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1 /*****************************************************************************
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2 multiIntersectBed.h
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3
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4 (c) 2010 - Aaron Quinlan, UVA
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5 - Assaf Gordon, CSHL
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6 Quinlan Laboratory
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7 Department of Public Health Sciences
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8 Center for Public Health Genomics
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9 University of Virginia
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10 aaronquinlan@gmail.com
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11
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12 Licenced under the GNU General Public License 2.0 license.
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13 ******************************************************************************/
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14 #ifndef MULTIINTERSECTBED_H
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15 #define MULTIINTERSECTBED_H
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16
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17 #include <vector>
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18 #include <string>
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19 #include "bedFile.h"
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20 #include "genomeFile.h"
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21 #include "intervalItem.h"
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22
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23 class MultiIntersectBed
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24 {
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25 private:
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26
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27 vector<string> filenames;
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28 vector<string> titles;
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29
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30 vector<BedFile*> input_files;
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31 vector<int> current_depth;
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32 vector<BED> current_item;
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33
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34 std::ostream &output;
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35
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36 INTERVALS_PRIORITY_QUEUE queue;
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37 std::string current_chrom;
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38 map<int, bool> files_with_coverage;
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39 int current_non_zero_inputs;
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40 bool print_empty_regions;
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41 bool haveTitles;
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42
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43 GenomeFile* genome_sizes;
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44
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45 std::string no_coverage_value;
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46
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47 public:
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48 MultiIntersectBed(std::ostream& _output,
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49 const vector<string>& _filenames,
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50 const vector<string>& _titles,
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51 bool _print_empty_regions,
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52 const std::string& _genomeFileName,
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53 const std::string& _no_coverage_value);
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54
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55 virtual ~MultiIntersectBed();
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56
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57 // Combines all interval files
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58 void MultiIntersect();
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59
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60 // Print the header line: chrom/start/end + name of each bedgraph file.
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61 void PrintHeader();
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62
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63
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64 private:
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65
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66 // Open all input files, initialize "current_XXX" vectors
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67 void OpenFiles();
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68
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69 // Close the input files.
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70 void CloseFiles();
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71
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72 /*
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73 Add an interval from BedGraph file 'index' into the queue.
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74 will only be added if it belongs to the current chromosome.
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75
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76 If the interval was added (=consumed), the next interval will be read from the file
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77 using 'LoadNextItem'
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78 */
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79 void AddInterval(int index);
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80
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81 /*
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82 Loads the next interval from Bed file 'index'.
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83 Stores it in 'current_bed_item' vector.
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84 */
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85 void LoadNextItem(int index);
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86
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87 /*
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88 Scans the 'current_bedgraph_item' vector,
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89 find the 'first' chromosome to use (different BedGraph files can start with different chromosomes).
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90 */
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91 std::string DetermineNextChrom();
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92
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93 /*
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94 Returns 'true' if ALL intervals from ALL BedGraph files were used
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95 */
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96 bool AllFilesDone();
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97
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98 /*
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99 Extract the next coordinate from the queue, and updates the current coverage information.
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100 If multiple interval share the same coordinate values, all of them are handled.
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101 If an END coordinate is consumed, the next interval (from the corresponding file) is read.
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102 */
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103 CHRPOS ConsumeNextCoordinate();
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104
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105 /*
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106 Updates the coverage information based on the given item.
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107 Item can be a START coordinate or an END coordiante.
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108 */
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109 void UpdateInformation(const IntervalItem &item);
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110
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111 /*
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112 prints chrom/start/end and the current depth coverage values of all the files.
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113 */
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114 void PrintCoverage(CHRPOS start, CHRPOS end);
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115
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116 /*
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117 prints chrom/start/end and the ZERO depth coverage values of all the files.
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118 */
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119 void PrintEmptyCoverage(CHRPOS start, CHRPOS end);
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120
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121 void DebugPrintQueue();
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122 };
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123
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124
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125 #endif
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