Changes in version 1.3.2
------------------------

BUGFIXES

      o Circularity (from LOCUS header information) is now applied
      	to all sources in the file.

      o Improved assertion related to id ordering in makeTxDbFromGenBank
        which passed in previous R version but was failing in recent ones

Changes in version 1.1.5
------------------------

MINOR CHANGES

      o Change vignette to use system file to retrieve sample file
      	in response to ROpenSci reviewer comment.

      o Change vignette builder from knitr to rmarkdown in response
      	to ROpenSci reviewer comment.
	

Changes in version 1.1.4
------------------------

BUGFIXES

      o Fix bug when mRNA features are present and not annototated with gene.
      	Addresses half of https://github.com/gmbecker/genbankr/issues/1 Will be
	backported to 1.0.4

      o Fix bug when joins include incomplete range (< or >).
      	Addresses second half of https://github.com/gmbecker/genbankr/issues/1
	Will be backported to 1.0.4

Changes in version 1.1.3
------------------------

BUGFIXES

      o Fix bug in .seqTypeFromLOCUS when accession has non-alphanumeric characters (will
      	be backported to version 1.0.3.


Changes in version 0.99.9
-------------------------

USER FACING CHANGES

      o use of genbankr and genbankr version are now listed in TxDb objects 
        created via makeTxDbFromGenBank.

BUGFIXES

      o NEWS file entries are now in most-recent-first order.

Changes in version 0.99.7
-------------------------

MAJOR USER FACING CHANGES

      o gene_id is now taken from locus_tag when present (in any features of a 
        given type) and gene is now only used as a backup when locus_tag is 
	absent for all features of that type.

USER VISIBLE CHANGES

     o gene_synonym added to set of attribute that are assumed multi-valued and
       always returned as a CharacterList column (without a warning).

BUGFIXES

     o Added Michael Lawrence as second author.


Changes in version 0.99.6
-------------------------

USER VISIBLE CHANGES

     o Added support for creating of TxDb objects from GenBankRecord objects

     o Added support for genpept files to readGenBank and parseGenBank

BUGFIXES

     o Fix bug where partial was not being passed down correctly when specified
       in readGenBank call.




Changes in version 0.99.5
-------------------------

MAJOR USER VISIBLE CHANGES

     o Move to single-class model with nullable sequence slot, class name 
       changed to GenBankRecord. Removed methods, etc for old classes

     o parseGenBank now accepts ret.anno and ret.seq to control whether the 
       the sequence and annotations are parsed. 

     o Change how repeated annotation fields within a single feature entry is
       handled. Known multivalue fields (currently db_xref and EC_number) 
       *always* return CharacterList. Others return CharacterList in case of 
       duplicate entries only, with a warning.

BUGFIXES
	
     o correctly support cases where arbitrary annotations appear more than once
       within a single feature. 

     o fix regression problem with handling GenBank files with no sequence
       information when ret.seq is TRUE

     o fix problem where tests weren't being invoked properly during check

     o More informative error message when non-existent filename is passed to 
       readGenBank or parseGenBank.

     o Fix bug when *all* variation features in a file lack /replace (for
       VRanges alt is a mandatory field).


Changes in version 0.99.4
-------------------------

BUGFIXES

     o Fix small documentation bugs to squash check warnings


Changes in version 0.99.2
-------------------------

USER VISIBLE CHANGES

     o Version number jump as part of Bioconductor submission process

     o Added runnable examples to (most) help files

     o Hook existing unit tests into Bioconductor testing harness
     
     o Add fastpass to extract sequence, in the form of seq.only argument to 
       parseGenBank, and getSeq methods for GBAccession and GenBankFile classes

BUGFIXES

     o Fix some accessor methods for GenBankFull which didn't call annotations()
       to grab GenBankAnnot object before accessing slots.


Changes in version 0.1.0
------------------------

USER VISIBLE CHANGES

     o Text argument now supports character vector of length 1 with embedded 
       newlines in addition to character vectors of length N without.

     o Added GBAccession class and constructor

     o If a GBAccession is passed to readGenBank's first argument (file), the 
       GenBank formatted content will be retrieved from NCBI using rentrez (if 
       available)

     o rentrez added to Suggests

     o added seqinfo capture and support for GenBankAnnot, GenBankFull, and 
       underlying G/VRanges

     o Added support for parsing more than one GenBank file/content block at 
       once, e.g. when a GBAccession vector of length > 1 is passed to 
       readGenBank.

BUGFIXES 

     o Seqnames are no longer appended with ":1" when only one source
       (/chromosome/plasmid/etc) is present in the file.

     o Ensure correct (matching) transcript ids are manufactured when both mRNA
       and CDS features are annotated in the file. Ensure generated transcript 
       ids include gene identity when known.


Changes in version 0.0.8
------------------------

USER VISIBLE CHANGES

     o When gene label is NA in (any) CDS annotations, temporary grouping 
       variable is used to inferm "transcripts"

     o non-valued attributes (e.g. "/pseudo") are now imported as logical 
       columns, with presence corresponding to TRUE and absence corresponding to
       FALSE

BUGFIXES 

     o non-valued attributes are no longer appended to the value of the previous
       attribute.


Changes in version 0.0.7
------------------------

USER VISIBLE CHANGES

     o When "gene" label is missing in gene and CDS annotations (happens in 
       plasmid files), locus_tag is used as the gene identifier for both.

BUGFIXES

     o Fix error when a subset of CDS annotations do not have translation 
       information.


Changes in version 0.0.6
------------------------

USER VISIBLE CHANGES

     o Genbank files which do not contain origin sequence are now supported. 
       Variation features in such files are ignored with a warning
