indexTabix: Compress and index tabix-compatible files.

Description Usage Arguments Value Author(s) References Examples

Description

Index (with indexTabix) files that have been sorted into ascending sequence, start and end position ordering.

Usage

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indexTabix(file,
           format=c("gff", "bed", "sam", "vcf", "vcf4", "psltbl"),
           seq=integer(), start=integer(), end=integer(),
           skip=0L, comment="#", zeroBased=FALSE, ...)

Arguments

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 format is missing, then seq indicates the column in which the ‘sequence’ identifier (e.g., chrq) is to be found.

start

If format is missing, start indicates the column containing the start coordinate of the feature to be indexed.

end

If format is missing, end indicates the column containing the ending coordinate of the feature to be indexed.

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.

Value

The return value of indexTabix is an updated instance of file reflecting the newly-created index file.

Author(s)

Martin Morgan <mtmorgan@fhcrc.org>.

References

http://samtools.sourceforge.net/tabix.shtml

Examples

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from <- system.file("extdata", "ex1.sam", package="Rsamtools",
                    mustWork=TRUE)
to <- tempfile()
zipped <- bgzip(from, to)
idx <- indexTabix(zipped, "sam")

tab <- TabixFile(zipped, idx) 


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