r-bioc-variantannotation 1.24.2-1 / usr / lib / R / site-library / VariantAnnotation / NEWS

CHANGES IN VERSION 1.24.0
------------------------

NEW FEATURES

    o Add subset,VCF-method that knows about info()

    o Add alt,ref accessors for VRangesList 

MODIFICATIONS

    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)