(Legacy) GappedReads objects
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
GappedReads objects are typically created when reading a file
containing aligned reads with the
In the code snippets below,
x is a GappedReads object.
qseq(x): Extracts the sequences of the queries as a
greads_file <- system.file("extdata", "ex1.bam", package="Rsamtools") greads <- readGappedReads(greads_file) greads qseq(greads)