case class RichAlignment(record: Alignment) extends Product with Serializable
An enriched version of an Avro Alignment.
- record
The underlying read.
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new
RichAlignment(record: Alignment)
- record
The underlying read.
Value Members
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final
def
!=(arg0: Any): Boolean
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final
def
##(): Int
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final
def
==(arg0: Any): Boolean
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final
def
asInstanceOf[T0]: T0
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def
clone(): AnyRef
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final
def
eq(arg0: AnyRef): Boolean
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def
fivePrimePosition: Long
- returns
The position of the five prime end of the read.
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def
fivePrimeReferencePosition: ReferencePosition
- returns
The position of the five prime end of the read, wrapped as a reference position.
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final
def
getClass(): Class[_]
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final
def
isInstanceOf[T0]: Boolean
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def
isMismatchAtReferencePosition(pos: ReferencePosition): Option[Boolean]
- pos
The reference position to check for a mismatch.
- returns
Returns true if this read overlaps the given reference position, and the base aligned at this position is a mismatch against the reference genome..
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lazy val
mdTag: Option[MdTag]
The MdTag if the read is mapped, None otherwise
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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
overlapsReferencePosition(pos: ReferencePosition): Boolean
- pos
The reference position to check for overlap.
- returns
Returns true if this read overlaps the given reference position.
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lazy val
qualityScoreValues: Array[Int]
The quality scores as a list of integers.
The quality scores as a list of integers. Assumes Illumina (33) encoding.
- val record: Alignment
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lazy val
samtoolsCigar: Cigar
Parses the text CIGAR representation of the alignment.
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final
def
synchronized[T0](arg0: ⇒ T0): T0
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lazy val
tags: Seq[Attribute]
On access, parses the attribute tags ("key:type:value" triples) into usable records.
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lazy val
unclippedEnd: Long
The position of the unclipped end if the read is mapped, None otherwise.
The position of the unclipped end if the read is mapped, None otherwise.
- Note
The unclipped position assumes that any clipped bases would've been aligned as an alignment match.
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lazy val
unclippedStart: Long
The position of the unclipped start if the read is mapped, None otherwise.
The position of the unclipped start if the read is mapped, None otherwise.
- Note
The unclipped position assumes that any clipped bases would've been aligned as an alignment match.
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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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def
wait(): Unit
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def
finalize(): Unit
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