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1 // ***************************************************************************
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2 // BamIndex.h (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: 19 November 2010 (DB)
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7 // ---------------------------------------------------------------------------
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8 // Provides basic BAM index interface
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9 // ***************************************************************************
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10
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11 #ifndef BAM_INDEX_H
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12 #define BAM_INDEX_H
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13
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14 #include <api_global.h>
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15 #include <BamAux.h>
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16 #include <iostream>
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17 #include <string>
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18 #include <vector>
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19
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20 namespace BamTools {
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21
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22 class BamReader;
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23 class BgzfData;
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24
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25 namespace Internal {
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26 class BamStandardIndex;
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27 class BamToolsIndex;
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28 } // namespace Internal
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29
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30 // --------------------------------------------------
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31 // BamIndex base class
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32 class API_EXPORT BamIndex {
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33
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34 // specify index-caching behavior
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35 //
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36 // @FullIndexCaching - store entire index file contents in memory
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37 // @LimitedIndexCaching - store only index data for current reference
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38 // being processed
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39 // @NoIndexCaching - do not store any index data. Load as needed to
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40 // calculate jump offset
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41 public: enum BamIndexCacheMode { FullIndexCaching = 0
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42 , LimitedIndexCaching
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43 , NoIndexCaching
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44 };
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45
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46 // ctor & dtor
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47 public:
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48 BamIndex(BamTools::BgzfData* bgzf, BamTools::BamReader* reader);
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49 virtual ~BamIndex(void);
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50
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51 // index interface
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52 public:
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53 // creates index data (in-memory) from current reader data
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54 virtual bool Build(void) =0;
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55 // returns supported file extension
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56 virtual const std::string Extension(void) const =0;
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57 // returns whether reference has alignments or no
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58 virtual bool HasAlignments(const int& referenceID) const =0;
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59 // attempts to use index to jump to region; returns success/fail
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60 // a "successful" jump indicates no error, but not whether this region has data
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61 // * thus, the method sets a flag to indicate whether there are alignments
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62 // available after the jump position
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63 virtual bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion) =0;
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64 // loads existing data from file into memory
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65 virtual bool Load(const std::string& filename);
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66 // change the index caching behavior
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67 virtual void SetCacheMode(const BamIndexCacheMode mode);
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68 // writes in-memory index data out to file
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69 // N.B. - (this is the original BAM filename, method will modify it to use applicable extension)
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70 virtual bool Write(const std::string& bamFilename);
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71
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72 // derived-classes MUST provide implementation
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73 protected:
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74 // clear all current index offset data in memory
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75 virtual void ClearAllData(void) =0;
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76 // return file position after header metadata
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77 virtual const off_t DataBeginOffset(void) const =0;
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78 // return true if all index data is cached
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79 virtual bool HasFullDataCache(void) const =0;
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80 // clears index data from all references except the first
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81 virtual void KeepOnlyFirstReferenceOffsets(void) =0;
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82 // load index data for all references, return true if loaded OK
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83 // @saveData - save data in memory if true, just read & discard if false
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84 virtual bool LoadAllReferences(bool saveData = true) =0;
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85 // load first reference from file, return true if loaded OK
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86 // @saveData - save data in memory if true, just read & discard if false
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87 virtual bool LoadFirstReference(bool saveData = true) =0;
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88 // load header data from index file, return true if loaded OK
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89 virtual bool LoadHeader(void) =0;
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90 // position file pointer to first reference begin, return true if skipped OK
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91 virtual bool SkipToFirstReference(void) =0;
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92 // write index reference data
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93 virtual bool WriteAllReferences(void) =0;
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94 // write index header data
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95 virtual bool WriteHeader(void) =0;
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96
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97 // internal methods
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98 protected:
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99 // rewind index file to beginning of index data, return true if rewound OK
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100 bool Rewind(void);
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101
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102 private:
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103 // return true if FILE* is open
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104 bool IsOpen(void) const;
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105 // opens index file according to requested mode, return true if opened OK
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106 bool OpenIndexFile(const std::string& filename, const std::string& mode);
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107 // updates in-memory cache of index data, depending on current cache mode
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108 void UpdateCache(void);
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109
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110 // factory methods for returning proper BamIndex-derived type based on available index files
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111 public:
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112
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113 // returns index based on BAM filename 'stub'
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114 // checks first for preferred type, returns that type if found
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115 // (if not found, attmempts to load other type(s), returns 0 if NONE found)
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116 //
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117 // ** default preferred type is BamToolsIndex ** use this anytime it exists
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118 enum PreferredIndexType { BAMTOOLS = 0, STANDARD };
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119 static BamIndex* FromBamFilename(const std::string& bamFilename,
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120 BamTools::BgzfData* bgzf,
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121 BamTools::BamReader* reader,
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122 const BamIndex::PreferredIndexType& type = BamIndex::BAMTOOLS);
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123
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124 // returns index based on explicitly named index file (or 0 if not found)
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125 static BamIndex* FromIndexFilename(const std::string& indexFilename,
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126 BamTools::BgzfData* bgzf,
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127 BamTools::BamReader* reader);
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128
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129 // data members
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130 protected:
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131 BamTools::BgzfData* m_BGZF;
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132 BamTools::BamReader* m_reader;
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133 BamTools::RefVector m_references;
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134 BamIndex::BamIndexCacheMode m_cacheMode;
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135 FILE* m_indexStream;
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136
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137
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138 // friends
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139 friend class Internal::BamStandardIndex;
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140 friend class Internal::BamToolsIndex;
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141 };
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142
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143 } // namespace BamTools
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144
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145 #endif // BAM_INDEX_H
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