object DuplexConsensusCaller
Container for constant values and types used by the DuplexConsensusCaller
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case class
DuplexConsensusRead(id: String, bases: Array[Byte], quals: Array[Byte], errors: Array[Short], abConsensus: VanillaConsensusRead, baConsensus: Option[VanillaConsensusRead]) extends SimpleRead with Product with Serializable
Stores information about a consensus read.
Stores information about a consensus read. Bases, arrays, and the two single strand consensus reads (when present) must all be the same length.
- bases
the base calls of the consensus read
- quals
the calculated phred-scaled quality scores of the bases
- errors
the total number of raw read errors vs. the final consensus sequence at each base
- abConsensus
the AB consensus read from which the duplex was constructed
- baConsensus
the BA consensus read from which the duplex was constructed, if present. It may not be present if created from the AB strand reads only.
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- val ErrorRatePostUmi: PhredScore
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val
ErrorRatePreUmi: PhredScore
Various default values for the consensus caller.
- val FilterCollision: String
- val FilterFragments: String
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val
FilterMinReads: String
Additional filter strings used when rejecting reads.
- val FilterSsConsensus: String
- val MinInputBaseQuality: PhredScore
- val NoCall: Byte
- val NoCallQual: PhredScore
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