nl
.
biopet
.
tools
.
vcfstats
Args
Related Doc:
package vcfstats
case class
Args
(
inputFile:
File
=
null
,
outputDir:
File
=
null
,
referenceFile:
File
=
null
,
intervals:
Option
[
File
] =
None
,
infoTags:
List
[
VcfField
] =
Nil
,
genotypeTags:
List
[
VcfField
] =
Nil
,
binSize:
Int
=
10000000
,
maxContigsInSingleJob:
Int
=
250
,
writeBinStats:
Boolean
=
false
,
localThreads:
Int
=
1
,
notWriteContigStats:
Boolean
=
false
,
sparkMaster:
Option
[
String
] =
None
,
sparkConfigValues:
Map
[
String
,
String
] =
...
,
contigSampleOverlapPlots:
Boolean
=
false
,
sampleToSampleMinDepth:
Option
[
Int
] =
None
,
skipGeneral:
Boolean
=
false
,
skipGenotype:
Boolean
=
false
,
skipSampleDistributions:
Boolean
=
false
,
skipSampleCompare:
Boolean
=
false
)
extends
Product
with
Serializable
Linear Supertypes
Serializable
,
Serializable
,
Product
,
Equals
,
AnyRef
,
Any
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Inherited
Args
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Serializable
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All
Instance Constructors
new
Args
(
inputFile:
File
=
null
,
outputDir:
File
=
null
,
referenceFile:
File
=
null
,
intervals:
Option
[
File
] =
None
,
infoTags:
List
[
VcfField
] =
Nil
,
genotypeTags:
List
[
VcfField
] =
Nil
,
binSize:
Int
=
10000000
,
maxContigsInSingleJob:
Int
=
250
,
writeBinStats:
Boolean
=
false
,
localThreads:
Int
=
1
,
notWriteContigStats:
Boolean
=
false
,
sparkMaster:
Option
[
String
] =
None
,
sparkConfigValues:
Map
[
String
,
String
] =
...
,
contigSampleOverlapPlots:
Boolean
=
false
,
sampleToSampleMinDepth:
Option
[
Int
] =
None
,
skipGeneral:
Boolean
=
false
,
skipGenotype:
Boolean
=
false
,
skipSampleDistributions:
Boolean
=
false
,
skipSampleCompare:
Boolean
=
false
)
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
val
binSize
:
Int
def
clone
()
:
AnyRef
Attributes
protected[
java.lang
]
Definition Classes
AnyRef
Annotations
@throws
(
...
)
val
contigSampleOverlapPlots
:
Boolean
final
def
eq
(
arg0:
AnyRef
)
:
Boolean
Definition Classes
AnyRef
def
finalize
()
:
Unit
Attributes
protected[
java.lang
]
Definition Classes
AnyRef
Annotations
@throws
(
classOf[java.lang.Throwable]
)
val
genotypeTags
:
List
[
VcfField
]
final
def
getClass
()
:
Class
[_]
Definition Classes
AnyRef → Any
val
infoTags
:
List
[
VcfField
]
val
inputFile
:
File
val
intervals
:
Option
[
File
]
final
def
isInstanceOf
[
T0
]
:
Boolean
Definition Classes
Any
val
localThreads
:
Int
val
maxContigsInSingleJob
:
Int
final
def
ne
(
arg0:
AnyRef
)
:
Boolean
Definition Classes
AnyRef
val
notWriteContigStats
:
Boolean
final
def
notify
()
:
Unit
Definition Classes
AnyRef
final
def
notifyAll
()
:
Unit
Definition Classes
AnyRef
val
outputDir
:
File
val
referenceFile
:
File
val
sampleToSampleMinDepth
:
Option
[
Int
]
val
skipGeneral
:
Boolean
val
skipGenotype
:
Boolean
val
skipSampleCompare
:
Boolean
val
skipSampleDistributions
:
Boolean
val
sparkConfigValues
:
Map
[
String
,
String
]
val
sparkMaster
:
Option
[
String
]
final
def
synchronized
[
T0
]
(
arg0: ⇒
T0
)
:
T0
Definition Classes
AnyRef
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
(
...
)
val
writeBinStats
:
Boolean
Inherited from
Serializable
Inherited from
Serializable
Inherited from
Product
Inherited from
Equals
Inherited from
AnyRef
Inherited from
Any
Ungrouped