// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 19 November 2010 (DB)
+// Last modified: 24 February 2011 (DB)
// ---------------------------------------------------------------------------
// Provides basic BAM index interface
// ***************************************************************************
namespace BamTools {
class BamReader;
-class BgzfData;
namespace Internal {
- class BamStandardIndex;
- class BamToolsIndex;
+ class BamReaderPrivate;
} // namespace Internal
// --------------------------------------------------
// BamIndex base class
class API_EXPORT BamIndex {
- // specify index-caching behavior
- //
- // @FullIndexCaching - store entire index file contents in memory
- // @LimitedIndexCaching - store only index data for current reference
- // being processed
- // @NoIndexCaching - do not store any index data. Load as needed to
- // calculate jump offset
- public: enum BamIndexCacheMode { FullIndexCaching = 0
- , LimitedIndexCaching
- , NoIndexCaching
- };
+ // enums
+ public:
+ // specify index-caching behavior
+ enum IndexCacheMode { FullIndexCaching = 0 // store entire index file contents in memory
+ , LimitedIndexCaching // store only index data for current reference
+ , NoIndexCaching // do not store any index data between jumps
+ };
+
+ // list of supported BamIndex types
+ enum IndexType { BAMTOOLS = 0
+ , STANDARD
+ };
// ctor & dtor
public:
- BamIndex(BamTools::BgzfData* bgzf, BamTools::BamReader* reader);
+ BamIndex(void);
virtual ~BamIndex(void);
// index interface
public:
- // creates index data (in-memory) from current reader data
- virtual bool Build(void) =0;
+ // creates index data (in-memory) from @reader data
+ virtual bool Build(Internal::BamReaderPrivate* reader) =0;
// returns supported file extension
- virtual const std::string Extension(void) const =0;
+ virtual const std::string Extension(void) =0;
// returns whether reference has alignments or no
virtual bool HasAlignments(const int& referenceID) const =0;
- // attempts to use index to jump to region; returns success/fail
+ // attempts to use index data to jump to @region in @reader; returns success/fail
// a "successful" jump indicates no error, but not whether this region has data
- // * thus, the method sets a flag to indicate whether there are alignments
+ // * thus, the method sets a flag to indicate whether there are alignments
// available after the jump position
- virtual bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion) =0;
+ virtual bool Jump(Internal::BamReaderPrivate* reader,
+ const BamTools::BamRegion& region,
+ bool* hasAlignmentsInRegion) =0;
// loads existing data from file into memory
virtual bool Load(const std::string& filename);
// change the index caching behavior
- virtual void SetCacheMode(const BamIndexCacheMode mode);
+ virtual void SetCacheMode(const BamIndex::IndexCacheMode& mode);
// writes in-memory index data out to file
// N.B. - (this is the original BAM filename, method will modify it to use applicable extension)
virtual bool Write(const std::string& bamFilename);
-
+
// derived-classes MUST provide implementation
protected:
// clear all current index offset data in memory
virtual void ClearAllData(void) =0;
// return file position after header metadata
- virtual const off_t DataBeginOffset(void) const =0;
+ virtual off_t DataBeginOffset(void) const =0;
// return true if all index data is cached
virtual bool HasFullDataCache(void) const =0;
// clears index data from all references except the first
// write index header data
virtual bool WriteHeader(void) =0;
- // internal methods
+ // internal methods (but available to derived classes)
protected:
// rewind index file to beginning of index data, return true if rewound OK
bool Rewind(void);
// updates in-memory cache of index data, depending on current cache mode
void UpdateCache(void);
- // factory methods for returning proper BamIndex-derived type based on available index files
- public:
-
- // returns index based on BAM filename 'stub'
- // checks first for preferred type, returns that type if found
- // (if not found, attmempts to load other type(s), returns 0 if NONE found)
- //
- // ** default preferred type is BamToolsIndex ** use this anytime it exists
- enum PreferredIndexType { BAMTOOLS = 0, STANDARD };
- static BamIndex* FromBamFilename(const std::string& bamFilename,
- BamTools::BgzfData* bgzf,
- BamTools::BamReader* reader,
- const BamIndex::PreferredIndexType& type = BamIndex::BAMTOOLS);
-
- // returns index based on explicitly named index file (or 0 if not found)
- static BamIndex* FromIndexFilename(const std::string& indexFilename,
- BamTools::BgzfData* bgzf,
- BamTools::BamReader* reader);
-
// data members
protected:
- BamTools::BgzfData* m_BGZF;
- BamTools::BamReader* m_reader;
- BamTools::RefVector m_references;
- BamIndex::BamIndexCacheMode m_cacheMode;
FILE* m_indexStream;
-
-
- // friends
- friend class Internal::BamStandardIndex;
- friend class Internal::BamToolsIndex;
+ std::string m_indexFilename;
+ BamIndex::IndexCacheMode m_cacheMode;
};
} // namespace BamTools
projects / bamtools.git / blobdiff