inst/unitTests/off_test_bam_tally.R

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

test_bam_tally <- function() {
  f <- system.file("extdata", "test_data_aln",
                   "test_data_aln.concordant_uniq.bam", package = "gmapR")
  bf <- BamFile(f)
  
  bam_tally(bf, BamTallyParam(genome))
}

test_bam_tally_C <- function() {
  library(BSgenome.Dmelanogaster.UCSC.dm3)

  genome <- GmapGenome(Dmelanogaster, create = TRUE)

  library(pasillaBamSubset)
  bam <- untreated3_chr4()
  
  bf <- Rsamtools::BamFile(bam)
  which <- GRanges("chr4", IRanges(1e6, 1.3e6))
  gr <- bam_tally(bf, BamTallyParam(genome, indels=TRUE, which = which))
  gr <- bam_tally(bf, BamTallyParam(genome, variant_strand = 1L))
  gr <- bam_tally(bf, BamTallyParam(genome, which = which, variant_strand = 1L))
  empty <- GRanges("chr2L", IRanges(1e6, 2e6))
  gr <- bam_tally(bf, BamTallyParam(genome, which = empty))
  
  gr <- bam_tally(bf, BamTallyParam(genome, read_pos_breaks = c(1, 15, 30, 40)))

  genome <- GmapGenome("hg19_IGIS21")
  which <- GRanges("1", IRanges(1e6, 2e6))
  bam <- "~/share/data/R1047_LIB6635_SAM636095_L1_NXG2449.analyzed.bam"
  bf <- Rsamtools::BamFile(bam)
  gr <- bam_tally(bf, BamTallyParam(genome, which = which, variant_strand = 1L,
                                    read_pos_breaks = c(0L, 10L, 75L),
                                    indels = TRUE))
  
}