object GroupReadsByUmi

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  1. type MoleculeId = String

    A type to represent a unique ID assigned to a molecule.

  2. class PairedUmiAssigner extends AdjacencyUmiAssigner

    Version of the adjacency assigner that works for paired UMIs stored as a single tag of the form A-B where reads with A-B and B-A are related but not identical.

  3. case class ReadInfo (refIndex: Int, start1: Int, start2: Int, strand1: Boolean, strand2: Boolean, library: String) extends Product with Serializable

    A case class to represent all the information we need to order reads for duplicate marking / grouping.

  4. type Umi = String

    A type representing an actual UMI that is a string of DNA sequence.

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  4. val BottomStrandDuplex: String

    The suffix appended to molecular identifier reads from the "bottom strand" of the duplex molecule.

    The suffix appended to molecular identifier reads from the "bottom strand" of the duplex molecule. These reads have 5' coordinate for read 1 greater than the 5' coordinate for read 2.

  5. val TopStrandDuplex: String

    The suffix appended to molecular identifier reads from the "top strand" of the duplex molecule.

    The suffix appended to molecular identifier reads from the "top strand" of the duplex molecule. These reads have 5' coordinate for read 1 less than or equal to the 5' coordinate for read 2.

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  22. object ReadInfo extends Serializable

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