 
## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
 Change Log for package rbamtools
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Project   :     refGenome
Created   :     19.03.2012
Author    :     W. Kaisers
Content   :     Funktionality for importing and managing genomic reference data
                (Ucsc, Ensembl, Genbank)
                for usage in R
Version   :     1.2.8

Changelog :
05.06.12  :     addIsoforms and addEnsemble delete qualifier rows before
                (re-) inserting
06.06.12  :     Added correction in get_ens_attribute_df which removed a
                memory leak
                (Also the token_list module is now valgrind tested)

08.06.12  :     Added class refdb         (encapsulates database access)
09.06.12  :     Added class refDataLocations
                (encapuslates directory and file management)

13.06.12  :     Implementation updates for refGenome,ensembl,ucsc and
                genbank finished

26.11.12  :     Added function 'extractSeqids' and 'tableSeqids'
08.05.13  :     refGenome_1.0.0 on CRAN
09.05.13  :     Added class and function ensemblExons
06.06.13  :     Added strand and frame in 'getGenePositions'
17.07.13  :     Changed signature for 'extractByGeneName' 1.0.4
                (so generic can be used in 'spliceSites')

01.08.13  :     C-routines valgrind tested
04.08.13  :     getGenePositions changed (doBy): >116 sec to 3.9 sec
                runtime (1.0.6)

04.08.13  :     Added getSpliceTable, unifyJuncs (1.0.7)
05.08.13  :     Added getUnifiedJuncs, updated vignette (1.0.8)
06.08.13  :     New getSplicSite and unifyJuncs in C (1.0.10),
                valgrind tested

07.08.13  :     refGenome_1.1.0 on CRAN
08.08.13  :     Corrected generic for extractByGeneName (refGenome_1.1.0)

07.07.14  :     Added R_init_refGenome
08.07.14  :     Added overlapJuncs function (1.2.5)
10.07.14  :     Added tests which are executed in R CMD check
07.08.14  :     Added support for 'gene' entry in gtf table
                (New feature type in Ensembl 76)

25.02.15  :     Changed compilation mode of source code to C++11 (from C)
25.02.15  :     Added unifiedExons class and unifyRanges function (1.4.0)

30.06.15  :     New C++ based import of GTF files due to import errors
                in Ensembl 76 (1.4.2). The attributes table and
                associated functions are removed.
                
10.09.15  :     Added global seqid checks in overlapJuncs
22.09.15  :     Added transcript_biotype information (for Ensembl genomes)
                Unified Juncs now contain the information how many
                transcripts are classified as nonsense mediated decay.
                unifyJuncs now returns refJunctions
                (i.e. same class as passed object).
24.02.16  :     Added extractByGeneId function.
13.05.16  :     Added new classes: geneModel and geneList

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## END OF FILE
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