\r
// C++ includes\r
#include <string>\r
+#include <map>\r
+#include <utility> // for pair\r
\r
using namespace std;\r
\r
\r
namespace BamTools {\r
\r
-enum BamReaderState { START, END, CLOSED };\r
+// index mapping reference/position pairings to bamreaders and their alignments\r
+typedef multimap<pair<int, int>, pair<BamReader*, BamAlignment*> > AlignmentIndex;\r
\r
class BamMultiReader {\r
\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);\r
+ void Open(const vector<string> filenames, bool openIndexes = true);\r
// returns file pointers to beginning of alignments\r
bool Rewind(void);\r
\r
// ----------------------\r
\r
// returns unified SAM header text for all files\r
- const string GetUnifiedHeaderText(void) const;\r
+ const string GetHeaderText(void) const;\r
// returns number of reference sequences\r
const int GetReferenceCount(void) const;\r
// returns vector of reference objects\r
const BamTools::RefVector GetReferenceData(void) const;\r
// returns reference id (used for BamMultiReader::Jump()) for the given reference name\r
- //const int GetReferenceID(const std::string& refName) const;\r
+ const int GetReferenceID(const std::string& refName) const;\r
+ // validates that we have a congruent set of BAM files that are aligned against the same reference sequences\r
+ void ValidateReaders() const;\r
\r
// ----------------------\r
// BAM index operations\r
\r
// utility\r
void PrintFilenames(void);\r
- void UpdateAlignments(void);\r
-\r
+ void DumpAlignmentIndex(void);\r
\r
// private implementation\r
private:\r
- // TODO perhaps, for legibility, I should use a struct to wrap them all up\r
- // But this may actually make things more confusing, as I'm only\r
- // operating on them all simultaneously during GetNextAlignment\r
- // calls.\r
- // all these vectors are ordered the same\r
- // readers.at(N) refers to the same reader as alignments.at(N) and readerStates.at(N)\r
- vector<BamReader*> readers; // the set of readers which we operate on\r
- vector<BamAlignment*> alignments; // the equivalent set of alignments we use to step through the files\r
- vector<BamReaderState> readerStates; // states of the various readers\r
- // alignment position?\r
+\r
+ // the set of readers and alignments which we operate on, maintained throughout the life of this class\r
+ vector<pair<BamReader*, BamAlignment*> > readers;\r
+\r
+ // readers and alignments sorted by reference id and position, to keep track of the lowest (next) alignment\r
+ // when a reader reaches EOF, its entry is removed from this index\r
+ AlignmentIndex alignments;\r
+\r
vector<string> fileNames;\r
};\r
\r