
        **************************************************
        *                                                *
        *              1.0 SERIES NEWS                   *
        *                                                *
        **************************************************


		CHANGES IN GENOMINATOR VERSION 1.1

NEW FEATURES

    o	Included an example on working with priming weights to the
	vignette as well as a section on gene models.
    o	Added computePrimingWeights and addPrimingWeights; this is a
	method recentley developed by the authors to try to make RNA-Seq
	reads more uniformly distributed across expressed transcripts.
    o	makeGeneRepresentation has been added and made public.  This
	function computes Union, Union-intersetion, Background and Regions
	of constant expression (ROCEs) based on annotation.
    o	validAnnotation is now public.
    o	Initial rewrite of the "Working with the ShortRead package"
	vignette which will contain a fully workable analysis of data
	from the yeastRNASeq package.
    o	The NEWS files is now parsable by the R function call
	news(package = "Genominator").
    o	Changed importFromAlignedReads to have only one argument 'x'
	instead of 'alignedReads' and 'filenames'.
    o	Added functionality to importFromAlignedReads so that it is
	possible to immediately collapse several files together, at
	the cost of having them all in memory at the same time (this
	later point might be changed).
    o	Added groupBy to summarizeByAnnotation.
    o	Added to Bioconductor.
    o	Improved User Guide substantially
    o	Added CITATION file.

BUG FIXES

    o   Fixed a bug related to the deprecation of IRanges::matchMatrix.
    o   Fixed two bugs discovered by Elizabeth Purdom regarding wrong
	indexing in .writeRegionsTable and importToExpData. 
    o	Changed some internals of the plotting functionality to make
	it work with a GenomeGraphs update.
    o	The new version of DBI (0.2-5) fixes the name mangling of the
	SQL reserved keyword "end".  Workarounds for this mangling has
	been removed and Genominator now depends on DBI >= 0.2-5.
    o	Added a check to importToExpData so that only rows with
	non-missing values of (chr, location, strand) gets written to
	the database.
    o	Fixed the connection pool to be outside of individual ExpData
	objects. This elucidated a hitherto unknown bug where a user
	could inadvertently write to a read-only database. 
    o	(Internal) Changed a few tryCatch statements to use the SQL
	"... IF EXISTS ..." instead. 
    o	Changed the db and filename to be in sync: there is now only a
	dbFIlename slot in ExpData and all functions accept
	dbFilename.

		CHANGES IN GENOMINATOR VERSION 1.0

NEW FEATURES

    o	Changed underlying database model where now the database
	exists in two modes, either a read or write mode. This should
	be somewhat transparent to the end user.
    o	Added importFromAlignedRead which allows the importing of
	objects read using readAligned from ShortRead package.
    o	Added support for arbitrary index columns, this support allows
	for the inclusion of more complex types of reads, e.g. reads
	of different lengths or paired end reads. This support is
	preliminary, but should allow for a mix of representations.
    o	Added '$' and '[' methods to expData objects to directly query
	the database.
    o	Fixed vignette to more correctly describe splitByAnnotation.
    o	Added ability to filter the reads when importing an Eland export file.
    o	Added whereClause to summarizeExpData.
    o	Added sample = FALSE argument to plot function for goodness of
	fit plots. This allows one to plot fewer than all of the
	points for smaller pdfs.
    o	Added regionGoodnessOfFit.df to work with matrices or
	data.frames.
    o	Added in-memory ordering to importToExpData; this speeds things
	up considerably when indexing.

BUG FIXES

    o	Fixed bug where colnames are trashed when preserveColnames = T
	and bindAnno = T
    o	Modified fix below when we include "what" argument.
    o	Fixed bug in splitByAnnotation when expand = TRUE and
	addOverStrands = TRUE and only one strand was present in the
	sequencing reads.
    o	Fixed bug in splitByAnnotation when expand = TRUE where reads
	were lost.

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