inst/unitTests/test_bam_tally.R

In gmapR: An R interface to the GMAP/GSNAP/GSTRUCT suite

test_bam_tally <- function() {
  param <- BamTallyParam(TP53Genome(), TP53Which(), indels = TRUE)
  bam <- system.file("extdata/H1993.analyzed.bam", 
                     package="LungCancerLines", mustWork=TRUE)
  tallies <- bam_tally(bam, param)
  variants <- variantSummary(tallies, NULL, 0L)
}

test_IITs_not_created <- function() {
  gmapGenome <- GmapGenome(genome="NoGenome", directory = getwd())
  checkException(BamTallyParam(genome=gmapGenome,
                               which = GRanges()), silent = TRUE)
}