org
.
biodatageeks
.
sequila
.
pileup
.
model
ContigAggregate
Related Doc:
package model
case class
ContigAggregate
(
contig:
String
=
""
,
contigLen:
Int
=
0
,
events:
Array
[
Short
]
,
alts:
MultiLociAlts
,
quals:
MultiLociQuals
,
startPosition:
Int
=
0
,
maxPosition:
Int
=
0
,
shrinkedEventsArraySize:
Int
=
0
,
maxSeqLen:
Int
=
0
,
qualityCache:
QualityCache
,
conf:
Broadcast
[
Conf
]
)
extends
Product
with
Serializable
Events aggregation on contig
Linear Supertypes
Serializable
,
Serializable
,
Product
,
Equals
,
AnyRef
,
Any
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Inherited
ContigAggregate
Serializable
Serializable
Product
Equals
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Any
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Public
All
Instance Constructors
new
ContigAggregate
(
contig:
String
=
""
,
contigLen:
Int
=
0
,
events:
Array
[
Short
]
,
alts:
MultiLociAlts
,
quals:
MultiLociQuals
,
startPosition:
Int
=
0
,
maxPosition:
Int
=
0
,
shrinkedEventsArraySize:
Int
=
0
,
maxSeqLen:
Int
=
0
,
qualityCache:
QualityCache
,
conf:
Broadcast
[
Conf
]
)
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
def
addToCache
(
readQualSummary:
ReadQualSummary
)
:
Unit
val
alts
:
MultiLociAlts
val
altsKeyCache
:
TreeSet
[
Int
]
final
def
asInstanceOf
[
T0
]
:
T0
Definition Classes
Any
def
calculateAdjustedQuals
(
upd:
PartitionCorrections
)
:
MultiLociQuals
def
calculateMaxLength
(
allPositions:
Boolean
)
:
Int
def
clone
()
:
AnyRef
Attributes
protected[
java.lang
]
Definition Classes
AnyRef
Annotations
@throws
(
...
)
val
conf
:
Broadcast
[
Conf
]
val
contig
:
String
val
contigLen
:
Int
final
def
eq
(
arg0:
AnyRef
)
:
Boolean
Definition Classes
AnyRef
val
events
:
Array
[
Short
]
def
fillQualityForHigherAlts
(
upd:
PartitionCorrections
,
adjustedQuals:
MultiLociQuals
,
blacklist:
Set
[
Int
]
)
:
MultiLociQuals
def
fillQualityForLowerAlts
(
upd:
PartitionCorrections
,
qualsInterim:
MultiLociQuals
,
blacklist:
Set
[
Int
]
,
conf:
Broadcast
[
Conf
]
)
:
MultiLociQuals
def
finalize
()
:
Unit
Attributes
protected[
java.lang
]
Definition Classes
AnyRef
Annotations
@throws
(
classOf[java.lang.Throwable]
)
def
getAdjustedAggregate
(
b:
Broadcast
[
FullCorrections
]
)
:
ContigAggregate
def
getAltPositionsForRange
(
start:
Int
,
end:
Int
)
:
SortedSet
[
Int
]
final
def
getClass
()
:
Class
[_]
Definition Classes
AnyRef → Any
def
getPileupUpdate
:
PileupUpdate
def
getRange
:
Range
def
getTail
:
Tail
def
hasAltOnPosition
(
pos:
Int
)
:
Boolean
final
def
isInstanceOf
[
T0
]
:
Boolean
Definition Classes
Any
val
maxPosition
:
Int
val
maxSeqLen
:
Int
final
def
ne
(
arg0:
AnyRef
)
:
Boolean
Definition Classes
AnyRef
final
def
notify
()
:
Unit
Definition Classes
AnyRef
final
def
notifyAll
()
:
Unit
Definition Classes
AnyRef
val
qualityCache
:
QualityCache
val
quals
:
MultiLociQuals
val
shrinkedEventsArraySize
:
Int
val
startPosition
:
Int
final
def
synchronized
[
T0
]
(
arg0: ⇒
T0
)
:
T0
Definition Classes
AnyRef
def
trimQuals
:
MultiLociQuals
def
updateAlts
(
pos:
Int
,
alt:
Char
)
:
Unit
def
updateEvents
(
pos:
Int
,
startPart:
Int
,
delta:
Short
)
:
Unit
def
updateQuals
(
pos:
Int
,
alt:
Char
,
quality:
Byte
,
firstUpdate:
Boolean
=
false
,
updateMax:
Boolean
=
true
)
:
Unit
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
Serializable
Inherited from
Serializable
Inherited from
Product
Inherited from
Equals
Inherited from
AnyRef
Inherited from
Any
Ungrouped
Events aggregation on contig