// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 20 October 2010 (DB)
+// Last modified: 19 November 2010 (DB)
// ---------------------------------------------------------------------------
-// Provides index functionality - both for the standardized BAM index format
-// (".bai") as well as a BamTools-specific (nonstandard) index format (".bti").
+// Provides basic BAM index interface
// ***************************************************************************
#ifndef BAM_INDEX_H
class BamReader;
class BgzfData;
-
+
+namespace Internal {
+ class BamStandardIndex;
+ class BamToolsIndex;
+} // namespace Internal
+
// --------------------------------------------------
// BamIndex base class
class API_EXPORT BamIndex {
BamTools::RefVector m_references;
BamIndex::BamIndexCacheMode m_cacheMode;
FILE* m_indexStream;
-};
-
-// --------------------------------------------------
-// BamStandardIndex class
-//
-// implements standardized (per SAM/BAM spec) index file ops
-class BamStandardIndex : public BamIndex {
-
- // ctor & dtor
- public:
- BamStandardIndex(BamTools::BgzfData* bgzf,
- BamTools::BamReader* reader);
- ~BamStandardIndex(void);
-
- // interface (implements BamIndex virtual methods)
- public:
- // creates index data (in-memory) from current reader data
- bool Build(void);
- // returns supported file extension
- const std::string Extension(void) const { return std::string(".bai"); }
- // returns whether reference has alignments or no
- bool HasAlignments(const int& referenceID) const;
- // attempts to use index to jump to region; 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
- // available after the jump position
- bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion);
- protected:
- // clear all current index offset data in memory
- void ClearAllData(void);
- // return file position after header metadata
- const off_t DataBeginOffset(void) const;
- // return true if all index data is cached
- bool HasFullDataCache(void) const;
- // clears index data from all references except the first
- void KeepOnlyFirstReferenceOffsets(void);
- // load index data for all references, return true if loaded OK
- // @saveData - save data in memory if true, just read & discard if false
- bool LoadAllReferences(bool saveData = true);
- // load first reference from file, return true if loaded OK
- // @saveData - save data in memory if true, just read & discard if false
- bool LoadFirstReference(bool saveData = true);
- // load header data from index file, return true if loaded OK
- bool LoadHeader(void);
- // position file pointer to first reference begin, return true if skipped OK
- bool SkipToFirstReference(void);
- // write index reference data
- bool WriteAllReferences(void);
- // write index header data
- bool WriteHeader(void);
- // internal implementation
- private:
- struct BamStandardIndexPrivate;
- BamStandardIndexPrivate* d;
+ friend class Internal::BamStandardIndex;
+ friend class Internal::BamToolsIndex;
};
-// --------------------------------------------------
-// BamToolsIndex class
-//
-// implements BamTools-specific index file ops
-class BamToolsIndex : public BamIndex {
-
- // ctor & dtor
- public:
- BamToolsIndex(BamTools::BgzfData* bgzf,
- BamTools::BamReader* reader);
- ~BamToolsIndex(void);
-
- // interface (implements BamIndex virtual methods)
- public:
- // creates index data (in-memory) from current reader data
- bool Build(void);
- // returns supported file extension
- const std::string Extension(void) const { return std::string(".bti"); }
- // returns whether reference has alignments or no
- bool HasAlignments(const int& referenceID) const;
- // attempts to use index to jump to region; 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
- // available after the jump position
- bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion);
- protected:
- // clear all current index offset data in memory
- void ClearAllData(void);
- // return file position after header metadata
- const off_t DataBeginOffset(void) const;
- // return true if all index data is cached
- bool HasFullDataCache(void) const;
- // clears index data from all references except the first
- void KeepOnlyFirstReferenceOffsets(void);
- // load index data for all references, return true if loaded OK
- // @saveData - save data in memory if true, just read & discard if false
- bool LoadAllReferences(bool saveData = true);
- // load first reference from file, return true if loaded OK
- // @saveData - save data in memory if true, just read & discard if false
- bool LoadFirstReference(bool saveData = true);
- // load header data from index file, return true if loaded OK
- bool LoadHeader(void);
- // position file pointer to first reference begin, return true if skipped OK
- bool SkipToFirstReference(void);
- // write index reference data
- bool WriteAllReferences(void);
- // write index header data
- bool WriteHeader(void);
-
- // internal implementation
- private:
- struct BamToolsIndexPrivate;
- BamToolsIndexPrivate* d;
-};
-
-// --------------------------------------------------
-// BamIndex factory methods
-
-// 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
-inline
-BamIndex* BamIndex::FromBamFilename(const std::string& bamFilename,
- BamTools::BgzfData* bgzf,
- BamTools::BamReader* reader,
- const BamIndex::PreferredIndexType& type)
-{
- // ---------------------------------------------------
- // attempt to load preferred type first
-
- const std::string bamtoolsIndexFilename = bamFilename + ".bti";
- const bool bamtoolsIndexExists = BamTools::FileExists(bamtoolsIndexFilename);
- if ( (type == BamIndex::BAMTOOLS) && bamtoolsIndexExists )
- return new BamToolsIndex(bgzf, reader);
-
- const std::string standardIndexFilename = bamFilename + ".bai";
- const bool standardIndexExists = BamTools::FileExists(standardIndexFilename);
- if ( (type == BamIndex::STANDARD) && standardIndexExists )
- return new BamStandardIndex(bgzf, reader);
-
- // ----------------------------------------------------
- // preferred type could not be found, try other (non-preferred) types
- // if none found, return 0
-
- if ( bamtoolsIndexExists ) return new BamToolsIndex(bgzf, reader);
- if ( standardIndexExists ) return new BamStandardIndex(bgzf, reader);
- return 0;
-}
-
-// returns index based on explicitly named index file (or 0 if not found)
-inline
-BamIndex* BamIndex::FromIndexFilename(const std::string& indexFilename,
- BamTools::BgzfData* bgzf,
- BamTools::BamReader* reader)
-{
- // see if specified file exists
- const bool indexExists = BamTools::FileExists(indexFilename);
- if ( !indexExists ) return 0;
-
- const std::string bamtoolsIndexExtension(".bti");
- const std::string standardIndexExtension(".bai");
-
- // if has bamtoolsIndexExtension
- if ( indexFilename.find(bamtoolsIndexExtension) == (indexFilename.length() - bamtoolsIndexExtension.length()) )
- return new BamToolsIndex(bgzf, reader);
-
- // if has standardIndexExtension
- if ( indexFilename.find(standardIndexExtension) == (indexFilename.length() - standardIndexExtension.length()) )
- return new BamStandardIndex(bgzf, reader);
-
- // otherwise, unsupported file type
- return 0;
-}
-
} // namespace BamTools
#endif // BAM_INDEX_H
projects / bamtools.git / blobdiff