// Marth Lab, Department of Biology, Boston College\r
// All rights reserved.\r
// ---------------------------------------------------------------------------\r
-// Last modified: 8 December 2009 (DB)\r
+// Last modified: 17 August 2010 (DB)\r
// ---------------------------------------------------------------------------\r
// Uses BGZF routines were adapted from the bgzf.c code developed at the Broad\r
// Institute.\r
// closes the alignment archive\r
void Close(void);\r
// opens the alignment archive\r
- void Open(const std::string& filename, const std::string& samHeader, const BamTools::RefVector& referenceSequences);\r
+ bool Open(const std::string& filename, \r
+ const std::string& samHeader, \r
+ const BamTools::RefVector& referenceSequences, \r
+ bool writeUncompressed = false);\r
// saves the alignment to the alignment archive\r
void SaveAlignment(const BamTools::BamAlignment& al);\r
\r