1.6.0版本的变化 ------------------------ 新特性o VCF现在虚拟。具体的子类是折叠式dvcf和扩展式dvcf。o为字符和TabixFile添加filterVcf()泛型和方法。此方法使用FilterRules从另一个VCF文件创建一个VCF文件。增强显示，VCF方法与头信息。o Stephanie Gogarten添加了genotypeToSnpMatrix()泛型和CollapsedVCF和矩阵方法。o Chris Wallace添加了snpSummary()泛型和CollapsedVCF方法。o为VCF对象添加cbind和rbind。修改writeVcf，连接方法允许写入控制台和追加。o writeVcf,connection-method接受open="a"的连接，只在文件不存在时添加头文件。 o predictCoding and genotypeToSnpMatrix can now handle ALT as CharacterList. Structural variants are set to empty character (""). o When no INFO data are present in a vcf file, the info() slot is now an empty DataFrame. Previously an empty column named 'INFO' was returned. o Empty VCF class now has an empty VCFHeader o expand,CollapsedVCF-method expands 'geno' data with Number=A. o VCF class accessors "fixed", "info" now return DataFrame instead of GRanges. "rowData" returns fixed fileds as the mcols. o Updates to the vignette. DEPRECATED and DEFUNCT o Deprecate dbSNPFilter() and regionFilter(). o Deprecate MatrixToSnpMatrix(). BUG FIXES o Multiple bugs fixed in "locateVariants". o Multiple bugs fixed in "writeVcf". o Bug fixed in subsetting of VCF objects. o Bug fixed in "predictCoding" related to QUERYID column not mapping back to original indices (rows). CHANGES IN VERSION 1.4.0 ------------------------ NEW FEATURES o "summarizeVariants" for summarizing counts by sample o new VariantType 'PromoterVariants()' added to "locateVariants" MODIFICATIONS o "ref", "alt", "filt" and "qual" accessors for VCF-class now return a single variable instead of GRanges with variable as metadata CHANGES IN VERSION 1.2.0 ------------------------ NEW FEATURES o "readVcf" has genome argument, can be subset on ranges or VCF elements with "ScanVcfParam" o "scanVcfHeader" returns VCFHeader class with accessors fixed, info, geno, etc. o "writeVcf" writes out a VCF file from a VCF class o "locateVariants" methods - returns GRanges instead of DataFrame - 'region' argument allows specification of variants by region - output includes txID, geneID and cdsID - has cache argument for repeated calls over multiple vcf files o "predictCoding" methods - returns GRanges instead of DataFrame - output includes txID, geneID, cdsID, cds-based and protein-based coordinates CHANGES IN VERSION 1.0.0 ------------------------ NEW FEATURES o "readVcf" methods for reading and parsing VCF files into a SummarizedExperiment o "locateVariants" and "predictCoding" for identifying amino acid coding changes in nonsynonymous variants o "dbSNPFilter" and "regionFilter" for filtering variants on membership in dbSNP or on a particular location in the genome o access to PolyPhen and SIFT predictions through "keys" , "cols" and "select" methods. See ?SIFT or ?PolyPhen. BUG FIXES o No changes classified as 'bug fixes' (package under active development)