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1 // ***************************************************************************
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2 // BamReader_p.h (c) 2010 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 the basic functionality for reading BAM files
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9 // ***************************************************************************
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10
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11 #ifndef BAMREADER_P_H
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12 #define BAMREADER_P_H
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13
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14 // -------------
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15 // W A R N I N G
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16 // -------------
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17 //
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18 // This file is not part of the BamTools API. It exists purely as an
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19 // implementation detail. This header file may change from version to version
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20 // without notice, or even be removed.
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21 //
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22 // We mean it.
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23
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24 #include <BamAlignment.h>
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25 #include <BamIndex.h>
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26 #include <BGZF.h>
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27 #include <string>
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28
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29 namespace BamTools {
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30
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31 class BamReader;
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32
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33 namespace Internal {
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34
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35 class BamReaderPrivate {
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36
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37 // enums
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38 public: enum RegionState { BEFORE_REGION = 0
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39 , WITHIN_REGION
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40 , AFTER_REGION
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41 };
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42
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43 // ctor & dtor
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44 public:
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45 BamReaderPrivate(BamReader* parent);
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46 ~BamReaderPrivate(void);
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47
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48 // 'public' interface to BamReader
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49 public:
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50
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51 // file operations
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52 void Close(void);
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53 bool Open(const std::string& filename,
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54 const std::string& indexFilename,
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55 const bool lookForIndex,
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56 const bool preferStandardIndex);
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57 bool Rewind(void);
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58 bool SetRegion(const BamRegion& region);
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59
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60 // access alignment data
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61 bool GetNextAlignment(BamAlignment& bAlignment);
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62 bool GetNextAlignmentCore(BamAlignment& bAlignment);
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63
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64 // access auxiliary data
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65 const std::string GetHeaderText(void) const;
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66 int GetReferenceID(const std::string& refName) const;
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67
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68 // index operations
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69 bool CreateIndex(bool useStandardIndex);
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70 void SetIndexCacheMode(const BamIndex::BamIndexCacheMode mode);
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71
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72 // 'internal' methods
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73 public:
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74
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75 // ---------------------------------------
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76 // reading alignments and auxiliary data
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77
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78 // adjusts requested region if necessary (depending on where data actually begins)
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79 void AdjustRegion(BamRegion& region);
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80 // fills out character data for BamAlignment data
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81 bool BuildCharData(BamAlignment& bAlignment);
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82 // checks to see if alignment overlaps current region
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83 RegionState IsOverlap(BamAlignment& bAlignment);
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84 // retrieves header text from BAM file
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85 void LoadHeaderData(void);
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86 // retrieves BAM alignment under file pointer
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87 bool LoadNextAlignment(BamAlignment& bAlignment);
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88 // builds reference data structure from BAM file
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89 void LoadReferenceData(void);
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90 // mark references with 'HasAlignments' status
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91 void MarkReferences(void);
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92
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93 // ---------------------------------
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94 // index file handling
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95
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96 // clear out inernal index data structure
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97 void ClearIndex(void);
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98 // loads index from BAM index file
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99 bool LoadIndex(const bool lookForIndex, const bool preferStandardIndex);
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100
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101 // data members
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102 public:
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103
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104 // general file data
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105 BgzfData mBGZF;
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106 std::string HeaderText;
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107 BamIndex* Index;
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108 RefVector References;
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109 bool HasIndex;
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110 int64_t AlignmentsBeginOffset;
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111 std::string Filename;
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112 std::string IndexFilename;
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113
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114 // Internal::BamHeader* m_header;
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115
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116 // index caching mode
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117 BamIndex::BamIndexCacheMode IndexCacheMode;
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118
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119 // system data
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120 bool IsBigEndian;
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121
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122 // user-specified region values
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123 BamRegion Region;
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124 bool HasAlignmentsInRegion;
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125
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126 // parent BamReader
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127 BamReader* Parent;
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128
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129 // BAM character constants
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130 const char* DNA_LOOKUP;
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131 const char* CIGAR_LOOKUP;
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132 };
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133
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134 } // namespace Internal
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135 } // namespace BamTools
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136
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137 #endif // BAMREADER_P_H
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