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biopet.biopet
Commits
fb25247e
Commit
fb25247e
authored
Apr 05, 2017
by
Peter van 't Hof
Browse files
Fixing nullpointer
parent
a76b4665
Changes
2
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Side-by-side
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
View file @
fb25247e
...
@@ -97,6 +97,7 @@ class ShivaVariantcalling(val parent: Configurable) extends QScript
...
@@ -97,6 +97,7 @@ class ShivaVariantcalling(val parent: Configurable) extends QScript
cv
.
rod_priority_list
=
Some
(
callers
.
filter
(
_
.
mergeVcfResults
).
map
(
_
.
name
).
mkString
(
","
))
cv
.
rod_priority_list
=
Some
(
callers
.
filter
(
_
.
mergeVcfResults
).
map
(
_
.
name
).
mkString
(
","
))
for
(
caller
<-
callers
)
{
for
(
caller
<-
callers
)
{
caller
.
inputBams
=
inputBams
caller
.
inputBams
=
inputBams
caller
.
inputBqsrFiles
=
inputBqsrFiles
caller
.
namePrefix
=
namePrefix
caller
.
namePrefix
=
namePrefix
caller
.
outputDir
=
new
File
(
outputDir
,
caller
.
name
)
caller
.
outputDir
=
new
File
(
outputDir
,
caller
.
name
)
add
(
caller
)
add
(
caller
)
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/variantcallers/Variantcaller.scala
View file @
fb25247e
...
@@ -33,7 +33,7 @@ trait Variantcaller extends QScript with BiopetQScript with Reference {
...
@@ -33,7 +33,7 @@ trait Variantcaller extends QScript with BiopetQScript with Reference {
* Map of samplename -> (preprocessed) bam file
* Map of samplename -> (preprocessed) bam file
*/
*/
var
inputBams
:
Map
[
String
,
File
]
=
_
var
inputBams
:
Map
[
String
,
File
]
=
_
var
inputBqsrFiles
:
Map
[
String
,
File
]
=
_
var
inputBqsrFiles
:
Map
[
String
,
File
]
=
Map
()
def
init
()
=
{}
def
init
()
=
{}
...
...
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