--- /dev/null
+// ***************************************************************************
+// BamToolsIndex.h (c) 2010 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 19 November 2010 (DB)
+// ---------------------------------------------------------------------------
+// Provides index operations for the BamTools index format (".bti")
+// ***************************************************************************
+
+#ifndef BAMTOOLS_INDEX_FORMAT_H
+#define BAMTOOLS_INDEX_FORMAT_H
+
+// -------------
+// W A R N I N G
+// -------------
+//
+// This file is not part of the BamTools API. It exists purely as an
+// implementation detail. This header file may change from version to
+// version without notice, or even be removed.
+//
+// We mean it.
+
+#include <api/BamAux.h>
+#include <api/BamIndex.h>
+#include <map>
+#include <string>
+#include <vector>
+
+namespace BamTools {
+
+namespace Internal {
+
+// individual index offset entry
+struct BamToolsIndexEntry {
+
+ // data members
+ int32_t MaxEndPosition;
+ int64_t StartOffset;
+ int32_t StartPosition;
+
+ // ctor
+ BamToolsIndexEntry(const int32_t& maxEndPosition = 0,
+ const int64_t& startOffset = 0,
+ const int32_t& startPosition = 0)
+ : MaxEndPosition(maxEndPosition)
+ , StartOffset(startOffset)
+ , StartPosition(startPosition)
+ { }
+};
+
+// reference index entry
+struct BamToolsReferenceEntry {
+
+ // data members
+ bool HasAlignments;
+ std::vector<BamToolsIndexEntry> Offsets;
+
+ // ctor
+ BamToolsReferenceEntry(void)
+ : HasAlignments(false)
+ { }
+};
+
+// the actual index data structure
+typedef std::map<int, BamToolsReferenceEntry> BamToolsIndexData;
+
+class BamToolsIndex : public BamIndex {
+
+ // keep a list of any supported versions here
+ // (might be useful later to handle any 'legacy' versions if the format changes)
+ // listed for example like: BTI_1_0 = 1, BTI_1_1 = 2, BTI_1_2 = 3, BTI_2_0 = 4, and so on
+ //
+ // so a change introduced in (hypothetical) BTI_1_2 would be handled from then on by:
+ //
+ // if ( indexVersion >= BTI_1_2 )
+ // do something new
+ // else
+ // do the old thing
+ enum Version { BTI_1_0 = 1
+ , BTI_1_1
+ , BTI_1_2
+ };
+
+
+ // 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);
+ public:
+ // 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' methods
+ public:
+
+ // -----------------------
+ // index file operations
+
+ // check index file magic number, return true if OK
+ bool CheckMagicNumber(void);
+ // check index file version, return true if OK
+ bool CheckVersion(void);
+ // return true if FILE* is open
+ bool IsOpen(void) const;
+ // load a single index entry from file, return true if loaded OK
+ // @saveData - save data in memory if true, just read & discard if false
+ bool LoadIndexEntry(const int& refId, bool saveData = true);
+ // load a single reference from file, return true if loaded OK
+ // @saveData - save data in memory if true, just read & discard if false
+ bool LoadReference(const int& refId, bool saveData = true);
+ // loads number of references, return true if loaded OK
+ bool LoadReferenceCount(int& numReferences);
+ // position file pointer to desired reference begin, return true if skipped OK
+ bool SkipToReference(const int& refId);
+ // write current reference index data to new index file
+ bool WriteReferenceEntry(const BamToolsReferenceEntry& refEntry);
+ // write current index offset entry to new index file
+ bool WriteIndexEntry(const BamToolsIndexEntry& entry);
+
+ // -----------------------
+ // index data operations
+
+ // clear all index offset data for desired reference
+ void ClearReferenceOffsets(const int& refId);
+ // calculate BAM file offset for desired region
+ // return true if no error (*NOT* equivalent to "has alignments or valid offset")
+ // check @hasAlignmentsInRegion to determine this status
+ // @region - target region
+ // @offset - resulting seek target
+ // @hasAlignmentsInRegion - sometimes a file just lacks data in region, this flag indicates that status
+ bool GetOffset(const BamRegion& region, int64_t& offset, bool* hasAlignmentsInRegion);
+ // returns true if index cache has data for desired reference
+ bool IsDataLoaded(const int& refId) const;
+ // clears index data from all references except the one specified
+ void KeepOnlyReferenceOffsets(const int& refId);
+ // saves an index offset entry in memory
+ void SaveOffsetEntry(const int& refId, const BamToolsIndexEntry& entry);
+ // pre-allocates size for offset vector
+ void SetOffsetCount(const int& refId, const int& offsetCount);
+ // initializes index data structure to hold @count references
+ void SetReferenceCount(const int& count);
+
+ // data members
+ private:
+ int32_t m_blockSize;
+ BamToolsIndexData m_indexData;
+ off_t m_dataBeginOffset;
+ bool m_hasFullDataCache;
+ bool m_isBigEndian;
+ int32_t m_inputVersion; // Version is serialized as int
+ Version m_outputVersion;
+};
+
+} // namespace Internal
+} // namespace BamTools
+
+#endif // BAMTOOLS_INDEX_FORMAT_H
projects / bamtools.git / blobdiff