diff spp/src/BamReader.cpp @ 15:e689b83b0257 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spp/src/BamReader.cpp	Tue Nov 27 16:15:21 2012 -0500
@@ -0,0 +1,66 @@
+// ***************************************************************************
+// BamReader.cpp (c) 2009 Derek Barnett, Michael Str�mberg
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 22 November 2010 (DB)
+// ---------------------------------------------------------------------------
+// Provides the basic functionality for reading BAM files
+// ***************************************************************************
+
+#include <BamReader.h>
+#include <BamReader_p.h>
+using namespace BamTools;
+using namespace BamTools::Internal;
+
+#include <algorithm>
+#include <iostream>
+#include <iterator>
+#include <string>
+#include <vector>
+using namespace std;
+
+// constructor
+BamReader::BamReader(void) {
+    d = new BamReaderPrivate(this);
+}
+
+// destructor
+BamReader::~BamReader(void) {
+    delete d;
+    d = 0;
+}
+
+// file operations
+void BamReader::Close(void) { d->Close(); }
+bool BamReader::HasIndex(void) const { return d->HasIndex; }
+bool BamReader::IsIndexLoaded(void) const { return HasIndex(); }
+bool BamReader::IsOpen(void) const { return d->mBGZF.IsOpen; }
+bool BamReader::Jump(int refID, int position)  { return d->SetRegion( BamRegion(refID, position) ); }
+bool BamReader::Open(const std::string& filename,
+                     const std::string& indexFilename,
+                     const bool lookForIndex,
+                     const bool preferStandardIndex)
+{
+    return d->Open(filename, indexFilename, lookForIndex, preferStandardIndex);
+}
+bool BamReader::Rewind(void) { return d->Rewind(); }
+bool BamReader::SetRegion(const BamRegion& region) { return d->SetRegion(region); }
+bool BamReader::SetRegion(const int& leftRefID, const int& leftBound, const int& rightRefID, const int& rightBound) {
+    return d->SetRegion( BamRegion(leftRefID, leftBound, rightRefID, rightBound) );
+}
+
+// access alignment data
+bool BamReader::GetNextAlignment(BamAlignment& bAlignment) { return d->GetNextAlignment(bAlignment); }
+bool BamReader::GetNextAlignmentCore(BamAlignment& bAlignment) { return d->GetNextAlignmentCore(bAlignment); }
+
+// access auxiliary data
+const string BamReader::GetHeaderText(void) const { return d->GetHeaderText(); }
+int BamReader::GetReferenceCount(void) const { return d->References.size(); }
+const RefVector& BamReader::GetReferenceData(void) const { return d->References; }
+int BamReader::GetReferenceID(const string& refName) const { return d->GetReferenceID(refName); }
+const std::string BamReader::GetFilename(void) const { return d->Filename; }
+
+// index operations
+bool BamReader::CreateIndex(bool useStandardIndex) { return d->CreateIndex(useStandardIndex); }
+void BamReader::SetIndexCacheMode(const BamIndex::BamIndexCacheMode mode) { d->SetIndexCacheMode(mode); }