1 // ***************************************************************************
2 // BamStandardIndex.h (c) 2010 Derek Barnett
3 // Marth Lab, Department of Biology, Boston College
4 // ---------------------------------------------------------------------------
5 // Last modified: 10 November 2011 (DB)
6 // ---------------------------------------------------------------------------
7 // Provides index operations for the standardized BAM index format (".bai")
8 // ***************************************************************************
10 #ifndef BAM_STANDARD_INDEX_FORMAT_H
11 #define BAM_STANDARD_INDEX_FORMAT_H
17 // This file is not part of the BamTools API. It exists purely as an
18 // implementation detail. This header file may change from version to
19 // version without notice, or even be removed.
23 #include "api/BamAux.h"
24 #include "api/BamIndex.h"
25 #include "api/IBamIODevice.h"
34 // -----------------------------------------------------------------------------
35 // BamStandardIndex data structures
37 // defines start and end of a contiguous run of alignments
38 struct BaiAlignmentChunk {
45 BaiAlignmentChunk(const uint64_t& start = 0,
46 const uint64_t& stop = 0)
52 // comparison operator (for sorting)
54 bool operator<(const BaiAlignmentChunk& lhs, const BaiAlignmentChunk& rhs) {
55 return lhs.Start < rhs.Start;
58 // convenience typedef for a list of all alignment 'chunks' in a BAI bin
59 typedef std::vector<BaiAlignmentChunk> BaiAlignmentChunkVector;
61 // convenience typedef for a map of all BAI bins in a reference (ID => chunks)
62 typedef std::map<uint32_t, BaiAlignmentChunkVector> BaiBinMap;
64 // convenience typedef for a list of all 'linear offsets' in a reference
65 typedef std::vector<uint64_t> BaiLinearOffsetVector;
67 // contains all fields necessary for building, loading, & writing
68 // full BAI index data for a single reference
69 struct BaiReferenceEntry {
74 BaiLinearOffsetVector LinearOffsets;
77 BaiReferenceEntry(const int32_t& id = -1)
82 // provides (persistent) summary of BaiReferenceEntry's index data
83 struct BaiReferenceSummary {
88 uint64_t FirstBinFilePosition;
89 uint64_t FirstLinearOffsetFilePosition;
92 BaiReferenceSummary(void)
95 , FirstBinFilePosition(0)
96 , FirstLinearOffsetFilePosition(0)
100 // convenience typedef for describing a full BAI index file summary
101 typedef std::vector<BaiReferenceSummary> BaiFileSummary;
103 // end BamStandardIndex data structures
104 // -----------------------------------------------------------------------------
106 class BamStandardIndex : public BamIndex {
110 BamStandardIndex(Internal::BamReaderPrivate* reader);
111 ~BamStandardIndex(void);
113 // BamIndex implementation
115 // builds index from associated BAM file & writes out to index file
117 // returns whether reference has alignments or no
118 bool HasAlignments(const int& referenceID) const;
119 // attempts to use index data to jump to @region, returns success/fail
120 // a "successful" jump indicates no error, but not whether this region has data
121 // * thus, the method sets a flag to indicate whether there are alignments
122 // available after the jump position
123 bool Jump(const BamTools::BamRegion& region, bool* hasAlignmentsInRegion);
124 // loads existing data from file into memory
125 bool Load(const std::string& filename);
127 // returns format's file extension
128 static const std::string Extension(void);
134 void CheckMagicNumber(void);
135 void CloseFile(void);
136 bool IsDeviceOpen(void) const;
137 void OpenFile(const std::string& filename, IBamIODevice::OpenMode mode);
138 void Seek(const int64_t& position, const int origin);
139 int64_t Tell(void) const;
141 // BAI index building methods
142 void ClearReferenceEntry(BaiReferenceEntry& refEntry);
143 void SaveAlignmentChunkToBin(BaiBinMap& binMap,
144 const uint32_t& currentBin,
145 const uint64_t& currentOffset,
146 const uint64_t& lastOffset);
147 void SaveLinearOffsetEntry(BaiLinearOffsetVector& offsets,
148 const int& alignmentStartPosition,
149 const int& alignmentStopPosition,
150 const uint64_t& lastOffset);
152 // random-access methods
153 void AdjustRegion(const BamRegion& region, uint32_t& begin, uint32_t& end);
154 void CalculateCandidateBins(const uint32_t& begin,
156 std::set<uint16_t>& candidateBins);
157 void CalculateCandidateOffsets(const BaiReferenceSummary& refSummary,
158 const uint64_t& minOffset,
159 std::set<uint16_t>& candidateBins,
160 std::vector<int64_t>& offsets);
161 uint64_t CalculateMinOffset(const BaiReferenceSummary& refSummary, const uint32_t& begin);
162 void GetOffset(const BamRegion& region, int64_t& offset, bool* hasAlignmentsInRegion);
163 uint64_t LookupLinearOffset(const BaiReferenceSummary& refSummary, const int& index);
165 // BAI summary (create/load) methods
166 void ReserveForSummary(const int& numReferences);
167 void SaveBinsSummary(const int& refId, const int& numBins);
168 void SaveLinearOffsetsSummary(const int& refId, const int& numLinearOffsets);
169 void SkipBins(const int& numBins);
170 void SkipLinearOffsets(const int& numLinearOffsets);
171 void SummarizeBins(BaiReferenceSummary& refSummary);
172 void SummarizeIndexFile(void);
173 void SummarizeLinearOffsets(BaiReferenceSummary& refSummary);
174 void SummarizeReference(BaiReferenceSummary& refSummary);
176 // BAI full index input methods
177 void ReadBinID(uint32_t& binId);
178 void ReadBinIntoBuffer(uint32_t& binId, int32_t& numAlignmentChunks);
179 void ReadIntoBuffer(const unsigned int& bytesRequested);
180 void ReadLinearOffset(uint64_t& linearOffset);
181 void ReadNumAlignmentChunks(int& numAlignmentChunks);
182 void ReadNumBins(int& numBins);
183 void ReadNumLinearOffsets(int& numLinearOffsets);
184 void ReadNumReferences(int& numReferences);
186 // BAI full index output methods
187 void MergeAlignmentChunks(BaiAlignmentChunkVector& chunks);
188 void SortLinearOffsets(BaiLinearOffsetVector& linearOffsets);
189 void WriteAlignmentChunk(const BaiAlignmentChunk& chunk);
190 void WriteAlignmentChunks(BaiAlignmentChunkVector& chunks);
191 void WriteBin(const uint32_t& binId, BaiAlignmentChunkVector& chunks);
192 void WriteBins(const int& refId, BaiBinMap& bins);
193 void WriteHeader(void);
194 void WriteLinearOffsets(const int& refId, BaiLinearOffsetVector& linearOffsets);
195 void WriteReferenceEntry(BaiReferenceEntry& refEntry);
200 BaiFileSummary m_indexFileSummary;
203 unsigned int m_bufferLength;
205 IBamIODevice* Device;
210 RaiiWrapper m_resources;
214 // checks if the buffer is large enough to accomodate the requested size
215 static void CheckBufferSize(char*& buffer,
216 unsigned int& bufferLength,
217 const unsigned int& requestedBytes);
218 // checks if the buffer is large enough to accomodate the requested size
219 static void CheckBufferSize(unsigned char*& buffer,
220 unsigned int& bufferLength,
221 const unsigned int& requestedBytes);
224 static const int MAX_BIN;
225 static const int BAM_LIDX_SHIFT;
226 static const std::string BAI_EXTENSION;
227 static const char* const BAI_MAGIC;
228 static const int SIZEOF_ALIGNMENTCHUNK;
229 static const int SIZEOF_BINCORE;
230 static const int SIZEOF_LINEAROFFSET;
233 } // namespace Internal
234 } // namespace BamTools
236 #endif // BAM_STANDARD_INDEX_FORMAT_H