UmiConsensusCaller

Type Members

trait SimpleRead extends AnyRef

A trait that consensus reads must implement.
case class SourceRead(id: String, bases: Array[Byte], quals: Array[Byte], cigar: Cigar, sam: Option[SamRecord] = None) extends SimpleRead with Product with Serializable

Stores information about a read to be fed into a consensus.

Value Members

final def !=(arg0: Any): Boolean

Definition Classes
AnyRef → Any
final def ##(): Int

Definition Classes
AnyRef → Any
final def ==(arg0: Any): Boolean

Definition Classes
AnyRef → Any
val FilterInsufficientSupport: String

Filter reason for when there are too few reads to form a consensus.
val FilterLowQuality: String

Filter reason for when reads are rejected due to low quality.
val FilterMinorityAlignment: String

Filter reason for when reads are rejected for having a minority CIGAR.
val FilterOrphan: String

Filter reason for when reads are rejected due creation of orphaned consensus (i.e.
Filter reason for when reads are rejected due creation of orphaned consensus (i.e. R1 or R2 failed).
object ReadType extends Enumeration

The type of consensus read to output.
final def asInstanceOf[T0]: T0

Definition Classes
Any
def checkSortOrder(header: SAMFileHeader, source: Any, warn: (String) ⇒ Unit, error: (String) ⇒ Unit): Unit

Helper method to check that the input BAM is in the correct order for consensus calling.
Helper method to check that the input BAM is in the correct order for consensus calling. Will call the warn function if the sort order looks like it's probably compatible but it's not 100% sure. Will invoke the error function in cases where the sort order is definitely incompatible.
header
the header of the BAM file to be used for consensus calling
source
a path or string representing the source of the header
warn
a function to be called when any warnings are detected/emitted
error
a function to be called when any errors are encountered; should probably throw an exception!
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
final def eq(arg0: AnyRef): Boolean

Definition Classes
AnyRef
def equals(arg0: Any): Boolean

Definition Classes
AnyRef → Any
def finalize(): Unit

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( classOf[java.lang.Throwable] )
final def getClass(): Class[_]

Definition Classes
AnyRef → Any
def hashCode(): Int

Definition Classes
AnyRef → Any
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
def makePrefixFromSamHeader(header: SAMFileHeader): String

Attempts to construct a String that can be used as a prefix for consensus read names based on the contents of the incoming SAMFileHeader.
final def ne(arg0: AnyRef): Boolean

Definition Classes
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final def notify(): Unit

Definition Classes
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final def notifyAll(): Unit

Definition Classes
AnyRef
def outputHeader(in: SAMFileHeader, readGroupId: String, sortOrder: Option[SamOrder] = None): SAMFileHeader

Constructs an output header with a single read group for the a BAM.
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def toString(): String

Definition Classes
AnyRef → Any
final def wait(): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )
final def wait(arg0: Long, arg1: Int): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )
final def wait(arg0: Long): Unit

Definition Classes
AnyRef
Annotations
@throws( ... )

Related Docs: trait UmiConsensusCaller | package umi

object UmiConsensusCaller

Type Members

trait SimpleRead extends AnyRef

case class SourceRead(id: String, bases: Array[Byte], quals: Array[Byte], cigar: Cigar, sam: Option[SamRecord] = None) extends SimpleRead with Product with Serializable

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

val FilterInsufficientSupport: String

val FilterLowQuality: String

val FilterMinorityAlignment: String

val FilterOrphan: String

object ReadType extends Enumeration

final def asInstanceOf[T0]: T0

def checkSortOrder(header: SAMFileHeader, source: Any, warn: (String) ⇒ Unit, error: (String) ⇒ Unit): Unit

def clone(): AnyRef

final def eq(arg0: AnyRef): Boolean

def equals(arg0: Any): Boolean

def finalize(): Unit

final def getClass(): Class[_]

def hashCode(): Int

final def isInstanceOf[T0]: Boolean

def makePrefixFromSamHeader(header: SAMFileHeader): String

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

def outputHeader(in: SAMFileHeader, readGroupId: String, sortOrder: Option[SamOrder] = None): SAMFileHeader

final def synchronized[T0](arg0: ⇒ T0): T0

def toString(): String

final def wait(): Unit

final def wait(arg0: Long, arg1: Int): Unit

final def wait(arg0: Long): Unit

Inherited from AnyRef

Inherited from Any

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