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1 /*****************************************************************************
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2 bedGraphFile.cpp
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3
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4 (c) 2010 - Assaf Gordon
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5 Hall Laboratory
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6 Department of Biochemistry and Molecular Genetics
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7 University of Virginia
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8 aaronquinlan@gmail.com
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9
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10 Licenced under the GNU General Public License 2.0 license.
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11 ******************************************************************************/
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12 #ifndef BEDGRAPHFILE_H
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13 #define BEDGRAPHFILE_H
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14
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15 #include "gzstream.h"
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16 #include "lineFileUtilities.h"
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17 #include "fileType.h"
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18 #include <vector>
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19 #include <map>
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20 #include <set>
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21 #include <string>
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22 #include <iostream>
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23 #include <fstream>
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24 #include <sstream>
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25 #include <cstring>
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26 #include <algorithm>
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27 #include <limits.h>
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28 #include <stdint.h>
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29 #include <cstdio>
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30
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31 using namespace std;
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32
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33 //*************************************************
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34 // Data type tydedef
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35 //*************************************************
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36 #ifndef CHRPOS
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37 typedef uint32_t CHRPOS;
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38 #endif
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39
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40 #ifndef DEPTH
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41 typedef uint32_t DEPTH;
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42 #endif
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43
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44 /*
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45 Structure for regular BedGraph records
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46 */
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47 template <typename T>
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48 class BEDGRAPH
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49 {
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50 public:
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51 std::string chrom;
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52 CHRPOS start;
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53 CHRPOS end;
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54 T depth;
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55
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56 public:
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57 typedef T DEPTH_TYPE;
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58 // constructors
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59
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60 // Null
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61 BEDGRAPH() :
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62 start(0),
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63 end(0),
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64 depth(T())
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65 {}
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66
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67 // BEDGraph
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68 BEDGRAPH(string _chrom, CHRPOS _start, CHRPOS _end, T _depth) :
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69 chrom(_chrom),
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70 start(_start),
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71 end(_end),
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72 depth(_depth)
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73 {}
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74 }; // BEDGraph
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75
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76 typedef BEDGRAPH<int32_t> BEDGRAPH_INT;
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77 typedef BEDGRAPH<std::string> BEDGRAPH_STR;
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78 typedef BEDGRAPH<double> BEDGRAPH_FLOAT;
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79
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80 template <typename T>
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81 std::ostream& operator<< (std::ostream& strm, const BEDGRAPH<T>& bg)
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82 {
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83 strm << bg.chrom << "\t"
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84 << bg.start << "\t"
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85 << bg.end << "\t"
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86 << bg.depth;
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87 return strm;
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88 }
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89
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90 // enum to flag the state of a given line in a BEDGraph file.
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91 enum BedGraphLineStatus
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92 {
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93 BEDGRAPH_INVALID = -1,
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94 BEDGRAPH_HEADER = 0,
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95 BEDGRAPH_BLANK = 1,
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96 BEDGRAPH_VALID = 2
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97 };
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98
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99
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100 //************************************************
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101 // BedGraphFile Class methods and elements
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102 //************************************************
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103 class BedGraphFile {
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104
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105 public:
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106
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107 // Constructor
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108 BedGraphFile(string &);
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109
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110 // Destructor
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111 ~BedGraphFile(void);
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112
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113 // Open a BEDGraph file for reading (creates an istream pointer)
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114 void Open(void);
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115
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116 // Close an opened BED file.
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117 void Close(void);
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118
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119 // Get the next BED entry in an opened BED file.
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120 template <typename T>
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121 BedGraphLineStatus GetNextBedGraph (BEDGRAPH<T> &bedgraph, int &lineNum)
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122 {
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123 // make sure there are still lines to process.
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124 // if so, tokenize, validate and return the BED entry.
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125 if (_bedGraphStream->good()) {
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126 string bedGraphLine;
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127 vector<string> bedGraphFields;
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128
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129 // parse the bedStream pointer
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130 getline(*_bedGraphStream, bedGraphLine);
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131 if (_bedGraphStream->eof())
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132 return BEDGRAPH_INVALID;
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133 if (_bedGraphStream->bad()) {
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134 cerr << "Error while reading file '" << bedGraphFile << "' : "
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135 << strerror(errno) << endl;
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136 exit(1);
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137 }
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138 lineNum++;
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139
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140 // split into a string vector.
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141 Tokenize(bedGraphLine,bedGraphFields);
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142
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143 // load the BED struct as long as it's a valid BED entry.
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144 return parseLine(bedgraph, bedGraphFields, lineNum);
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145 }
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146
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147 // default if file is closed or EOF
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148 return BEDGRAPH_INVALID;
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149 }
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150
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151 // the bedfile with which this instance is associated
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152 string bedGraphFile;
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153
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154 private:
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155 // data
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156 istream *_bedGraphStream;
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157
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158 template <typename T>
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159 BedGraphLineStatus parseLine (BEDGRAPH<T> &bg, const vector<string> &lineVector, int &lineNum)
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160 {
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161 if (lineVector.size() == 0)
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162 return BEDGRAPH_BLANK;
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163
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164 if (lineVector[0].find("track") != string::npos ||
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165 lineVector[0].find("browser") != string::npos ||
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166 lineVector[0].find("#") != string::npos)
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167 return BEDGRAPH_HEADER;
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168
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169 if (lineVector.size() != 4)
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170 return BEDGRAPH_INVALID;
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171
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172 bg.chrom = lineVector[0];
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173
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174 stringstream str_start(lineVector[1]);
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175 if (! (str_start >> bg.start) ) {
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176 cerr << "Input error, failed to extract start value from '" << lineVector[1]
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177 << "' (column 2) in " << bedGraphFile << " line " << lineNum << endl;
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178 exit(1);
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179 }
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180
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181 stringstream str_end(lineVector[2]);
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182 if (! (str_end >> bg.end) ) {
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183 cerr << "Input error, failed to extract end value from '" << lineVector[2]
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184 << "' (column 3) in " << bedGraphFile << " line " << lineNum << endl;
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185 exit(1);
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186 }
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187
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188 stringstream str_depth(lineVector[3]);
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189 if (! (str_depth >> bg.depth) ) {
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190 cerr << "Input error, failed to extract depth value from '" << lineVector[3]
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191 << "' (column 4) in " << bedGraphFile << " line " << lineNum << endl;
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192 exit(1);
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193 }
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194
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195 return BEDGRAPH_VALID;
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196 }
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197 };
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198
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199 #endif /* BEDFILE_H */
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