22class BamReaderPrivate;
42 const std::string GetFilename()
const;
46 bool Jump(
int refID,
int position = 0);
48 bool Open(
const std::string& filename);
54 bool SetRegion(
const int& leftRefID,
const int& leftPosition,
const int& rightRefID,
55 const int& rightPosition);
71 const SamHeader& GetConstSamHeader()
const;
75 std::string GetHeaderText()
const;
82 int GetReferenceCount()
const;
84 const RefVector& GetReferenceData()
const;
86 int GetReferenceID(
const std::string& refName)
const;
95 bool HasIndex()
const;
99 bool OpenIndex(
const std::string& indexFilename);
108 std::string GetErrorString()
const;
112 Internal::BamReaderPrivate* d;