NEWS
GDSAnnotator 0.99.1
- 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
- New function 'seqToGDS_ANNOVAR()' for importing ANNOVAR-annotated VCF
files (from table_annovar.pl -vcfinput) into SeqArray GDS format
- 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)
- '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)
- 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
- Bug fix: ‘seqToGDS_FAVOR()' printed progress messages with
’verbose=FALSE'
- 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'
- 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'
GDSAnnotator 0.99.0