CHANGES IN VERSION 1.15 ----------------------- NEW FEATURES o Integrated with tabix via Rsamtools. BED and GFF export methods now generate a tabix index, if index=TRUE. Most import() methods gain a 'which' argument that takes advantage of tabix, when available. o Added wigToBigWig() function for efficient conversion of WIG to BigWig. o Added SeqinfoForBSGenome() and SeqinfoForUCSCGenome() for conveniently retrieving Seqinfo objects for a given genome. o Added support for FASTA import/export via Biostrings. o GTF and GVF files are now parsed as GFF. SIGNIFICANT USER-VISIBLE CHANGES o The import/export API is now based on RTLFile objects, which wrap a file path, URL or connection. There is an RTLFile subclass for every file format. This makes it easier to extend rtracklayer (export, import) with new file types. The existing API is still supported (and even encouraged for most uses). o Handle CSV attributes in GFF3 using CharacterList columns. o BED columns thickStart/thickEnd translate to an IRanges column named "thick". The blockStarts/Sizes/Count columns now map to a single RangesList "blocks" column. BUG FIXES o Numerous fixes in the import/export methods, as a result of implementing a full unit test suite. If something was not working for you in the past, please try again. o Compression and connections should now work fairly uniformly across file types. (start date: 29 March, 2012)