org
.
hammerlab
.
genomics
.
readsets
.
args
.
base
Base
Related Doc:
package base
trait
Base
extends
ReadFilters
with
InputArgs
Linear Supertypes
InputArgs
,
ReadFilters
,
LociInput
,
AnyRef
,
Any
Known Subclasses
Arguments
,
PathPrefixArg
,
PathsArgs
,
PrefixedPathsBase
,
PrefixedSingleSampleArgs
,
SingleSampleArgs
,
SingleSampleArgsI
Ordering
Alphabetic
By Inheritance
Inherited
Base
InputArgs
ReadFilters
LociInput
AnyRef
Any
Hide All
Show All
Visibility
Public
All
Abstract Value Members
abstract
def
includeDuplicates
:
Boolean
Definition Classes
ReadFilters
abstract
def
includeFailedQualityChecks
:
Boolean
Definition Classes
ReadFilters
abstract
def
includeSingleEnd
:
Boolean
Definition Classes
ReadFilters
abstract
def
lociFileOpt
:
Option
[
Path
]
Definition Classes
LociInput
abstract
def
lociStrOpt
:
Option
[
String
]
Definition Classes
LociInput
abstract
def
minAlignmentQualityOpt
:
Option
[
Int
]
Definition Classes
ReadFilters
abstract
def
noSequenceDictionary
:
Boolean
abstract
def
onlyMappedReads
:
Boolean
Definition Classes
ReadFilters
abstract
def
paths
:
Array
[
Path
]
Definition Classes
InputArgs
abstract
def
sampleNames
:
Array
[
Name
]
Definition Classes
InputArgs
abstract
def
splitSizeOpt
:
Option
[
Bytes
]
Definition Classes
ReadFilters
Concrete Value Members
final
def
!=
(
arg0:
Any
)
:
Boolean
Definition Classes
AnyRef → Any
final
def
##
()
:
Int
Definition Classes
AnyRef → Any
final
def
==
(
arg0:
Any
)
:
Boolean
Definition Classes
AnyRef → 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
lazy val
inputs
:
Inputs
Definition Classes
InputArgs
final
def
isInstanceOf
[
T0
]
:
Boolean
Definition Classes
Any
final
def
ne
(
arg0:
AnyRef
)
:
Boolean
Definition Classes
AnyRef
final
def
notify
()
:
Unit
Definition Classes
AnyRef
final
def
notifyAll
()
:
Unit
Definition Classes
AnyRef
def
parseConfig
(
implicit
conf:
Configuration
)
:
Config
Definition Classes
ReadFilters
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
InputArgs
Inherited from
ReadFilters
Inherited from
LociInput
Inherited from
AnyRef
Inherited from
Any
Ungrouped