1 // ***************************************************************************
2 // BamIndex.h (c) 2009 Derek Barnett
3 // Marth Lab, Department of Biology, Boston College
4 // ---------------------------------------------------------------------------
5 // Last modified: 10 October 2011 (DB)
6 // ---------------------------------------------------------------------------
7 // Provides basic BAM index interface
8 // ***************************************************************************
13 #include "api/api_global.h"
14 #include "api/BamAux.h"
20 class BamReaderPrivate;
21 } // namespace Internal
23 /*! \class BamTools::BamIndex
24 \brief Provides methods for generating & loading BAM index files.
26 This class straddles the line between public API and internal
27 implementation detail. Most client code should never have to use this
30 It is exposed to the public API to allow advanced users to implement
31 their own custom indexing schemes.
34 class API_EXPORT BamIndex {
39 // list of supported BamIndex types
40 enum IndexType { BAMTOOLS = 0
46 BamIndex(Internal::BamReaderPrivate* reader) : m_reader(reader) { }
47 virtual ~BamIndex(void) { }
51 // builds index from associated BAM file & writes out to index file
52 virtual bool Create(void) =0;
54 // returns a human-readable description of the last error encountered
55 std::string GetErrorString(void) { return m_errorString; }
57 // returns whether reference has alignments or no
58 virtual bool HasAlignments(const int& referenceID) const =0;
60 // attempts to use index data to jump to @region, returns success/fail
61 // a "successful" jump indicates no error, but not whether this region has data
62 // * thus, the method sets a flag to indicate whether there are alignments
63 // available after the jump position
64 virtual bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion) =0;
66 // loads existing data from file into memory
67 virtual bool Load(const std::string& filename) =0;
69 // returns the 'type' enum for derived index format
70 virtual BamIndex::IndexType Type(void) const =0;
76 void SetErrorString(const std::string& where, const std::string& what) const {
77 m_errorString = where + ": " + what;
82 Internal::BamReaderPrivate* m_reader; // copy, not owned
83 mutable std::string m_errorString;
88 } // namespace BamTools