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