headerTabix: Retrieve sequence names defined in a tabix file.

In Bioconductor/Rsamtools: Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

Retrieve sequence names defined in a tabix file.

Description

This function queries a tabix file, returning the names of the ‘sequences’ used as a key when creating the file.

Usage

headerTabix(file, ...)
## S4 method for signature 'character'
headerTabix(file, ...)

Arguments

file	A character(1) file path or TabixFile instance pointing to a ‘tabix’ file.
...	Additional arguments, currently ignored.

Value

A list(4) of the sequence names, column indicies used to sort the file, the number of lines skipped while indexing, and the comment character used while indexing.

Author(s)

Martin Morgan <[e-mail]>.

Examples

fl <- system.file("extdata", "example.gtf.gz", package="Rsamtools",
                  mustWork=TRUE)
headerTabix(fl)

Bioconductor/Rsamtools documentation built on Nov. 30, 2024, 8:15 a.m.