MdTag

Instance Constructors

new MdTag(start: Long, matches: List[NumericRange[Long]], mismatches: Map[Long, Char], deletions: Map[Long, Char])

start
Start position of the alignment.
matches
A list of the ranges over which the read has a perfect sequence match.
mismatches
A map of all the locations where a base mismatched.
deletions
A map of all locations where a base was deleted.

Value Members

final def !=(arg0: AnyRef): Boolean

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

Definition Classes
Any
final def ##(): Int

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

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

Definition Classes
Any
final def asInstanceOf[T0]: T0

Definition Classes
Any
def canEqual(other: Any): Boolean

We can check equality against MdTags.
We can check equality against MdTags.
other
Object to see if we can compare against.
returns
Returns True if the object is an MdTag.

Definition Classes
MdTag → Equals
def clone(): AnyRef

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( ... )
def countOfMismatches: Int

Returns the number of mismatches against the reference.
Returns the number of mismatches against the reference.
returns
Number of mismatches against the reference
def deletedBase(pos: Long): Option[Char]

Returns the base that was deleted at a position.
Returns the base that was deleted at a position.
pos
Reference based position.
returns
The base that was deleted at this position in the reference.
val deletions: Map[Long, Char]

A map of all locations where a base was deleted.
def end(): Long

Returns the end position of the record described by this MD tag.
Returns the end position of the record described by this MD tag.
returns
The reference based end position of this tag.
final def eq(arg0: AnyRef): Boolean

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

We implement equality checking by seeing whether two MD tags are at the same position and have the same value.
We implement equality checking by seeing whether two MD tags are at the same position and have the same value.
other
An object to compare to.
returns
True if the object is an MD tag at the same position and with the same string value. Else, false.

Definition Classes
MdTag → Equals → 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 getReference(read: RichAlignmentRecord, withGaps: Boolean = false): String

Given a read, returns the reference.
Given a read, returns the reference.
read
A read for which one desires the reference sequence.
withGaps
If true, applies INDEL gaps to the reference. Else, returns the raw reference sequence.
returns
A string corresponding to the reference overlapping this read.
def hasMismatches: Boolean

Returns whether this read has any mismatches against the reference.
Returns whether this read has any mismatches against the reference.
returns
True if this read has mismatches. We do not return true if the read has no mismatches but has deletions.
def hashCode(): Int

returns
We implement hashing by hashing the string representation of the MD tag.

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

Definition Classes
Any
def isMatch(pos: ReferencePosition): Boolean

Returns whether a base is a match against the reference.
Returns whether a base is a match against the reference.
pos
ReferencePosition object describing where to check.
returns
True if base matches reference. False means that the base may be either a mismatch or a deletion.
def isMatch(pos: Long): Boolean

Returns whether a base is a match against the reference.
Returns whether a base is a match against the reference.
pos
Reference based position to check.
returns
True if base matches reference. False means that the base may be either a mismatch or a deletion.
val matches: List[NumericRange[Long]]

A list of the ranges over which the read has a perfect sequence match.
def mismatchedBase(pos: Long): Option[Char]

Returns the mismatched base at a position.
Returns the mismatched base at a position.
pos
Reference based position.
returns
The base at this position in the reference.
val mismatches: Map[Long, Char]

A map of all the locations where a base mismatched.
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
val start: Long

Start position of the alignment.
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def toString(): String

Converts an MdTag object to a properly formatted MD string.
Converts an MdTag object to a properly formatted MD string.
returns
MD string corresponding to [0-9]+(([A-Z]|\^[A-Z]+)[0-9]+)

Definition Classes
MdTag → AnyRef → Any
See also
http://zenfractal.com/2013/06/19/playing-with-matches/
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( ... )

case class MdTag(start: Long, matches: List[NumericRange[Long]], mismatches: Map[Long, Char], deletions: Map[Long, Char]) extends Product with Serializable

Instance Constructors

new MdTag(start: Long, matches: List[NumericRange[Long]], mismatches: Map[Long, Char], deletions: Map[Long, Char])

Value Members

final def !=(arg0: AnyRef): Boolean

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: AnyRef): Boolean

final def ==(arg0: Any): Boolean

final def asInstanceOf[T0]: T0

def canEqual(other: Any): Boolean

def clone(): AnyRef

def countOfMismatches: Int

def deletedBase(pos: Long): Option[Char]

val deletions: Map[Long, Char]

def end(): Long

final def eq(arg0: AnyRef): Boolean

def equals(other: Any): Boolean

def finalize(): Unit

final def getClass(): Class[_]

def getReference(read: RichAlignmentRecord, withGaps: Boolean = false): String

def hasMismatches: Boolean

def hashCode(): Int

final def isInstanceOf[T0]: Boolean

def isMatch(pos: ReferencePosition): Boolean

def isMatch(pos: Long): Boolean

val matches: List[NumericRange[Long]]

def mismatchedBase(pos: Long): Option[Char]

val mismatches: Map[Long, Char]

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

val start: Long

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 Serializable

Inherited from Serializable

Inherited from Product

Inherited from Equals

Inherited from AnyRef

Inherited from Any

Ungrouped