--- a/BEDTools-Version-2.14.3/src/multiIntersectBed/multiIntersectBed.cpp	Thu Nov 03 10:25:04 2011 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,289 +0,0 @@
-/*****************************************************************************
-  unionBedGraphs.cpp
-
-  (c) 2010 - Assaf Gordon, CSHL
-           - Aaron Quinlan, UVA
-  Hall Laboratory
-  Department of Biochemistry and Molecular Genetics
-  University of Virginia
-  aaronquinlan@gmail.com
-
-  Licenced under the GNU General Public License 2.0 license.
-******************************************************************************/
-#include <cassert>
-#include <cstring>
-#include <cstdlib>
-#include <iostream>
-#include <algorithm>
-
-#include "bedFile.h"
-#include "multiIntersectBed.h"
-
-using namespace std;
-
-
-MultiIntersectBed::MultiIntersectBed(std::ostream& _output,
-                            const vector<string>& _filenames,
-                            const vector<string>& _titles,
-                            bool _print_empty_regions,
-                            const std::string& _genome_size_filename,
-                            const std::string& _no_coverage_value   ) :
-    filenames(_filenames),
-    titles(_titles),
-    output(_output),
-    current_non_zero_inputs(0),
-    print_empty_regions(_print_empty_regions),
-    haveTitles(false),
-    genome_sizes(NULL),
-    no_coverage_value(_no_coverage_value)
-{
-    if (print_empty_regions) {
-        assert(!_genome_size_filename.empty());
-
-        genome_sizes = new GenomeFile(_genome_size_filename);
-    }
-    
-    if (titles.size() > 0) {
-        haveTitles = true;
-    }
-}
-
-
-MultiIntersectBed::~MultiIntersectBed() {
-    CloseFiles();
-    if (genome_sizes) {
-        delete genome_sizes;
-        genome_sizes = NULL ;
-    }
-}
-
-
-void MultiIntersectBed::MultiIntersect() {
-    OpenFiles();
-
-    // Add the first interval from each file
-    for(size_t i = 0;i < input_files.size(); ++i)
-        LoadNextItem(i);
-
-    // Chromosome loop - once per chromosome
-    do {
-        // Find the first chromosome to use
-        current_chrom = DetermineNextChrom();
-
-        // Populate the queue with initial values from all files
-        // (if they belong to the correct chromosome)
-        for(size_t i = 0; i < input_files.size(); ++i)
-            AddInterval(i);
-
-        CHRPOS current_start = ConsumeNextCoordinate();
-
-        // User wanted empty regions, and the first coordinate is not 0 - print a dummy empty coverage
-        if (print_empty_regions && current_start > 0)
-            PrintEmptyCoverage(0,current_start);
-
-        // Intervals loop - until all intervals (of current chromosome) from all files are used.
-        do {
-            CHRPOS current_end = queue.top().coord;
-            PrintCoverage(current_start, current_end);
-            current_start = ConsumeNextCoordinate();
-        } while (!queue.empty());
-
-        // User wanted empty regions, and the last coordinate is not the last coordinate of the chromosome
-            // print a dummy empty coverage
-        if (print_empty_regions) {
-            CHRPOS chrom_size = genome_sizes->getChromSize(current_chrom);
-            if (current_start < chrom_size)
-                PrintEmptyCoverage(current_start, chrom_size);
-        }
-
-    } while (!AllFilesDone());
-}
-
-
-CHRPOS MultiIntersectBed::ConsumeNextCoordinate() {
-    assert(!queue.empty());
-
-    CHRPOS new_position = queue.top().coord;
-    do {
-        IntervalItem item = queue.top();
-        UpdateInformation(item);
-        queue.pop();
-    } while (!queue.empty() && queue.top().coord == new_position);
-
-    return new_position;
-}
-
-
-void MultiIntersectBed::UpdateInformation(const IntervalItem &item) {
-    // Update the depth coverage for this file
-
-    // Which coordinate is it - start or end?
-    switch (item.coord_type)
-    {
-    case START:
-        current_depth[item.source_index] = 1;
-        current_non_zero_inputs++;
-        files_with_coverage[item.source_index] = true;
-        break;
-    case END:
-        //Read the next interval from this file
-        AddInterval(item.source_index);
-        current_depth[item.source_index] = 0;
-        current_non_zero_inputs--;
-        files_with_coverage.erase(item.source_index);
-        break;
-    default:
-        assert(0);
-    }
-}
-
-
-void MultiIntersectBed::AddInterval(int index) {
-    assert(static_cast<unsigned int>(index) < input_files.size());
-
-    //This file has no more intervals
-    if (current_item[index].chrom.empty())
-        return;
-
-    //If the next interval belongs to a different chrom, don't add it
-    if (current_item[index].chrom!=current_chrom)
-        return;
-
-    const BED &bed(current_item[index]);
-
-    IntervalItem start_item(index, START, bed.start);
-    IntervalItem end_item(index, END, bed.end);
-
-    queue.push(start_item);
-    queue.push(end_item);
-
-    LoadNextItem(index);
-}
-
-
-void MultiIntersectBed::PrintHeader() {
-    output << "chrom\tstart\tend\tnum\tlist" ;
-    for (size_t i=0;i<titles.size();++i)
-        output << "\t" <<titles[i];
-    output << endl;
-}
-
-
-void MultiIntersectBed::PrintCoverage(CHRPOS start, CHRPOS end) {
-    if ( current_non_zero_inputs == 0 && ! print_empty_regions )
-        return ;
-
-    output << current_chrom << "\t"
-        << start << "\t"
-        << end   << "\t"
-        << current_non_zero_inputs << "\t";
-    
-    ostringstream file_list_string;
-    ostringstream file_bool_string;
-    int depth_count = 0;
-    for (size_t i = 0; i < current_depth.size(); ++i)
-    {
-        if (current_depth[i] > 0) {
-            if (depth_count < current_non_zero_inputs - 1) {
-                if (!haveTitles)
-                    file_list_string << i+1 << ",";
-                else 
-                    file_list_string << titles[i] << ",";
-            }
-            else {
-                if (!haveTitles)
-                    file_list_string << i+1;
-                else 
-                    file_list_string << titles[i];
-            }
-            depth_count++;
-        }
-        file_bool_string << "\t" << current_depth[i];
-    }
-    if (current_non_zero_inputs > 0) {
-        cout << file_list_string.str() << file_bool_string.str() << endl;
-    }
-    else {
-        cout << "none" << file_bool_string.str() << endl;
-    }
-}
-
-
-void MultiIntersectBed::PrintEmptyCoverage(CHRPOS start, CHRPOS end) {
-    output << current_chrom << "\t"
-        << start << "\t"
-        << end   << "\t"
-        << "0"   << "\t" << "none";
-        
-    for (size_t i=0;i<current_depth.size();++i)
-        output << "\t0";
-
-    output << endl;
-}
-
-
-void MultiIntersectBed::LoadNextItem(int index) {
-    assert(static_cast<unsigned int>(index) < input_files.size());
-
-    current_item[index].chrom="";
-
-    BedFile *file = input_files[index];
-    BED merged_bed;
-    int lineNum = 0;
-    //
-    // TO DO: Do the mergeing on the fly.  How best to do this?
-    // 
-    // IDEA: Implement a Merge class with GetNextMerge element.
-    //
-
-    while (file->GetNextMergedBed(merged_bed, lineNum))
-    {
-        current_item[index] = merged_bed;
-        break;
-    }
-}
-
-
-bool MultiIntersectBed::AllFilesDone() {
-    for (size_t i=0;i<current_item.size();++i)
-        if (!current_item[i].chrom.empty())
-            return false;
-    return true;
-}
-
-
-string MultiIntersectBed::DetermineNextChrom() {
-    string next_chrom;
-    for (size_t i=0;i<current_item.size();++i) {
-        if (current_item[i].chrom.empty())
-            continue;
-
-        if (next_chrom.empty())
-            next_chrom = current_item[i].chrom;
-        else
-            if (current_item[i].chrom < next_chrom)
-                next_chrom = current_item[i].chrom ;
-    }
-    return next_chrom;
-}
-
-
-void MultiIntersectBed::OpenFiles() {
-    for (size_t i = 0; i < filenames.size(); ++i) {
-        BedFile *file = new BedFile(filenames[i]);
-        file->Open();
-        input_files.push_back(file);
-        current_depth.push_back(0);
-    }
-    current_item.resize(filenames.size());
-}
-
-
-void MultiIntersectBed::CloseFiles() {
-    for (size_t i=0; i < input_files.size(); ++i) {
-        BedFile *file = input_files[i];
-        delete file;
-        input_files[i] = NULL ;
-    }
-    input_files.clear();
-}