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