1.30版本的变化- - - - - - - - - - - - - - - - - - - - - - - - o readGFF添加新功能(),一个快速和灵活的人造石铺地面/ GTF解析器实现c .看到了什么? readGFF获得更多信息。重要用户可见的变化o import.gff()现在使用readGFF()内部使它快至少5倍在大多数用例和显著减少内存占用。1.26版本的变化- - - - - - - - - - - - - - - - - - - - - - - - o ucscGenomes新特性()检索生物信息o新函数exportToTabix()出口一个农庄tabix-indexed标签分隔文件,其中包含所有的元数据列。使用进口,TabixFile特定范围的数据加载到一个农庄。o大佬导入/导出/从整数/数字/ RleList现在更有效率,并使用一个更高效的存储格式在权贵文件,如果可能的话。重要用户可见现在在BSgenome o BSgenome出口变化方法。BUG修复o处理报价在GFF3现在与规范一致。1.22版本的变化- - - - - - - - - - - - - - - - - - - - - - - -新特性导入,BigWigFile收益一个asRle参数,返回数据作为RleList(假设瓷砖序列);速度远远超过导入一个农庄和调用报道()。o增加出口、RleList BigWigFile直接方法(而且更有效)的输出RleLists大佬文件(如保险)。重要用户可见的变化o UCSCData现在扩展了农庄组织而不是RangedData(感谢Herve) BUG修复o处理不同的set - cookie套管头字段; 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)