MappedRead

Instance Constructors

new MappedRead(name: String, sequence: Bases, baseQualities: IndexedSeq[Byte], isDuplicate: Boolean, contigName: ContigName, alignmentQuality: Int, start: Locus, cigar: Cigar, failedVendorQualityChecks: Boolean, isPositiveStrand: Boolean, isPaired: Boolean)

contigName
the contig name (e.g. "chr12") that this read was mapped to.
alignmentQuality
the mapping quality, phred scaled.
start
the (0-based) reference locus that the first base in this read aligns to.
cigar
parsed samtools CIGAR object.

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
lazy val alignmentLikelihood: Double
val alignmentQuality: Int

the mapping quality, phred scaled.
final def asInstanceOf[T0]: T0

Definition Classes
Any
def asMappedRead: Some[MappedRead]

Definition Classes
MappedRead → Read
val baseQualities: IndexedSeq[Byte]

The base qualities, phred scaled.
The base qualities, phred scaled. These are numbers, and are NOT character encoded.

Definition Classes
MappedRead → Read
val cigar: Cigar

parsed samtools CIGAR object.
lazy val cigarElements: Vector[CigarElement]

Individual components of the CIGAR string (e.g.
Individual components of the CIGAR string (e.g. "10M"), parsed, and as a Scala buffer.
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
def contains(locus: Locus): Boolean

Definition Classes
Interval
val contigName: ContigName

the contig name (e.g.
the contig name (e.g. "chr12") that this read was mapped to.

Definition Classes
MappedRead → HasContig
val end: Locus

The end of the alignment, exclusive.
The end of the alignment, exclusive. This is the first reference locus AFTER the locus corresponding to the last base in this read.

Definition Classes
MappedRead → Interval
final def eq(arg0: AnyRef): Boolean

Definition Classes
AnyRef
val failedVendorQualityChecks: Boolean

Whether the read failed predefined vendor checks for quality
Whether the read failed predefined vendor checks for quality

Definition Classes
MappedRead → Read
def finalize(): Unit

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

Definition Classes
AnyRef → Any
val isDuplicate: Boolean

Is this read a duplicate of another?
Is this read a duplicate of another?

Definition Classes
MappedRead → Read
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
def isMapped: Boolean

Is this read mapped?
Is this read mapped?

Definition Classes
MappedRead → Read
val isPaired: Boolean

Whether read is from a paired-end library
Whether read is from a paired-end library

Definition Classes
MappedRead → Read
val isPositiveStrand: Boolean
def iterator(): Iterator[Locus]

Definition Classes
Interval
def length: NumLoci

Definition Classes
Interval
val name: String

Definition Classes
MappedRead → Read
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
def overlaps(other: Region): Boolean

Definition Classes
Region
def overlapsLocus(locus: Locus, halfWindowSize: WindowSize): Boolean

Definition Classes
Region
val sequence: Bases

The nucleotide sequence.
The nucleotide sequence.

Definition Classes
MappedRead → Read
val start: Locus

the (0-based) reference locus that the first base in this read aligns to.
the (0-based) reference locus that the first base in this read aligns to.

Definition Classes
MappedRead → Interval
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def toString(): String

Definition Classes
MappedRead → Region → Interval → AnyRef → Any
def unclippedEnd: Locus

The end of the read's alignment, including any final clipped bases, exclusive.
def unclippedStart: Locus

A read can be "clipped", meaning that some prefix or suffix of it did not align.
A read can be "clipped", meaning that some prefix or suffix of it did not align. This is the start of the whole read's alignment, including any initial clipped bases.
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 Doc: package reads

Instance Constructors

new MappedRead(name: String, sequence: Bases, baseQualities: IndexedSeq[Byte], isDuplicate: Boolean, contigName: ContigName, alignmentQuality: Int, start: Locus, cigar: Cigar, failedVendorQualityChecks: Boolean, isPositiveStrand: Boolean, isPaired: Boolean)

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

lazy val alignmentLikelihood: Double

val alignmentQuality: Int

final def asInstanceOf[T0]: T0

def asMappedRead: Some[MappedRead]

val baseQualities: IndexedSeq[Byte]

val cigar: Cigar

lazy val cigarElements: Vector[CigarElement]

def clone(): AnyRef

def contains(locus: Locus): Boolean

val contigName: ContigName

val end: Locus

final def eq(arg0: AnyRef): Boolean

val failedVendorQualityChecks: Boolean

def finalize(): Unit

final def getClass(): Class[_]

val isDuplicate: Boolean

final def isInstanceOf[T0]: Boolean

def isMapped: Boolean

val isPaired: Boolean

val isPositiveStrand: Boolean

def iterator(): Iterator[Locus]

def length: NumLoci

val name: String

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

def overlaps(other: Region): Boolean

def overlapsLocus(locus: Locus, halfWindowSize: WindowSize): Boolean

val sequence: Bases

val start: Locus

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

def toString(): String

def unclippedEnd: Locus

def unclippedStart: Locus

final def wait(): Unit

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

final def wait(arg0: Long): Unit

Inherited from Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from Region

Inherited from Interval

Inherited from HasContig

Inherited from Read

Inherited from AnyRef

Inherited from Any

Ungrouped