context("Testing the SamSource object functionality")
samFile <- file.path( "goodSamFiles", "pe.sam" )
describe( "SamSource() constructs create correct objects", {
samSourceData <- list(name="aSourceName", type="file", host="bioinfo.unc.edu")
it( "Works for list input", {
obj <- SamSource( samSourceData )
expect_equal(samSourceName(obj), samSourceData$name )
expect_equal(samSourceHost(obj), samSourceData$host )
expect_equal(samSourceType(obj), samSourceData$type )
})
it( "Works for character input", {
obj <- SamSource( samSourceData$name,
host= samSourceData$host, type= samSourceData$type )
expect_equal(samSourceName(obj), samSourceData$name )
expect_equal(samSourceHost(obj), samSourceData$host )
expect_equal(samSourceType(obj), samSourceData$type )
})
})
describe( "Test fixtures for use in the test_sam testthat file", {
it( "Provides 'samFile' as a generic input sam file.", {
expect_true( file.exists( samFile ))
})
})
describe( "Can construct a source object", {
expect_output( sam <- Sam(samFile) )
it( "Can consturct a source object from a Sam object", {
source <- SamSource(sam)
expect_s3_class(source, "SamSource")
expect_s3_class(source, "list")
})
it( "Can consturct a source object from a SamReads object", {
source <- SamSource(SamReads(sam))
expect_s3_class(source, "SamSource")
expect_equal(source, SamSource(sam))
})
it( "Can consturct a source object from a SamHeader object", {
source <- SamSource(SamHeader(sam))
expect_s3_class(source, "SamSource")
expect_equal(source, SamSource(sam))
})
})
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