TabixInput {Rsamtools} | R Documentation

## Operations on ‘tabix’ (indexed, tab-delimited) files.

### Description

Scan compressed, sorted, tabix-indexed, tab-delimited files.

### Usage

    scanTabix(file, ..., param)
    ## S4 method for signature 'character,IntegerRangesList'
    scanTabix(file, ..., param)
    ## S4 method for signature 'character,GRanges'
    scanTabix(file, ..., param)

### Arguments

`file` | The character() file name(s) of the tabix file be processed, or more flexibly an instance of class `TabixFile`.
`param` | A instance of `GRanges` or `IntegerRangesList` providing the sequence names and regions to be parsed.
`...` | Additional arguments, currently ignored.

### Value

`scanTabix` returns a list, with one element per region. Each element of the list is a character vector representing records in the region.

### Error

`scanTabix` signals errors using `signalCondition`. The following errors are signaled:

`scanTabix_param`

  `yieldSize(file)` must be NA when more than one range is specified.

`scanTabix_io`

  A read error occured while inputing the tabix file. This might be because the file is corrupt, or of incorrect format (e.g., when `path` points to a plain text file but `index` is present, implying that `path` should be a `bgzip`ed file. The error message may include an error code representing the logical OR of these cryptic signals: 1, BGZF_ERR_ZLIB; 2, BGZF_ERR_HEADER; 4, BGZF_ERR_IO; 8, BGZF_ERR_MISUSE.

### Author(s)

Martin Morgan <mtmorgan@fhcrc.org>.

### References

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

### Examples

    example(TabixFile)

[Package Rsamtools version 2.2.3 Index]