c

com.fulcrumgenomics.bam

PileupBuilder

class PileupBuilder extends AnyRef

Class that provides methods to build and filter Pileups.

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Inherited
  1. PileupBuilder
  2. AnyRef
  3. Any
Implicitly
  1. by any2stringadd
  2. by StringFormat
  3. by Ensuring
  4. by ArrowAssoc
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Visibility
  1. Public
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Instance Constructors

  1. new PileupBuilder(dict: SAMSequenceDictionary, minMapQ: Int = 20, minBaseQ: Int = 20, mappedPairsOnly: Boolean = true, includeDuplicates: Boolean = false, includeSecondaryAlignments: Boolean = false, includeSupplementalAlignments: Boolean = false)

    dict

    the SAMSequenceDictionary for the reference sequence

    minMapQ

    the minimum MAPQ to allow a read to contribute to the pileup

    minBaseQ

    the minimum base quality to allow a base to contribute to the pileup

    mappedPairsOnly

    if true only allow reads from read-pairs with both reads mapped to contribute to the pileup

    includeDuplicates

    if true allow reads flagged as duplicates to contribute to the pileup

    includeSecondaryAlignments

    if true allow secondary alignments to contribute to the pileup

    includeSupplementalAlignments

    if true allow supplemental alignments to contribute to the pileup

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 PileupBuilder to any2stringadd[PileupBuilder] performed by method any2stringadd in scala.Predef.
    Definition Classes
    any2stringadd
  4. def ->[B](y: B): (PileupBuilder, B)
    Implicit
    This member is added by an implicit conversion from PileupBuilder to ArrowAssoc[PileupBuilder] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc
    Annotations
    @inline()
  5. final def ==(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  6. def accepts(entry: PileupEntry): Boolean

    Checks to see if all read filters accept the read.

    Checks to see if all read filters accept the read.

    Attributes
    protected
  7. def accepts(rec: SAMRecord): Boolean

    Checks to see if all read filters accept the read.

    Checks to see if all read filters accept the read.

    Attributes
    protected
  8. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  9. def build(iterator: Iterator[SAMRecord], refName: String, pos: Int): Pileup[PileupEntry]

    Constructs a pileup, at the single requested position, from the records returned by the iterator.

    Constructs a pileup, at the single requested position, from the records returned by the iterator.

    iterator

    an Iterator of SAMRecords that may or may not overlap the position

    refName

    the name of the reference sequence/contig/chrom on which the position resides

    pos

    the 1-based position on the reference sequence at which to construct the pileup

  10. def clone(): AnyRef
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  11. def ensuring(cond: (PileupBuilder) ⇒ Boolean, msg: ⇒ Any): PileupBuilder
    Implicit
    This member is added by an implicit conversion from PileupBuilder to Ensuring[PileupBuilder] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  12. def ensuring(cond: (PileupBuilder) ⇒ Boolean): PileupBuilder
    Implicit
    This member is added by an implicit conversion from PileupBuilder to Ensuring[PileupBuilder] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  13. def ensuring(cond: Boolean, msg: ⇒ Any): PileupBuilder
    Implicit
    This member is added by an implicit conversion from PileupBuilder to Ensuring[PileupBuilder] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  14. def ensuring(cond: Boolean): PileupBuilder
    Implicit
    This member is added by an implicit conversion from PileupBuilder to Ensuring[PileupBuilder] performed by method Ensuring in scala.Predef.
    Definition Classes
    Ensuring
  15. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  16. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  17. def finalize(): Unit
    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  18. def formatted(fmtstr: String): String
    Implicit
    This member is added by an implicit conversion from PileupBuilder to StringFormat[PileupBuilder] performed by method StringFormat in scala.Predef.
    Definition Classes
    StringFormat
    Annotations
    @inline()
  19. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
  20. def hashCode(): Int
    Definition Classes
    AnyRef → Any
  21. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  22. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  23. final def notify(): Unit
    Definition Classes
    AnyRef
  24. final def notifyAll(): Unit
    Definition Classes
    AnyRef
  25. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  26. def toString(): String
    Definition Classes
    AnyRef → Any
  27. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  28. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  29. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  30. def withBaseFilter(f: (PileupEntry) ⇒ Boolean): PileupBuilder

    Adds a base level filter to the set of filters.

  31. def withReadFilter(f: (SAMRecord) ⇒ Boolean): PileupBuilder

    Adds a read level filter to the set of filters.

  32. def →[B](y: B): (PileupBuilder, B)
    Implicit
    This member is added by an implicit conversion from PileupBuilder to ArrowAssoc[PileupBuilder] performed by method ArrowAssoc in scala.Predef.
    Definition Classes
    ArrowAssoc

Inherited from AnyRef

Inherited from Any

Inherited by implicit conversion any2stringadd from PileupBuilder to any2stringadd[PileupBuilder]

Inherited by implicit conversion StringFormat from PileupBuilder to StringFormat[PileupBuilder]

Inherited by implicit conversion Ensuring from PileupBuilder to Ensuring[PileupBuilder]

Inherited by implicit conversion ArrowAssoc from PileupBuilder to ArrowAssoc[PileupBuilder]

Ungrouped