// ***************************************************************************
// BamMultiReader_p.h (c) 2010 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 17 January 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Functionality for simultaneously reading multiple BAM files
// *************************************************************************
//
// We mean it.
-#include <api/BamMultiReader.h>
+#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:
+ typedef std::pair<BamReader*, BamAlignment*> ReaderAlignment;
+
// constructor / destructor
public:
BamMultiReaderPrivate(void);
public:
// file operations
- void Close(void);
- bool Open(const std::vector<std::string>& filenames,
- bool openIndexes = true,
- bool coreMode = false,
- bool preferStandardIndex = false);
- bool IsIndexLoaded(void) const;
+ bool Close(void);
+ bool CloseFile(const std::string& filename);
+ const std::vector<std::string> Filenames(void) const;
bool Jump(int refID, int position = 0);
- void PrintFilenames(void) const;
- bool SetRegion(const BamRegion& region);
+ bool Open(const std::vector<std::string>& filenames);
+ bool OpenFile(const std::string& filename);
bool Rewind(void);
+ bool SetRegion(const BamRegion& region);
// access alignment data
bool GetNextAlignment(BamAlignment& al);
bool GetNextAlignmentCore(BamAlignment& al);
bool HasOpenReaders(void);
- void SetSortOrder(const BamMultiReader::SortOrder& order);
// access auxiliary data
- const std::string GetHeaderText(void) const;
- const int GetReferenceCount(void) const;
+ SamHeader GetHeader(void) const;
+ std::string GetHeaderText(void) const;
+ int GetReferenceCount(void) const;
const BamTools::RefVector GetReferenceData(void) const;
- const int GetReferenceID(const std::string& refName) const;
+ int GetReferenceID(const std::string& refName) const;
// BAM index operations
- bool CreateIndexes(bool useStandardIndex = true);
- void SetIndexCacheMode(const BamIndex::BamIndexCacheMode mode);
-
- // internal methods
- private:
- IBamMultiMerger* CreateMergerForCurrentSortOrder(void) const;
- const std::string ExtractReadGroup(const std::string& headerLine) const;
- bool LoadNextAlignment(BamAlignment& al, bool coreMode);
- void SaveNextAlignment(BamTools::BamReader* reader, BamTools::BamAlignment* alignment);
- const std::vector<std::string> SplitHeaderText(const std::string& headerText) const;
- // updates our alignment cache
- void UpdateAlignments(void);
- // validates that we have a congruent set of BAM files that are aligned against the same reference sequences
- void ValidateReaders(void) const;
+ bool CreateIndexes(const BamIndex::IndexType& type = BamIndex::STANDARD);
+ bool HasIndexes(void) const;
+ bool LocateIndexes(const BamIndex::IndexType& preferredType = BamIndex::STANDARD);
+ bool OpenIndexes(const std::vector<std::string>& indexFilenames);
+ void SetIndexCacheMode(const BamIndex::IndexCacheMode mode);
- // data members
+ // error handling
+ std::string GetErrorString(void) const;
+
+ // 'internal' methods
public:
- typedef std::pair<BamReader*, BamAlignment*> ReaderAlignment;
- std::vector<ReaderAlignment> m_readers;
- IBamMultiMerger* m_alignments;
- bool m_isCoreMode;
- BamMultiReader::SortOrder m_sortOrder;
+ 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);
+ void SetErrorString(const std::string& where, const std::string& what) const; //
+ bool UpdateAlignmentCache(void);
+ bool ValidateReaders(void) const;
+
+ // data members
+ public:
+ std::vector<MergeItem> m_readers;
+ IMultiMerger* m_alignmentCache;
+ mutable std::string m_errorString;
};
} // namespace Internal