Changes in version 0.99.2 o The conversion functions are renamed in camelCase, following the naming of `SeqArray::seqVCF2GDS()`: `seqToGDS_FAVOR()` => `seqFAVOR2GDS()`, `seqToGDS_FAVOR_tar()` => `seqFAVORTar2GDS()`, `seqToGDS_gnomAD()` => `seqGnomAD2GDS()`, `seqToGDS_VEP()` => `seqVEP2GDS()`, `seqToGDS_SnpEff()` => `seqSnpEff2GDS()` and `seqToGDS_ANNOVAR()` => `seqANNOVAR2GDS()` o New help page `?GDSAnnotator-extdata` describing the example data; 'inst/script' is renamed to 'inst/scripts' o Internal code reorganized into smaller functions, without changing the outputs; the benchmark script is removed from 'inst' Changes in version 0.99.1 o New functions `seqAnnotStat()`, `seqAnnotReport()` and `seqAnnotGeneTable()` for generating a VEP/SnpEff-like summary report from GDS files: `seqAnnotStat()` collects all summary statistics in a single pass over the file (the counters are additive, so multiple GDS files, e.g., one per chromosome, can be summarized together), and `seqAnnotReport()` renders them as a report in HTML (plain HTML tables and inline SVG charts, no additional package is required), Markdown (pipe tables) or R Markdown (the charts are drawn at knit time) format; 'parallel' splits the variants between multiple processes, and the per-process counters are merged afterwards o New function `seqToGDS_ANNOVAR()` for importing ANNOVAR-annotated VCF files (from table_annovar.pl -vcfinput) into SeqArray GDS format o new 'bsize' in `seqAnnotate()` and `seqAnnotateGDS()` to split the variants into blocks when 'add_to_gds' is TRUE or a file name: the annotation data are loaded and written block by block, so the memory usage no longer depends on the total number of variants (requiring the block writing in `SeqArray::seqAddValue()`, SeqArray_v1.53.2) o `seqAnnotate()` accepts the `VCF` objects of the package VariantAnnotation (CollapsedVCF and ExpandedVCF), annotating one row per alternative allele; `seqAnnotateVCF()` does the same after reading the file (VariantAnnotation is a suggested package, loaded on demand) o Bug fix: `seqAnnotate()` failed when 'varnm' was missing for a data.frame, DataFrame or IRanges input, instead of using all the annotations of the first annotation file o Bug fix: `seqToGDS_FAVOR()` printed progress messages with 'verbose=FALSE' o The categories of each counter in `seqAnnotStat()` are stored as plain named numeric vectors in a fixed order, so that the output is identical regardless of 'parallel' and 'bsize' o Explicit exports in NAMESPACE; the examples write to `tempfile()`; the provenance of the example data in 'inst/extdata' is documented in 'inst/script'; new package help page `?GDSAnnotator` Changes in version 0.99.0 o Initial package