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biopet.biopet
Commits
8ee74c1b
Commit
8ee74c1b
authored
Jul 10, 2017
by
Peter van 't Hof
Browse files
Fixing own comments
parent
b60bb0f4
Changes
3
Hide whitespace changes
Inline
Side-by-side
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/CommandLineGATK.scala
View file @
8ee74c1b
...
...
@@ -421,5 +421,8 @@ trait CommandLineGATK extends BiopetJavaCommandLineFunction with Reference with
object
CommandLineGATK
{
def
isFileWithTag
(
file
:
File
,
tag
:
String
)
:
Boolean
=
file
.
isInstanceOf
[
TaggedFile
]
&&
file
.
asInstanceOf
[
TaggedFile
].
tag
==
tag
def
isFileWithTag
(
file
:
File
,
tag
:
String
)
:
Boolean
=
file
match
{
case
f
:
TaggedFile
=>
f
.
tag
==
tag
case
_
=>
false
}
}
\ No newline at end of file
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/Logging.scala
View file @
8ee74c1b
...
...
@@ -38,10 +38,17 @@ object Logging {
private
[
biopet
]
val
errors
:
ListBuffer
[
Exception
]
=
ListBuffer
()
def
addError
(
error
:
String
,
debug
:
String
=
null
,
cause
:
Exception
=
null
)
:
Unit
=
{
val
msg
=
error
+
(
if
(
debug
!=
null
&&
logger
.
isDebugEnabled
)
"; "
+
debug
else
""
)
logger
.
error
(
msg
,
cause
)
errors
.
append
(
if
(
cause
!=
null
)
new
Exception
(
msg
,
cause
)
else
new
Exception
(
msg
))
def
addError
(
error
:
String
,
debug
:
Option
[
String
]
=
None
,
cause
:
Option
[
Exception
]
=
None
)
:
Unit
=
{
val
msg
=
error
+
debug
.
map
(
"; "
+
_
).
getOrElse
(
""
)
cause
match
{
case
Some
(
e
)
=>
logger
.
error
(
msg
,
e
)
errors
.
append
(
new
Exception
(
msg
,
e
))
case
_
=>
logger
.
error
(
msg
)
errors
.
append
(
new
Exception
(
msg
))
}
}
def
checkErrors
(
debug
:
Boolean
=
false
)
:
Unit
=
{
...
...
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaVariantcalling.scala
View file @
8ee74c1b
...
...
@@ -160,8 +160,10 @@ class ShivaVariantcalling(val parent: Configurable)
caller
.
namePrefix
=
namePrefix
caller
.
outputDir
=
new
File
(
outputDir
,
caller
.
name
)
caller
.
genders
=
genders
if
(
caller
.
isInstanceOf
[
SomaticVariantCaller
])
caller
.
asInstanceOf
[
SomaticVariantCaller
].
tnPairs
=
tumorSamples
caller
match
{
case
c
:
SomaticVariantCaller
=>
c
.
tnPairs
=
tumorSamples
case
_
=>
}
add
(
caller
)
addStats
(
caller
.
outputFile
,
caller
.
name
)
...
...
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