CHANGES IN VERSION 1.30
-----------------------

NEW FEATURES

    o Add readGFF(), a fast and flexible GFF/GTF parser implemented in C. See
      ?readGFF for more information.

SIGNIFICANT USER-VISIBLE CHANGES

    o import.gff() now uses readGFF() internally which makes it at least 5x
      faster in most use cases and dramatically reduces its memory footprint.


CHANGES IN VERSION 1.26
-----------------------

NEW FEATURES

    o ucscGenomes() retrieves organism information

    o New function exportToTabix() exports a GRanges to a
      tabix-indexed tab separated file that contains all of the
      metadata columns. Use import,TabixFile to load specific ranges
      of data back into a GRanges.

    o BigWig import/export to/from Integer/Numeric/RleList is now much
      more efficient, and uses a more efficient storage format within
      the BigWig file, when possible.

SIGNIFICANT USER-VISIBLE CHANGES

    o BSgenome export methods are now in BSgenome.

BUG FIXES

    o Handling of quotes in GFF3 is now consistent with the spec.

CHANGES IN VERSION 1.22
-----------------------

NEW FEATURES

    o import,BigWigFile gains an asRle parameter that returns the data as an
      RleList (assuming it tiles the sequence); much faster than importing a
      GRanges and calling coverage() on it.

    o add export,RleList,BigWigFile method for direct (and much more
      efficient) output of RleLists (like coverage) to BigWig files.

SIGNIFICANT USER-VISIBLE CHANGES

    o UCSCData now extends GRanges instead of RangedData (thanks Herve)
    
BUG FIXES

    o handle different Set-Cookie header field casing; often due to proxies
      (thanks to Altuna Akalin)
    o attempt to more gracefully handle UCSC truncation of large data downloads
    o handle re-directs due to UCSC mirroring (thanks Martin Morgan)
    
CHANGES IN VERSION 1.20
-----------------------

NEW FEATURES

    o Table query interface supports multiple query ranges.

    o Files (RTLFile objects) can be directly uploaded to UCSC, via track<-.

SIGNIFICANT USER-VISIBLE CHANGES

    o All methods with asRangedData argument now have it default to
      FALSE, instead of TRUE. A warning is issued if the argument is
      missing. Eventually, we will drop all support for RangedData
      import (export will still work via automatic coercion to
      GRanges).
    
BUG FIXES

    o Chromosome list for a genome is now downloaded from the table
      browser, instead of the Genome Browser page. This supports
      genomes with more than 1000 contigs.

    o BEDX+Y formats now work when a track line is present, and the
      extraCols argument is used for the column names.

    o path.expand() is now called for paths passed off to the Kent library.

    o Order of metadata columns upon GFF import no longer depends on LC_COLLATE.
    
CHANGES IN VERSION 1.17
-----------------------

NEW FEATURES

    o Export of GappedAlignments objects as BAM files. There is also a
      corresponding import method.

    o Support for BEDX+Y import using the extraCols parameter to import.

    o Direct export of RleList objects to BigWig files.
    
CHANGES IN VERSION 1.15
-----------------------

NEW FEATURES

    o Integrated with tabix via Rsamtools. BED and GFF export methods
      now generate a tabix index, if index=TRUE. Most import() methods
      gain a 'which' argument that takes advantage of tabix, when
      available.
      
    o Added wigToBigWig() function for efficient conversion of WIG to BigWig.
    
    o Added SeqinfoForBSGenome() and SeqinfoForUCSCGenome() for
      conveniently retrieving Seqinfo objects for a given genome.
    
    o Added support for FASTA import/export via Biostrings.

    o GTF and GVF files are now parsed as GFF.

SIGNIFICANT USER-VISIBLE CHANGES

    o The import/export API is now based on RTLFile objects, which
      wrap a file path, URL or connection. There is an RTLFile
      subclass for every file format. This makes it easier to extend
      rtracklayer (export, import) with new file types. The existing
      API is still supported (and even encouraged for most uses).

    o Handle CSV attributes in GFF3 using CharacterList columns.

    o BED columns thickStart/thickEnd translate to an IRanges column
      named "thick". The blockStarts/Sizes/Count columns now map to a
      single RangesList "blocks" column.
    
BUG FIXES

    o Numerous fixes in the import/export methods, as a result of
      implementing a full unit test suite. If something was not
      working for you in the past, please try again.

    o Compression and connections should now work fairly uniformly
      across file types.

(start date: 29 March, 2012)
