trait UmiConsensusCaller[C <: SimpleRead] extends AnyRef

A trait that can be mixed in by any consensus caller that works at the read level, mapping incoming SAMRecords into consensus SAMRecords.

C

Internally, the type of lightweight consensus read that is used prior to rebuilding SAMRecords.

Linear Supertypes
AnyRef, Any
Known Subclasses
DuplexConsensusCaller, VanillaUmiConsensusCaller
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Inherited
  1. UmiConsensusCaller
  2. AnyRef
  3. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
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Abstract Value Members

  1. abstract def consensusSamRecordsFromSamRecords(recs: Seq[SAMRecord]): Seq[SAMRecord]

    Takes in all the reads for a source molecule and, if possible, generates one or more output consensus reads as SAM records.

    Takes in all the reads for a source molecule and, if possible, generates one or more output consensus reads as SAM records.

    recs

    the full set of source SAMRecords for a source molecule

    returns

    a seq of consensus SAM records, may be empty

    Attributes
    protected
  2. abstract def readGroupId: String

    A RG.ID to apply to all generated reads.

    A RG.ID to apply to all generated reads.

    Attributes
    protected
  3. abstract val readNamePrefix: String

    A prefix to use on all read names.

    A prefix to use on all read names. If None then a suitable prefix will be synthesized.

    Attributes
    protected
  4. abstract def sourceMoleculeId(rec: SAMRecord): String

    Needs to be implemented to return a value from a SAMRecord that represents the unit of grouping, e.g.

    Needs to be implemented to return a value from a SAMRecord that represents the unit of grouping, e.g. the MI tag for vanilla UMI data and the MI tag minus the /?? suffix for duplex data.

    rec

    a SAMRecord

    returns

    an identified for the source molecule

    Attributes
    protected[com.fulcrumgenomics.umi]

Concrete Value Members

  1. final def !=(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  2. final def ##(): Int
    Definition Classes
    AnyRef → Any
  3. def +(other: String): String
    Implicit
    This member is added by an implicit conversion from UmiConsensusCaller[C] to any2stringadd[UmiConsensusCaller[C]] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (UmiConsensusCaller[C], B)
    Implicit
    This member is added by an implicit conversion from UmiConsensusCaller[C] to ArrowAssoc[UmiConsensusCaller[C]] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  5. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  6. val NoCall: Byte
    Attributes
    protected
  7. val NoCallQual: PhredScore
    Attributes
    protected
  8. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  9. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  10. def consensusReadsConstructed: Long

    Returns the number of consensus reads constructed by this caller.

  11. final def consensusReadsFromSamRecords(recs: Seq[SAMRecord]): Seq[SAMRecord]

    Takes in all the reads for a source molecule and, if possible, generates one or more output consensus reads as SAM records.

    Takes in all the reads for a source molecule and, if possible, generates one or more output consensus reads as SAM records.

    recs

    the full set of source SAMRecords for a source molecule

    returns

    a seq of consensus SAM records, may be empty

  12. def createSamRecord(read: C, readType: ReadType): SAMRecord

    Creates a SAMRecord from the called consensus base and qualities.

    Creates a SAMRecord from the called consensus base and qualities.

    Attributes
    protected
  13. def ensuring(cond: (UmiConsensusCaller[C]) ⇒ Boolean, msg: ⇒ Any): UmiConsensusCaller[C]
    Implicit
    This member is added by an implicit conversion from UmiConsensusCaller[C] to Ensuring[UmiConsensusCaller[C]] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  14. def ensuring(cond: (UmiConsensusCaller[C]) ⇒ Boolean): UmiConsensusCaller[C]
    Implicit
    This member is added by an implicit conversion from UmiConsensusCaller[C] to Ensuring[UmiConsensusCaller[C]] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  15. def ensuring(cond: Boolean, msg: ⇒ Any): UmiConsensusCaller[C]
    Implicit
    This member is added by an implicit conversion from UmiConsensusCaller[C] to Ensuring[UmiConsensusCaller[C]] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  16. def ensuring(cond: Boolean): UmiConsensusCaller[C]
    Implicit
    This member is added by an implicit conversion from UmiConsensusCaller[C] to Ensuring[UmiConsensusCaller[C]] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  17. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  18. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  19. def filterToMostCommonAlignment(recs: Seq[SAMRecord]): Seq[SAMRecord]

    Takes in a non-empty seq of SAMRecords and filters them such that the returned seq only contains those reads that share the most common alignment of the read sequence to the reference.

    Takes in a non-empty seq of SAMRecords and filters them such that the returned seq only contains those reads that share the most common alignment of the read sequence to the reference. If two or more different alignments share equal numbers of reads, the 'most common' will be an arbitrary pick amongst those alignments, and the group of reads with that alignment will be returned.

    For the purposes of this method all that is implied by "same alignment" is that any insertions or deletions are at the same position and of the same length. This is done to allow for differential read length (either due to sequencing or untracked hard-clipping of adapters) and for differential soft-clipping at the starts and ends of reads.

    NOTE: filtered out reads are sent to the rejectRecords() method and do not need further handling

    Attributes
    protected[com.fulcrumgenomics.umi]
  20. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  21. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from UmiConsensusCaller[C] to StringFormat[UmiConsensusCaller[C]] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  22. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  23. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  24. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  25. def logStatistics(logger: Logger): Unit

    Logs statistics about how many reads were seen, and how many were filtered/discarded due to various filters.

  26. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  27. final def notify(): Unit
    Definition Classes
    AnyRef
  28. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  29. def readsFilteredInsufficientSupport: Long

    Returns the number of raw reads filtered out due to there being insufficient reads present to build the necessary set of consensus reads.

  30. def readsFilteredMinorityAlignment: Long

    Returns the number of raw reads filtered out because their alignment disagreed with the majority alignment of all raw reads for the same source molecule.

  31. def rejectRecords(recs: Traversable[SAMRecord]): Unit

    Records that the supplied records were rejected, and not used to build a consensus read.

    Records that the supplied records were rejected, and not used to build a consensus read.

    Attributes
    protected
  32. def subGroupRecords(records: Seq[SAMRecord]): (Seq[SAMRecord], Seq[SAMRecord], Seq[SAMRecord])

    Split records into those that should make a single-end consensus read, first of pair consensus read, and second of pair consensus read, respectively.

    Split records into those that should make a single-end consensus read, first of pair consensus read, and second of pair consensus read, respectively. The default method is to use the SAM flag to find unpaired reads, first of pair reads, and second of pair reads.

    Attributes
    protected
  33. def sum(ss: Array[Short]): Int

    Sums a short array into an Int to avoid overflow.

    Sums a short array into an Int to avoid overflow.

    Attributes
    protected
  34. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  35. def toSourceRead(rec: SAMRecord, minBaseQuality: PhredScore): Option[SourceRead]

    Converts from a SAMRecord into a SourceRead.

    Converts from a SAMRecord into a SourceRead. During conversion the record is end-trimmed to remove Ns and bases below the minBaseQuality. Remaining bases that are below minBaseQuality are then masked to Ns.

    returns

    Some(SourceRead) if there are any called bases with quality > minBaseQuality, else None

    Attributes
    protected[com.fulcrumgenomics.umi]
  36. def toString(): String
    Definition Classes
    AnyRef → Any
  37. def totalReads: Long

    Returns the total number of input reads examined by the consensus caller so far.

  38. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  39. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  40. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  41. def →[B](y: B): (UmiConsensusCaller[C], B)
    Implicit
    This member is added by an implicit conversion from UmiConsensusCaller[C] to ArrowAssoc[UmiConsensusCaller[C]] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion any2stringadd from UmiConsensusCaller[C] to any2stringadd[UmiConsensusCaller[C]]

Inherited by implicit conversion StringFormat from UmiConsensusCaller[C] to StringFormat[UmiConsensusCaller[C]]

Inherited by implicit conversion Ensuring from UmiConsensusCaller[C] to Ensuring[UmiConsensusCaller[C]]

Inherited by implicit conversion ArrowAssoc from UmiConsensusCaller[C] to ArrowAssoc[UmiConsensusCaller[C]]

Ungrouped