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biopet.biopet
Commits
51f89433
Commit
51f89433
authored
Apr 11, 2016
by
Peter van 't Hof
Browse files
Added spec parsing unit test
parent
33b1aeb1
Changes
7
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public/gwas-test/src/test/resources/specs/files.specs
0 → 100644
View file @
51f89433
{
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
public/gwas-test/src/test/resources/specs/test.gens
0 → 100644
View file @
51f89433
public/gwas-test/src/test/resources/specs/test.gens_info
0 → 100644
View file @
51f89433
public/gwas-test/src/test/resources/specs/test.gens_info_by_sample
0 → 100644
View file @
51f89433
public/gwas-test/src/test/resources/specs/test.gens_summary
0 → 100644
View file @
51f89433
public/gwas-test/src/test/resources/specs/test.gens_warnings
0 → 100644
View file @
51f89433
public/gwas-test/src/test/scala/nl/lumc/sasc/biopet/pipelines/gwastest/GwasTestTest.scala
View file @
51f89433
...
...
@@ -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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