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  • package com
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  • package fulcrumgenomics
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  • package umi
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    fulcrumgenomics
  • object ConsensusTags

    Object that encapsulates the various consensus related tags that are added to consensus reads at both the per-read and per-base level.

    Object that encapsulates the various consensus related tags that are added to consensus reads at both the per-read and per-base level.

    Currently only contains tags for single-strand consensus reads, but with a view to using the following names for consistency if/when we add duplex calling: Value AB BA Final --------------------- -- -- ----- per-read-depth aD bD cD per-read-min-depth aM bM cM per-read-error-rate aE bE cE per-base-depth ad bd cd per-base-error-count ae be ce per-base-bases ac bc bases per-base-quals aq bq quals The second letter in the tag is lower case if it is per-base, upper case if it is per-read.

    Definition Classes
    umi
  • PerBase
  • PerRead

object PerBase

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  4. val AbConsensusBases: String

    The single-stranded consensus from the AB raw reads.

  5. val AbConsensusQuals: String

    The phred-scaled qualities, as phred-33 ascii values, of the single-stranded consensus from the AB raw reads.

  6. val AbRawReadCount: String
  7. val AbRawReadErrors: String
  8. val AllPerBaseTags: Seq[String]

    The set of all per-base tags.

  9. val BaConsensusBases: String

    The single-stranded consensus from the BA raw reads.

  10. val BaConsensusQuals: String

    The phred-scaled qualities, as phred-33 ascii values, of the single-stranded consensus from the BA raw reads.

  11. val BaRawReadCount: String
  12. val BaRawReadErrors: String
  13. val RawReadCount: String

    The per-base number of raw-reads contributing to the consensus (stored as a short[]).

  14. val RawReadErrors: String

    The number of bases at each position that disagreed with the final consensus call (stored as a short[]).

    The number of bases at each position that disagreed with the final consensus call (stored as a short[]). If the final consensus call is a no call (N), then we use the most likely consensus base instead of the final call.

  15. val TagsToReverse: Seq[String]

    The set of the per-base tags produced by the consensus caller that need to be reversed after alignment.

  16. val TagsToReverseComplement: Seq[String]

    The set of the per-base tags produced by the consensus caller that need to be reverse complemented after alignment.

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