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biopet.biopet
Commits
e32832d3
Commit
e32832d3
authored
Jul 24, 2017
by
pjvan_thof
Browse files
Changing name blah ;)
parent
28db4a1e
Changes
1
Hide whitespace changes
Inline
Side-by-side
biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/VcfStatsTest.scala
View file @
e32832d3
...
...
@@ -246,24 +246,24 @@ class VcfStatsTest extends TestNGSuite with Matchers {
def
testCheckGeneral
()
:
Unit
=
{
val
record
=
new
VCFFileReader
(
new
File
(
resourcePath
(
"/chrQ.vcf.gz"
))).
iterator
().
next
()
val
blah
=
checkGeneral
(
record
,
List
())
blah
.
get
(
"SampleDistribution-NonInformative"
)
shouldEqual
Some
(
Map
(
0
->
1
))
blah
.
get
(
"SampleDistribution-Called"
)
shouldEqual
Some
(
Map
(
3
->
1
))
blah
.
get
(
"SampleDistribution-Mixed"
)
shouldEqual
Some
(
Map
(
0
->
1
))
blah
.
get
(
"SampleDistribution-Hom"
)
shouldEqual
Some
(
Map
(
1
->
1
))
blah
.
get
(
"SampleDistribution-HomRef"
)
shouldEqual
Some
(
Map
(
1
->
1
))
blah
.
get
(
"SampleDistribution-Available"
)
shouldEqual
Some
(
Map
(
3
->
1
))
blah
.
get
(
"QUAL"
)
shouldEqual
Some
(
Map
(
1541
->
1
))
blah
.
get
(
"SampleDistribution-HetNonRef"
)
shouldEqual
Some
(
Map
(
0
->
1
))
blah
.
get
(
"SampleDistribution-Het"
)
shouldEqual
Some
(
Map
(
2
->
1
))
blah
.
get
(
"SampleDistribution-NoCall"
)
shouldEqual
Some
(
Map
(
0
->
1
))
blah
.
get
(
"SampleDistribution-Filtered"
)
shouldEqual
Some
(
Map
(
0
->
1
))
blah
.
get
(
"SampleDistribution-HomVar"
)
shouldEqual
Some
(
Map
(
0
->
1
))
blah
.
get
(
"SampleDistribution-Variant"
)
shouldEqual
Some
(
Map
(
2
->
1
))
blah
.
get
(
"general"
)
should
not
be
empty
val
general
=
blah
(
"general"
)
val
generalStats
=
checkGeneral
(
record
,
List
())
generalStats
.
get
(
"SampleDistribution-NonInformative"
)
shouldEqual
Some
(
Map
(
0
->
1
))
generalStats
.
get
(
"SampleDistribution-Called"
)
shouldEqual
Some
(
Map
(
3
->
1
))
generalStats
.
get
(
"SampleDistribution-Mixed"
)
shouldEqual
Some
(
Map
(
0
->
1
))
generalStats
.
get
(
"SampleDistribution-Hom"
)
shouldEqual
Some
(
Map
(
1
->
1
))
generalStats
.
get
(
"SampleDistribution-HomRef"
)
shouldEqual
Some
(
Map
(
1
->
1
))
generalStats
.
get
(
"SampleDistribution-Available"
)
shouldEqual
Some
(
Map
(
3
->
1
))
generalStats
.
get
(
"QUAL"
)
shouldEqual
Some
(
Map
(
1541
->
1
))
generalStats
.
get
(
"SampleDistribution-HetNonRef"
)
shouldEqual
Some
(
Map
(
0
->
1
))
generalStats
.
get
(
"SampleDistribution-Het"
)
shouldEqual
Some
(
Map
(
2
->
1
))
generalStats
.
get
(
"SampleDistribution-NoCall"
)
shouldEqual
Some
(
Map
(
0
->
1
))
generalStats
.
get
(
"SampleDistribution-Filtered"
)
shouldEqual
Some
(
Map
(
0
->
1
))
generalStats
.
get
(
"SampleDistribution-HomVar"
)
shouldEqual
Some
(
Map
(
0
->
1
))
generalStats
.
get
(
"SampleDistribution-Variant"
)
shouldEqual
Some
(
Map
(
2
->
1
))
generalStats
.
get
(
"general"
)
should
not
be
empty
val
general
=
generalStats
(
"general"
)
general
.
get
(
"PolymorphicInSamples"
)
shouldEqual
Some
(
1
)
general
.
get
(
"ComplexIndel"
)
shouldEqual
Some
(
0
)
...
...
@@ -285,7 +285,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
general
.
get
(
"Symbolic"
)
shouldEqual
Some
(
0
)
general
.
get
(
"SimpleInsertion"
)
shouldEqual
Some
(
1
)
val
total
=
blah
val
total
=
generalStats
total
.
get
(
"SampleDistribution-NonInformative"
)
shouldEqual
Some
(
Map
(
0
->
1
))
total
.
get
(
"SampleDistribution-Called"
)
shouldEqual
Some
(
Map
(
3
->
1
))
total
.
get
(
"SampleDistribution-Mixed"
)
shouldEqual
Some
(
Map
(
0
->
1
))
...
...
@@ -300,8 +300,8 @@ class VcfStatsTest extends TestNGSuite with Matchers {
total
.
get
(
"SampleDistribution-HomVar"
)
shouldEqual
Some
(
Map
(
0
->
1
))
total
.
get
(
"SampleDistribution-Variant"
)
shouldEqual
Some
(
Map
(
2
->
1
))
blah
.
get
(
"general"
)
should
not
be
empty
val
totGeneral
=
blah
(
"general"
)
generalStats
.
get
(
"general"
)
should
not
be
empty
val
totGeneral
=
generalStats
(
"general"
)
totGeneral
.
get
(
"PolymorphicInSamples"
)
shouldEqual
Some
(
1
)
totGeneral
.
get
(
"ComplexIndel"
)
shouldEqual
Some
(
0
)
...
...
@@ -330,17 +330,17 @@ class VcfStatsTest extends TestNGSuite with Matchers {
val
genotype
=
record
.
getGenotype
(
0
)
val
blah
=
checkGenotype
(
record
,
genotype
,
List
())
val
genotypeStats
=
checkGenotype
(
record
,
genotype
,
List
())
blah
.
get
(
"GQ"
)
shouldEqual
Some
(
Map
(
99
->
1
))
blah
.
get
(
"AD"
)
shouldEqual
Some
(
Map
(
24
->
1
,
21
->
1
))
blah
.
get
(
"AD-used"
)
shouldEqual
Some
(
Map
(
24
->
1
,
21
->
1
))
blah
.
get
(
"DP"
)
shouldEqual
Some
(
Map
(
45
->
1
))
blah
.
get
(
"AD-alt"
)
shouldEqual
Some
(
Map
(
21
->
1
))
blah
.
get
(
"AD-ref"
)
shouldEqual
Some
(
Map
(
24
->
1
))
blah
.
get
(
"general"
)
should
not
be
empty
genotypeStats
.
get
(
"GQ"
)
shouldEqual
Some
(
Map
(
99
->
1
))
genotypeStats
.
get
(
"AD"
)
shouldEqual
Some
(
Map
(
24
->
1
,
21
->
1
))
genotypeStats
.
get
(
"AD-used"
)
shouldEqual
Some
(
Map
(
24
->
1
,
21
->
1
))
genotypeStats
.
get
(
"DP"
)
shouldEqual
Some
(
Map
(
45
->
1
))
genotypeStats
.
get
(
"AD-alt"
)
shouldEqual
Some
(
Map
(
21
->
1
))
genotypeStats
.
get
(
"AD-ref"
)
shouldEqual
Some
(
Map
(
24
->
1
))
genotypeStats
.
get
(
"general"
)
should
not
be
empty
val
general
=
blah
(
"general"
)
val
general
=
genotypeStats
(
"general"
)
general
.
get
(
"Hom"
)
shouldEqual
Some
(
0
)
general
.
get
(
"NoCall"
)
shouldEqual
Some
(
0
)
general
.
get
(
"Variant"
)
shouldEqual
Some
(
1
)
...
...
@@ -355,7 +355,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
general
.
get
(
"Het"
)
shouldEqual
Some
(
1
)
general
.
get
(
"HetNonRef"
)
shouldEqual
Some
(
0
)
val
total
=
blah
val
total
=
genotypeStats
total
.
get
(
"GQ"
)
shouldEqual
Some
(
Map
(
99
->
1
))
total
.
get
(
"AD"
)
shouldEqual
Some
(
Map
(
24
->
1
,
21
->
1
))
total
.
get
(
"AD-used"
)
shouldEqual
Some
(
Map
(
24
->
1
,
21
->
1
))
...
...
@@ -364,7 +364,7 @@ class VcfStatsTest extends TestNGSuite with Matchers {
total
.
get
(
"AD-ref"
)
shouldEqual
Some
(
Map
(
24
->
1
))
total
.
get
(
"general"
)
should
not
be
empty
val
totGeneral
=
blah
(
"general"
)
val
totGeneral
=
genotypeStats
(
"general"
)
totGeneral
.
get
(
"Hom"
)
shouldEqual
Some
(
0
)
totGeneral
.
get
(
"NoCall"
)
shouldEqual
Some
(
0
)
totGeneral
.
get
(
"Variant"
)
shouldEqual
Some
(
1
)
...
...
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