Compress and index tabix-compatible files.
Index (with indexTabix) files that have been sorted into
ascending sequence, start and end position ordering.
indexTabix(file,
format=c("gff", "bed", "sam", "vcf", "vcf4", "psltbl"),
seq=integer(), start=integer(), end=integer(),
skip=0L, comment="#", zeroBased=FALSE, ...)file |
A characater(1) path to a sorted, bgzip-compressed file. |
format |
The format of the data in the compressed file. A characater(1) matching one of the types named in the function signature. |
seq |
If |
start |
If |
end |
If |
skip |
The number of lines to be skipped at the beginning of the file. |
comment |
A single character which, when present as the first character in a line, indicates that the line is to be omitted. from indexing. |
zeroBased |
A logical(1) indicating whether coordinats in the file are zero-based. |
... |
Additional arguments. |
The return value of indexTabix is an updated instance of
file reflecting the newly-created index file.
Martin Morgan <mtmorgan@fhcrc.org>.
from <- system.file("extdata", "ex1.sam", package="Rsamtools",
mustWork=TRUE)
to <- tempfile()
zipped <- bgzip(from, to)
idx <- indexTabix(zipped, "sam")
tab <- TabixFile(zipped, idx)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.