// Marth Lab, Department of Biology, Boston College\r
// All rights reserved.\r
// ---------------------------------------------------------------------------\r
-// Last modified: 18 September 2010 (DB)\r
+// Last modified: 19 November 2010 (DB)\r
// ---------------------------------------------------------------------------\r
// Functionality for simultaneously reading multiple BAM files\r
// ***************************************************************************\r
#ifndef BAMMULTIREADER_H\r
#define BAMMULTIREADER_H\r
\r
-#include <string>\r
+#include <api/api_global.h>\r
+#include <api/BamReader.h>\r
#include <map>\r
-#include <utility>\r
#include <sstream>\r
-#include "BamReader.h"\r
+#include <string>\r
+#include <utility>\r
\r
namespace BamTools {\r
\r
// index mapping reference/position pairings to bamreaders and their alignments\r
typedef std::multimap<std::pair<int, int>, std::pair<BamReader*, BamAlignment*> > AlignmentIndex;\r
\r
-class BamMultiReader {\r
+class API_EXPORT BamMultiReader {\r
\r
// constructor / destructor\r
public:\r
// creates index for BAM files which lack them, saves to files (default = bamFilename + ".bai")\r
bool CreateIndexes(bool useStandardIndex = true);\r
\r
+ // sets the index caching mode for the readers\r
+ void SetIndexCacheMode(const BamIndex::BamIndexCacheMode mode);\r
+\r
//const int GetReferenceID(const string& refName) const;\r
\r
// utility\r