1 // ***************************************************************************
2 // BamReader_p.cpp (c) 2009 Derek Barnett
3 // Marth Lab, Department of Biology, Boston College
4 // ---------------------------------------------------------------------------
5 // Last modified: 10 October 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/IBamIODevice.h"
13 #include "api/internal/BamDeviceFactory_p.h"
14 #include "api/internal/BamException_p.h"
15 #include "api/internal/BamHeader_p.h"
16 #include "api/internal/BamRandomAccessController_p.h"
17 #include "api/internal/BamReader_p.h"
18 #include "api/internal/BamStandardIndex_p.h"
19 #include "api/internal/BamToolsIndex_p.h"
20 using namespace BamTools;
21 using namespace BamTools::Internal;
31 BamReaderPrivate::BamReaderPrivate(BamReader* parent)
32 : m_alignmentsBeginOffset(0)
35 m_isBigEndian = BamTools::SystemIsBigEndian();
39 BamReaderPrivate::~BamReaderPrivate(void) {
43 // closes the BAM file
44 bool BamReaderPrivate::Close(void) {
53 // close random access controller
54 m_randomAccessController.Close();
56 // if stream is open, attempt close
60 } catch ( BamException& e ) {
61 const string streamError = e.what();
62 const string message = string("encountered error closing BAM file: \n\t") + streamError;
63 SetErrorString("BamReader::Close", message);
72 // creates an index file of requested type on current BAM file
73 bool BamReaderPrivate::CreateIndex(const BamIndex::IndexType& type) {
75 // skip if BAM file not open
77 SetErrorString("BamReader::CreateIndex", "cannot create index on unopened BAM file");
81 // attempt to create index
82 if ( m_randomAccessController.CreateIndex(this, type) )
85 const string bracError = m_randomAccessController.GetErrorString();
86 const string message = string("could not create index: \n\t") + bracError;
87 SetErrorString("BamReader::CreateIndex", message);
92 // return path & filename of current BAM file
93 const string BamReaderPrivate::Filename(void) const {
97 string BamReaderPrivate::GetErrorString(void) const {
101 // return header data as std::string
102 string BamReaderPrivate::GetHeaderText(void) const {
103 return m_header.ToString();
106 // return header data as SamHeader object
107 SamHeader BamReaderPrivate::GetSamHeader(void) const {
108 return m_header.ToSamHeader();
111 // get next alignment (with character data fully parsed)
112 bool BamReaderPrivate::GetNextAlignment(BamAlignment& alignment) {
114 // if valid alignment found
115 if ( GetNextAlignmentCore(alignment) ) {
117 // store alignment's "source" filename
118 alignment.Filename = m_filename;
120 // return success/failure of parsing char data
121 if ( alignment.BuildCharData() )
124 const string alError = alignment.GetErrorString();
125 const string message = string("could not populate alignment data: \n\t") + alError;
126 SetErrorString("BamReader::GetNextAlignment", message);
131 // no valid alignment found
135 // retrieves next available alignment core data (returns success/fail)
136 // ** DOES NOT populate any character data fields (read name, bases, qualities, tag data, filename)
137 // these can be accessed, if necessary, from the supportData
138 // useful for operations requiring ONLY positional or other alignment-related information
139 bool BamReaderPrivate::GetNextAlignmentCore(BamAlignment& alignment) {
141 // skip if stream not opened
142 if ( !m_stream.IsOpen() )
147 // skip if region is set but has no alignments
148 if ( m_randomAccessController.HasRegion() &&
149 !m_randomAccessController.RegionHasAlignments() )
154 // if can't read next alignment
155 if ( !LoadNextAlignment(alignment) )
158 // check alignment's region-overlap state
159 BamRandomAccessController::RegionState state = m_randomAccessController.AlignmentState(alignment);
161 // if alignment starts after region, no need to keep reading
162 if ( state == BamRandomAccessController::AfterRegion )
165 // read until overlap is found
166 while ( state != BamRandomAccessController::OverlapsRegion ) {
168 // if can't read next alignment
169 if ( !LoadNextAlignment(alignment) )
172 // check alignment's region-overlap state
173 state = m_randomAccessController.AlignmentState(alignment);
175 // if alignment starts after region, no need to keep reading
176 if ( state == BamRandomAccessController::AfterRegion )
180 // if we get here, we found the next 'valid' alignment
181 // (e.g. overlaps current region if one was set, simply the next alignment if not)
182 alignment.SupportData.HasCoreOnly = true;
185 } catch ( BamException& e ) {
186 const string streamError = e.what();
187 const string message = string("encountered error reading BAM alignment: \n\t") + streamError;
188 SetErrorString("BamReader::GetNextAlignmentCore", message);
193 int BamReaderPrivate::GetReferenceCount(void) const {
194 return m_references.size();
197 const RefVector& BamReaderPrivate::GetReferenceData(void) const {
201 // returns RefID for given RefName (returns References.size() if not found)
202 int BamReaderPrivate::GetReferenceID(const string& refName) const {
204 // retrieve names from reference data
205 vector<string> refNames;
206 RefVector::const_iterator refIter = m_references.begin();
207 RefVector::const_iterator refEnd = m_references.end();
208 for ( ; refIter != refEnd; ++refIter)
209 refNames.push_back( (*refIter).RefName );
211 // return 'index-of' refName (or -1 if not found)
212 int index = distance(refNames.begin(), find(refNames.begin(), refNames.end(), refName));
213 if ( index == (int)m_references.size() ) return -1;
217 bool BamReaderPrivate::HasIndex(void) const {
218 return m_randomAccessController.HasIndex();
221 bool BamReaderPrivate::IsOpen(void) const {
222 return m_stream.IsOpen();
225 // load BAM header data
226 void BamReaderPrivate::LoadHeaderData(void) {
227 m_header.Load(&m_stream);
230 // populates BamAlignment with alignment data under file pointer, returns success/fail
231 bool BamReaderPrivate::LoadNextAlignment(BamAlignment& alignment) {
233 // read in the 'block length' value, make sure it's not zero
234 char buffer[sizeof(uint32_t)];
235 m_stream.Read(buffer, sizeof(uint32_t));
236 alignment.SupportData.BlockLength = BamTools::UnpackUnsignedInt(buffer);
237 if ( m_isBigEndian ) BamTools::SwapEndian_32(alignment.SupportData.BlockLength);
238 if ( alignment.SupportData.BlockLength == 0 )
241 // read in core alignment data, make sure the right size of data was read
242 char x[Constants::BAM_CORE_SIZE];
243 if ( m_stream.Read(x, Constants::BAM_CORE_SIZE) != Constants::BAM_CORE_SIZE )
246 // swap core endian-ness if necessary
247 if ( m_isBigEndian ) {
248 for ( unsigned int i = 0; i < Constants::BAM_CORE_SIZE; i+=sizeof(uint32_t) )
249 BamTools::SwapEndian_32p(&x[i]);
252 // set BamAlignment 'core' and 'support' data
253 alignment.RefID = BamTools::UnpackSignedInt(&x[0]);
254 alignment.Position = BamTools::UnpackSignedInt(&x[4]);
256 unsigned int tempValue = BamTools::UnpackUnsignedInt(&x[8]);
257 alignment.Bin = tempValue >> 16;
258 alignment.MapQuality = tempValue >> 8 & 0xff;
259 alignment.SupportData.QueryNameLength = tempValue & 0xff;
261 tempValue = BamTools::UnpackUnsignedInt(&x[12]);
262 alignment.AlignmentFlag = tempValue >> 16;
263 alignment.SupportData.NumCigarOperations = tempValue & 0xffff;
265 alignment.SupportData.QuerySequenceLength = BamTools::UnpackUnsignedInt(&x[16]);
266 alignment.MateRefID = BamTools::UnpackSignedInt(&x[20]);
267 alignment.MatePosition = BamTools::UnpackSignedInt(&x[24]);
268 alignment.InsertSize = BamTools::UnpackSignedInt(&x[28]);
270 // set BamAlignment length
271 alignment.Length = alignment.SupportData.QuerySequenceLength;
273 // read in character data - make sure proper data size was read
274 bool readCharDataOK = false;
275 const unsigned int dataLength = alignment.SupportData.BlockLength - Constants::BAM_CORE_SIZE;
276 RaiiBuffer allCharData(dataLength);
278 if ( m_stream.Read(allCharData.Buffer, dataLength) == dataLength ) {
280 // store 'allCharData' in supportData structure
281 alignment.SupportData.AllCharData.assign((const char*)allCharData.Buffer, dataLength);
284 readCharDataOK = true;
287 // need to calculate this here so that BamAlignment::GetEndPosition() performs correctly,
288 // even when GetNextAlignmentCore() is called
289 const unsigned int cigarDataOffset = alignment.SupportData.QueryNameLength;
290 uint32_t* cigarData = (uint32_t*)(allCharData.Buffer + cigarDataOffset);
292 alignment.CigarData.clear();
293 alignment.CigarData.reserve(alignment.SupportData.NumCigarOperations);
294 for ( unsigned int i = 0; i < alignment.SupportData.NumCigarOperations; ++i ) {
296 // swap endian-ness if necessary
297 if ( m_isBigEndian ) BamTools::SwapEndian_32(cigarData[i]);
299 // build CigarOp structure
300 op.Length = (cigarData[i] >> Constants::BAM_CIGAR_SHIFT);
301 op.Type = Constants::BAM_CIGAR_LOOKUP[ (cigarData[i] & Constants::BAM_CIGAR_MASK) ];
304 alignment.CigarData.push_back(op);
308 // return success/failure
309 return readCharDataOK;
312 // loads reference data from BAM file
313 bool BamReaderPrivate::LoadReferenceData(void) {
315 // get number of reference sequences
316 char buffer[sizeof(uint32_t)];
317 m_stream.Read(buffer, sizeof(uint32_t));
318 uint32_t numberRefSeqs = BamTools::UnpackUnsignedInt(buffer);
319 if ( m_isBigEndian ) BamTools::SwapEndian_32(numberRefSeqs);
320 m_references.reserve((int)numberRefSeqs);
322 // iterate over all references in header
323 for ( unsigned int i = 0; i != numberRefSeqs; ++i ) {
325 // get length of reference name
326 m_stream.Read(buffer, sizeof(uint32_t));
327 uint32_t refNameLength = BamTools::UnpackUnsignedInt(buffer);
328 if ( m_isBigEndian ) BamTools::SwapEndian_32(refNameLength);
329 RaiiBuffer refName(refNameLength);
331 // get reference name and reference sequence length
332 m_stream.Read(refName.Buffer, refNameLength);
333 m_stream.Read(buffer, sizeof(int32_t));
334 int32_t refLength = BamTools::UnpackSignedInt(buffer);
335 if ( m_isBigEndian ) BamTools::SwapEndian_32(refLength);
337 // store data for reference
339 aReference.RefName = (string)((const char*)refName.Buffer);
340 aReference.RefLength = refLength;
341 m_references.push_back(aReference);
348 bool BamReaderPrivate::LocateIndex(const BamIndex::IndexType& preferredType) {
350 if ( m_randomAccessController.LocateIndex(this, preferredType) )
353 const string bracError = m_randomAccessController.GetErrorString();
354 const string message = string("could not locate index: \n\t") + bracError;
355 SetErrorString("BamReader::LocateIndex", message);
360 // opens BAM file (and index)
361 bool BamReaderPrivate::Open(const string& filename) {
365 // make sure we're starting with fresh state
369 m_stream.Open(filename, IBamIODevice::ReadOnly);
376 // store filename & offset of first alignment
377 m_filename = filename;
378 m_alignmentsBeginOffset = m_stream.Tell();
383 } catch ( BamException& e ) {
384 const string error = e.what();
385 const string message = string("could not open file: ") + filename +
387 SetErrorString("BamReader::Open", message);
392 bool BamReaderPrivate::OpenIndex(const std::string& indexFilename) {
394 if ( m_randomAccessController.OpenIndex(indexFilename, this) )
397 const string bracError = m_randomAccessController.GetErrorString();
398 const string message = string("could not open index: \n\t") + bracError;
399 SetErrorString("BamReader::OpenIndex", message);
404 // returns BAM file pointer to beginning of alignment data
405 bool BamReaderPrivate::Rewind(void) {
408 m_randomAccessController.ClearRegion();
410 // return status of seeking back to first alignment
411 if ( Seek(m_alignmentsBeginOffset) )
414 const string currentError = m_errorString;
415 const string message = string("could not rewind: \n\t") + currentError;
416 SetErrorString("BamReader::Rewind", message);
421 bool BamReaderPrivate::Seek(const int64_t& position) {
423 // skip if BAM file not open
425 SetErrorString("BamReader::Seek", "cannot seek on unopened BAM file");
430 m_stream.Seek(position);
433 catch ( BamException& e ) {
434 const string streamError = e.what();
435 const string message = string("could not seek in BAM file: \n\t") + streamError;
436 SetErrorString("BamReader::Seek", message);
441 void BamReaderPrivate::SetErrorString(const string& where, const string& what) {
442 static const string SEPARATOR = ": ";
443 m_errorString = where + SEPARATOR + what;
446 void BamReaderPrivate::SetIndex(BamIndex* index) {
447 m_randomAccessController.SetIndex(index);
450 // change the index caching behavior
451 void BamReaderPrivate::SetIndexCacheMode(const BamIndex::IndexCacheMode& mode) {
452 m_randomAccessController.SetIndexCacheMode(mode);
455 // sets current region & attempts to jump to it
456 // returns success/failure
457 bool BamReaderPrivate::SetRegion(const BamRegion& region) {
459 if ( m_randomAccessController.SetRegion(region, m_references.size()) )
462 const string bracError = m_randomAccessController.GetErrorString();
463 const string message = string("could not set region: \n\t") + bracError;
464 SetErrorString("BamReader::SetRegion", message);
469 int64_t BamReaderPrivate::Tell(void) const {
470 return m_stream.Tell();