// BamAlignment.h (c) 2009 Derek Barnett
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 4 December 2012 (DB)
+// Last modified: 25 July 2013 (DB)
// ---------------------------------------------------------------------------
// Provides the BamAlignment data structure
// ***************************************************************************
public:
std::string Name; // read name
int32_t Length; // length of query sequence
- std::string QueryBases; // 'original' sequence (as reported from sequencing machine)
- std::string AlignedBases; // 'aligned' sequence (includes any indels, padding, clipping)
+ std::string QueryBases; // 'original' sequence (contained in BAM file)
+ std::string AlignedBases; // 'aligned' sequence (QueryBases plus deletion, padding, clipping chars)
std::string Qualities; // FASTQ qualities (ASCII characters, not numeric values)
std::string TagData; // tag data (use provided methods to query/modify)
int32_t RefID; // ID number for reference sequence