Rsamtools: seqnamesTabix – R documentation

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seqnamesTabix

Retrieve sequence names defined in a tabix file.

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

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

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

A character() vector of sequence names present in the file.

Martin Morgan <mtmorgan@fhcrc.org>.

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

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

v2.6.0

Artistic-2.0 | file LICENSE

Authors

Martin Morgan, Hervé Pagès, Valerie Obenchain, Nathaniel Hayden

Initial release