org
.
biodatageeks
.
sequila
.
pileup
Pileup
Related Doc:
package pileup
class
Pileup
[
T <:
BDGAlignInputFormat
]
extends
BDGAlignFileReaderWriter
[
T
]
Linear Supertypes
BDGAlignFileReaderWriter
[
T
],
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Inherited
Pileup
BDGAlignFileReaderWriter
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Instance Constructors
new
Pileup
(
spark:
SparkSession
)
(
implicit
c:
ClassTag
[
T
]
)
Value Members
final
def
!=
(
arg0:
Any
)
:
Boolean
Definition Classes
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final
def
##
()
:
Int
Definition Classes
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final
def
==
(
arg0:
Any
)
:
Boolean
Definition Classes
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final
def
asInstanceOf
[
T0
]
:
T0
Definition Classes
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def
clone
()
:
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Attributes
protected[
java.lang
]
Definition Classes
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Annotations
@throws
(
...
)
val
confMap
:
HashMap
[
String
,
String
]
Definition Classes
BDGAlignFileReaderWriter
final
def
eq
(
arg0:
AnyRef
)
:
Boolean
Definition Classes
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def
equals
(
arg0:
Any
)
:
Boolean
Definition Classes
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def
finalize
()
:
Unit
Attributes
protected[
java.lang
]
Definition Classes
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Annotations
@throws
(
classOf[java.lang.Throwable]
)
final
def
getClass
()
:
Class
[_]
Definition Classes
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def
handlePileup
(
tableName:
String
,
sampleId:
String
,
refPath:
String
,
output:
Seq
[
Attribute
]
,
conf:
Conf
)
:
RDD
[
InternalRow
]
def
hashCode
()
:
Int
Definition Classes
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final
def
isInstanceOf
[
T0
]
:
Boolean
Definition Classes
Any
val
logger
:
Logger
final
def
ne
(
arg0:
AnyRef
)
:
Boolean
Definition Classes
AnyRef
final
def
notify
()
:
Unit
Definition Classes
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final
def
notifyAll
()
:
Unit
Definition Classes
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def
readBAMFile
(
sqlContext:
SQLContext
,
path:
String
,
refPath:
Option
[
String
] =
None
)
(
implicit
c:
ClassTag
[
T
]
)
:
RDD
[
SAMRecord
]
Definition Classes
BDGAlignFileReaderWriter
def
readBAMFileToBAMBDGRecord
(
sqlContext:
SQLContext
,
path:
String
,
requiredColumns:
Array
[
String
]
)
(
implicit
c:
ClassTag
[
T
]
)
:
RDD
[
Row
]
Definition Classes
BDGAlignFileReaderWriter
def
setConf
(
key:
String
,
value:
String
)
:
HashMap
[
String
,
String
]
Definition Classes
BDGAlignFileReaderWriter
def
setLocalConf
(
sqlContext:
SQLContext
)
:
HashMap
[
String
,
String
]
Definition Classes
BDGAlignFileReaderWriter
final
def
synchronized
[
T0
]
(
arg0: ⇒
T0
)
:
T0
Definition Classes
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def
toString
()
:
String
Definition Classes
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final
def
wait
()
:
Unit
Definition Classes
AnyRef
Annotations
@throws
(
...
)
final
def
wait
(
arg0:
Long
,
arg1:
Int
)
:
Unit
Definition Classes
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Annotations
@throws
(
...
)
final
def
wait
(
arg0:
Long
)
:
Unit
Definition Classes
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Annotations
@throws
(
...
)
Inherited from
BDGAlignFileReaderWriter
[
T
]
Inherited from
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