X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2FBamMultiReader.h;h=4f8c133fca2bf32cdc3551c7724dc554c43ed510;hb=3fe66b92028b60629826d827ee9058405fa7e4be;hp=43ef56a86c6d0a8cfead8ba12155443ab1e7ee76;hpb=daf64972794dbbdae4bea6a0495578708c86363b;p=bamtools.git diff --git a/src/api/BamMultiReader.h b/src/api/BamMultiReader.h index 43ef56a..4f8c133 100644 --- a/src/api/BamMultiReader.h +++ b/src/api/BamMultiReader.h @@ -1,9 +1,8 @@ // *************************************************************************** // BamMultiReader.h (c) 2010 Erik Garrison, Derek Barnett // Marth Lab, Department of Biology, Boston College -// All rights reserved. // --------------------------------------------------------------------------- -// Last modified: 1 October 2011 (DB) +// Last modified: 14 January 2013 (DB) // --------------------------------------------------------------------------- // Convenience class for reading multiple BAM files. // *************************************************************************** @@ -11,8 +10,8 @@ #ifndef BAMMULTIREADER_H #define BAMMULTIREADER_H -#include -#include +#include "api/api_global.h" +#include "api/BamReader.h" #include #include #include @@ -26,6 +25,14 @@ namespace Internal { class API_EXPORT BamMultiReader { + // enums + public: + // possible merge order strategies + enum MergeOrder { RoundRobinMerge = 0 + , MergeByCoordinate + , MergeByName + }; + // constructor / destructor public: BamMultiReader(void); @@ -39,11 +46,13 @@ class API_EXPORT BamMultiReader { // ---------------------- // closes all open BAM files - void Close(void); + bool Close(void); // close only the requested BAM file - void CloseFile(const std::string& filename); + bool CloseFile(const std::string& filename); // returns list of filenames for all open BAM files const std::vector Filenames(void) const; + // returns curent merge order strategy + BamMultiReader::MergeOrder GetMergeOrder(void) const; // returns true if multireader has any open BAM files bool HasOpenReaders(void) const; // performs random-access jump within current BAM files @@ -54,6 +63,8 @@ class API_EXPORT BamMultiReader { bool OpenFile(const std::string& filename); // returns file pointers to beginning of alignments bool Rewind(void); + // sets an explicit merge order, regardless of the BAM files' SO header tag + bool SetExplicitMergeOrder(BamMultiReader::MergeOrder order); // sets the target region of interest bool SetRegion(const BamRegion& region); // sets the target region of interest @@ -98,8 +109,13 @@ class API_EXPORT BamMultiReader { bool LocateIndexes(const BamIndex::IndexType& preferredType = BamIndex::STANDARD); // opens index files for current BAM files. bool OpenIndexes(const std::vector& indexFilenames); - // changes the caching behavior of the index data - void SetIndexCacheMode(const BamIndex::IndexCacheMode& mode); + + // ---------------------- + // error handling + // ---------------------- + + // returns a human-readable description of the last error that occurred + std::string GetErrorString(void) const; // private implementation private: