版本1.30的变化-----------------------新功能o添加readGFF()，一个快速和灵活的GFF/GTF解析器实现在C.参见?readGFF以获得更多信息。import.gff()现在在内部使用readGFF()，这使得它在大多数用例中至少快了5倍，并极大地减少了它的内存占用。版本1.26的变化-----------------------新功能o ucscGenomes()检索生物体信息o新函数exportToTabix()将GRanges导出到一个包含所有元数据列的表索引选项卡分离文件。使用import、TabixFile将特定范围的数据加载回grange。o BigWig导入/导出到/从Integer/Numeric/RleList现在更加高效，并在可能的情况下在BigWig文件中使用更高效的存储格式。显著的用户可见的变化BSgenome导出方法现在在BSgenome。BUG修复o在GFF3中的引号处理现在与规范一致。1.22版本的变化-----------------------新功能o导入，BigWigFile获得一个asRle参数，返回数据作为RleList(假设它瓷砖序列);比导入GRanges并在其上调用coverage()快得多。o添加export,RleList,BigWigFile方法，直接(更有效)输出RleList(如覆盖)到BigWig文件。显著的用户可见的变化UCSCData现在扩展GRanges而不是RangedData(感谢Herve)错误修复处理不同的Set-Cookie报头字段套管; often due to proxies (thanks to Altuna Akalin) o attempt to more gracefully handle UCSC truncation of large data downloads o handle re-directs due to UCSC mirroring (thanks Martin Morgan) CHANGES IN VERSION 1.20 ----------------------- NEW FEATURES o Table query interface supports multiple query ranges. o Files (RTLFile objects) can be directly uploaded to UCSC, via track<-. SIGNIFICANT USER-VISIBLE CHANGES o All methods with asRangedData argument now have it default to FALSE, instead of TRUE. A warning is issued if the argument is missing. Eventually, we will drop all support for RangedData import (export will still work via automatic coercion to GRanges). BUG FIXES o Chromosome list for a genome is now downloaded from the table browser, instead of the Genome Browser page. This supports genomes with more than 1000 contigs. o BEDX+Y formats now work when a track line is present, and the extraCols argument is used for the column names. o path.expand() is now called for paths passed off to the Kent library. o Order of metadata columns upon GFF import no longer depends on LC_COLLATE. CHANGES IN VERSION 1.17 ----------------------- NEW FEATURES o Export of GappedAlignments objects as BAM files. There is also a corresponding import method. o Support for BEDX+Y import using the extraCols parameter to import. o Direct export of RleList objects to BigWig files. 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)