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NEWS
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CHANGES IN VERSION 1.36.0
-------------------------
NEW FEATURES
o ref<-, alt<-, qual<- and filt<- allow replacement value length
recycling
CHANGES IN VERSION 1.28.0
------------------------
NEW FEATURES
o 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'
o Add vcfFields method for character, VCFHeader, VcfFile and VCF
to return all available vcf fields in CharacterList().
o Add support for single breakend notation (thanks d-cameron)
BUG FIXES
o .formatInfo() now return a column with all 'NA' for a missing value
instead of dropping the column.
CHANGES IN VERSION 1.26.0
------------------------
MODIFICATIONS
o Clarify fixed fields must be
o Following renaming of RangesList class -> IntegerRangesList
o Updates to accommodate change to '[<-' method for SummarizedExperiment
o DP4 assumed to come from INFO field
o Extract altDepth and totalDepth from DP4 GENO field when present
o predictCoding() now respects 'alt_init_codons' at the start of CDS
region only
o Remove error message in 'rowRanges<-' and 'mcol<-' methods that
check for fixed column name.
CHANGES IN VERSION 1.24.0
------------------------
NEW FEATURES
o Add subset,VCF-method that knows about info()
o Add alt,ref accessors for VRangesList
o More efficient show,VCF-method
o 'rowRanges<-' and 'mcols<-' on VCF class behave as they do
on RangedSummarizedExperiment
o info,VCFHeader() and geno,VCFHeader() return a DataFrame with
the correct columns in the case of empty
BUG FIXES
o Fix "ref<-" recycling on VRanges
o Fix bug in locateVariants(); code to fetch IntronVariants() was
incorrectly fetching IntergenicVariants()
o Fix bug in rbind,VCF,VCF-method
CHANGES IN VERSION 1.22.0
------------------------
NEW FEATURES
o add import() wrapper for VCF files
o add support for Number='R' in vcf parsing
o add indexVcf() and methods for character,VcfFile,VcfFileList
MODIFICATIONS
o throw message() instead of warning() when non-nucleotide
variations are set to NA
o replace 'force=TRUE' with 'pruning.mode="coarse"' in seqlevels() setter
o add 'pruning.mode' argument to keepSeqlevels() in man page example
o idempotent VcfFile()
o add 'idType' arg to IntergenicVariants() constructor
o modify locateVariants man page example to work around
issue that distance,GRanges,TxDb does not support gene ranges on
multiple chromosomes
o modify VcfFile() constructor to detect index file if not specified
o order vignettes from intro to advanced; use BiocStyle::latex2()
o remove unused SNPlocs.Hsapiens.dbSNP.20110815 from the Suggests field
o follow rename change in S4Vectors from vector_OR_factor to
vector_or_factor
o pass classDef to .RsamtoolsFileList; VariantAnnotation may not be
on the search path
BUG FIXES
o fix expansion of 'A' fields when there are multiple columns
CHANGES IN VERSION 1.20.0
------------------------
NEW FEATURES
o add import() wrapper for VCF files
MODIFICATIONS
o use now-public R_GetConnection
o remove defunct readVcfLongForm() generic
o remove 'genome' argument from readVcf()
o improvements to VCF to VRanges coercion
o support Varscan2 AD/RD convention when coercing VCF to VRanges
o use [["FT"]] to avoid picking up FTZ field
o summarizeVariants() recognize '.' as missing GT field
o document scanVcfheader() behavior for duplicate row names
BUG FIXES
o ensure only 1 matching hub resource selected in filterVcf vignette
o fix check for FILT == "PASS"
o correct column alignment in makeVRangesFromGRanges()
o fix check for AD conformance
CHANGES IN VERSION 1.19.0
------------------------
NEW FEATURES
o add SnpMatrixToVCF()
o add patch from Stephanie Gogarten to support 'PL' in genotypeToSnpMatrix()
MODIFICATIONS
o move getSeq,XStringSet-method from VariantAnnotation to BSgenome
o update filterVcf vignette
o remove 'pivot' export
o 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()
o update summarizeVariants() to comply with new SummarizedExperiment
rownames requirement
o defunct VRangesScanVcfParam() and restrictToSNV()
o use elementNROWS() instead of elementLengths()
o 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.
o 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
o export PLtoGP()
o VariantAnnotation 100% RangedData-free
BUG FIXES
o use short path names in src/Makevars.win
CHANGES IN VERSION 1.18.0
------------------------
MODIFICATIONS
o defunct VRangesScanVcfParam()
o defunct restrictToSNV()
BUG FIXES
o scanVcf,character,missing-method ignores blank data lines.
o Build path for C code made robust on Windows.
CHANGES IN VERSION 1.16.0
------------------------
NEW FEATURES
o support REF and ALT values ".", "+" and "-" in predictCoding()
o return non-translated characters in VARCODON in predictCoding() output
o add 'verbose' option to readVcf() and friends
o writeVcf() writes 'fileformat' header line always
o readVcf() converts REF and ALT values "*" and "I" to '' and '.'
MODIFICATIONS
o VRanges uses '*' strand by default
o coerce 'alt' to DNStringSet for predictCoding,VRanges-method
o add detail to documentation for 'ignore.strand' in predictCoding()
o be robust to single requrested INFO column not present in vcf file
o replace old SummarizedExperiment class from GenomicRanges with the
new new RangedSummarizedExperiment from SummarizedExperiment
package
o return strand of 'subject' for intronic variants in locateVariants()
BUG FIXES
o writeVcf() does not duplicate header lines when chunking
o remove extra tab after INFO when no FORMAT data are present
o filteVcf() supports 'param' with ranges
CHANGES IN VERSION 1.14.0
------------------------
NEW FEATURES
o gVCF support:
- missing END header written out with writeVcf()
- expand() handles <NON_REF> 'REF' value
o support 'Type=Character' in INFO header fields
o add 'row.names' argument to expand()
o add 'Efficient Usage' section to readVcf() man page
o efficiency improvements to info(..., row.names=)
- anyDuplicated() less expensive than any(duplicated())
- use row.names=FALSE when not needed, e.g., show()
o add genotypeCodesToNucleotides()
o add support for gvcf in isSNP family of functions
o add VcfFile and VcfFileList classes
o support 'Type=Character' of unspecified length (.)
o add isDelins() from Robert Castelo
o add makeVRangesFromGRanges() from Thomas Sandmann
MODIFICATIONS
o 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
o 'ALT' in expandedVCF output is DNAStringSet, not *List
o remove .listCumsum() and .listCumsumShifted() helpers
o add multiple INFO field unit test from Julian Gehring
o add additional expand() unit tests
o modify readVccfAsVRanges() to use ScanVcfParam() as the
'param'; deprecate VRangesScanVcfParam
o replace mapCoords() with mapToTranscripts()
o change 'CDSID' output from integer to IntegerList in
locateVariants() and predictCoding()
o add readVcf,character,ANY,ANY; remove readVcf,character,ANY,ScanVcfParam
o replace rowData() accessor with rowRanges()
o replace 'rowData' argument with 'rowRanges' (construct SE, VCF classes)
o replace getTranscriptSeqs() with extractTranscripts()
BUG FIXES
o readVcf() properly handles Seqinfo class as 'genome'
o allow 'ignore.strand' to pass through mapCoords()
o writeVcf() no longer ignores rows with no genotype field
o expand() properly handles
- less than all INFO fields are selected
- VCF has only one row
- only one INFO column
o don't call path() on non-*File objects
o split (relist) of VRanges now yields a CompressedVRangesList
o predictCoding() now ignores zero-width ranges
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 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)