org
.
hammerlab
.
genomics
.
readsets
.
args
Base
trait
Base
extends
ReadFilterArgs
with
NoSequenceDictionaryArgs
Linear Supertypes
NoSequenceDictionaryArgs
,
ReadFilterArgs
,
LociArgs
,
AnyRef
,
Any
Known Subclasses
Arguments
,
SingleSampleArgs
,
TumorNormalReadsArgs
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Base
NoSequenceDictionaryArgs
ReadFilterArgs
LociArgs
AnyRef
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Abstract Value Members
abstract
def
paths
:
Array
[
String
]
abstract
def
sampleNames
:
Array
[
String
]
Concrete Value Members
final
def
!=
(
arg0:
AnyRef
)
:
Boolean
Definition Classes
AnyRef
final
def
!=
(
arg0:
Any
)
:
Boolean
Definition Classes
Any
final
def
##
()
:
Int
Definition Classes
AnyRef → Any
final
def
==
(
arg0:
AnyRef
)
:
Boolean
Definition Classes
AnyRef
final
def
==
(
arg0:
Any
)
:
Boolean
Definition Classes
Any
final
def
asInstanceOf
[
T0
]
:
T0
Definition Classes
Any
def
clone
()
:
AnyRef
Attributes
protected[
java.lang
]
Definition Classes
AnyRef
Annotations
@throws
(
...
)
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]
)
final
def
getClass
()
:
Class
[_]
Definition Classes
AnyRef → Any
def
hashCode
()
:
Int
Definition Classes
AnyRef → Any
var
includeDuplicates
:
Boolean
Definition Classes
ReadFilterArgs
var
includeFailedQualityChecks
:
Boolean
Definition Classes
ReadFilterArgs
var
includeSingleEnd
:
Boolean
Definition Classes
ReadFilterArgs
lazy val
inputs
:
PerSample
[
Input
]
final
def
isInstanceOf
[
T0
]
:
Boolean
Definition Classes
Any
var
lociFileOpt
:
Option
[
String
]
Definition Classes
LociArgs
var
lociStrOpt
:
Option
[
String
]
Definition Classes
LociArgs
var
minAlignmentQualityOpt
:
Option
[
Int
]
Definition Classes
ReadFilterArgs
final
def
ne
(
arg0:
AnyRef
)
:
Boolean
Definition Classes
AnyRef
var
noSequenceDictionary
:
Boolean
Definition Classes
NoSequenceDictionaryArgs
final
def
notify
()
:
Unit
Definition Classes
AnyRef
final
def
notifyAll
()
:
Unit
Definition Classes
AnyRef
var
onlyMappedReads
:
Boolean
Definition Classes
ReadFilterArgs
def
parseConfig
(
hadoopConfiguration:
Configuration
)
:
InputConfig
Definition Classes
ReadFilterArgs
var
splitSize
:
Option
[
String
]
Definition Classes
ReadFilterArgs
final
def
synchronized
[
T0
]
(
arg0: ⇒
T0
)
:
T0
Definition Classes
AnyRef
def
toString
()
:
String
Definition Classes
AnyRef → Any
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
(
...
)
Inherited from
NoSequenceDictionaryArgs
Inherited from
ReadFilterArgs
Inherited from
LociArgs
Inherited from
AnyRef
Inherited from
Any
Ungrouped