CHANGES IN VERSION 1.12.0 ------------------------ NEW FEATURES o allow GRanges in 'rowData' to hold user-defined metadata cols (i.e., cols other than paramRangeID, REF, ALT, etc.) o add isSNV() family of functions o add faster method for converting a list matrix to an array o add 'c' method for typed Rle classes so class is preserved o add CITATION file o rework writeVCF(): - FORMAT and genotype fields are parsed in C - output file is written from C - chunking added for large VCFs MODIFICATIONS o add 'row.names' to readVcf() o deprecate restrictToSNV(); replaced by isSNV() family o remove use of seqapply() o show info / geno headers without splitting across blocks o use mapCoords() in predictCoding() and locateVariants() o deprecate refLocsToLocalLocs() o propagate strand in predictCoding() o replace deprecated seqsplit() with splitAsList() o ensure GT field, if present, comes first in VCF output o modify DESCRIPTION Author and Maintainer fileds with @R o add 'row.names' to info,VCF-method BUG FIXES o modify expand() to work with no 'info' fields are imported o remove duplicate rows from .splicesites() o fix handling of real-valued NAs in geno omatrix construction in writeVcf() CHANGES IN VERSION 1.10.0 ------------------------ NEW FEATURES o add support for ##contig in VCF header o add 'meta<-', 'info<-', 'geno<-' replacement methods for VCFHeader o add 'header<-' replacement method for VCF o add strand to output from locationVariants() o add support for writeVcf() to process Rle data in geno matrix o readVcf() now parses 'geno' fields with Number=G as ((#alleles + 1) * (#alleles + 2)) / 2 o writeVcf() now sorts the VCF when 'index=TRUE' o add 'fixed<-,VCFHeader,DataFrameList' method o add convenience functions for reading VCF into VRanges o add Rplinkseq test script o add 'isSNV', 'isInsertion', 'isDeletion', 'isIndel', 'isTransition', 'isPrecise', 'isSV' and 'isSubstitution' generics o add 'isSNV', 'isInsertion', 'isDeletion', 'isIndel' methods for VRanges and VCF classes o add match methods between ExpandedVCF and VRanges o add support for VRanges %in% TabixFile MODIFICATIONS o expand,VCF-method ignores 'AD' header of 'AD' geno is NULL o add support for SIFT.Hsapiens.dbSNP137 o remove locateVariants() dependence on chr7-sub.vcf.gz o modify expand() to handle 'AD' field where 'Number' is integer o rename readVRangesFromVCF() to readVcfAsVRanges() o remove check for circular chromosomes in locateVariants() and predictCoding() and refLocsToLocalLocs() o modify filterVcf() to handle ranges in ScanVcfParam o pass 'genetic.code' through predictCoding() o change default to 'row.names=TRUE' for readGT(), readGeno(), and readInfo() o fixed() on empty VCF now returns DataFrame with column names and data types vs an empty DataFrame o update biocViews o modify 'show,VCF' to represent empty values in XStringSet with '.' o replace rtracklayer:::pasteCollapse with unstrsplit() DEPRECATED and DEFUNCT o remove defunct dbSNPFilter(), regionfilter() and MatrixToSnpMatrix() o deprecate defunct readVcfLongForm() BUG FIXES o modify expand.geno() to handle case where header and geno don't match o modify writeVcf() to write out rownames with ":" character instead of treating as missing o fix how sample names were passed from 'ScanVcfParam' to scanVcf() o fix bug in 'show,VCF' method o fix bugs in VRanges -> VCF coercion methods o fix bug in lightweight read* functions that were ignoring samples in ScanVcfParam o fix bug in writeVcf() when no 'ALT' is present CHANGES IN VERSION 1.8.0 ------------------------ NEW FEATURES o Add 'upstream' and 'downstream' arguments to IntergenicVariants() constructor. o Add 'samples' argument to ScanVcfParam(). o Add readGT(), readGeno() and readInfo(). o Add VRanges, VRangesList, SimpleVRangesList, and CompressedVRangesList classes. o Add coercion VRanges -> VCF and VCF -> VRanges. o Add methods for VRanges family: altDepth(), refDepth(), totalDepth(), altFraction() called(), hardFilters(), sampleNames(), softFilterMatrix() isIndel(), resetFilter(). o Add stackedSamples,VRangesList method. MODIFICATIONS o VCF validity method now requires the number of rows in info() to match the length of rowData(). o PRECEDEID and FOLLOWID from locateVariants() are now CharacterLists with all genes in 'upstream' and 'downstream' range. o Modify rownames on rowData() GRanges to CHRAM:POS_REF/ALT for variants with no ID. o readVcf() returns info() and geno() in the order specified in the ScanVcfParam. o Work on scanVcf(): - free parse memory at first opportunity - define it_next in .c rather than .h - parse ALT "." in C - hash incoming strings - parse only param-requested 'fixed', 'info', 'geno' fields o Add dimnames<-,VCF method to prevent 'fixed' fields from being copied into 'rowData' when new rownames or colnames were assigned. o Support read/write for an emtpy VCF. o readVcf(file=character, ...) method attempts coercion to TabixFile. o Support for read/write an emtpy VCF. o Add performance section to vignette; convert to BiocStyle. o expand,CompressedVcf method expands geno() field 'AD' to length ALT + 1. The expanded field is a (n x y x 2) array. o 'genome' argument to readVcf() can be a character(1) or Seqinfo object. DEPRECATED and DEFUNCT o Defunct dbSNPFilter(), regionFilter() and MatrixToSnpMatrix(). o Deprecate readVcfLongForm(). BUG FIXES o Fix bug in compatibility of read/writeVcf() when no INFO are columns present. o Fix bug in locateVariants() when 'features' has no txid and cdsid. o Fix bug in asVCF() when writing header lines. o Fix bug in "expand" methods for VCF to handle multiple 'A' columns in info(). CHANGES IN VERSION 1.6.0 ------------------------ NEW FEATURES o VCF is now VIRTUAL. Concrete subclasses are CollapsedVCF and ExpandedVCF. o Add filterVcf() generic and methods for character and TabixFile. This method creates one VCF file from another, using FilterRules. o Enhance show,VCF method with header information. o Stephanie Gogarten added genotypeToSnpMatrix() generic and CollapsedVCF and matrix methods. o Chris Wallace added snpSummary() generic and CollapsedVCF method. o Add cbind and rbind for VCF objects. MODIFICATIONS o writeVcf,connection-method allows writing to console and appending. o writeVcf,connection-method accepts connections with open="a", only adding a header if the file does not already exist. 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)