indexTabix {Rsamtools} | R Documentation

## Compress and index tabix-compatible files.

### Description

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

### Usage

    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

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

    tab <- TabixFile(zipped, idx)

[Package Rsamtools version 2.2.3 Index]