// BamMultiReader_p.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 9 September 2011 (DB)
+// Last modified: 7 October 2011 (DB)
// ---------------------------------------------------------------------------
// Functionality for simultaneously reading multiple BAM files
// *************************************************************************
#include <api/SamHeader.h>
#include <api/BamMultiReader.h>
+#include <api/internal/BamMultiMerger_p.h>
#include <string>
#include <vector>
namespace BamTools {
namespace Internal {
-class IBamMultiMerger;
-
class BamMultiReaderPrivate {
// typedefs
public:
// file operations
- void Close(void);
- void CloseFile(const std::string& filename);
- void CloseFiles(const std::vector<std::string>& filenames);
+ bool Close(void);
+ bool CloseFile(const std::string& filename);
const std::vector<std::string> Filenames(void) const;
bool Jump(int refID, int position = 0);
bool Open(const std::vector<std::string>& filenames);
bool OpenFile(const std::string& filename);
- void PrintFilenames(void) const;
bool Rewind(void);
bool SetRegion(const BamRegion& region);
bool GetNextAlignment(BamAlignment& al);
bool GetNextAlignmentCore(BamAlignment& al);
bool HasOpenReaders(void);
- void SetSortOrder(const BamMultiReader::SortOrder& order);
// access auxiliary data
SamHeader GetHeader(void) const;
bool OpenIndexes(const std::vector<std::string>& indexFilenames);
void SetIndexCacheMode(const BamIndex::IndexCacheMode mode);
+ // error handling
+ std::string GetErrorString(void) const;
+
// 'internal' methods
public:
- IBamMultiMerger* CreateMergerForCurrentSortOrder(void) const;
- const std::string ExtractReadGroup(const std::string& headerLine) const;
- bool HasAlignmentData(void) const;
- bool LoadNextAlignment(BamReader* reader, BamAlignment* alignment);
- ReaderAlignment OpenReader(const std::string& filename, bool* ok);
+
+ bool CloseFiles(const std::vector<std::string>& filenames);
+ IMultiMerger* CreateAlignmentCache(void) const;
bool PopNextCachedAlignment(BamAlignment& al, const bool needCharData);
bool RewindReaders(void);
void SaveNextAlignment(BamReader* reader, BamAlignment* alignment);
- const std::vector<std::string> SplitHeaderText(const std::string& headerText) const;
- void UpdateAlignmentCache(void);
- void ValidateReaders(void) const;
+ void SetErrorString(const std::string& where, const std::string& what) const; //
+ bool UpdateAlignmentCache(void);
+ bool ValidateReaders(void) const;
// data members
- public:
- std::vector<ReaderAlignment> m_readers;
- IBamMultiMerger* m_alignments;
- BamMultiReader::SortOrder m_sortOrder;
+ public:
+ std::vector<MergeItem> m_readers;
+ IMultiMerger* m_alignmentCache;
+ mutable std::string m_errorString;
};
} // namespace Internal