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)
