getCoverageInRange: Get Coverage in Range
In PacificBiosciences/R-pbh5: Interface to Pacific Biosciences HDF5 Files

Description Usage Arguments Value Examples

Return a vector of length end - start + 1 of the number of reads overalapping that range.

1	getCoverageInRange(cmpH5, refSeq, refStart, refEnd, idx = NULL)

`cmpH5`	An object of class `PacBioCmpH5`
`refSeq`	Which reference sequence to use.
`refStart`	The start of the range (1-based inclusive).
`refEnd`	The end of the range (1-based inclusive).
`idx`	The indices alignments from the alignmentIndex to use. This argument can be used to filter certain alignments.

A vector of length end - start + 1

  require(pbh5)  
  cmpH5 <- PacBioCmpH5(system.file("h5_files",  "aligned_reads.cmp.h5",
  package = "pbh5"))
  coverage <- getCoverageInRange(cmpH5, 1, 1000, 2000)
  boxplot(coverage, ylab = "Pileup Coverage")