                        Dear Emacs, please make this -*-Text-*- mode!
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        *              1.0 SERIES NEWS                   *
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	Changes in Genominator Version 1.0.3

BUG FIXES
o The newly released DBI version 0.2-5 fixed a name mangling bug
  whereby a column name  of "end" would be silently changed to
  "end__1".  This columnname was used internally in Genominator so a
  change was warranted.  Genominator now depends explicitely on
  DBI >= 0.2-5. 
o An oversight in the vignette build process left a big temporary
  database in the build directory which was getting packaged as a part
  of the final build.  This has been fixed, reducing the size of
  the source tarball from 34M to 2M and also reducing the size of the
  installation by a similar amount.


                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.

