X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=src%2Fapi%2FBamMultiReader.h;h=43ef56a86c6d0a8cfead8ba12155443ab1e7ee76;hb=daf64972794dbbdae4bea6a0495578708c86363b;hp=cc49ec8eb2076469be2585bdf978bd603acec8a3;hpb=038f0e1dda24b2d6765cc8c878b7dbdc5f922ed6;p=bamtools.git diff --git a/src/api/BamMultiReader.h b/src/api/BamMultiReader.h index cc49ec8..43ef56a 100644 --- a/src/api/BamMultiReader.h +++ b/src/api/BamMultiReader.h @@ -3,7 +3,7 @@ // Marth Lab, Department of Biology, Boston College // All rights reserved. // --------------------------------------------------------------------------- -// Last modified: 15 March 2011 (DB) +// Last modified: 1 October 2011 (DB) // --------------------------------------------------------------------------- // Convenience class for reading multiple BAM files. // *************************************************************************** @@ -26,12 +26,6 @@ namespace Internal { class API_EXPORT BamMultiReader { - public: - enum SortOrder { SortedByPosition = 0 - , SortedByReadName - , Unsorted - }; - // constructor / destructor public: BamMultiReader(void); @@ -74,12 +68,9 @@ class API_EXPORT BamMultiReader { // retrieves next available alignment bool GetNextAlignment(BamAlignment& alignment); - // retrieves next available alignmnet (without populating the alignment's string data fields) + // retrieves next available alignment (without populating the alignment's string data fields) bool GetNextAlignmentCore(BamAlignment& alignment); - // sets the expected sorting order for reading across multiple BAM files - void SetSortOrder(const SortOrder& order); - // ---------------------- // access auxiliary data // ---------------------- @@ -110,13 +101,6 @@ class API_EXPORT BamMultiReader { // changes the caching behavior of the index data void SetIndexCacheMode(const BamIndex::IndexCacheMode& mode); - // deprecated methods - public: - // returns \c true if all BAM files have index data available. - bool IsIndexLoaded(void) const; - // convenience method for printing filenames to stdout - void PrintFilenames(void) const; - // private implementation private: Internal::BamMultiReaderPrivate* d;