// ***************************************************************************
// BamReader_p.cpp (c) 2009 Derek Barnett
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 10 May 2011 (DB)
+// Last modified: 10 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides the basic functionality for reading BAM files
// ***************************************************************************
-#include <api/BamConstants.h>
-#include <api/BamReader.h>
-#include <api/IBamIODevice.h>
-#include <api/internal/BamDeviceFactory_p.h>
-#include <api/internal/BamHeader_p.h>
-#include <api/internal/BamRandomAccessController_p.h>
-#include <api/internal/BamReader_p.h>
-#include <api/internal/BamStandardIndex_p.h>
-#include <api/internal/BamToolsIndex_p.h>
-#include <api/internal/BgzfStream_p.h>
+#include "api/BamConstants.h"
+#include "api/BamReader.h"
+#include "api/IBamIODevice.h"
+#include "api/internal/BamDeviceFactory_p.h"
+#include "api/internal/BamException_p.h"
+#include "api/internal/BamHeader_p.h"
+#include "api/internal/BamRandomAccessController_p.h"
+#include "api/internal/BamReader_p.h"
+#include "api/internal/BamStandardIndex_p.h"
+#include "api/internal/BamToolsIndex_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
#include <algorithm>
+#include <cassert>
#include <iostream>
#include <iterator>
#include <vector>
}
// closes the BAM file
-void BamReaderPrivate::Close(void) {
+bool BamReaderPrivate::Close(void) {
- // clear header & reference data
+ // clear BAM metadata
m_references.clear();
m_header.Clear();
- // close internal
- m_randomAccessController.Close();
- m_stream.Close();
-
// clear filename
m_filename.clear();
+
+ // close random access controller
+ m_randomAccessController.Close();
+
+ // if stream is open, attempt close
+ if ( IsOpen() ) {
+ try {
+ m_stream.Close();
+ } catch ( BamException& e ) {
+ const string streamError = e.what();
+ const string message = string("encountered error closing BAM file: \n\t") + streamError;
+ SetErrorString("BamReader::Close", message);
+ return false;
+ }
+ }
+
+ // return success
+ return true;
}
// creates an index file of requested type on current BAM file
bool BamReaderPrivate::CreateIndex(const BamIndex::IndexType& type) {
- if ( !IsOpen() ) return false;
- return m_randomAccessController.CreateIndex(this, type);
+
+ // skip if BAM file not open
+ if ( !IsOpen() ) {
+ SetErrorString("BamReader::CreateIndex", "cannot create index on unopened BAM file");
+ return false;
+ }
+
+ // attempt to create index
+ if ( m_randomAccessController.CreateIndex(this, type) )
+ return true;
+ else {
+ const string bracError = m_randomAccessController.GetErrorString();
+ const string message = string("could not create index: \n\t") + bracError;
+ SetErrorString("BamReader::CreateIndex", message);
+ return false;
+ }
}
// return path & filename of current BAM file
return m_filename;
}
+string BamReaderPrivate::GetErrorString(void) const {
+ return m_errorString;
+}
+
// return header data as std::string
string BamReaderPrivate::GetHeaderText(void) const {
return m_header.ToString();
alignment.Filename = m_filename;
// return success/failure of parsing char data
- return alignment.BuildCharData();
+ if ( alignment.BuildCharData() )
+ return true;
+ else {
+ const string alError = alignment.GetErrorString();
+ const string message = string("could not populate alignment data: \n\t") + alError;
+ SetErrorString("BamReader::GetNextAlignment", message);
+ return false;
+ }
}
// no valid alignment found
// useful for operations requiring ONLY positional or other alignment-related information
bool BamReaderPrivate::GetNextAlignmentCore(BamAlignment& alignment) {
+ // skip if stream not opened
if ( !m_stream.IsOpen() )
return false;
- // skip if region is set but has no alignments
- if ( m_randomAccessController.HasRegion() &&
- !m_randomAccessController.RegionHasAlignments() )
- {
- return false;
- }
-
- // if can't read next alignment
- if ( !LoadNextAlignment(alignment) )
- return false;
-
- // check alignment's region-overlap state
- BamRandomAccessController::RegionState state = m_randomAccessController.AlignmentState(alignment);
+ try {
- // if alignment starts after region, no need to keep reading
- if ( state == BamRandomAccessController::AfterRegion )
- return false;
-
- // read until overlap is found
- while ( state != BamRandomAccessController::OverlapsRegion ) {
+ // skip if region is set but has no alignments
+ if ( m_randomAccessController.HasRegion() &&
+ !m_randomAccessController.RegionHasAlignments() )
+ {
+ return false;
+ }
// if can't read next alignment
if ( !LoadNextAlignment(alignment) )
return false;
// check alignment's region-overlap state
- state = m_randomAccessController.AlignmentState(alignment);
+ BamRandomAccessController::RegionState state = m_randomAccessController.AlignmentState(alignment);
// if alignment starts after region, no need to keep reading
if ( state == BamRandomAccessController::AfterRegion )
return false;
- }
- // if we get here, we found the next 'valid' alignment
- // (e.g. overlaps current region if one was set, simply the next alignment if not)
- alignment.SupportData.HasCoreOnly = true;
- return true;
+ // read until overlap is found
+ while ( state != BamRandomAccessController::OverlapsRegion ) {
+
+ // if can't read next alignment
+ if ( !LoadNextAlignment(alignment) )
+ return false;
+
+ // check alignment's region-overlap state
+ state = m_randomAccessController.AlignmentState(alignment);
+
+ // if alignment starts after region, no need to keep reading
+ if ( state == BamRandomAccessController::AfterRegion )
+ return false;
+ }
+
+ // if we get here, we found the next 'valid' alignment
+ // (e.g. overlaps current region if one was set, simply the next alignment if not)
+ alignment.SupportData.HasCoreOnly = true;
+ return true;
+
+ } catch ( BamException& e ) {
+ const string streamError = e.what();
+ const string message = string("encountered error reading BAM alignment: \n\t") + streamError;
+ SetErrorString("BamReader::GetNextAlignmentCore", message);
+ return false;
+ }
}
int BamReaderPrivate::GetReferenceCount(void) const {
}
// load BAM header data
-bool BamReaderPrivate::LoadHeaderData(void) {
- return m_header.Load(&m_stream);
+void BamReaderPrivate::LoadHeaderData(void) {
+ m_header.Load(&m_stream);
}
// populates BamAlignment with alignment data under file pointer, returns success/fail
m_stream.Read(buffer, sizeof(uint32_t));
alignment.SupportData.BlockLength = BamTools::UnpackUnsignedInt(buffer);
if ( m_isBigEndian ) BamTools::SwapEndian_32(alignment.SupportData.BlockLength);
- if ( alignment.SupportData.BlockLength == 0 ) return false;
+ if ( alignment.SupportData.BlockLength == 0 )
+ return false;
// read in core alignment data, make sure the right size of data was read
char x[Constants::BAM_CORE_SIZE];
// read in character data - make sure proper data size was read
bool readCharDataOK = false;
const unsigned int dataLength = alignment.SupportData.BlockLength - Constants::BAM_CORE_SIZE;
- char* allCharData = (char*)calloc(sizeof(char), dataLength);
+ RaiiBuffer allCharData(dataLength);
- if ( m_stream.Read(allCharData, dataLength) == dataLength ) {
+ if ( m_stream.Read(allCharData.Buffer, dataLength) == dataLength ) {
// store 'allCharData' in supportData structure
- alignment.SupportData.AllCharData.assign((const char*)allCharData, dataLength);
+ alignment.SupportData.AllCharData.assign((const char*)allCharData.Buffer, dataLength);
// set success flag
readCharDataOK = true;
// need to calculate this here so that BamAlignment::GetEndPosition() performs correctly,
// even when GetNextAlignmentCore() is called
const unsigned int cigarDataOffset = alignment.SupportData.QueryNameLength;
- uint32_t* cigarData = (uint32_t*)(allCharData + cigarDataOffset);
+ uint32_t* cigarData = (uint32_t*)(allCharData.Buffer + cigarDataOffset);
CigarOp op;
alignment.CigarData.clear();
alignment.CigarData.reserve(alignment.SupportData.NumCigarOperations);
}
}
- // clean up & return parsing success/failure
- free(allCharData);
+ // return success/failure
return readCharDataOK;
}
m_stream.Read(buffer, sizeof(uint32_t));
uint32_t refNameLength = BamTools::UnpackUnsignedInt(buffer);
if ( m_isBigEndian ) BamTools::SwapEndian_32(refNameLength);
- char* refName = (char*)calloc(refNameLength, 1);
+ RaiiBuffer refName(refNameLength);
// get reference name and reference sequence length
- m_stream.Read(refName, refNameLength);
+ m_stream.Read(refName.Buffer, refNameLength);
m_stream.Read(buffer, sizeof(int32_t));
int32_t refLength = BamTools::UnpackSignedInt(buffer);
if ( m_isBigEndian ) BamTools::SwapEndian_32(refLength);
// store data for reference
RefData aReference;
- aReference.RefName = (string)((const char*)refName);
+ aReference.RefName = (string)((const char*)refName.Buffer);
aReference.RefLength = refLength;
m_references.push_back(aReference);
-
- // clean up calloc-ed temp variable
- free(refName);
}
// return success
}
bool BamReaderPrivate::LocateIndex(const BamIndex::IndexType& preferredType) {
- return m_randomAccessController.LocateIndex(this, preferredType);
+
+ if ( m_randomAccessController.LocateIndex(this, preferredType) )
+ return true;
+ else {
+ const string bracError = m_randomAccessController.GetErrorString();
+ const string message = string("could not locate index: \n\t") + bracError;
+ SetErrorString("BamReader::LocateIndex", message);
+ return false;
+ }
}
// opens BAM file (and index)
bool BamReaderPrivate::Open(const string& filename) {
- // make sure we're starting with a fresh slate
- Close();
+ try {
- // attempt to open BgzfStream for reading
- if ( !m_stream.Open(filename, IBamIODevice::ReadOnly) ) {
- cerr << "BamReader ERROR: Could not open BGZF stream for " << filename << endl;
- return false;
- }
-
- // attempt to load header data
- if ( !LoadHeaderData() ) {
- cerr << "BamReader ERROR: Could not load header data for " << filename << endl;
+ // make sure we're starting with fresh state
Close();
- return false;
- }
- // attempt to load reference data
- if ( !LoadReferenceData() ) {
- cerr << "BamReader ERROR: Could not load reference data for " << filename << endl;
- Close();
- return false;
- }
+ // open BgzfStream
+ m_stream.Open(filename, IBamIODevice::ReadOnly);
+ assert(m_stream);
- // if all OK, store filename & offset of first alignment
- m_filename = filename;
- m_alignmentsBeginOffset = m_stream.Tell();
+ // load BAM metadata
+ LoadHeaderData();
+ LoadReferenceData();
- // return success
- return true;
+ // store filename & offset of first alignment
+ m_filename = filename;
+ m_alignmentsBeginOffset = m_stream.Tell();
+
+ // return success
+ return true;
+
+ } catch ( BamException& e ) {
+ const string error = e.what();
+ const string message = string("could not open file: ") + filename +
+ "\n\t" + error;
+ SetErrorString("BamReader::Open", message);
+ return false;
+ }
}
bool BamReaderPrivate::OpenIndex(const std::string& indexFilename) {
- return m_randomAccessController.OpenIndex(indexFilename, this);
+
+ if ( m_randomAccessController.OpenIndex(indexFilename, this) )
+ return true;
+ else {
+ const string bracError = m_randomAccessController.GetErrorString();
+ const string message = string("could not open index: \n\t") + bracError;
+ SetErrorString("BamReader::OpenIndex", message);
+ return false;
+ }
}
// returns BAM file pointer to beginning of alignment data
bool BamReaderPrivate::Rewind(void) {
- if ( !m_stream.IsOpen() )
- return false;
+ // reset region
+ m_randomAccessController.ClearRegion();
- // attempt rewind to first alignment
- if ( !m_stream.Seek(m_alignmentsBeginOffset) )
+ // return status of seeking back to first alignment
+ if ( Seek(m_alignmentsBeginOffset) )
+ return true;
+ else {
+ const string currentError = m_errorString;
+ const string message = string("could not rewind: \n\t") + currentError;
+ SetErrorString("BamReader::Rewind", message);
return false;
+ }
+}
- // verify that we can read first alignment
- BamAlignment al;
- if ( !LoadNextAlignment(al) )
- return false;
+bool BamReaderPrivate::Seek(const int64_t& position) {
- // reset region
- m_randomAccessController.ClearRegion();
+ // skip if BAM file not open
+ if ( !IsOpen() ) {
+ SetErrorString("BamReader::Seek", "cannot seek on unopened BAM file");
+ return false;
+ }
- // rewind back to beginning of first alignment
- // return success/fail of seek
- return m_stream.Seek(m_alignmentsBeginOffset);
+ try {
+ m_stream.Seek(position);
+ return true;
+ }
+ catch ( BamException& e ) {
+ const string streamError = e.what();
+ const string message = string("could not seek in BAM file: \n\t") + streamError;
+ SetErrorString("BamReader::Seek", message);
+ return false;
+ }
}
-bool BamReaderPrivate::Seek(const int64_t& position) {
- return m_stream.Seek(position);
+void BamReaderPrivate::SetErrorString(const string& where, const string& what) {
+ static const string SEPARATOR = ": ";
+ m_errorString = where + SEPARATOR + what;
}
void BamReaderPrivate::SetIndex(BamIndex* index) {
m_randomAccessController.SetIndex(index);
}
-// change the index caching behavior
-void BamReaderPrivate::SetIndexCacheMode(const BamIndex::IndexCacheMode& mode) {
- m_randomAccessController.SetIndexCacheMode(mode);
-}
-
// sets current region & attempts to jump to it
// returns success/failure
bool BamReaderPrivate::SetRegion(const BamRegion& region) {
- return m_randomAccessController.SetRegion(this, region, m_references.size());
+
+ if ( m_randomAccessController.SetRegion(region, m_references.size()) )
+ return true;
+ else {
+ const string bracError = m_randomAccessController.GetErrorString();
+ const string message = string("could not set region: \n\t") + bracError;
+ SetErrorString("BamReader::SetRegion", message);
+ return false;
+ }
}
int64_t BamReaderPrivate::Tell(void) const {
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