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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spp/src/BamWriter.cpp	Tue Nov 27 16:15:21 2012 -0500
@@ -0,0 +1,47 @@
+// ***************************************************************************
+// BamWriter.cpp (c) 2009 Michael Str�mberg, Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 22 November 2010 (DB)
+// ---------------------------------------------------------------------------
+// Provides the basic functionality for producing BAM files
+// ***************************************************************************
+
+#include <BamWriter.h>
+#include <BamWriter_p.h>
+using namespace BamTools;
+using namespace BamTools::Internal;
+
+#include <iostream>
+using namespace std;
+
+// constructor
+BamWriter::BamWriter(void) {
+    d = new BamWriterPrivate;
+}
+
+// destructor
+BamWriter::~BamWriter(void) {
+    delete d;
+    d = 0;
+}
+
+// closes the alignment archive
+void BamWriter::Close(void) {
+    d->Close();
+}
+
+// opens the alignment archive
+bool BamWriter::Open(const string& filename,
+                     const string& samHeader,
+                     const RefVector& referenceSequences,
+                     bool isWriteUncompressed)
+{
+    return d->Open(filename, samHeader, referenceSequences, isWriteUncompressed);
+}
+
+// saves the alignment to the alignment archive
+void BamWriter::SaveAlignment(const BamAlignment& al) {
+    d->SaveAlignment(al);
+}