getAlignmentBlock: Returns a Specified Alignment Block

In PacificBiosciences/R-pbh5: Interface to Pacific Biosciences HDF5 Files

Description

Returns a view of the MSA for a group of reads.

Usage

  getAlignmentBlock(cmpH5, ref, refStart, refEnd, idx = 1:nrow(cmpH5))

Arguments

cmpH5	An object of class PacBioCmpH5.
ref	Reference sequence
refStart	Reference start point.
refEnd	Reference end point.
idx	Which alignments to return

Value

Returns a matrix of characters.

Examples

  require(pbh5)
   cmpH5 <- PacBioCmpH5(system.file("h5_files",  "aligned_reads.cmp.h5",
                        package = "pbh5"))
  getAlignmentBlock(cmpH5, 1, 20, 40)

PacificBiosciences/R-pbh5 documentation built on May 7, 2019, 11:54 p.m.