GappedReads-class {GenomicAlignments} | R Documentation

## (Legacy) GappedReads objects

### Description

The GappedReads class extends the GAlignments class.

A GappedReads object contains all the information contained in a GAlignments object plus the sequences of the queries. Those sequences can be accessed via the `qseq` accessor.

### Constructor

GappedReads objects are typically created when reading a file containing aligned reads with the `readGappedReads` function.

### Accessors

In the code snippets below, `x` is a GappedReads object.

  `qseq(x)`: Extracts the sequences of the queries as a `DNAStringSet` object.

### Author(s)

Hervé Pagès

### References

http://samtools.sourceforge.net/

### See Also

- GAlignments objects.

- `readGappedReads`.

### Examples

    greads_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
    greads <- readGappedReads(greads_file)
    greads
    qseq(greads)

[Package GenomicAlignments version 1.20.1 Index]