org
.
bdgenomics
.
cannoli
.
cli
BwaArgs
Related Doc:
package cli
class
BwaArgs
extends
BwaFnArgs
with
ADAMSaveAnyArgs
with
ParquetArgs
Bwa command line arguments.
Linear Supertypes
ParquetArgs
,
ADAMSaveAnyArgs
,
SaveArgs
,
ParquetRDDArgs
,
BwaFnArgs
,
Args4jBase
,
AnyRef
,
Any
Ordering
Alphabetic
By Inheritance
Inherited
BwaArgs
ParquetArgs
ADAMSaveAnyArgs
SaveArgs
ParquetRDDArgs
BwaFnArgs
Args4jBase
AnyRef
Any
Hide All
Show All
Visibility
Public
All
Instance Constructors
new
BwaArgs
()
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
var
addFiles
:
Boolean
Definition Classes
BwaFnArgs
var
asFragments
:
Boolean
final
def
asInstanceOf
[
T0
]
:
T0
Definition Classes
Any
var
asSingleFile
:
Boolean
Definition Classes
BwaArgs
→ ADAMSaveAnyArgs
var
blockSize
:
Int
Definition Classes
ParquetArgs → ParquetRDDArgs
def
clone
()
:
AnyRef
Attributes
protected[
java.lang
]
Definition Classes
AnyRef
Annotations
@throws
(
...
)
var
compressionCodec
:
CompressionCodecName
Definition Classes
ParquetArgs → ParquetRDDArgs
var
deferMerging
:
Boolean
Definition Classes
BwaArgs
→ ADAMSaveAnyArgs
var
disableDictionaryEncoding
:
Boolean
Definition Classes
ParquetArgs → ParquetRDDArgs
var
disableFastConcat
:
Boolean
Definition Classes
BwaArgs
→ ADAMSaveAnyArgs
var
doPrintUsage
:
Boolean
Definition Classes
Args4jBase
final
def
eq
(
arg0:
AnyRef
)
:
Boolean
Definition Classes
AnyRef
def
equals
(
arg0:
Any
)
:
Boolean
Definition Classes
AnyRef → Any
var
executable
:
String
Definition Classes
BwaFnArgs
def
finalize
()
:
Unit
Attributes
protected[
java.lang
]
Definition Classes
AnyRef
Annotations
@throws
(
classOf[java.lang.Throwable]
)
var
forceLoadIfastq
:
Boolean
var
forceLoadParquet
:
Boolean
final
def
getClass
()
:
Class
[_]
Definition Classes
AnyRef → Any
def
hashCode
()
:
Int
Definition Classes
AnyRef → Any
var
image
:
String
Definition Classes
BwaFnArgs
var
indexPath
:
String
Definition Classes
BwaFnArgs
var
inputPath
:
String
final
def
isInstanceOf
[
T0
]
:
Boolean
Definition Classes
Any
var
logLevel
:
String
Definition Classes
ParquetArgs
final
def
ne
(
arg0:
AnyRef
)
:
Boolean
Definition Classes
AnyRef
final
def
notify
()
:
Unit
Definition Classes
AnyRef
final
def
notifyAll
()
:
Unit
Definition Classes
AnyRef
var
outputPath
:
String
Definition Classes
BwaArgs
→ SaveArgs
var
pageSize
:
Int
Definition Classes
ParquetArgs → ParquetRDDArgs
var
printMetrics
:
Boolean
Definition Classes
Args4jBase
var
sample
:
String
Definition Classes
BwaFnArgs
var
sequenceDictionary
:
String
var
sortFastqOutput
:
Boolean
Definition Classes
BwaArgs
→ ADAMSaveAnyArgs
var
stringency
:
String
var
sudo
:
Boolean
Definition Classes
BwaFnArgs
final
def
synchronized
[
T0
]
(
arg0: ⇒
T0
)
:
T0
Definition Classes
AnyRef
def
toString
()
:
String
Definition Classes
AnyRef → Any
var
useDocker
:
Boolean
Definition Classes
BwaFnArgs
var
useSingularity
:
Boolean
Definition Classes
BwaFnArgs
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
ParquetArgs
Inherited from
ADAMSaveAnyArgs
Inherited from
SaveArgs
Inherited from
ParquetRDDArgs
Inherited from
BwaFnArgs
Inherited from
Args4jBase
Inherited from
AnyRef
Inherited from
Any
Ungrouped
Bwa command line arguments.