getTemplateSpan: Functions to get information about the alignments.
In PacificBiosciences/R-pbh5: Interface to Pacific Biosciences HDF5 Files

Description Usage Arguments Value Examples

These functions retrieve information about alignments. Namely, position, length, and accuracy.

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  getTemplateSpan(cmpH5, idx = seq.int(1, nrow(cmpH5)))
  getAccuracy(cmpH5, idx = seq.int(1, nrow(cmpH5)),
              denominator = getReadLength)

`cmpH5`	An object of class `PacBioCmpH5`.
`idx`	The indices of the alignments to retrieve.
`denominator`	What to divide the number of errors by.

Return numeric vectors of length: length(idx).

  require(pbh5)
  cmpH5 <- PacBioCmpH5(system.file("h5_files",  "aligned_reads.cmp.h5", package = "pbh5"))
  tStrand <- getTemplateStrand(cmpH5)
  tStart <- getTemplateStart(cmpH5)
  tEnd <- getTemplateEnd(cmpH5)
  tSpan <- getTemplateSpan(cmpH5)
  matrix <- cbind(tStart, tEnd, tSpan)
  head(matrix, 10)