// Marth Lab, Department of Biology, Boston College\r
// All rights reserved.\r
// ---------------------------------------------------------------------------\r
-// Last modified: 14 April 2010 (DB)\r
+// Last modified: 8 June 2010 (DB)\r
// ---------------------------------------------------------------------------\r
// Provides the basic constants, data structures, etc. for using BAM files\r
// ***************************************************************************\r
// ----------------------------------------------------------------\r
// Auxiliary data structs & typedefs\r
\r
+struct BamAlignmentSupportData {\r
+ \r
+ // data members\r
+ std::string AllCharData;\r
+ uint32_t BlockLength;\r
+ uint32_t NumCigarOperations;\r
+ uint32_t QueryNameLength;\r
+ uint32_t QuerySequenceLength;\r
+ \r
+ // constructor\r
+ BamAlignmentSupportData(void)\r
+ : BlockLength(0)\r
+ , NumCigarOperations(0)\r
+ , QueryNameLength(0)\r
+ , QuerySequenceLength(0)\r
+ { }\r
+};\r
+\r
struct CigarOp {\r
+ \r
+ // data members\r
char Type; // Operation type (MIDNSHP)\r
uint32_t Length; // Operation length (number of bases)\r
+ \r
+ // constructor\r
+ CigarOp(const char type = '\0', \r
+ const uint32_t length = 0) \r
+ : Type(type)\r
+ , Length(length) \r
+ { }\r
};\r
\r
struct RefData {\r