// BamRandomAccessController_p.cpp (c) 2011 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 5 April 2011(DB)
+// Last modified: 10 October 2011(DB)
// ---------------------------------------------------------------------------
// Manages random access operations in a BAM file
// **************************************************************************
-#include <api/BamIndex.h>
-#include <api/internal/BamRandomAccessController_p.h>
-#include <api/internal/BamReader_p.h>
-#include <api/internal/BamIndexFactory_p.h>
+#include "api/BamIndex.h"
+#include "api/internal/BamException_p.h"
+#include "api/internal/BamRandomAccessController_p.h"
+#include "api/internal/BamReader_p.h"
+#include "api/internal/BamIndexFactory_p.h"
using namespace BamTools;
using namespace BamTools::Internal;
-#include <iostream>
+#include <cassert>
+#include <sstream>
using namespace std;
BamRandomAccessController::BamRandomAccessController(void)
// if alignment starts at or after left bound position
if ( alignment.Position >= m_region.LeftPosition) {
- if ( m_region.isRightBoundSpecified() && // right bound is specified AND
- m_region.LeftRefID == m_region.RightRefID && // left & right bounds on same reference AND
- alignment.Position > m_region.RightPosition ) // alignment starts after right bound position
+ if ( m_region.isRightBoundSpecified() && // right bound is specified AND
+ m_region.LeftRefID == m_region.RightRefID && // left & right bounds on same reference AND
+ alignment.Position >= m_region.RightPosition ) // alignment starts on or after right bound position
return AfterRegion;
// otherwise, alignment overlaps region
else {
// if alignment overlaps left bound position
- if ( alignment.GetEndPosition() >= m_region.LeftPosition )
+ if ( alignment.GetEndPosition() > m_region.LeftPosition )
return OverlapsRegion;
else
return BeforeRegion;
// alignment is on right bound reference
else {
- // if alignment starts on or before right bound position
- if ( alignment.Position <= m_region.RightPosition )
+ // if alignment starts before right bound position
+ if ( alignment.Position < m_region.RightPosition )
return OverlapsRegion;
else
return AfterRegion;
}
}
- // otherwise, alignment starts after left bound and there is no right bound
+ // otherwise, alignment starts after left bound and there is no right bound given
else return OverlapsRegion;
}
}
}
void BamRandomAccessController::ClearIndex(void) {
- delete m_index;
- m_index = 0;
+ if ( m_index ) {
+ delete m_index;
+ m_index = 0;
+ }
}
void BamRandomAccessController::ClearRegion(void) {
}
bool BamRandomAccessController::CreateIndex(BamReaderPrivate* reader,
- const BamIndex::IndexType& type) {
-
+ const BamIndex::IndexType& type)
+{
// skip if reader is invalid
- if ( reader == 0 )
+ assert(reader);
+ if ( !reader->IsOpen() ) {
+ SetErrorString("BamRandomAccessController::CreateIndex",
+ "cannot create index for unopened reader");
return false;
+ }
// create new index of requested type
BamIndex* newIndex = BamIndexFactory::CreateIndexOfType(type, reader);
if ( newIndex == 0 ) {
- cerr << "BamRandomAccessController ERROR: could not create index of type " << type << endl;
+ stringstream s("");
+ s << "could not create index of type: " << type;
+ SetErrorString("BamRandomAccessController::CreateIndex", s.str());
return false;
}
// attempt to build index from current BamReader file
if ( !newIndex->Create() ) {
- cerr << "BamRandomAccessController ERROR: could not create index for BAM file: "
- << reader->Filename() << endl;
+ const string indexError = newIndex->GetErrorString();
+ const string message = "could not create index: \n\t" + indexError;
+ SetErrorString("BamRandomAccessController::CreateIndex", message);
return false;
}
return true;
}
+string BamRandomAccessController::GetErrorString(void) const {
+ return m_errorString;
+}
+
bool BamRandomAccessController::HasIndex(void) const {
return ( m_index != 0 );
}
const BamIndex::IndexType& preferredType)
{
// look up index filename, deferring to preferredType if possible
+ assert(reader);
const string& indexFilename = BamIndexFactory::FindIndexFilename(reader->Filename(), preferredType);
// if no index file found (of any type)
if ( indexFilename.empty() ) {
- cerr << "BamRandomAccessController WARNING: "
- << "could not find index file for BAM: "
- << reader->Filename() << endl;
+ const string message = string("could not find index file for:") + reader->Filename();
+ SetErrorString("BamRandomAccessController::LocateIndex", message);
return false;
}
// attempt create new index of type based on filename
BamIndex* index = BamIndexFactory::CreateIndexFromFilename(indexFilename, reader);
if ( index == 0 ) {
- cerr << "BamRandomAccessController ERROR: could not create index for file: " << indexFilename << endl;
+ const string message = string("could not open index file: ") + indexFilename;
+ SetErrorString("BamRandomAccessController::OpenIndex", message);
return false;
}
// attempt to load data from index file
if ( !index->Load(indexFilename) ) {
- cerr << "BamRandomAccessController ERROR: could not load index data from file: " << indexFilename << endl;
+ const string indexError = index->GetErrorString();
+ const string message = string("could not load index data from file: ") + indexFilename +
+ "\n\t" + indexError;
+ SetErrorString("BamRandomAccessController::OpenIndex", message);
return false;
}
return m_hasAlignmentsInRegion;
}
+void BamRandomAccessController::SetErrorString(const string& where, const string& what) {
+ m_errorString = where + ": " + what;
+}
+
void BamRandomAccessController::SetIndex(BamIndex* index) {
if ( m_index )
ClearIndex();
m_index->SetCacheMode(mode);
}
-bool BamRandomAccessController::SetRegion(BamReaderPrivate* reader,
- const BamRegion& region,
- const int& referenceCount)
-{
+bool BamRandomAccessController::SetRegion(const BamRegion& region, const int& referenceCount) {
+
// store region
m_region = region;
// cannot jump when no index is available
- if ( !HasIndex() )
+ if ( !HasIndex() ) {
+ SetErrorString("BamRandomAccessController", "cannot jump if no index data available");
return false;
+ }
// adjust region as necessary to reflect where data actually begins
AdjustRegion(referenceCount);
// if no data present, return true
// * Not an error, but future attempts to access alignments in this region will not return data
// Returning true is useful in a BamMultiReader setting where some BAM files may
- // lack alignments in regions where other BAMs do have data.
+ // lack alignments in regions where other files still have data available.
if ( !m_hasAlignmentsInRegion )
return true;
// This covers 'corner case' where a region is requested that lies beyond the last
// alignment on a reference. If this occurs, any subsequent calls to GetNextAlignment[Core]
// will not return data. BamMultiReader will still be able to successfully pull alignments
- // from a region from multiple files even if one or more have no data.
- return m_index->Jump(m_region, &m_hasAlignmentsInRegion);
+ // from a region from other files even if this one has no data.
+ if ( !m_index->Jump(m_region, &m_hasAlignmentsInRegion) ) {
+ const string indexError = m_index->GetErrorString();
+ const string message = string("could not set region\n\t") + indexError;
+ SetErrorString("BamRandomAccessController::OpenIndex", message);
+ return false;
+ }
+ else
+ return true;
}
projects / bamtools.git / blobdiff