Commit 51f89433 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added spec parsing unit test

parent 33b1aeb1
{
files = (
{
chromosome = "chrQ";
name = "imputation_06/test";
orig = "imputation_03/LLS_Offspring_Partners_Final_37_Overlap_chr1";
},
{
chromosome = "chrQ";
name = "imputation_06/test";
orig = "imputation_03/LLS_Offspring_Partners_Final_37_Overlap_chr1";
},
{
chromosome = "chrQ";
name = "imputation_06/test";
orig = "imputation_03/LLS_Offspring_Partners_Final_37_Overlap_chr22";
},
{
chromosome = "chrQ";
name = "imputation_06/test";
orig = "imputation_03/LLS_Offspring_Partners_Final_37_Overlap_chr22";
}
);
jids = ( "2102064" );
type = "tped3col";
}
\ No newline at end of file
......@@ -32,6 +32,35 @@ class GwasTestTest extends TestNGSuite with Matchers {
pipeline.script()
}
@Test
def testFromGens: Unit = {
val pipeline = initPipeline(GwasTestTest.config ++
Map("input_gens" -> List(Map("genotypes" -> GwasTestTest.vcfFile, "contig" -> "chrQ"))
)
)
pipeline.script()
}
@Test
def testWrongContig: Unit = {
val pipeline = initPipeline(GwasTestTest.config ++
Map("input_gens" -> List(Map("genotypes" -> GwasTestTest.vcfFile, "contig" -> "chrBla"))
)
)
intercept[IllegalStateException] {
pipeline.script()
}
}
@Test
def testFromSpecs: Unit = {
val pipeline = initPipeline(GwasTestTest.config ++
Map("imute_specs_file" -> GwasTestTest.resourcePath("/specs/files.specs"))
)
pipeline.script()
}
@Test
def testEmpty: Unit = {
val pipeline = initPipeline(GwasTestTest.config)
......
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