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 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.
                


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