tests/testthat/test_writeToFasta.R

In cancer-genomics/trellis: Somatic structural variant analysis

context("writeToFasta")

test_that("writeToFasta", {
  path <- system.file("extdata", package="svbams")
  tags <- readRDS(file.path(path, "tags.34bd277.rds"))
  fa.file <- tempfile()
  expect_true(writeToFasta(tags, fa.file))
  if(FALSE){
    writeToFasta(tags, file.path(path, "fasta_34bd277.txt"))
  }
  fa <- read.delim(fa.file)
  expected <- read.delim(file.path(path, "fasta_34bd277.txt"))
  expect_identical(fa, expected)
})

test_that("umapped_read", {
  path <- system.file("extdata", package="svbams")
  rlist <- readRDS(file.path(path, "filterRearrangementList.37be188.rds"))
  query <- uncouple(linkedBins(rlist))
  extdata <- system.file("extdata", package="svbams")
  bam.file <- file.path(extdata, "cgov44t_revised.bam")
  unmapped <- unmapped_read(bam.file, query, yield_size=200000, maxgap=200)
  if(FALSE){
    saveRDS(unmapped, file="unmapped.34bd277.rds")
  }
  expected <- readRDS(file.path(path, "unmapped.34bd277.rds"))
  expect_true(sum(unmapped$snms %in% expected$snms) == 86)
})