dagr
.
pipelines
GermlineVariantCallingPipeline
Related Doc:
package pipelines
class
GermlineVariantCallingPipeline
extends
Pipeline
Pipeline to call germline variants in a set of regions
Annotations
@ClpAnnotation
()
Linear Supertypes
Pipeline
,
LazyLogging
,
Task
,
Dependable
,
AnyRef
,
Any
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By Inheritance
Inherited
GermlineVariantCallingPipeline
Pipeline
LazyLogging
Task
Dependable
AnyRef
Any
Implicitly
by any2stringadd
by StringFormat
by Ensuring
by ArrowAssoc
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Visibility
Public
All
Instance Constructors
new
GermlineVariantCallingPipeline
(
in:
PathToBam
,
out:
Path
,
intervals:
Option
[
PathToIntervals
] =
None
,
ref:
PathToFasta
,
dbsnp:
Option
[
PathToVcf
] =
None
,
keepIntermediates:
Boolean
=
false
,
useGatk:
Boolean
=
true
,
truthVcf:
Option
[
PathToVcf
] =
None
,
truthIntervals:
List
[
PathToIntervals
] =
Nil
)
Value Members
final
def
!=
(
arg0:
Any
)
:
Boolean
Definition Classes
AnyRef → Any
def
!=>
(
other:
Dependable
)
:
Unit
Definition Classes
Task → Dependable
final
def
##
()
:
Int
Definition Classes
AnyRef → Any
def
+
(
other:
String
)
:
String
Implicit information
This member is added by an implicit conversion from
GermlineVariantCallingPipeline
to
any2stringadd
[
GermlineVariantCallingPipeline
] performed by method any2stringadd in scala.Predef.
Definition Classes
any2stringadd
def
->
[
B
]
(
y:
B
)
: (
GermlineVariantCallingPipeline
,
B
)
Implicit information
This member is added by an implicit conversion from
GermlineVariantCallingPipeline
to
ArrowAssoc
[
GermlineVariantCallingPipeline
] performed by method ArrowAssoc in scala.Predef.
Definition Classes
ArrowAssoc
Annotations
@inline
()
def
::
(
other:
Option
[
Dependable
]
)
:
Dependable
Definition Classes
Dependable
def
::
(
other:
Dependable
)
:
Dependable
Definition Classes
Dependable
final
def
==
(
arg0:
Any
)
:
Boolean
Definition Classes
AnyRef → Any
final
def
==>
(
other:
Option
[
Dependable
]
)
:
Dependable
Definition Classes
Dependable
final
def
==>
(
other:
Dependable
)
:
Dependable
Definition Classes
Dependable
def
addDependent
(
dependent:
Dependable
)
:
Unit
Definition Classes
Task → Dependable
def
allTasks
:
Traversable
[
Task
]
Definition Classes
Task → Dependable
final
def
asInstanceOf
[
T0
]
:
T0
Definition Classes
Any
def
build
()
:
Unit
Definition Classes
GermlineVariantCallingPipeline
→ Pipeline
def
clone
()
:
AnyRef
Attributes
protected[
java.lang
]
Definition Classes
AnyRef
Annotations
@throws
(
...
)
def
contains
(
task:
Task
)
:
Boolean
Definition Classes
Pipeline
val
dbsnp
:
Option
[
PathToVcf
]
def
ensuring
(
cond: (
GermlineVariantCallingPipeline
) ⇒
Boolean
,
msg: ⇒
Any
)
:
GermlineVariantCallingPipeline
Implicit information
This member is added by an implicit conversion from
GermlineVariantCallingPipeline
to
Ensuring
[
GermlineVariantCallingPipeline
] performed by method Ensuring in scala.Predef.
Definition Classes
Ensuring
def
ensuring
(
cond: (
GermlineVariantCallingPipeline
) ⇒
Boolean
)
:
GermlineVariantCallingPipeline
Implicit information
This member is added by an implicit conversion from
GermlineVariantCallingPipeline
to
Ensuring
[
GermlineVariantCallingPipeline
] performed by method Ensuring in scala.Predef.
Definition Classes
Ensuring
def
ensuring
(
cond:
Boolean
,
msg: ⇒
Any
)
:
GermlineVariantCallingPipeline
Implicit information
This member is added by an implicit conversion from
GermlineVariantCallingPipeline
to
Ensuring
[
GermlineVariantCallingPipeline
] performed by method Ensuring in scala.Predef.
Definition Classes
Ensuring
def
ensuring
(
cond:
Boolean
)
:
GermlineVariantCallingPipeline
Implicit information
This member is added by an implicit conversion from
GermlineVariantCallingPipeline
to
Ensuring
[
GermlineVariantCallingPipeline
] performed by method Ensuring in scala.Predef.
Definition Classes
Ensuring
final
def
eq
(
arg0:
AnyRef
)
:
Boolean
Definition Classes
AnyRef
def
equals
(
arg0:
Any
)
:
Boolean
Definition Classes
AnyRef → Any
def
finalize
()
:
Unit
Attributes
protected[
java.lang
]
Definition Classes
AnyRef
Annotations
@throws
(
classOf[java.lang.Throwable]
)
def
formatted
(
fmtstr:
String
)
:
String
Implicit information
This member is added by an implicit conversion from
GermlineVariantCallingPipeline
to
StringFormat
[
GermlineVariantCallingPipeline
] performed by method StringFormat in scala.Predef.
Definition Classes
StringFormat
Annotations
@inline
()
final
def
getClass
()
:
Class
[_]
Definition Classes
AnyRef → Any
final
def
getTasks
:
Traversable
[_ <:
Task
]
Definition Classes
Pipeline → Task
def
hashCode
()
:
Int
Definition Classes
AnyRef → Any
def
headTasks
:
Traversable
[
Task
]
Definition Classes
Task → Dependable
val
in
:
PathToBam
val
intervals
:
Option
[
PathToIntervals
]
final
def
isInstanceOf
[
T0
]
:
Boolean
Definition Classes
Any
val
keepIntermediates
:
Boolean
lazy val
logger
:
Logger
Attributes
protected
Definition Classes
LazyLogging
var
name
:
String
Definition Classes
Task
final
def
ne
(
arg0:
AnyRef
)
:
Boolean
Definition Classes
AnyRef
final
def
notify
()
:
Unit
Definition Classes
AnyRef
final
def
notifyAll
()
:
Unit
Definition Classes
AnyRef
def
onComplete
(
exitCode:
Int
)
:
Boolean
Definition Classes
Task
val
out
:
Path
val
outputDirectory
:
Option
[
Path
]
Definition Classes
Pipeline
val
ref
:
PathToFasta
def
removeDependency
(
task:
Task
)
:
Boolean
Definition Classes
Task
val
root
:
Dependable
Definition Classes
Pipeline
final
def
synchronized
[
T0
]
(
arg0: ⇒
T0
)
:
T0
Definition Classes
AnyRef
def
tailTasks
:
Traversable
[
Task
]
Definition Classes
Task → Dependable
def
tasksDependedOn
:
Traversable
[
Task
]
Attributes
protected[
dagr.core
]
Definition Classes
Task
def
tasksDependingOnThisTask
:
Traversable
[
Task
]
Attributes
protected[
dagr.core
]
Definition Classes
Task
def
toString
()
:
String
Definition Classes
AnyRef → Any
val
truthIntervals
:
List
[
PathToIntervals
]
val
truthVcf
:
Option
[
PathToVcf
]
val
useGatk
:
Boolean
final
def
wait
()
:
Unit
Definition Classes
AnyRef
Annotations
@throws
(
...
)
final
def
wait
(
arg0:
Long
,
arg1:
Int
)
:
Unit
Definition Classes
AnyRef
Annotations
@throws
(
...
)
final
def
wait
(
arg0:
Long
)
:
Unit
Definition Classes
AnyRef
Annotations
@throws
(
...
)
def
withName
(
name:
String
)
:
GermlineVariantCallingPipeline
.this.type
Definition Classes
Task
def
→
[
B
]
(
y:
B
)
: (
GermlineVariantCallingPipeline
,
B
)
Implicit information
This member is added by an implicit conversion from
GermlineVariantCallingPipeline
to
ArrowAssoc
[
GermlineVariantCallingPipeline
] performed by method ArrowAssoc in scala.Predef.
Definition Classes
ArrowAssoc
Inherited from
Pipeline
Inherited from
LazyLogging
Inherited from
Task
Inherited from
Dependable
Inherited from
AnyRef
Inherited from
Any
Inherited by implicit conversion any2stringadd from
GermlineVariantCallingPipeline
to
any2stringadd
[
GermlineVariantCallingPipeline
]
Inherited by implicit conversion StringFormat from
GermlineVariantCallingPipeline
to
StringFormat
[
GermlineVariantCallingPipeline
]
Inherited by implicit conversion Ensuring from
GermlineVariantCallingPipeline
to
Ensuring
[
GermlineVariantCallingPipeline
]
Inherited by implicit conversion ArrowAssoc from
GermlineVariantCallingPipeline
to
ArrowAssoc
[
GermlineVariantCallingPipeline
]
Ungrouped
Pipeline to call germline variants in a set of regions