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1 // ***************************************************************************
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2 // BamMultiReader.h (c) 2010 Erik Garrison, 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: 15 March 2011 (DB)
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7 // ---------------------------------------------------------------------------
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8 // Convenience class for reading multiple BAM files.
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9 // ***************************************************************************
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10
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11 #ifndef BAMMULTIREADER_H
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12 #define BAMMULTIREADER_H
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13
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14 #include <api/api_global.h>
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15 #include <api/BamReader.h>
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16 #include <map>
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17 #include <sstream>
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18 #include <string>
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19 #include <utility>
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20
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21 namespace BamTools {
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22
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23 namespace Internal {
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24 class BamMultiReaderPrivate;
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25 } // namespace Internal
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26
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27 class API_EXPORT BamMultiReader {
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28
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29 public:
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30 enum SortOrder { SortedByPosition = 0
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31 , SortedByReadName
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32 , Unsorted
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33 };
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34
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35 // constructor / destructor
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36 public:
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37 BamMultiReader(void);
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38 ~BamMultiReader(void);
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39
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40 // public interface
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41 public:
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42
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43 // ----------------------
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44 // BAM file operations
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45 // ----------------------
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46
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47 // closes all open BAM files
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48 void Close(void);
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49 // close only the requested BAM file
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50 void CloseFile(const std::string& filename);
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51 // returns list of filenames for all open BAM files
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52 const std::vector<std::string> Filenames(void) const;
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53 // returns true if multireader has any open BAM files
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54 bool HasOpenReaders(void) const;
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55 // performs random-access jump within current BAM files
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56 bool Jump(int refID, int position = 0);
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57 // opens BAM files
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58 bool Open(const std::vector<std::string>& filenames);
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59 // opens a single BAM file, adding to any other current BAM files
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60 bool OpenFile(const std::string& filename);
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61 // returns file pointers to beginning of alignments
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62 bool Rewind(void);
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63 // sets the target region of interest
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64 bool SetRegion(const BamRegion& region);
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65 // sets the target region of interest
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66 bool SetRegion(const int& leftRefID,
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67 const int& leftPosition,
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68 const int& rightRefID,
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69 const int& rightPosition);
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70
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71 // ----------------------
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72 // access alignment data
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73 // ----------------------
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74
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75 // retrieves next available alignment
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76 bool GetNextAlignment(BamAlignment& alignment);
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77 // retrieves next available alignmnet (without populating the alignment's string data fields)
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78 bool GetNextAlignmentCore(BamAlignment& alignment);
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79
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80 // sets the expected sorting order for reading across multiple BAM files
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81 void SetSortOrder(const SortOrder& order);
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82
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83 // ----------------------
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84 // access auxiliary data
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85 // ----------------------
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86
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87 // returns unified SAM header for all files
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88 SamHeader GetHeader(void) const;
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89 // returns unified SAM header text for all files
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90 std::string GetHeaderText(void) const;
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91 // returns number of reference sequences
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92 int GetReferenceCount(void) const;
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93 // returns all reference sequence entries.
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94 const BamTools::RefVector GetReferenceData(void) const;
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95 // returns the ID of the reference with this name.
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96 int GetReferenceID(const std::string& refName) const;
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97
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98 // ----------------------
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99 // BAM index operations
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100 // ----------------------
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101
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102 // creates index files for current BAM files
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103 bool CreateIndexes(const BamIndex::IndexType& type = BamIndex::STANDARD);
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104 // returns true if all BAM files have index data available
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105 bool HasIndexes(void) const;
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106 // looks for index files that match current BAM files
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107 bool LocateIndexes(const BamIndex::IndexType& preferredType = BamIndex::STANDARD);
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108 // opens index files for current BAM files.
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109 bool OpenIndexes(const std::vector<std::string>& indexFilenames);
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110 // changes the caching behavior of the index data
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111 void SetIndexCacheMode(const BamIndex::IndexCacheMode& mode);
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112
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113 // deprecated methods
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114 public:
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115 // returns \c true if all BAM files have index data available.
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116 bool IsIndexLoaded(void) const;
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117 // convenience method for printing filenames to stdout
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118 void PrintFilenames(void) const;
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119
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120 // private implementation
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121 private:
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122 Internal::BamMultiReaderPrivate* d;
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123 };
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124
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125 } // namespace BamTools
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126
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127 #endif // BAMMULTIREADER_H
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