// Marth Lab, Department of Biology, Boston College\r
// All rights reserved.\r
// ---------------------------------------------------------------------------\r
-// Last modified: 19 November 2010 (DB)\r
+// Last modified: 23 December 2010 (DB)\r
// ---------------------------------------------------------------------------\r
// Functionality for simultaneously reading multiple BAM files\r
// ***************************************************************************\r
\r
namespace BamTools {\r
\r
-// index mapping reference/position pairings to bamreaders and their alignments\r
-typedef std::multimap<std::pair<int, int>, std::pair<BamReader*, BamAlignment*> > AlignmentIndex;\r
+namespace Internal {\r
+ class BamMultiReaderPrivate;\r
+} // namespace Internal\r
\r
class API_EXPORT BamMultiReader {\r
\r
// public interface\r
public:\r
\r
- // positioning\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
- // @preferStandardIndex - look for standard BAM index ".bai" first. If false, \r
- // will look for BamTools index ".bti". \r
- bool Open(const std::vector<std::string>& filenames, bool openIndexes = true, bool coreMode = false, bool preferStandardIndex = false);\r
-\r
+ // @preferStandardIndex - look for standard BAM index ".bai" first. If false,\r
+ // will look for BamTools index ".bti".\r
+ bool Open(const std::vector<std::string>& filenames,\r
+ bool openIndexes = true,\r
+ bool coreMode = false,\r
+ bool preferStandardIndex = false);\r
// returns whether underlying BAM readers ALL have an index loaded\r
// this is useful to indicate whether Jump() or SetRegion() are possible\r
bool IsIndexLoaded(void) const;\r
- \r
// performs random-access jump to reference, position\r
bool Jump(int refID, int position = 0);\r
-\r
+ // list files associated with this multireader\r
+ void PrintFilenames(void) const;\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
+ bool SetRegion(const int& leftRefID,\r
+ const int& leftBound,\r
+ const int& rightRefID,\r
+ const int& rightBound);\r
// returns file pointers to beginning of alignments\r
bool Rewind(void);\r
\r
// ----------------------\r
// access alignment data\r
// ----------------------\r
- // updates the reference id marker to match the lower limit of our readers\r
- void UpdateReferenceID(void);\r
\r
// retrieves next available alignment (returns success/fail) from all files\r
- bool GetNextAlignment(BamAlignment&);\r
+ bool GetNextAlignment(BamAlignment& alignment);\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
+ bool GetNextAlignmentCore(BamAlignment& alignment);\r
// ... should this be private?\r
bool HasOpenReaders(void);\r
+ // set sort order for merging BAM files (i.e. which alignment from the files is 'next'?)\r
+ // default behavior is to sort by position, use this method to handle BAMs sorted by read name\r
+ enum SortOrder { SortedByPosition = 0, SortedByReadName};\r
+ void SetSortOrder(const SortOrder& order);\r
\r
// ----------------------\r
// access auxiliary data\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
- // 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
// creates index for BAM files which lack them, saves to files (default = bamFilename + ".bai")\r
bool CreateIndexes(bool useStandardIndex = true);\r
-\r
// sets the index caching mode for the readers\r
void SetIndexCacheMode(const BamIndex::BamIndexCacheMode mode);\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
-\r
- // the set of readers and alignments which we operate on, maintained throughout the life of this class\r
- std::vector<std::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
- std::vector<std::string> fileNames;\r
+ Internal::BamMultiReaderPrivate* d;\r
};\r
\r
} // namespace BamTools\r
projects / bamtools.git / blobdiff