CHANGES IN VERSION 1.30.0 ------------------------ o add support for Ensembl release 99 CHANGES IN VERSION 1.28.0 ------------------------ o add support for Ensembl release 97/98 CHANGES IN VERSION 1.26.0 ------------------------ o add support for Ensembl release 95/96 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