1 // ***************************************************************************
2 // BamReader_p.cpp (c) 2009 Derek Barnett
3 // Marth Lab, Department of Biology, Boston College
4 // ---------------------------------------------------------------------------
5 // Last modified: 10 May 2011 (DB)
6 // ---------------------------------------------------------------------------
7 // Provides the basic functionality for reading BAM files
8 // ***************************************************************************
10 #include <api/BamConstants.h>
11 #include <api/BamReader.h>
12 #include <api/internal/BamHeader_p.h>
13 #include <api/internal/BamRandomAccessController_p.h>
14 #include <api/internal/BamReader_p.h>
15 #include <api/internal/BamStandardIndex_p.h>
16 #include <api/internal/BamToolsIndex_p.h>
17 #include <api/internal/BgzfStream_p.h>
18 using namespace BamTools;
19 using namespace BamTools::Internal;
28 BamReaderPrivate::BamReaderPrivate(BamReader* parent)
29 : m_alignmentsBeginOffset(0)
32 m_isBigEndian = BamTools::SystemIsBigEndian();
36 BamReaderPrivate::~BamReaderPrivate(void) {
40 // closes the BAM file
41 void BamReaderPrivate::Close(void) {
43 // clear header & reference data
48 m_randomAccessController.Close();
55 // creates an index file of requested type on current BAM file
56 bool BamReaderPrivate::CreateIndex(const BamIndex::IndexType& type) {
57 if ( !IsOpen() ) return false;
58 return m_randomAccessController.CreateIndex(this, type);
61 // return path & filename of current BAM file
62 const string BamReaderPrivate::Filename(void) const {
66 // return header data as std::string
67 string BamReaderPrivate::GetHeaderText(void) const {
68 return m_header.ToString();
71 // return header data as SamHeader object
72 SamHeader BamReaderPrivate::GetSamHeader(void) const {
73 return m_header.ToSamHeader();
76 // get next alignment (with character data fully parsed)
77 bool BamReaderPrivate::GetNextAlignment(BamAlignment& alignment) {
79 // if valid alignment found
80 if ( GetNextAlignmentCore(alignment) ) {
82 // store alignment's "source" filename
83 alignment.Filename = m_filename;
85 // return success/failure of parsing char data
86 return alignment.BuildCharData();
89 // no valid alignment found
93 // retrieves next available alignment core data (returns success/fail)
94 // ** DOES NOT populate any character data fields (read name, bases, qualities, tag data, filename)
95 // these can be accessed, if necessary, from the supportData
96 // useful for operations requiring ONLY positional or other alignment-related information
97 bool BamReaderPrivate::GetNextAlignmentCore(BamAlignment& alignment) {
99 // skip if region is set but has no alignments
100 if ( m_randomAccessController.HasRegion() &&
101 !m_randomAccessController.RegionHasAlignments() )
106 // if can't read next alignment
107 if ( !LoadNextAlignment(alignment) )
110 // check alignment's region-overlap state
111 BamRandomAccessController::RegionState state = m_randomAccessController.AlignmentState(alignment);
113 // if alignment starts after region, no need to keep reading
114 if ( state == BamRandomAccessController::AfterRegion )
117 // read until overlap is found
118 while ( state != BamRandomAccessController::OverlapsRegion ) {
120 // if can't read next alignment
121 if ( !LoadNextAlignment(alignment) )
124 // check alignment's region-overlap state
125 state = m_randomAccessController.AlignmentState(alignment);
127 // if alignment starts after region, no need to keep reading
128 if ( state == BamRandomAccessController::AfterRegion )
132 // if we get here, we found the next 'valid' alignment
133 // (e.g. overlaps current region if one was set, simply the next alignment if not)
134 alignment.SupportData.HasCoreOnly = true;
138 int BamReaderPrivate::GetReferenceCount(void) const {
139 return m_references.size();
142 const RefVector& BamReaderPrivate::GetReferenceData(void) const {
146 // returns RefID for given RefName (returns References.size() if not found)
147 int BamReaderPrivate::GetReferenceID(const string& refName) const {
149 // retrieve names from reference data
150 vector<string> refNames;
151 RefVector::const_iterator refIter = m_references.begin();
152 RefVector::const_iterator refEnd = m_references.end();
153 for ( ; refIter != refEnd; ++refIter)
154 refNames.push_back( (*refIter).RefName );
156 // return 'index-of' refName (or -1 if not found)
157 int index = distance(refNames.begin(), find(refNames.begin(), refNames.end(), refName));
158 if ( index == (int)m_references.size() ) return -1;
162 bool BamReaderPrivate::HasIndex(void) const {
163 return m_randomAccessController.HasIndex();
166 bool BamReaderPrivate::IsOpen(void) const {
167 return m_stream.IsOpen;
170 // load BAM header data
171 bool BamReaderPrivate::LoadHeaderData(void) {
172 return m_header.Load(&m_stream);
175 // populates BamAlignment with alignment data under file pointer, returns success/fail
176 bool BamReaderPrivate::LoadNextAlignment(BamAlignment& alignment) {
178 // read in the 'block length' value, make sure it's not zero
179 char buffer[sizeof(uint32_t)];
180 m_stream.Read(buffer, sizeof(uint32_t));
181 alignment.SupportData.BlockLength = BamTools::UnpackUnsignedInt(buffer);
182 if ( m_isBigEndian ) BamTools::SwapEndian_32(alignment.SupportData.BlockLength);
183 if ( alignment.SupportData.BlockLength == 0 ) return false;
185 // read in core alignment data, make sure the right size of data was read
186 char x[Constants::BAM_CORE_SIZE];
187 if ( m_stream.Read(x, Constants::BAM_CORE_SIZE) != Constants::BAM_CORE_SIZE )
190 // swap core endian-ness if necessary
191 if ( m_isBigEndian ) {
192 for ( int i = 0; i < Constants::BAM_CORE_SIZE; i+=sizeof(uint32_t) )
193 BamTools::SwapEndian_32p(&x[i]);
196 // set BamAlignment 'core' and 'support' data
197 alignment.RefID = BamTools::UnpackSignedInt(&x[0]);
198 alignment.Position = BamTools::UnpackSignedInt(&x[4]);
200 unsigned int tempValue = BamTools::UnpackUnsignedInt(&x[8]);
201 alignment.Bin = tempValue >> 16;
202 alignment.MapQuality = tempValue >> 8 & 0xff;
203 alignment.SupportData.QueryNameLength = tempValue & 0xff;
205 tempValue = BamTools::UnpackUnsignedInt(&x[12]);
206 alignment.AlignmentFlag = tempValue >> 16;
207 alignment.SupportData.NumCigarOperations = tempValue & 0xffff;
209 alignment.SupportData.QuerySequenceLength = BamTools::UnpackUnsignedInt(&x[16]);
210 alignment.MateRefID = BamTools::UnpackSignedInt(&x[20]);
211 alignment.MatePosition = BamTools::UnpackSignedInt(&x[24]);
212 alignment.InsertSize = BamTools::UnpackSignedInt(&x[28]);
214 // set BamAlignment length
215 alignment.Length = alignment.SupportData.QuerySequenceLength;
217 // read in character data - make sure proper data size was read
218 bool readCharDataOK = false;
219 const unsigned int dataLength = alignment.SupportData.BlockLength - Constants::BAM_CORE_SIZE;
220 char* allCharData = (char*)calloc(sizeof(char), dataLength);
222 if ( m_stream.Read(allCharData, dataLength) == (signed int)dataLength ) {
224 // store 'allCharData' in supportData structure
225 alignment.SupportData.AllCharData.assign((const char*)allCharData, dataLength);
228 readCharDataOK = true;
231 // need to calculate this here so that BamAlignment::GetEndPosition() performs correctly,
232 // even when GetNextAlignmentCore() is called
233 const unsigned int cigarDataOffset = alignment.SupportData.QueryNameLength;
234 uint32_t* cigarData = (uint32_t*)(allCharData + cigarDataOffset);
236 alignment.CigarData.clear();
237 alignment.CigarData.reserve(alignment.SupportData.NumCigarOperations);
238 for ( unsigned int i = 0; i < alignment.SupportData.NumCigarOperations; ++i ) {
240 // swap endian-ness if necessary
241 if ( m_isBigEndian ) BamTools::SwapEndian_32(cigarData[i]);
243 // build CigarOp structure
244 op.Length = (cigarData[i] >> Constants::BAM_CIGAR_SHIFT);
245 op.Type = Constants::BAM_CIGAR_LOOKUP[ (cigarData[i] & Constants::BAM_CIGAR_MASK) ];
248 alignment.CigarData.push_back(op);
252 // clean up & return parsing success/failure
254 return readCharDataOK;
257 // loads reference data from BAM file
258 bool BamReaderPrivate::LoadReferenceData(void) {
260 // get number of reference sequences
261 char buffer[sizeof(uint32_t)];
262 m_stream.Read(buffer, sizeof(uint32_t));
263 uint32_t numberRefSeqs = BamTools::UnpackUnsignedInt(buffer);
264 if ( m_isBigEndian ) BamTools::SwapEndian_32(numberRefSeqs);
265 m_references.reserve((int)numberRefSeqs);
267 // iterate over all references in header
268 for ( unsigned int i = 0; i != numberRefSeqs; ++i ) {
270 // get length of reference name
271 m_stream.Read(buffer, sizeof(uint32_t));
272 uint32_t refNameLength = BamTools::UnpackUnsignedInt(buffer);
273 if ( m_isBigEndian ) BamTools::SwapEndian_32(refNameLength);
274 char* refName = (char*)calloc(refNameLength, 1);
276 // get reference name and reference sequence length
277 m_stream.Read(refName, refNameLength);
278 m_stream.Read(buffer, sizeof(int32_t));
279 int32_t refLength = BamTools::UnpackSignedInt(buffer);
280 if ( m_isBigEndian ) BamTools::SwapEndian_32(refLength);
282 // store data for reference
284 aReference.RefName = (string)((const char*)refName);
285 aReference.RefLength = refLength;
286 m_references.push_back(aReference);
288 // clean up calloc-ed temp variable
296 bool BamReaderPrivate::LocateIndex(const BamIndex::IndexType& preferredType) {
297 return m_randomAccessController.LocateIndex(this, preferredType);
300 // opens BAM file (and index)
301 bool BamReaderPrivate::Open(const string& filename) {
303 // close current BAM file if open
304 if ( m_stream.IsOpen )
307 // attempt to open BgzfStream for reading
308 if ( !m_stream.Open(filename, "rb") ) {
309 cerr << "BamReader ERROR: Could not open BGZF stream for " << filename << endl;
313 // attempt to load header data
314 if ( !LoadHeaderData() ) {
315 cerr << "BamReader ERROR: Could not load header data for " << filename << endl;
320 // attempt to load reference data
321 if ( !LoadReferenceData() ) {
322 cerr << "BamReader ERROR: Could not load reference data for " << filename << endl;
327 // if all OK, store filename & offset of first alignment
328 m_filename = filename;
329 m_alignmentsBeginOffset = m_stream.Tell();
335 bool BamReaderPrivate::OpenIndex(const std::string& indexFilename) {
336 return m_randomAccessController.OpenIndex(indexFilename, this);
339 // returns BAM file pointer to beginning of alignment data
340 bool BamReaderPrivate::Rewind(void) {
342 // attempt rewind to first alignment
343 if ( !m_stream.Seek(m_alignmentsBeginOffset) )
346 // verify that we can read first alignment
348 if ( !LoadNextAlignment(al) )
352 m_randomAccessController.ClearRegion();
354 // rewind back to beginning of first alignment
355 // return success/fail of seek
356 return m_stream.Seek(m_alignmentsBeginOffset);
359 bool BamReaderPrivate::Seek(const int64_t& position) {
360 return m_stream.Seek(position);
363 void BamReaderPrivate::SetIndex(BamIndex* index) {
364 m_randomAccessController.SetIndex(index);
367 // change the index caching behavior
368 void BamReaderPrivate::SetIndexCacheMode(const BamIndex::IndexCacheMode& mode) {
369 m_randomAccessController.SetIndexCacheMode(mode);
372 // sets current region & attempts to jump to it
373 // returns success/failure
374 bool BamReaderPrivate::SetRegion(const BamRegion& region) {
375 return m_randomAccessController.SetRegion(this, region, m_references.size());
378 int64_t BamReaderPrivate::Tell(void) const {
379 return m_stream.Tell();