NEWS

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VariantAnnotation 1.36.0

NEW FEATURES

• ref<-, alt<-, qual<- and filt<- allow replacement value length recycling

VariantAnnotation 1.28.0

NEW FEATURES

• Update package to support VCF format version 4.3 - SAMPLE field lines can now have key 'SAMPLE' or 'META'. To avoid a name clash, the existing 'META' DataFrame has been split by row into separate DataFrames. The 'meta(VCFHeader)' getter now returns one DataFrame per unique key in the header. - PEDIGREE header line now begins with 'ID'
• Add vcfFields method for character, VCFHeader, VcfFile and VCF to return all available vcf fields in CharacterList().
• Add support for single breakend notation (thanks d-cameron)

BUG FIXES

• .formatInfo() now return a column with all 'NA' for a missing value instead of dropping the column.

VariantAnnotation 1.26.0

MODIFICATIONS

• Clarify fixed fields must be
• Following renaming of RangesList class -> IntegerRangesList
• Updates to accommodate change to '[<-' method for SummarizedExperiment
• DP4 assumed to come from INFO field
• Extract altDepth and totalDepth from DP4 GENO field when present
• predictCoding() now respects 'alt_init_codons' at the start of CDS region only
• Remove error message in 'rowRanges<-' and 'mcol<-' methods that check for fixed column name.

VariantAnnotation 1.24.0

NEW FEATURES

• Add subset,VCF-method that knows about info()
• Add alt,ref accessors for VRangesList
• More efficient show,VCF-method
• 'rowRanges<-' and 'mcols<-' on VCF class behave as they do on RangedSummarizedExperiment
• info,VCFHeader() and geno,VCFHeader() return a DataFrame with the correct columns in the case of empty

BUG FIXES

• Fix "ref<-" recycling on VRanges
• Fix bug in locateVariants(); code to fetch IntronVariants() was incorrectly fetching IntergenicVariants()
• Fix bug in rbind,VCF,VCF-method

VariantAnnotation 1.22.0

NEW FEATURES

• add import() wrapper for VCF files
• add support for Number='R' in vcf parsing
• add indexVcf() and methods for character,VcfFile,VcfFileList

MODIFICATIONS

• throw message() instead of warning() when non-nucleotide variations are set to NA
• replace 'force=TRUE' with 'pruning.mode="coarse"' in seqlevels() setter
• add 'pruning.mode' argument to keepSeqlevels() in man page example
• idempotent VcfFile()
• add 'idType' arg to IntergenicVariants() constructor
• modify locateVariants man page example to work around issue that distance,GRanges,TxDb does not support gene ranges on multiple chromosomes
• modify VcfFile() constructor to detect index file if not specified
• order vignettes from intro to advanced; use BiocStyle::latex2()
• remove unused SNPlocs.Hsapiens.dbSNP.20110815 from the Suggests field
• follow rename change in S4Vectors from vector_OR_factor to vector_or_factor
• pass classDef to .RsamtoolsFileList; VariantAnnotation may not be on the search path

BUG FIXES

• fix expansion of 'A' fields when there are multiple columns

VariantAnnotation 1.20.0

NEW FEATURES

• add import() wrapper for VCF files

MODIFICATIONS

• use now-public R_GetConnection
• remove defunct readVcfLongForm() generic
• remove 'genome' argument from readVcf()
• improvements to VCF to VRanges coercion
• support Varscan2 AD/RD convention when coercing VCF to VRanges
• use [["FT"]] to avoid picking up FTZ field
• summarizeVariants() recognize '.' as missing GT field
• document scanVcfheader() behavior for duplicate row names

BUG FIXES

• ensure only 1 matching hub resource selected in filterVcf vignette
• fix check for FILT == "PASS"
• correct column alignment in makeVRangesFromGRanges()
• fix check for AD conformance

VariantAnnotation 1.19.0

NEW FEATURES

• add SnpMatrixToVCF()
• add patch from Stephanie Gogarten to support 'PL' in genotypeToSnpMatrix()

MODIFICATIONS

• move getSeq,XStringSet-method from VariantAnnotation to BSgenome
• update filterVcf vignette
• remove 'pivot' export
• work on readVcf(): - 5X speedup for readVcf (at least in one case) by not using "==" to compare a list to a character (the list gets coerced to character, which is expensive for huge VCFs) - avoiding relist.list()
• update summarizeVariants() to comply with new SummarizedExperiment rownames requirement
• defunct VRangesScanVcfParam() and restrictToSNV()
• use elementNROWS() instead of elementLengths()
• togroup(x) now only works on a ManyToOneGrouping object so replace togroup(x, ...) calls with togroup(PartitioningByWidth(x), ...) when 'x' is a list-like object that is not a ManyToOneGrouping object.
• drop validity assertion that altDepth must be NA when alt is NA there are VCFs in the wild that use e.g. "*" for alt, but include depth
• export PLtoGP()
• VariantAnnotation 100% RangedData-free

BUG FIXES

• use short path names in src/Makevars.win

VariantAnnotation 1.18.0

MODIFICATIONS

• defunct VRangesScanVcfParam()
• defunct restrictToSNV()

BUG FIXES

• scanVcf,character,missing-method ignores blank data lines.
• Build path for C code made robust on Windows.

VariantAnnotation 1.16.0

NEW FEATURES

• support REF and ALT values ".", "+" and "-" in predictCoding()
• return non-translated characters in VARCODON in predictCoding() output
• add 'verbose' option to readVcf() and friends
• writeVcf() writes 'fileformat' header line always
• readVcf() converts REF and ALT values "*" and "I" to ” and '.'

MODIFICATIONS

• VRanges uses '*' strand by default
• coerce 'alt' to DNStringSet for predictCoding,VRanges-method
• add detail to documentation for 'ignore.strand' in predictCoding()
• be robust to single requrested INFO column not present in vcf file
• replace old SummarizedExperiment class from GenomicRanges with the new new RangedSummarizedExperiment from SummarizedExperiment package
• return strand of 'subject' for intronic variants in locateVariants()

BUG FIXES

• writeVcf() does not duplicate header lines when chunking
• remove extra tab after INFO when no FORMAT data are present
• filteVcf() supports 'param' with ranges

VariantAnnotation 1.14.0

NEW FEATURES

• gVCF support: - missing END header written out with writeVcf() - expand() handles NON_REF 'REF' value
• support 'Type=Character' in INFO header fields
• add 'row.names' argument to expand()
• add 'Efficient Usage' section to readVcf() man page
• efficiency improvements to info(..., row.names=) - anyDuplicated() less expensive than any(duplicated()) - use row.names=FALSE when not needed, e.g., show()
• add genotypeCodesToNucleotides()
• add support for gvcf in isSNP family of functions
• add VcfFile and VcfFileList classes
• support 'Type=Character' of unspecified length (.)
• add isDelins() from Robert Castelo
• add makeVRangesFromGRanges() from Thomas Sandmann

MODIFICATIONS

• VCFHeader support: - SAMPLE and PEDIGREE header fields are now parsed - meta(VCFHeader) returns DataFrameList instead of DataFrame - show(VCFHeader) displays the outer list names in meta - fixed(VCFHeader) returns 'ALT' and 'REF' if present
• 'ALT' in expandedVCF output is DNAStringSet, not *List
• remove .listCumsum() and .listCumsumShifted() helpers
• add multiple INFO field unit test from Julian Gehring
• add additional expand() unit tests
• modify readVccfAsVRanges() to use ScanVcfParam() as the 'param'; deprecate VRangesScanVcfParam
• replace mapCoords() with mapToTranscripts()
• change 'CDSID' output from integer to IntegerList in locateVariants() and predictCoding()
• add readVcf,character,ANY,ANY; remove readVcf,character,ANY,ScanVcfParam
• replace rowData() accessor with rowRanges()
• replace 'rowData' argument with 'rowRanges' (construct SE, VCF classes)
• replace getTranscriptSeqs() with extractTranscripts()

BUG FIXES

• readVcf() properly handles Seqinfo class as 'genome'
• allow 'ignore.strand' to pass through mapCoords()
• writeVcf() no longer ignores rows with no genotype field
• expand() properly handles - less than all INFO fields are selected - VCF has only one row - only one INFO column
• don't call path() on non-*File objects
• split (relist) of VRanges now yields a CompressedVRangesList
• predictCoding() now ignores zero-width ranges

VariantAnnotation 1.12.0

NEW FEATURES

• allow GRanges in 'rowData' to hold user-defined metadata cols (i.e., cols other than paramRangeID, REF, ALT, etc.)
• add isSNV() family of functions
• add faster method for converting a list matrix to an array
• add 'c' method for typed Rle classes so class is preserved
• add CITATION file
• rework writeVCF(): - FORMAT and genotype fields are parsed in C - output file is written from C - chunking added for large VCFs

MODIFICATIONS

• add 'row.names' to readVcf()
• deprecate restrictToSNV(); replaced by isSNV() family
• remove use of seqapply()
• show info / geno headers without splitting across blocks
• use mapCoords() in predictCoding() and locateVariants()
• deprecate refLocsToLocalLocs()
• propagate strand in predictCoding()
• replace deprecated seqsplit() with splitAsList()
• ensure GT field, if present, comes first in VCF output
• modify DESCRIPTION Author and Maintainer fileds with @R
• add 'row.names' to info,VCF-method

BUG FIXES

• modify expand() to work with no 'info' fields are imported
• remove duplicate rows from .splicesites()
• fix handling of real-valued NAs in geno omatrix construction in writeVcf()

VariantAnnotation 1.10.0

NEW FEATURES

• add support for ##contig in VCF header
• add 'meta<-', 'info<-', 'geno<-' replacement methods for VCFHeader
• add 'header<-' replacement method for VCF
• add strand to output from locationVariants()
• add support for writeVcf() to process Rle data in geno matrix
• readVcf() now parses 'geno' fields with Number=G as ((#alleles + 1) * (#alleles + 2)) / 2
• writeVcf() now sorts the VCF when 'index=TRUE'
• add 'fixed<-,VCFHeader,DataFrameList' method
• add convenience functions for reading VCF into VRanges
• add Rplinkseq test script
• add 'isSNV', 'isInsertion', 'isDeletion', 'isIndel', 'isTransition', 'isPrecise', 'isSV' and 'isSubstitution' generics
• add 'isSNV', 'isInsertion', 'isDeletion', 'isIndel' methods for VRanges and VCF classes
• add match methods between ExpandedVCF and VRanges
• add support for VRanges %in% TabixFile

MODIFICATIONS

• expand,VCF-method ignores 'AD' header of 'AD' geno is NULL
• add support for SIFT.Hsapiens.dbSNP137
• remove locateVariants() dependence on chr7-sub.vcf.gz
• modify expand() to handle 'AD' field where 'Number' is integer
• rename readVRangesFromVCF() to readVcfAsVRanges()
• remove check for circular chromosomes in locateVariants() and predictCoding() and refLocsToLocalLocs()
• modify filterVcf() to handle ranges in ScanVcfParam
• pass 'genetic.code' through predictCoding()
• change default to 'row.names=TRUE' for readGT(), readGeno(), and readInfo()
• fixed() on empty VCF now returns DataFrame with column names and data types vs an empty DataFrame
• update biocViews
• modify 'show,VCF' to represent empty values in XStringSet with '.'
• replace rtracklayer:::pasteCollapse with unstrsplit()

DEPRECATED and DEFUNCT

• remove defunct dbSNPFilter(), regionfilter() and MatrixToSnpMatrix()
• defunct readVcfLongForm()

BUG FIXES

• modify expand.geno() to handle case where header and geno don't match
• modify writeVcf() to write out rownames with ":" character instead of treating as missing
• fix how sample names were passed from 'ScanVcfParam' to scanVcf()
• fix bug in 'show,VCF' method
• fix bugs in VRanges -> VCF coercion methods
• fix bug in lightweight read* functions that were ignoring samples in ScanVcfParam
• fix bug in writeVcf() when no 'ALT' is present

VariantAnnotation 1.8.0

NEW FEATURES

• Add 'upstream' and 'downstream' arguments to IntergenicVariants() constructor.
• Add 'samples' argument to ScanVcfParam().
• Add readGT(), readGeno() and readInfo().
• Add VRanges, VRangesList, SimpleVRangesList, and CompressedVRangesList classes.
• Add coercion VRanges -> VCF and VCF -> VRanges.
• Add methods for VRanges family: altDepth(), refDepth(), totalDepth(), altFraction() called(), hardFilters(), sampleNames(), softFilterMatrix() isIndel(), resetFilter().
• Add stackedSamples,VRangesList method.

MODIFICATIONS

• VCF validity method now requires the number of rows in info() to match the length of rowData().
• PRECEDEID and FOLLOWID from locateVariants() are now CharacterLists with all genes in 'upstream' and 'downstream' range.
• Modify rownames on rowData() GRanges to CHRAM:POS_REF/ALT for variants with no ID.
• readVcf() returns info() and geno() in the order specified in the ScanVcfParam.
• 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
• Add dimnames<-,VCF method to prevent 'fixed' fields from being copied into 'rowData' when new rownames or colnames were assigned.
• Support read/write for an emtpy VCF.
• readVcf(file=character, ...) method attempts coercion to TabixFile.
• Support for read/write an emtpy VCF.
• Add performance section to vignette; convert to BiocStyle.
• expand,CompressedVcf method expands geno() field 'AD' to length ALT + 1. The expanded field is a (n x y x 2) array.
• 'genome' argument to readVcf() can be a character(1) or Seqinfo object.

DEPRECATED and DEFUNCT

• Defunct dbSNPFilter(), regionFilter() and MatrixToSnpMatrix().
• Deprecate readVcfLongForm().

BUG FIXES

• Fix bug in compatibility of read/writeVcf() when no INFO are columns present.
• Fix bug in locateVariants() when 'features' has no txid and cdsid.
• Fix bug in asVCF() when writing header lines.
• Fix bug in "expand" methods for VCF to handle multiple 'A' columns in info().

VariantAnnotation 1.6.0

NEW FEATURES

• VCF is now VIRTUAL. Concrete subclasses are CollapsedVCF and ExpandedVCF.
• Add filterVcf() generic and methods for character and TabixFile. This method creates one VCF file from another, using FilterRules.
• Enhance show,VCF method with header information.
• Stephanie Gogarten added genotypeToSnpMatrix() generic and CollapsedVCF and matrix methods.
• Chris Wallace added snpSummary() generic and CollapsedVCF method.
• Add cbind and rbind for VCF objects.

MODIFICATIONS

• writeVcf,connection-method allows writing to console and appending.
• writeVcf,connection-method accepts connections with open="a", only adding a header if the file does not already exist.
• predictCoding and genotypeToSnpMatrix can now handle ALT as CharacterList. Structural variants are set to empty character ("").
• 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.
• Empty VCF class now has an empty VCFHeader
• expand,CollapsedVCF-method expands 'geno' data with Number=A.
• VCF class accessors "fixed", "info" now return DataFrame instead of GRanges. "rowData" returns fixed fileds as the mcols.
• Updates to the vignette.

DEPRECATED and DEFUNCT

• Deprecate dbSNPFilter() and regionFilter().
• Deprecate MatrixToSnpMatrix().

BUG FIXES

• Multiple bugs fixed in "locateVariants".
• Multiple bugs fixed in "writeVcf".
• Bug fixed in subsetting of VCF objects.
• Bug fixed in "predictCoding" related to QUERYID column not mapping back to original indices (rows).

VariantAnnotation 1.4.0

NEW FEATURES

• "summarizeVariants" for summarizing counts by sample
• new VariantType 'PromoterVariants()' added to "locateVariants"

MODIFICATIONS

• "ref", "alt", "filt" and "qual" accessors for VCF-class now return a single variable instead of GRanges with variable as metadata

VariantAnnotation 1.2.0

NEW FEATURES

• "readVcf" has genome argument, can be subset on ranges or VCF elements with "ScanVcfParam"
• "scanVcfHeader" returns VCFHeader class with accessors fixed, info, geno, etc.
• "writeVcf" writes out a VCF file from a VCF class
• "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
• "predictCoding" methods - returns GRanges instead of DataFrame - output includes txID, geneID, cdsID, cds-based and protein-based coordinates

VariantAnnotation 1.0.0

NEW FEATURES

• "readVcf" methods for reading and parsing VCF files into a SummarizedExperiment
• "locateVariants" and "predictCoding" for identifying amino acid coding changes in nonsynonymous variants
• "dbSNPFilter" and "regionFilter" for filtering variants on membership in dbSNP or on a particular location in the genome
• access to PolyPhen and SIFT predictions through "keys" , "cols" and "select" methods. See ?SIFT or ?PolyPhen.

BUG FIXES

• No changes classified as 'bug fixes' (package under active development)