Check and ensure that a VCF is bgzipped and indexed — detect

Internal helpers used by read_vcf() to work with VCF files that are suitable for parallel reading with SeqArray, i.e. bgzip- compressed and Tabix-indexed.

detect_indexing() checks whether a VCF file:

is bgzip-compressed (.vcf.gz);
has an existing Tabix index (.tbi or .csi);
and that the index can be opened without error.

indexing_vcf() ensures that a VCF file is bgzip-compressed and indexed with Tabix. If the file is not .vcf.gz, it is compressed with Rsamtools::bgzip(); if no index is found, it is created via Rsamtools::indexTabix().

The typical workflow is to first call detect_indexing() and, if it returns TRUE, to run indexing_vcf() to make the VCF compatible with parallel chunked reading.

Usage

detect_indexing(vcf)

indexing_vcf(vcf, bcftools.path = "bcftools", verbose = TRUE)

Arguments

vcf: (character) Path to a VCF file. Can be plain text (.vcf) or bgzipped (.vcf.gz).
bcftools.path: Default: bcftools.path = "bcftools".
verbose: Default: verbose = TRUE.

Value

detect_indexing(): (logical) TRUE if the VCF needs compression and/or indexing (i.e. is not ready for parallel reading), FALSE if it is already bgzipped and indexed with a readable Tabix index.
indexing_vcf(): (character) The path to the bgzipped and Tabix-indexed VCF.

Details

These functions are designed for internal use and are not exported. indexing_vcf() emits user-friendly progress messages via cli when compression or indexing is required, but remains quiet when files are already compliant.

Examples

if (FALSE) { # \dontrun{
if (detect_indexing(vcf)) {
  vcf <- indexing_vcf(vcf)
}
} # }