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NEWS
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NEWS
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CHANGES IN VERSION 1.24.0
------------------------
NEW FEATURES
o add support for Ensembl release 94 (this should also encompass 93)
CHANGES IN VERSION 1.22.0
------------------------
NEW FEATURES
o add support for Ensembl release 92
o add support for Ensembl release 91
MODIFICATIONS
o The default 'host' is not specified, defaulting to vep default of
'ensembldb.ensembl.org'. The default previously was 'useastdb.ensembl.org'
Users in the US may find connection and transfer speeds quicker using the
East coast mirror, 'useastdb.ensembl.org'. It was updated because the
mirror only supports current and current minus one vep version, and to
bring the default in line with the default of vep.
CHANGES IN VERSION 1.20.0
------------------------
NEW FEATURES
o add support for Ensembl release 90
MODIFICATIONS
o param object is now VEPFlags instead of VEPParam; a more generalized
object with a single flags=list() argument to control ensembl vep runtime
options
CHANGES IN VERSION 1.16.0
------------------------
NOTE: As of Ensembl release 88 the name of the script was changed
from variant_effect_predictor.pl to vep.
NEW FEATURES
o add support for Ensembl release 85-88
MODIFICATIONS
o document parseCSQToGRanges() behavior when no 'CSQ' data are found
o parseCSQToGRanges() returns mcols with names from CSQ field when
CSQ is present but empty
o add DBI perl module to SystemRequirements
CHANGES IN VERSION 1.14.0
------------------------
NEW FEATURES
o add support for Ensembl release 85 and 86
CHANGES IN VERSION 1.12.0
------------------------
NEW FEATURES
o add support for Ensembl release 82 and 84
MODIFICATIONS
o elementLengths was renamed -> elementNROWS in S4Vectors
o mark as unsupported on windows; Ensembl release 84 requires tabix
CHANGES IN VERSION 1.10.0
------------------------
NEW FEATURES
o VEPParam78 class supports Ensembl 80
CHANGES IN VERSION 1.8.0
------------------------
NEW FEATURES
o Add VEPParam78 class to support Ensembl 78
o Add 'flag_pick', 'flag_pick_allele', 'pick_order' and 'tsl' flags
MODIFICATIONS
o Add new biocViews terms
CHANGES IN VERSION 1.6.0
------------------------
NEW FEATURES
o Add VEPParam77 class to support Ensembl 77
CHANGES IN VERSION 1.4.0
------------------------
NEW FEATURES
o VEPParam is now VIRTUAL with subclasses VECParam67 and
VEPParam73
o Add helpers currentVEP() and supportedVEP()
o Add VEPParam75 class
MODIFICATIONS
o Modify VEPParam to support Ensembl versions 67 and 73
o Add slots 'scriptPath' and 'version' to VEPParam
o New man page for runtime options
o Update biocViews terms