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1 // ***************************************************************************
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2 // BamIndex.cpp (c) 2009 Derek Barnett
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3 // Marth Lab, Department of Biology, Boston College
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4 // All rights reserved.
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5 // ---------------------------------------------------------------------------
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6 // Last modified: 22 November 2010 (DB)
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7 // ---------------------------------------------------------------------------
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8 // Provides index functionality - both for the default (standardized) BAM
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9 // index format (.bai) as well as a BamTools-specific (nonstandard) index
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10 // format (.bti).
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11 // ***************************************************************************
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12
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13 #include <BamIndex.h>
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14 #include <BamReader.h>
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15 #include <BGZF.h>
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16 #include <BamStandardIndex_p.h>
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17 #include <BamToolsIndex_p.h>
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18 using namespace BamTools;
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19 using namespace BamTools::Internal;
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20
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21 #include <cstdio>
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22 #include <cstdlib>
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23 #include <algorithm>
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24 #include <iostream>
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25 #include <map>
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26 using namespace std;
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27
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28 // --------------------------------------------------
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29 // BamIndex factory methods
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30
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31 // returns index based on BAM filename 'stub'
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32 // checks first for preferred type, returns that type if found
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33 // (if not found, attmempts to load other type(s), returns 0 if NONE found)
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34 //
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35 // ** default preferred type is BamToolsIndex ** use this anytime it exists
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36 BamIndex* BamIndex::FromBamFilename(const std::string& bamFilename,
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37 BamTools::BgzfData* bgzf,
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38 BamTools::BamReader* reader,
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39 const BamIndex::PreferredIndexType& type)
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40 {
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41 // ---------------------------------------------------
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42 // attempt to load preferred type first
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43
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44 const std::string bamtoolsIndexFilename = bamFilename + ".bti";
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45 const bool bamtoolsIndexExists = BamTools::FileExists(bamtoolsIndexFilename);
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46 if ( (type == BamIndex::BAMTOOLS) && bamtoolsIndexExists )
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47 return new BamToolsIndex(bgzf, reader);
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48
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49 const std::string standardIndexFilename = bamFilename + ".bai";
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50 const bool standardIndexExists = BamTools::FileExists(standardIndexFilename);
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51 if ( (type == BamIndex::STANDARD) && standardIndexExists )
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52 return new BamStandardIndex(bgzf, reader);
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53
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54 // ----------------------------------------------------
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55 // preferred type could not be found, try other (non-preferred) types
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56 // if none found, return 0
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57
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58 if ( bamtoolsIndexExists ) return new BamToolsIndex(bgzf, reader);
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59 if ( standardIndexExists ) return new BamStandardIndex(bgzf, reader);
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60 return 0;
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61 }
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62
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63 // returns index based on explicitly named index file (or 0 if not found)
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64 BamIndex* BamIndex::FromIndexFilename(const std::string& indexFilename,
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65 BamTools::BgzfData* bgzf,
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66 BamTools::BamReader* reader)
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67 {
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68 // see if specified file exists
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69 const bool indexExists = BamTools::FileExists(indexFilename);
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70 if ( !indexExists ) return 0;
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71
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72 const std::string bamtoolsIndexExtension(".bti");
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73 const std::string standardIndexExtension(".bai");
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74
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75 // if has bamtoolsIndexExtension
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76 if ( indexFilename.find(bamtoolsIndexExtension) == (indexFilename.length() - bamtoolsIndexExtension.length()) )
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77 return new BamToolsIndex(bgzf, reader);
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78
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79 // if has standardIndexExtension
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80 if ( indexFilename.find(standardIndexExtension) == (indexFilename.length() - standardIndexExtension.length()) )
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81 return new BamStandardIndex(bgzf, reader);
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82
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83 // otherwise, unsupported file type
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84 return 0;
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85 }
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86
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87 // -------------------------------
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88 // BamIndex implementation
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89
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90 // ctor
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91 BamIndex::BamIndex(BamTools::BgzfData* bgzf, BamTools::BamReader* reader)
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92 : m_BGZF(bgzf)
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93 , m_reader(reader)
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94 , m_cacheMode(BamIndex::LimitedIndexCaching)
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95 , m_indexStream(0)
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96 {
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97 if ( m_reader && m_reader->IsOpen() )
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98 m_references = m_reader->GetReferenceData();
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99 }
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100
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101 // dtor
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102 BamIndex::~BamIndex(void) {
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103 if ( IsOpen() )
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104 fclose(m_indexStream);
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105 }
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106
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107 // return true if FILE* is open
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108 bool BamIndex::IsOpen(void) const {
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109 return ( m_indexStream != 0 );
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110 }
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111
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112 // loads existing data from file into memory
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113 bool BamIndex::Load(const string& filename) {
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114
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115 // open index file, abort on error
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116 if ( !OpenIndexFile(filename, "rb") ) {
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117 fprintf(stderr, "ERROR: Unable to open the BAM index file %s for reading.\n", filename.c_str());
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118 return false;
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119 }
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120
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121 // check magic number
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122 if ( !LoadHeader() ) {
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123 fclose(m_indexStream);
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124 return false;
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125 }
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126
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127 // load reference data (but only keep in memory if full caching requested)
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128 bool saveInitialLoad = ( m_cacheMode == BamIndex::FullIndexCaching );
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129 if ( !LoadAllReferences(saveInitialLoad) ) {
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130 fclose(m_indexStream);
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131 return false;
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132 }
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133
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134 // update index cache based on selected mode
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135 UpdateCache();
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136
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137 // return success
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138 return true;
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139 }
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140
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141 // opens index file for reading/writing, return true if opened OK
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142 bool BamIndex::OpenIndexFile(const string& filename, const string& mode) {
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143 m_indexStream = fopen(filename.c_str(), mode.c_str());
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144 return ( m_indexStream != 0 );
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145 }
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146
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147 // rewind index file to beginning of index data, return true if rewound OK
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148 bool BamIndex::Rewind(void) {
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149 return ( fseek64(m_indexStream, DataBeginOffset(), SEEK_SET) == 0 );
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150 }
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151
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152 // change the index caching behavior
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153 void BamIndex::SetCacheMode(const BamIndexCacheMode mode) {
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154 if ( mode != m_cacheMode ) {
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155 m_cacheMode = mode;
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156 UpdateCache();
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157 }
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158 }
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159
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160 // updates in-memory cache of index data, depending on current cache mode
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161 void BamIndex::UpdateCache(void) {
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162
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163 // skip if file not open
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164 if ( !IsOpen() ) return;
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165
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166 // reflect requested cache mode behavior
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167 switch ( m_cacheMode ) {
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168
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169 case (BamIndex::FullIndexCaching) :
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170 Rewind();
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171 LoadAllReferences(true);
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172 break;
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173
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174 case (BamIndex::LimitedIndexCaching) :
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175 if ( HasFullDataCache() )
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176 KeepOnlyFirstReferenceOffsets();
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177 else {
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178 ClearAllData();
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179 SkipToFirstReference();
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180 LoadFirstReference(true);
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181 }
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182 break;
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183 case(BamIndex::NoIndexCaching) :
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184 ClearAllData();
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185 break;
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186 default :
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187 // unreachable
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188 ;
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189 }
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190 }
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191
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192 // writes in-memory index data out to file
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193 bool BamIndex::Write(const string& bamFilename) {
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194
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195 // open index file for writing
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196 string indexFilename = bamFilename + Extension();
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197 if ( !OpenIndexFile(indexFilename, "wb") ) {
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198 fprintf(stderr, "ERROR: Could not open file to save index.\n");
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199 return false;
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200 }
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201
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202 // write index header data
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203 if ( !WriteHeader() ) {
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204 fprintf(stderr, "ERROR: There was a problem writing index metadata to new index file.\n");
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205 fflush(m_indexStream);
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206 fclose(m_indexStream);
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207 exit(1);
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208 }
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209
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210 // write main index data
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211 if ( !WriteAllReferences() ) {
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212 fprintf(stderr, "ERROR: There was a problem writing index data to new index file.\n");
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213 fflush(m_indexStream);
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214 fclose(m_indexStream);
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215 exit(1);
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216 }
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217
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218 // flush any remaining output, rewind file, and return success
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219 fflush(m_indexStream);
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220 fclose(m_indexStream);
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221
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222 // re-open index file for later reading
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223 if ( !OpenIndexFile(indexFilename, "rb") ) {
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224 fprintf(stderr, "ERROR: Could not open newly created index file for reading.\n");
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225 return false;
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226 }
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227
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228 // return success/failure of write
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229 return true;
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230 }
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