GenomicAlignments (version 1.2.2)

GappedReads-class: (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.

Arguments

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.

References

http://samtools.sourceforge.net/

See Also

Examples

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

Run the code above in your browser using DataCamp Workspace