| Type: | Package |
| Title: | Fast Genetic Variant Call Format File Header Intelligence and Audit |
| Version: | 0.1.0 |
| License: | GPL-3 |
| Language: | en-GB |
| Description: | Streams and parses variant call format file headers without reading full files. Provides structured metadata, validation, inference, and HTML reporting. For details on the specifications used see Danecek et al. (2021) <doi:10.1093/gigascience/giab008>. |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.3.3 |
| Suggests: | knitr, rmarkdown, testthat (≥ 3.0.0), xml2 |
| VignetteBuilder: | knitr |
| Config/testthat/edition: | 3 |
| NeedsCompilation: | no |
| Packaged: | 2026-03-02 10:45:05 UTC; akira |
| Author: | Dylan Lawless 
[aut, cre, cph] |
| Maintainer: | Dylan Lawless <admin@switzerlandomics.ch> |
| Depends: | R (≥ 3.5.0) |
| Repository: | CRAN |
| Date/Publication: | 2026-03-06 13:10:02 UTC |
Parse a VCF header into a structured object
Description
Reads only the header portion of a VCF or gzipped VCF file and returns
a structured vcf_hdr object containing parsed metadata, field
definitions, sample names, warnings, and errors.
Usage
parse_vcf_header(path)
Arguments
path |
Path to a VCF or |
Value
A vcf_hdr object.
Print a vcf_hdr object
Description
Print a vcf_hdr object
Usage
## S3 method for class 'vcf_hdr'
print(x, ...)
Arguments
x |
A |
... |
Unused. |
Value
Invisibly returns x.
Read the header lines from a VCF file
Description
Read the header lines from a VCF file
Usage
read_vcf_header(path)
Arguments
path |
Path to a VCF file. |
Value
A character vector of header lines.
Generate an HTML report from a parsed VCF header
Description
Writes an HTML summary report for a parsed vcf_hdr object.
Usage
vcfheader(
x,
file = NULL,
spec_index = NULL,
manual_defs = NULL,
spec_sections = NULL,
input_path = NULL,
brand_svg = NULL
)
Arguments
x |
A |
file |
Output HTML file path. If |
spec_index |
Optional specification index object or path to an |
manual_defs |
Optional manual definition list. |
spec_sections |
Optional specification section list. |
input_path |
Optional input file path used when deriving the output path. |
brand_svg |
Optional path to an SVG logo or inline SVG markup. |
Value
Invisibly returns the output file path.