final case class SamMapping(record: SAMRecord, firstOfPairStrandOnTranscript: Orientation) extends GenericFeature with Product with Serializable
A Feature representing a mapped SAM record.
The Blocks of this SamMapping are the aligned blocks of the SAM record translated to zero-based half-open intervals.
If the sequencing library is strand specific, the Orientation of this Feature is the transcription strand of the entire fragment the record came from. For example, if the reads are unpaired and strand-specific, and always map to the transcription strand for this library, then this SamMapping will have Orientation Plus for a read mapped to the plus strand or Minus for a read mapped to the minus strand. If the reads are paired and read 1 always gives the transcription strand for this library, and we have a pair of records with read 1 mapped to the plus strand and read 2 mapped to the minus strand, then the entire fragment was transcribed from the plus strand, so the Orientation of both SamMappings is Plus.
If the library is not RNA-seq or is not strand specific, the Orientation is Unstranded.
- record
The SAM record
- firstOfPairStrandOnTranscript
Strand relative to transcription strand of read 1 (if reads are paired) or all reads (if unpaired). If read 1 maps to the transcription strand, this parameter should be Plus. If read 1 maps to the opposite of the transcription strand, this parameter should be Minus. If reads are not strand-specific, this parameter should be Unstranded.
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Instance Constructors
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new
SamMapping(record: SAMRecord, firstOfPairStrandOnTranscript: Orientation)
- record
The SAM record
- firstOfPairStrandOnTranscript
Strand relative to transcription strand of read 1 (if reads are paired) or all reads (if unpaired). If read 1 maps to the transcription strand, this parameter should be Plus. If read 1 maps to the opposite of the transcription strand, this parameter should be Minus. If reads are not strand-specific, this parameter should be Unstranded.
Value Members
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final
def
!=(arg0: Any): Boolean
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final
def
##(): Int
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def
<(that: Feature): Boolean
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def
<=(that: Feature): Boolean
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final
def
==(arg0: Any): Boolean
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def
>(that: Feature): Boolean
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def
>=(that: Feature): Boolean
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final
def
addBlock(block: Block): Feature
Returns a GenericFeature representing this with a new Block merged in.
Returns a GenericFeature representing this with a new Block merged in.
The underlying Region of the returned Feature is the result of calling Region.addBlock on the underlying Region of this Feature. The name of the returned Feature is None.
- block
Block to add
- returns
GenericFeature whose underlying Region has the new Block merged in, with name None
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final
def
asInstanceOf[T0]: T0
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val
blocks: Region
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def
canEqual(other: Any): Boolean
Returns true if other is an instance of GenericFeature, false otherwise.
Returns true if other is an instance of GenericFeature, false otherwise.
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def
clone(): AnyRef
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def
compare(that: Feature): Int
Returns the result of comparing this GenericFeature to another Feature.
Returns the result of comparing this GenericFeature to another Feature.
First compare the underlying Regions with Region.compare. If that result is non-zero, return it.
Next, compare the names. If both names are defined, use regular ordering on Strings. Otherwise, compare according to an ordering where name defined comes before name not defined. If the name comparison is non-zero, return it.
Next, compare the classes. The ordering used is GenericFeature < Transcript < MessengerRNA.
- that
Other Feature to compare
- returns
Negative integer if this is less than other, zero if neither is greater, positive integer if this is greater than other
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def
compareTo(that: Feature): Int
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def
contains(other: Feature): Boolean
Returns a boolean value representing whether this Feature contains another Feature.
-
def
containsCompatibleIntrons(other: Feature): Boolean
Returns a boolean value representing whether this Feature contains another Feature and their introns are compatible.
Returns a boolean value representing whether this Feature contains another Feature and their introns are compatible.
That is, no INTERNAL block boundary for one of the Features can fall strictly within a Block of the other Feature.
- other
Other Feature
- returns
True if this Feature contains the other and their introns are compatible, false otherwise
- Definition Classes
- Feature
-
def
distance(other: Feature): Int
Returns the distance between this Feature and another Feature.
Returns the distance between this Feature and another Feature.
Orientation is ignored.
If the spans of the Features (including introns) overlap, 0 is returned. Otherwise, if the other Feature lies to the right of this Feature, distance is defined as the first position of the other Feature minus the last position of this Feature. The definition is similar for the opposite direction. Therefore, the returned distance is a nonnegative number.
If the Features are on different chromosomes, an IllegalArgumentException is thrown.
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- Feature
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final
def
eq(arg0: AnyRef): Boolean
- Definition Classes
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def
equals(other: Any): Boolean
Returns an equality comparison of this with another object.
Returns an equality comparison of this with another object.
Returns true if other is a GenericFeature that can equal this according to GenericFeature.canEqual, the underlying Regions are equal, and the names are equal. Returns false otherwise.
- other
Other object
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True if this equals other, false otherwise
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def
finalize(): Unit
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- val firstOfPairStrandOnTranscript: Orientation
-
def
getBlocks: List[Block]
Returns the list of Blocks of the underlying Region as in Region.blocks.
Returns the list of Blocks of the underlying Region as in Region.blocks.
- Definition Classes
- Feature
-
def
getChr: String
Returns the chromosome name.
Returns the chromosome name.
- Definition Classes
- Feature
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final
def
getClass(): Class[_]
- Definition Classes
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def
getEnd: Int
Returns the end position of the underlying Region as in Region.end.
Returns the end position of the underlying Region as in Region.end.
- Definition Classes
- Feature
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def
getOrientation: Orientation
Returns the orientation of the underlying Region as in Region.orientation.
Returns the orientation of the underlying Region as in Region.orientation.
- Definition Classes
- Feature
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def
getStart: Int
Returns the start position of the underlying Region as in Region.start.
Returns the start position of the underlying Region as in Region.start.
- Definition Classes
- Feature
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lazy val
hashCode: Int
A hashCode based on the underlying Region and name.
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- GenericFeature → AnyRef → Any
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def
hc: Int
- Attributes
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- GenericFeature
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final
def
intersection(other: Feature): Option[Feature]
Returns a GenericFeature representing the intersection of this with another Feature.
Returns a GenericFeature representing the intersection of this with another Feature.
If the underlying Regions do not overlap according to Region.overlaps, returns None.
Otherwise, the returned feature has underlying Region equal to the intersection of the two underlying Regions as computed by Region.intersection. The returned feature has name None.
- other
Other Feature
- returns
GenericFeature calculated as the intersection of the underlying Regions with name None, or None if the underlying Regions do not overlap
- Definition Classes
- GenericFeature → Feature
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final
def
isInstanceOf[T0]: Boolean
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final
def
minus(other: Feature): Option[Feature]
Returns a GenericFeature representing this minus the overlap with another Feature.
Returns a GenericFeature representing this minus the overlap with another Feature.
If the underlying Region of this Feature is contained in the underlying Region of the other, returns None.
Otherwise, the returned Feature has underlying Region equal to the result of Region.minus on the two underlying Regions. The returned Feature has name None.
- other
Other Feature
- returns
GenericFeature calculated as the subtraction of the underlying Regions with name None, or None if that subtraction is empty
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val
name: Option[String]
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final
def
ne(arg0: AnyRef): Boolean
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final
def
notify(): Unit
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final
def
notifyAll(): Unit
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def
numBlocks: Int
Returns the number of Blocks in the underlying region.
-
def
overlaps(other: Feature): Boolean
Returns a boolean value representing whether this Feature overlaps another Feature.
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def
overlapsCompatibleIntrons(other: Feature): Boolean
Returns a boolean value representing whether this Feature overlaps another Feature and their introns are compatible.
Returns a boolean value representing whether this Feature overlaps another Feature and their introns are compatible.
That is, no INTERNAL block boundary for one of the Features can fall strictly within a Block of the other Feature.
- other
Other Feature
- returns
True if the Features overlap and their introns are compatible, false otherwise
- Definition Classes
- Feature
-
def
overlapsSpan(other: Feature): Boolean
Returns a boolean value representing whether the span of this Feature overlaps the span of another Feature.
- val record: SAMRecord
-
final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
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def
toString(): String
Returns a string representation of this GenericFeature.
Returns a string representation of this GenericFeature.
- Definition Classes
- GenericFeature → AnyRef → Any
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final
def
union(other: Feature): Feature
Returns a GenericFeature representing the union of this with another Feature.
Returns a GenericFeature representing the union of this with another Feature.
The returned feature has underlying Region equal to the union of the two underlying Regions as computed by Region.union. The returned feature has name None.
- other
Other Feature
- returns
GenericFeature calculated as the union of the underlying Regions, with name None
- Definition Classes
- GenericFeature → Feature
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final
def
wait(): Unit
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final
def
wait(arg0: Long, arg1: Int): Unit
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final
def
wait(arg0: Long): Unit
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