// Marth Lab, Department of Biology, Boston College\r
// All rights reserved.\r
// ---------------------------------------------------------------------------\r
-// Last modified: 22 February 2010 (EG)\r
+// Last modified: 20 July 2010 (DB)\r
// ---------------------------------------------------------------------------\r
// Functionality for simultaneously reading multiple BAM files\r
// ***************************************************************************\r
int CurrentRefID;\r
int CurrentLeft;\r
\r
+ // region under analysis, specified using SetRegion\r
+ BamRegion Region;\r
+\r
// ----------------------\r
// BAM file operations\r
// ----------------------\r
\r
// close BAM files\r
void Close(void);\r
+\r
+ // opens BAM files (and optional BAM index files, if provided)\r
+ // @openIndexes - triggers index opening, useful for suppressing\r
+ // error messages during merging of files in which we may not have\r
+ // indexes.\r
+ // @coreMode - setup our first alignments using GetNextAlignmentCore();\r
+ // also useful for merging\r
+ bool Open(const vector<string> filenames, bool openIndexes = true, bool coreMode = false, bool useDefaultIndex = true);\r
+\r
// performs random-access jump to reference, position\r
bool Jump(int refID, int position = 0);\r
- // opens BAM files (and optional BAM index files, if provided)\r
- //void Open(const vector<std::string&> filenames, const vector<std::string&> indexFilenames);\r
- void Open(const vector<string> filenames, bool openIndexes = true);\r
+\r
+ // sets the target region\r
+ bool SetRegion(const BamRegion& region);\r
+ bool SetRegion(const int&, const int&, const int&, const int&); // convenience function to above\r
+\r
// returns file pointers to beginning of alignments\r
bool Rewind(void);\r
\r
\r
// retrieves next available alignment (returns success/fail) from all files\r
bool GetNextAlignment(BamAlignment&);\r
+ // retrieves next available alignment (returns success/fail) from all files\r
+ // and populates the support data with information about the alignment\r
+ // *** BUT DOES NOT PARSE CHARACTER DATA FROM THE ALIGNMENT\r
+ bool GetNextAlignmentCore(BamAlignment&);\r
// ... should this be private?\r
bool HasOpenReaders(void);\r
\r
// ----------------------\r
\r
// creates index for BAM files which lack them, saves to files (default = bamFilename + ".bai")\r
- bool CreateIndexes(void);\r
+ bool CreateIndexes(bool useDefaultIndex = true);\r
\r
//const int GetReferenceID(const string& refName) const;\r
\r
// utility\r
void PrintFilenames(void);\r
void DumpAlignmentIndex(void);\r
+ void UpdateAlignments(void); // updates our alignment cache\r
\r
// private implementation\r
private:\r