// BamAlignment.h (c) 2009 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 10 October 2011 (DB)
+// Last modified: 12 October 2011 (DB)
// ---------------------------------------------------------------------------
// Provides the BamAlignment data structure
// ***************************************************************************
// returns a description of the last error that occurred
std::string GetErrorString(void) const;
+ // retrieves the size, read locations and reference locations of soft-clip operations
+ bool GetSoftClips(std::vector<int>& clipSizes,
+ std::vector<int>& readPositions,
+ std::vector<int>& genomePositions,
+ bool usePadded = false) const;
+
// public data fields
public:
std::string Name; // read name