case class BaseEntry(rec: SamRecord, offset: Int) extends PileupEntry with Product with Serializable
Pileup entry representing a match or mismatch.
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def
!=(arg0: Any): Boolean
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final
def
##(): Int
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def
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def
asInstanceOf[T0]: T0
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- val base: Byte
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def
baseInReadOrientation: Byte
Returns the base as it was read on the sequencer.
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clone(): AnyRef
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- def ensuring(cond: (BaseEntry) ⇒ Boolean, msg: ⇒ Any): BaseEntry
- def ensuring(cond: (BaseEntry) ⇒ Boolean): BaseEntry
- def ensuring(cond: Boolean, msg: ⇒ Any): BaseEntry
- def ensuring(cond: Boolean): BaseEntry
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def
eq(arg0: AnyRef): Boolean
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finalize(): Unit
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def
notifyAll(): Unit
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val
offset: Int
The zero-based offset within the com.fulcrumgenomics.bam.api.SamRecord that is represented.
The zero-based offset within the com.fulcrumgenomics.bam.api.SamRecord that is represented. For matches and mismatches this is the offset of the base in question. For deletions it is the base prior to the deleted sequence. For insertions it is the first inserted base in the read.
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- BaseEntry → PileupEntry
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def
positionInRead: Int
Returns the 1-based position within the read in the read's current orientation.
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def
positionInReadInReadOrder: Int
Returns the 1-based position within the read in the order the read was sequenced.
Returns the 1-based position within the read in the order the read was sequenced. This can be thought of as the offset from the 5' end plus one.
- val qual: Byte
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val
rec: SamRecord
The SamRecord that the pileup entry represents.
The SamRecord that the pileup entry represents.
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- BaseEntry → PileupEntry
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def
synchronized[T0](arg0: ⇒ T0): T0
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wait(arg0: Long, arg1: Int): Unit
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def
wait(arg0: Long): Unit
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