class PileupBuilder extends AnyRef
Class that provides methods to build and filter Pileups.
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Instance Constructors
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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
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final
def
!=(arg0: Any): Boolean
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final
def
##(): Int
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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
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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.
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- @inline()
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final
def
==(arg0: Any): Boolean
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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
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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
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final
def
asInstanceOf[T0]: T0
- Definition Classes
- Any
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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
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def
clone(): AnyRef
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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
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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
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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
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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
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final
def
eq(arg0: AnyRef): Boolean
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def
equals(arg0: Any): Boolean
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def
finalize(): Unit
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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
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- @inline()
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final
def
getClass(): Class[_]
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def
hashCode(): Int
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final
def
isInstanceOf[T0]: Boolean
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final
def
ne(arg0: AnyRef): Boolean
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final
def
notify(): Unit
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final
def
notifyAll(): Unit
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final
def
synchronized[T0](arg0: ⇒ T0): T0
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def
toString(): String
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final
def
wait(): Unit
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final
def
wait(arg0: Long, arg1: Int): Unit
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final
def
wait(arg0: Long): Unit
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def
withBaseFilter(f: (PileupEntry) ⇒ Boolean): PileupBuilder
Adds a base level filter to the set of filters.
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def
withReadFilter(f: (SamRecord) ⇒ Boolean): PileupBuilder
Adds a read level filter to the set of filters.
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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