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1 /*****************************************************************************
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2 bedToBam.cpp
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3
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4 (c) 2009 - Aaron Quinlan
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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 #include "lineFileUtilities.h"
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13 #include "bedFile.h"
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14 #include "genomeFile.h"
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15 #include "version.h"
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16
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17
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18 #include "api/BamReader.h"
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19 #include "api/BamAux.h"
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20 #include "api/BamWriter.h"
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21 using namespace BamTools;
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22
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23 #include <vector>
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24 #include <iostream>
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25 #include <fstream>
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26 #include <stdlib.h>
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27
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28 using namespace std;
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29
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30
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31 // define our program name
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32 #define PROGRAM_NAME "bedToBam"
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33
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34 // define our parameter checking macro
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35 #define PARAMETER_CHECK(param, paramLen, actualLen) (strncmp(argv[i], param, min(actualLen, paramLen))== 0) && (actualLen == paramLen)
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36
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37
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38 // function declarations
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39 void ShowHelp(void);
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40 void ProcessBed(istream &bedInput, BedFile *bed, GenomeFile *genome, bool isBED12, int mapQual, bool uncompressedBam);
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41 void ConvertBedToBam(const BED &bed, BamAlignment &bam, map<string, int> &chromToId, bool isBED12, int mapQual, int lineNum);
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42 void MakeBamHeader(const string &genomeFile, RefVector &refs, string &header, map<string, int> &chromToInt);
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43 int reg2bin(int beg, int end);
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44
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45
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46
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47 int main(int argc, char* argv[]) {
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48
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49 // our configuration variables
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50 bool showHelp = false;
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51
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52 // input files
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53 string bedFile = "stdin";
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54 string genomeFile;
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55
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56 unsigned int mapQual = 255;
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57
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58 bool haveBed = true;
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59 bool haveGenome = false;
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60 bool haveMapQual = false;
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61 bool isBED12 = false;
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62 bool uncompressedBam = false;
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63
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64 for(int i = 1; i < argc; i++) {
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65 int parameterLength = (int)strlen(argv[i]);
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66
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67 if((PARAMETER_CHECK("-h", 2, parameterLength)) ||
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68 (PARAMETER_CHECK("--help", 5, parameterLength))) {
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69 showHelp = true;
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70 }
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71 }
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72
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73 if(showHelp) ShowHelp();
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74
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75 // do some parsing (all of these parameters require 2 strings)
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76 for(int i = 1; i < argc; i++) {
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77
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78 int parameterLength = (int)strlen(argv[i]);
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79
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80 if(PARAMETER_CHECK("-i", 2, parameterLength)) {
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81 if ((i+1) < argc) {
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82 bedFile = argv[i + 1];
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83 i++;
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84 }
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85 }
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86 else if(PARAMETER_CHECK("-g", 2, parameterLength)) {
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87 if ((i+1) < argc) {
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88 haveGenome = true;
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89 genomeFile = argv[i + 1];
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90 i++;
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91 }
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92 }
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93 else if(PARAMETER_CHECK("-mapq", 5, parameterLength)) {
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94 haveMapQual = true;
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95 if ((i+1) < argc) {
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96 mapQual = atoi(argv[i + 1]);
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97 i++;
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98 }
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99 }
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100 else if(PARAMETER_CHECK("-bed12", 6, parameterLength)) {
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101 isBED12 = true;
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102 }
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103 else if(PARAMETER_CHECK("-ubam", 5, parameterLength)) {
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104 uncompressedBam = true;
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105 }
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106 else {
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107 cerr << endl << "*****ERROR: Unrecognized parameter: " << argv[i] << " *****" << endl << endl;
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108 showHelp = true;
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109 }
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110 }
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111
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112 // make sure we have an input files
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113 if (!haveBed ) {
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114 cerr << endl << "*****" << endl << "*****ERROR: Need -i (BED) file. " << endl << "*****" << endl;
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115 showHelp = true;
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116 }
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117 if (!haveGenome ) {
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118 cerr << endl << "*****" << endl << "*****ERROR: Need -g (genome) file. " << endl << "*****" << endl;
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119 showHelp = true;
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120 }
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121 if (mapQual < 0 || mapQual > 255) {
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122 cerr << endl << "*****" << endl << "*****ERROR: MAPQ must be in range [0,255]. " << endl << "*****" << endl;
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123 showHelp = true;
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124 }
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125
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126
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127 if (!showHelp) {
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128 BedFile *bed = new BedFile(bedFile);
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129 GenomeFile *genome = new GenomeFile(genomeFile);
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130
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131 ProcessBed(cin, bed, genome, isBED12, mapQual, uncompressedBam);
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132 }
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133 else {
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134 ShowHelp();
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135 }
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136 }
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137
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138
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139 void ShowHelp(void) {
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140
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141 cerr << endl << "Program: " << PROGRAM_NAME << " (v" << VERSION << ")" << endl;
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142
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143 cerr << "Author: Aaron Quinlan (aaronquinlan@gmail.com)" << endl;
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144
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145 cerr << "Summary: Converts feature records to BAM format." << endl << endl;
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146
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147 cerr << "Usage: " << PROGRAM_NAME << " [OPTIONS] -i <bed/gff/vcf> -g <genome>" << endl << endl;
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148
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149 cerr << "Options: " << endl;
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150
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151 cerr << "\t-mapq\t" << "Set the mappinq quality for the BAM records." << endl;
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152 cerr << "\t\t(INT) Default: 255" << endl << endl;
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153
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154 cerr << "\t-bed12\t" << "The BED file is in BED12 format. The BAM CIGAR" << endl;
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155 cerr << "\t\tstring will reflect BED \"blocks\"." << endl << endl;
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156
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157 cerr << "\t-ubam\t" << "Write uncompressed BAM output. Default is to write compressed BAM." << endl << endl;
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158
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159 cerr << "Notes: " << endl;
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160 cerr << "\t(1) BED files must be at least BED4 to be amenable to BAM (needs name field)." << endl << endl;
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161
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162
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163 // end the program here
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164 exit(1);
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165 }
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166
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167
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168 void ProcessBed(istream &bedInput, BedFile *bed, GenomeFile *genome, bool isBED12, int mapQual, bool uncompressedBam) {
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169
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170 BamWriter *writer = new BamWriter();
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171
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172 // build a BAM header from the genomeFile
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173 RefVector refs;
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174 string bamHeader;
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175 map<string, int, std::less<string> > chromToId;
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176 MakeBamHeader(genome->getGenomeFileName(), refs, bamHeader, chromToId);
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177
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178 // set compression mode
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179 BamWriter::CompressionMode compressionMode = BamWriter::Compressed;
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180 if ( uncompressedBam ) compressionMode = BamWriter::Uncompressed;
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181 writer->SetCompressionMode(compressionMode);
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182 // open a BAM and add the reference headers to the BAM file
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183 writer->Open("stdout", bamHeader, refs);
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184
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185
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186 // process each BED entry and convert to BAM
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187 BED bedEntry, nullBed;
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188 int lineNum = 0;
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189 BedLineStatus bedStatus;
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190 // open the BED file for reading.
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191 bed->Open();
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192 while ((bedStatus = bed->GetNextBed(bedEntry, lineNum)) != BED_INVALID) {
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193 if (bedStatus == BED_VALID) {
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194 BamAlignment bamEntry;
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195 if (bed->bedType >= 4) {
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196 ConvertBedToBam(bedEntry, bamEntry, chromToId, isBED12, mapQual, lineNum);
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197 writer->SaveAlignment(bamEntry);
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198 }
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199 else {
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200 cerr << "Error: BED entry without name found at line: " << lineNum << ". Exiting!" << endl;
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201 exit (1);
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202 }
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203 bedEntry = nullBed;
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204 }
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205 }
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206 //close up
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207 bed->Close();
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208 writer->Close();
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209 }
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210
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211
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212 void ConvertBedToBam(const BED &bed, BamAlignment &bam, map<string, int, std::less<string> > &chromToId,
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213 bool isBED12, int mapQual, int lineNum) {
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214
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215 bam.Name = bed.name;
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216 bam.Position = bed.start;
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217 bam.Bin = reg2bin(bed.start, bed.end);
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218
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219 // hard-code the sequence and qualities.
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220 int bedLength = bed.end - bed.start;
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221
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222 // set dummy seq and qual strings. the input is BED,
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223 // so the sequence is inherently the same as it's
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224 // reference genome.
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225 // Thanks to James M. Ward for pointing this out.
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226 bam.QueryBases = "";
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227 bam.Qualities = "";
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228
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229 // chrom and map quality
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230 bam.RefID = chromToId[bed.chrom];
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231 bam.MapQuality = mapQual;
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232
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233 // set the BAM FLAG
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234 bam.AlignmentFlag = 0;
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235 if (bed.strand == "-")
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236 bam.SetIsReverseStrand(true);
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237
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238 bam.MatePosition = -1;
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239 bam.InsertSize = 0;
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240 bam.MateRefID = -1;
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241
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242 bam.CigarData.clear();
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243
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244 if (isBED12 == false) {
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245 CigarOp cOp;
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246 cOp.Type = 'M';
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247 cOp.Length = bedLength;
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248 bam.CigarData.push_back(cOp);
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249 }
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250 // we're being told that the input is BED12.
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251 else{
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252
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253 // does it smell like BED12? if so, process it.
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254 if (bed.otherFields.size() == 6) {
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255
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256 // extract the relevant BED fields to convert BED12 to BAM
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257 // namely: blockCount, blockStarts, blockEnds
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258 unsigned int blockCount = atoi(bed.otherFields[3].c_str());
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259
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260 vector<int> blockSizes, blockStarts;
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261 Tokenize(bed.otherFields[4], blockSizes, ",");
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262 Tokenize(bed.otherFields[5], blockStarts, ",");
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263
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264 // make sure this is a well-formed BED12 entry.
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265 if (blockSizes.size() != blockCount) {
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266 cerr << "Error: Number of BED blocks does not match blockCount at line: " << lineNum << ". Exiting!" << endl;
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267 exit (1);
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268 }
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269 else {
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270 // does the first block start after the bed.start?
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271 // if so, we need to do some "splicing"
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272 if (blockStarts[0] > 0) {
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273 CigarOp cOp;
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274 cOp.Length = blockStarts[0];
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275 cOp.Type = 'N';
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276 bam.CigarData.push_back(cOp);
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277 }
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278 // handle the "middle" blocks
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279 for (unsigned int i = 0; i < blockCount - 1; ++i) {
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280 CigarOp cOp;
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281 cOp.Length = blockSizes[i];
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282 cOp.Type = 'M';
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283 bam.CigarData.push_back(cOp);
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284
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285 if (blockStarts[i+1] > (blockStarts[i] + blockSizes[i])) {
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286 CigarOp cOp;
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287 cOp.Length = (blockStarts[i+1] - (blockStarts[i] + blockSizes[i]));
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288 cOp.Type = 'N';
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289 bam.CigarData.push_back(cOp);
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290 }
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291 }
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292 // handle the last block.
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293 CigarOp cOp;
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294 cOp.Length = blockSizes[blockCount - 1];
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295 cOp.Type = 'M';
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296 bam.CigarData.push_back(cOp);
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297 }
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298 }
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299 // it doesn't smell like BED12. complain.
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300 else {
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301 cerr << "You've indicated that the input file is in BED12 format, yet the relevant fields cannot be found. Exiting." << endl << endl;
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302 exit(1);
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303 }
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304 }
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305 }
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306
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307
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308 void MakeBamHeader(const string &genomeFile, RefVector &refs, string &header,
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309 map<string, int, std::less<string> > &chromToId) {
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310
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311 // make a genome map of the genome file.
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312 GenomeFile genome(genomeFile);
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313
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314 header += "@HD\tVN:1.0\tSO:unsorted\n";
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315 header += "@PG\tID:BEDTools_bedToBam\tVN:V";
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316 header += VERSION;
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317 header += "\n";
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318
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319 int chromId = 0;
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320 vector<string> chromList = genome.getChromList();
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321 sort(chromList.begin(), chromList.end());
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322
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323 // create a BAM header (@SQ) entry for each chrom in the BEDTools genome file.
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324 vector<string>::const_iterator genomeItr = chromList.begin();
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325 vector<string>::const_iterator genomeEnd = chromList.end();
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326 for (; genomeItr != genomeEnd; ++genomeItr) {
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327 chromToId[*genomeItr] = chromId;
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328 chromId++;
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329
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330 // add to the header text
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331 int size = genome.getChromSize(*genomeItr);
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332 string chromLine = "@SQ\tSN:" + *genomeItr + "\tAS:" + genomeFile + "\tLN:" + ToString(size) + "\n";
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333 header += chromLine;
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334
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335 // create a chrom entry and add it to
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336 // the RefVector
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337 RefData chrom;
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338 chrom.RefName = *genomeItr;
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339 chrom.RefLength = size;
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340 refs.push_back(chrom);
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341 }
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342 }
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343
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344
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345 /* Taken directly from the SAMTools spec
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346 calculate bin given an alignment in [beg,end) (zero-based, half-close, half-open) */
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347 int reg2bin(int beg, int end) {
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348 --end;
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349 if (beg>>14 == end>>14) return ((1<<15)-1)/7 + (beg>>14);
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350 if (beg>>17 == end>>17) return ((1<<12)-1)/7 + (beg>>17);
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351 if (beg>>20 == end>>20) return ((1<<9)-1)/7 + (beg>>20);
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352 if (beg>>23 == end>>23) return ((1<<6)-1)/7 + (beg>>23);
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353 if (beg>>26 == end>>26) return ((1<<3)-1)/7 + (beg>>26);
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354 return 0;
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355 }
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356
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357
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