nl
.
biopet
.
tools
.
tenxkit
VariantCall
Related Docs:
class VariantCall
|
package tenxkit
object
VariantCall
extends
Logging
with
Serializable
Linear Supertypes
Serializable
,
Serializable
,
Logging
,
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,
Any
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VariantCall
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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
(
...
)
def
createFromBases
(
contig:
Int
,
position:
Int
,
bases:
PositionBases
,
referenceRegion:
ReferenceRegion
,
minCellAlleleCoverage:
Int
)
:
Option
[
VariantCall
]
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]
)
def
fromPartitionedVcf
(
directory:
File
,
dict:
Broadcast
[
SAMSequenceDictionary
]
,
sampleMap:
Broadcast
[
Map
[
String
,
Int
]]
)
(
implicit
sc:
SparkContext
)
:
RDD
[
VariantCall
]
def
fromVariantContext
(
variant:
VariantContext
,
dict:
SAMSequenceDictionary
,
sampleMap:
Map
[
String
,
Int
]
)
:
VariantCall
def
fromVcfFile
(
inputFile:
File
,
dict:
Broadcast
[
SAMSequenceDictionary
]
,
sampleMap:
Broadcast
[
Map
[
String
,
Int
]]
,
binsize:
Int
)
(
implicit
sc:
SparkContext
)
:
RDD
[
VariantCall
]
final
def
getClass
()
:
Class
[_]
Definition Classes
AnyRef → Any
def
hashCode
()
:
Int
Definition Classes
AnyRef → Any
final
def
isInstanceOf
[
T0
]
:
Boolean
Definition Classes
Any
def
logger
:
Logger
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
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
(
...
)
def
writeToPartitionedVcf
(
rdd:
RDD
[
VariantCall
]
,
outputDir:
File
,
correctCells:
Broadcast
[
IndexedSeq
[
String
]]
,
dict:
Broadcast
[
SAMSequenceDictionary
]
,
vcfHeader:
Broadcast
[
VCFHeader
]
,
seqError:
Float
)
:
Unit
Writes variants to a partitioned vcf file
Inherited from
Serializable
Inherited from
Serializable
Inherited from
Logging
Inherited from
AnyRef
Inherited from
Any
Ungrouped