- // opens BAM file (and optional BAM index file, if provided)\r
- // @lookForIndex - if no indexFilename provided, look in BAM file's directory for an existing index file\r
- // default behavior is to skip index file search if no index filename given\r
- // @preferStandardIndex - if true, give priority in index file searching to standard BAM index (*.bai)\r
- // default behavior is to prefer the BamToolsIndex (*.bti) if both are available\r
- bool Open(const std::string& filename, \r
- const std::string& indexFilename = "", \r
- const bool lookForIndex = false, \r
- const bool preferStandardIndex = false);\r
- // returns file pointer to beginning of alignments\r
+ // opens a BAM file\r
+ bool Open(const std::string& filename);\r
+ // returns internal file pointer to beginning of alignment data\r