAILURE);

+	}

+	int i;

+	for (i=0; i<columns_names.size()-1; i++)

+		out << columns_names[i] << "\t";

+	out << columns_names[i] << endl;

+

+	out.precision(15);

+	Bins2Values::iterator it;

+	for (it=bins2values.begin(); it!=bins2values.end(); ++it) {

+		vector<double> & values = it->second;

+		out << it->first;

+		if (optional_write) {

+			// assume there are at least two values associated with each bin

+			// for example, when we have three associated values, they can be

+			// (1) methylation_count

+			// (2) unmethylation_count

+			// (3) number of reads

+			double n = values[0] + values[1];

+			double v;

+			if (n==0) v=0;

+			else v=values[0]/n;

+			out << "\t" << v << "\t" << n;

+		}

+		for (i=0; i<values.size(); i++)

+			out << "\t" << values[i];

+		out << endl;

+	}

+	out.close();

+}

+

+// Bins2Value: a map of bin_index -> a value. bin_index is always 1-base

+void create_Bins2Value(int num_bins, double init_value, Bins2Value & bins2value)

+{

+	for (int bin_index=1; bin_index<=num_bins; bin_index++)

+		bins2value[bin_index] = init_value;

+}

+

+ostream& operator<<(ostream& out, Bins2Value& bins2value) {

+	out << "bin_index" << "\t" << "value" << endl;

+	out.precision(15);

+	Bins2Value::iterator it;

+	for (it=bins2value.begin(); it!=bins2value.end(); ++it)

+		out << it->first << "\t" << it->second << endl;

+	return(out);

+}

+

+void write_Bins2Value(Bins2Value & bins2value, string output_file)

+{

+	ofstream out;

+	out.open(output_file.c_str());

+	if (out.fail()){

+	  Rcpp::Rcerr << "Error: Unable to write " << output_file << " in write_Bins2Value()" << endl;

+	  // exit(EXIT_FAILURE);

+	}

+	out << "bin_index" << "\t" << "value" << endl;

+	out.precision(15);

+	Bins2Value::iterator it;

+	for (it=bins2value.begin(); it!=bins2value.end(); ++it)

+		out << it->first << "\t" << it->second << endl;

+	out.close();

+}

+

new file mode 100644

@@ -0,0 +1,322 @@

+#include <Rcpp.h>

+using namespace Rcpp;

+

+#include <cstdlib>

+#include <sstream>

+#include <iostream>

+#include <fstream>

+#include <map>

+#include <vector>

+#include <string>

+#include <cmath>

+#include <cstdlib>

+#include <boost/algorithm/string.hpp>

+#include <boost/assign.hpp>

+#include "data_types.h"

+

+using namespace std;

+using namespace boost;

+

+//

+// bins (or features) annotation format

+//

+//1. file of bins (features) annotation: "biomarkers.all_bins"

+//Each line is a bin (or feature). All columns are delimited by TAB. There is one header line.

+//Column 1: marker_index, 1-based index. Those bins that are not markers, are indexed as 0.

+//Column 2: chr

+//Column 3: start coordinate of read (1-base)

+//Column 4: end coordinate of read (1-base). The range of the bin is [start, end)

+//Column 5: marker_type. "I" is Marker_type_I, "II" is Marker_type_II, "-" is the complementary bin, only facilitating the searching.

+//

+// The following is an example file

+//

+//marker_index    chr     start   end     marker_type

+//0       chr1    1       855266  -

+//1       chr1    855266  855766  II

+//0       chr1    855766  969796  -

+//2       chr1    969796  970296  II

+//0       chr1    970296  1099044 -

+//3       chr1    1099044 1099544 II

+//0       chr1    1099544 1109315 -

+//4       chr1    1109315 1109815 II

+//

+void read_bins_annot_file(string input_bins_annot_file, Bins_end_coord & bins_end_coord,

+	Bins_index & bins_index, Bins_info & bins_info, bool has_header_line=true)

+{

+	ifstream fin;

+	fin.open(input_bins_annot_file.c_str());

+	if (fin.fail()){

+	  Rcpp::Rcerr << "Error: Unable to open " << input_bins_annot_file << " in read_bins_annot_file()" << endl;

+	  // exit(EXIT_FAILURE);

+  }

+	string line;

+	if (has_header_line)

+		// skip the first header line

+		getline(fin, line);

+	unsigned long i=0;

+	string old_chr;

+	while (!fin.eof()) {

+		getline(fin, line);

+		if (line.empty()) {

+			// this is the last line of the file

+			break;

+		}

+		//cout << line << endl;

+

+		vector<string> strs1;

+		split(strs1, line, is_any_of("\t"));

+		int bin_index = atoi(strs1[0].c_str());

+		string chr = strs1[1];

+		//int start_coord = atoi(strs1[2].c_str()); // start coordinate

+		int end_coord = atoi(strs1[3].c_str()); // end coordinate

+		if (i==0) {

+			// this is the first bin of all the genome, so we initialize old_chr

+			old_chr = chr;

+		}

+		if (chr.compare(old_chr)!=0) {

+			// This is the 1st bin of the new chromosome

+			old_chr = chr;

+			bins_end_coord.insert(make_pair(chr, vector<unsigned int>()));

+			bins_index.insert(make_pair(chr, vector<int >()));

+			bins_info.insert(make_pair(chr, vector<string >()));

+		}

+		vector<unsigned int> & coords = bins_end_coord[chr];

+		coords.push_back( end_coord );

+		vector<int> & indexes = bins_index[chr];

+		indexes.push_back( bin_index );

+		vector<string> & infos = bins_info[chr];

+		infos.push_back( line );

+		i++;

+	}

+	Rcpp::Rcerr << "#bins=" << i << endl;

+}

+

+int get_num_of_non_void_bins(Bins_index & bins_index, vector<int> & returned_markers_index)

+{

+	int num_of_non_void_bins = 0;

+	Bins_index::iterator it;

+	for (it=bins_index.begin(); it!=bins_index.end(); ++it) {

+		vector<int> & bins_of_chr = it->second;

+		for (int i=0; i<bins_of_chr.size(); i++)

+			if (bins_of_chr[i] > 0) {

+				num_of_non_void_bins++;

+				returned_markers_index.push_back( bins_of_chr[i] );

+			}

+	}

+	return num_of_non_void_bins;

+}

+

+// We find out the index of the bin with the range [bin_start_coord, bin_end_coord), where both "bin_start_coord" and "bin_end_coord" are 0-base.

+// Returned bin_internal_index is 0-base. If not found, return -1

+int find_exact_bin(Bins_end_coord & bins_end_coord, string chr, unsigned int bin_start_coord, unsigned int bin_end_coord) {

+	int bin_internal_index=-1;

+	vector<unsigned int> & coords_bins_of_chr = bins_end_coord[chr]; // a vector of end coordinates (1-base) of this chr.

+	vector<unsigned int>::iterator bin_it = find( coords_bins_of_chr.begin(), coords_bins_of_chr.end(), bin_end_coord);

+	if (bin_it!=coords_bins_of_chr.end()) {

+		// found

+		bin_internal_index = bin_it-coords_bins_of_chr.begin();

+	}

+	return bin_internal_index;

+}

+

+// We find out the index of the bin with the range [bin_start_coord, bin_end_coord), where the input paramter "position" (1-base) falls into this bin.

+// Returned bin_internal_index is 0-base. If not found, return -1

+int find_bin_of_position(Bins_end_coord & bins_end_coord, string chr, unsigned int position) {

+	int bin_internal_index=-1;

+	if ( bins_end_coord.find(chr) == bins_end_coord.end() ) {

+		// chr name is not found in binning system

+		bin_internal_index = -1;

+	} else {

+		vector<unsigned int> & coords_bins_of_chr = bins_end_coord[chr]; // a vector of end coordinates (1-base) of this chr.

+		vector<unsigned int>::iterator bin_it = lower_bound( coords_bins_of_chr.begin(), coords_bins_of_chr.end(), position);

+		if (position==*bin_it) bin_it++;

+		bin_internal_index = bin_it - coords_bins_of_chr.begin(); // bin_internal_index is 0-base

+		if (bin_internal_index==coords_bins_of_chr.size()) {

+			//cerr << "position(1-base): " << position << " doesn't exist in " << chr << endl;

+			bin_internal_index=-1;

+		}

+	}

+	return bin_internal_index;

+}

+

+// Each bin is in the range [ bins_end_coord[i-1], bins_end_coord[i] )

+// Given a query region, we want to know which bin has overlap with this query region. If there is overlap,

+// return (1) bin index, and (2) the overlap length

+// ongoing devevloping

+int find_overlap_bin(Bins_end_coord & bins_end_coord, string query_region_chr, unsigned int query_region_start_coord,

+	unsigned int query_region_end_coord, int & overlap_length)

+{

+	int bin_internal_index = -1;

+	overlap_length = -1;

+	if ( bins_end_coord.find(query_region_chr) != bins_end_coord.end() ) {

+		// chr name is found in binning system

+		bin_internal_index = find_bin_of_position(bins_end_coord, query_region_chr, query_region_start_coord);

+		if (bin_internal_index != -1) {

+			unsigned int bin_end_coord = bins_end_coord[query_region_chr][bin_internal_index];

+			if ( query_region_end_coord > bin_end_coord )

+				overlap_length = bin_end_coord - query_region_start_coord + 1;

+			else

+				overlap_length = query_region_end_coord - query_region_start_coord + 1;

+		}

+	}

+	return bin_internal_index;

+}

+

+void print_uint_vec( ostream& os, vector<unsigned int>& v, int len )

+{

+	int i;

+	if (len>v.size() || len==0) len=v.size();

+	if (len==0 || v.size()==0) {

+		os << "[" << "]";

+	} else {

+		os << "[";

+		for (i=0; i<len-1; i++)

+			os << v[i] << ",";

+		os << v[i] << "]";

+	}

+}

+

+void print_bins( ostream& os, Bins_end_coord & bins_end_coord, Bins_index & bins_index, Bins_info & bins_info) {

+	Bins_end_coord::iterator it;

+	for (it=bins_end_coord.begin(); it!=bins_end_coord.end(); ++it) {

+		string chr = it->first;

+		vector<unsigned int> coords=it->second;

+		vector<int> indexes=bins_index[chr];

+		vector<string> infos=bins_info[chr];

+		int n_bins = coords.size();

+		for (int i=0; i<n_bins; i++) {

+			os << indexes[i] << "\t" << chr << "\t" << coords[i] << "\t'" << infos[i] << "'"  << endl;

+		}

+	}

+}

+

+/*

+void print_bins_fullinfo( Bins_FullInfo & bins_fullinfo ) {

+	Bins_FullInfo::iterator: it;

+	for (it=bins.begin(); it!=bins.end(); ++it) {

+		cout << it.first << "\t";

+		print_int_vec(cout, it.second, it.second.size());

+		cout << endl;

+	}

+}

+*/

+

+// Bins2Values: a map of bin_index -> a vector of values. bin_index is always 1-base

+void create_Bins2Values(int num_bins, int num_of_values, double init_value, Bins2Values & bins2values)

+{

+	for (int bin_index=1; bin_index<=num_bins; bin_index++) {

+		vector<double> values;

+		for (int i=0; i<num_of_values; i++)

+			values.push_back( init_value );

+		bins2values[bin_index] = values;

+	}

+}

+

+// Bins2Values: a map of marker_index -> a vector of values.

+void create_Bins2Values(vector<int> markers_index, int num_of_values, double init_value, Bins2Values & bins2values)

+{

+	int num_bins = markers_index.size();

+	for (int ibin=0; ibin<num_bins; ibin++) {

+		vector<double> values;

+		for (int i=0; i<num_of_values; i++)

+			values.push_back( init_value );

+		bins2values[markers_index[ibin]] = values;

+	}

+}

+

+void print_Bins2Values(Bins2Values & bins2values)

+{

+	// cout.precision(15);

+	Bins2Values::iterator it;

+	for (it=bins2values.begin(); it!=bins2values.end(); ++it) {

+		vector<double> & values = it->second;