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biopet.biopet
Commits
d22fc2f7
Commit
d22fc2f7
authored
Jul 10, 2017
by
Peter van 't Hof
Browse files
Fixing unit tests
parent
5760560d
Changes
2
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Inline
Side-by-side
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/ConfigUtils.scala
View file @
d22fc2f7
...
...
@@ -416,7 +416,8 @@ object ConfigUtils extends Logging {
Logging
.
addError
(
"Value does not exist but is required, key: "
+
value
.
requestIndex
.
key
+
" namespace: "
+
value
.
requestIndex
.
module
,
if
(
value
.
requestIndex
.
path
!=
Nil
)
Some
(
" path: "
+
value
.
requestIndex
.
path
.
mkString
(
"->"
))
if
(
value
.
requestIndex
.
path
!=
Nil
)
Some
(
" path: "
+
value
.
requestIndex
.
path
.
mkString
(
"->"
))
else
None
)
exist
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
View file @
d22fc2f7
...
...
@@ -73,10 +73,11 @@ class ShivaVariantcalling(val parent: Configurable)
//TODO: this needs changed when the sample/library refactoring is beeing done
if
(
Option
(
genders
).
isEmpty
)
genders
=
{
inputBams
.
keys
.
map
{
sampleName
=>
val
gender
:
String
=
config
(
"gender"
,
path
=
"samples"
::
sampleName
::
"tags"
::
Nil
)
val
gender
:
Option
[
String
]
=
config
(
"gender"
,
path
=
"samples"
::
sampleName
::
"tags"
::
Nil
)
sampleName
->
(
gender
match
{
case
"male"
=>
Gender
.
Male
case
"female"
=>
Gender
.
Female
case
Some
(
"male"
)
=>
Gender
.
Male
case
Some
(
"female"
)
=>
Gender
.
Female
case
_
=>
Gender
.
Unknown
})
}.
toMap
...
...
@@ -86,7 +87,7 @@ class ShivaVariantcalling(val parent: Configurable)
if
(
Option
(
tumorSamples
).
isEmpty
)
tumorSamples
=
inputBams
.
keys
.
filter
(
name
=>
config
(
"type"
,
path
=
"samples"
::
name
::
"tags"
::
Nil
).
asString
.
toLowerCase
==
"tumor"
)
config
(
"type"
,
path
=
"samples"
::
name
::
"tags"
::
Nil
,
default
=
"normal"
).
asString
.
toLowerCase
==
"tumor"
)
.
map
{
tumorSample
=>
val
normal
:
String
=
config
(
"normal"
,
path
=
"samples"
::
tumorSample
::
"tags"
::
Nil
)
if
(!
inputBams
.
keySet
.
contains
(
normal
))
...
...
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