case class Template(r1: Option[SamRecord], r2: Option[SamRecord], r1Supplementals: Seq[SamRecord] = Nil, r2Supplementals: Seq[SamRecord] = Nil, r1Secondaries: Seq[SamRecord] = Nil, r2Secondaries: Seq[SamRecord] = Nil) extends Product with Serializable
Class that represents all reads from a template within a BAM file.
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def
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- def ->[B](y: B): (Template, B)
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def
allReads: Iterator[SamRecord]
Returns an iterator of all reads for the template.
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def
allSupplementaryAndSecondary: Iterator[SamRecord]
Returns an iterator over all records that are not the primary r1 and r2.
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- def ensuring(cond: (Template) ⇒ Boolean, msg: ⇒ Any): Template
- def ensuring(cond: (Template) ⇒ Boolean): Template
- def ensuring(cond: Boolean, msg: ⇒ Any): Template
- def ensuring(cond: Boolean): Template
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def
isInstanceOf[T0]: Boolean
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val
name: String
Gets the query name of the template (assumes all records have the same read name).
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def
pairOrientation: Option[PairOrientation]
If both the R1 and R2 are present and mapped to the same chromosome returns the pair orientation, else None.
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def
primaryReads: Iterator[SamRecord]
Returns an iterator over all non-secondary non-supplementary reads.
- val r1: Option[SamRecord]
- val r1Secondaries: Seq[SamRecord]
- val r1Supplementals: Seq[SamRecord]
- val r2: Option[SamRecord]
- val r2Secondaries: Seq[SamRecord]
- val r2Supplementals: Seq[SamRecord]
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lazy val
readCount: Int
The total count of records for the template.
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final
def
synchronized[T0](arg0: ⇒ T0): T0
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def
unmapped: Template
Produces a copy of the template that has had mapping information removed.
Produces a copy of the template that has had mapping information removed. Discards secondary and supplementary records, and retains the primary records after un-mapping them. Auxillary tags listed in Bams.AlignmentTags are removed from all records. Lastly the
OAtag is added to reads to record the Original Alignment. -
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wait(arg0: Long): Unit
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- def →[B](y: B): (Template, B)