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heuermh
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commands
CountAlignmentsPerRead
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object CountAlignmentsPerRead
|
package commands
class
CountAlignmentsPerRead
extends
BDGSparkCommand
[
CountAlignmentsPerReadArgs
] with
Logging
Count alignments per read ADAM command.
Linear Supertypes
BDGSparkCommand
[
CountAlignmentsPerReadArgs
],
Logging
,
BDGCommand
,
Runnable
,
AnyRef
,
Any
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Inherited
CountAlignmentsPerRead
BDGSparkCommand
Logging
BDGCommand
Runnable
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Any
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Instance Constructors
new
CountAlignmentsPerRead
(
args:
CountAlignmentsPerReadArgs
)
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
val
args
:
CountAlignmentsPerReadArgs
Attributes
protected
Definition Classes
CountAlignmentsPerRead
→ BDGSparkCommand
final
def
asInstanceOf
[
T0
]
:
T0
Definition Classes
Any
def
clone
()
:
AnyRef
Attributes
protected[
java.lang
]
Definition Classes
AnyRef
Annotations
@throws
(
...
)
val
companion
:
CountAlignmentsPerRead
.type
Definition Classes
CountAlignmentsPerRead
→ BDGCommand
def
debug
(
mkr:
Marker
,
msg: ⇒
Any
,
t: ⇒
Throwable
)
:
Unit
Attributes
protected
Definition Classes
Logging
def
debug
(
msg: ⇒
Any
,
t: ⇒
Throwable
)
:
Unit
Attributes
protected
Definition Classes
Logging
def
debug
(
msg: ⇒
Any
)
:
Unit
Attributes
protected
Definition Classes
Logging
final
def
eq
(
arg0:
AnyRef
)
:
Boolean
Definition Classes
AnyRef
def
equals
(
arg0:
Any
)
:
Boolean
Definition Classes
AnyRef → Any
def
error
(
mkr:
Marker
,
msg: ⇒
Any
,
t: ⇒
Throwable
)
:
Unit
Attributes
protected
Definition Classes
Logging
def
error
(
msg: ⇒
Any
,
t: ⇒
Throwable
)
:
Unit
Attributes
protected
Definition Classes
Logging
def
error
(
msg: ⇒
Any
)
:
Unit
Attributes
protected
Definition Classes
Logging
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
def
info
(
mkr:
Marker
,
msg: ⇒
Any
,
t: ⇒
Throwable
)
:
Unit
Attributes
protected
Definition Classes
Logging
def
info
(
msg: ⇒
Any
,
t: ⇒
Throwable
)
:
Unit
Attributes
protected
Definition Classes
Logging
def
info
(
msg: ⇒
Any
)
:
Unit
Attributes
protected
Definition Classes
Logging
def
initializeMetrics
(
sc:
SparkContext
)
:
Option
[
MetricsListener
]
Definition Classes
BDGSparkCommand
def
isDebugEnabled
:
Boolean
Attributes
protected
Definition Classes
Logging
def
isErrorEnabled
:
Boolean
Attributes
protected
Definition Classes
Logging
def
isInfoEnabled
:
Boolean
Attributes
protected
Definition Classes
Logging
final
def
isInstanceOf
[
T0
]
:
Boolean
Definition Classes
Any
def
isTraceEnabled
:
Boolean
Attributes
protected
Definition Classes
Logging
def
isWarnEnabled
:
Boolean
Attributes
protected
Definition Classes
Logging
def
logger
:
Logger
Attributes
protected
Definition Classes
Logging
def
loggerName
:
String
Attributes
protected
Definition Classes
Logging
final
def
ne
(
arg0:
AnyRef
)
:
Boolean
Definition Classes
AnyRef
final
def
notify
()
:
Unit
Definition Classes
AnyRef
final
def
notifyAll
()
:
Unit
Definition Classes
AnyRef
def
printMetrics
(
totalTime:
Long
,
metricsListener:
Option
[
MetricsListener
]
)
:
Unit
Definition Classes
BDGSparkCommand
def
run
(
sc:
SparkContext
)
:
Unit
Definition Classes
CountAlignmentsPerRead
→ BDGSparkCommand
def
run
()
:
Unit
Definition Classes
BDGSparkCommand → Runnable
final
def
synchronized
[
T0
]
(
arg0: ⇒
T0
)
:
T0
Definition Classes
AnyRef
def
toString
()
:
String
Definition Classes
AnyRef → Any
def
trace
(
mkr:
Marker
,
msg: ⇒
Any
,
t: ⇒
Throwable
)
:
Unit
Attributes
protected
Definition Classes
Logging
def
trace
(
msg: ⇒
Any
,
t: ⇒
Throwable
)
:
Unit
Attributes
protected
Definition Classes
Logging
def
trace
(
msg: ⇒
Any
)
:
Unit
Attributes
protected
Definition Classes
Logging
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
warn
(
mkr:
Marker
,
msg: ⇒
Any
,
t: ⇒
Throwable
)
:
Unit
Attributes
protected
Definition Classes
Logging
def
warn
(
msg: ⇒
Any
,
t: ⇒
Throwable
)
:
Unit
Attributes
protected
Definition Classes
Logging
def
warn
(
msg: ⇒
Any
)
:
Unit
Attributes
protected
Definition Classes
Logging
Inherited from
BDGSparkCommand
[
CountAlignmentsPerReadArgs
]
Inherited from
Logging
Inherited from
BDGCommand
Inherited from
Runnable
Inherited from
AnyRef
Inherited from
Any
Ungrouped
Count alignments per read ADAM command.