SequenceRecord

Metadata about a single reference sequence.

name: The name of this reference in the assembly.
length: The length of the sequence for this reference.
url: If available, the URI from which the reference sequence was obtained.
md5: If available, the MD5 checksum uniquely representing this reference as a lower-case hexadecimal string, calculated as the MD5 of the upper-case sequence excluding all whitespace characters (equivalent to SQ:M5 in SAM).
refseq: If available, the REFSEQ ID for the reference.
genbank: If available, the Genbank ID for the reference.
assembly: If available, the name of the assembly for this reference.
species: If available, the species that this reference is for.
index: If available, the number of this reference in a set of references.

Linear Supertypes

Product, Equals, Serializable, Serializable, AnyRef, Any

Instance Constructors

new SequenceRecord(name: String, length: Long, url: Option[String], md5: Option[String], refseq: Option[String], genbank: Option[String], assembly: Option[String], species: Option[String], index: Option[Int])

name
The name of this reference in the assembly.
length
The length of the sequence for this reference.
url
If available, the URI from which the reference sequence was obtained.
md5
If available, the MD5 checksum uniquely representing this reference as a lower-case hexadecimal string, calculated as the MD5 of the upper-case sequence excluding all whitespace characters (equivalent to SQ:M5 in SAM).
refseq
If available, the REFSEQ ID for the reference.
genbank
If available, the Genbank ID for the reference.
assembly
If available, the name of the assembly for this reference.
species
If available, the species that this reference is for.
index
If available, the number of this reference in a set of references.

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
final def asInstanceOf[T0]: T0

Definition Classes
Any
val assembly: Option[String]

If available, the name of the assembly for this reference.
def clone(): AnyRef

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

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

Definition Classes
SequenceRecord → Equals → AnyRef → Any
def finalize(): Unit

Attributes
protected[java.lang]
Definition Classes
AnyRef
Annotations
@throws( classOf[java.lang.Throwable] )
val genbank: Option[String]

If available, the Genbank ID for the reference.
final def getClass(): Class[_]

Definition Classes
AnyRef → Any
val index: Option[Int]

If available, the number of this reference in a set of references.
final def isInstanceOf[T0]: Boolean

Definition Classes
Any
val length: Long

The length of the sequence for this reference.
val md5: Option[String]

If available, the MD5 checksum uniquely representing this reference as a lower-case hexadecimal string, calculated as the MD5 of the upper-case sequence excluding all whitespace characters (equivalent to SQ:M5 in SAM).
val name: String

The name of this reference in the assembly.
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
val refseq: Option[String]

If available, the REFSEQ ID for the reference.
val species: Option[String]

If available, the species that this reference is for.
def stripIndex: SequenceRecord

returns
Returns a new sequence record with the index unset.
final def synchronized[T0](arg0: ⇒ T0): T0

Definition Classes
AnyRef
def toADAMReference: Reference

returns
Builds an Avro Reference representation from this record.
def toSAMSequenceRecord: SAMSequenceRecord

Converts this sequence record into a SAM sequence record.
Converts this sequence record into a SAM sequence record.
returns
A SAM formatted sequence record.
def toString(): String

Definition Classes
SequenceRecord → AnyRef → Any
val url: Option[String]

If available, the URI from which the reference sequence was obtained.
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: object SequenceRecord | package models

case class SequenceRecord(name: String, length: Long, url: Option[String], md5: Option[String], refseq: Option[String], genbank: Option[String], assembly: Option[String], species: Option[String], index: Option[Int]) extends Serializable with Product

Instance Constructors

new SequenceRecord(name: String, length: Long, url: Option[String], md5: Option[String], refseq: Option[String], genbank: Option[String], assembly: Option[String], species: Option[String], index: Option[Int])

Value Members

final def !=(arg0: Any): Boolean

final def ##(): Int

final def ==(arg0: Any): Boolean

final def asInstanceOf[T0]: T0

val assembly: Option[String]

def clone(): AnyRef

final def eq(arg0: AnyRef): Boolean

def equals(o: Any): Boolean

def finalize(): Unit

val genbank: Option[String]

final def getClass(): Class[_]

val index: Option[Int]

final def isInstanceOf[T0]: Boolean

val length: Long

val md5: Option[String]

val name: String

final def ne(arg0: AnyRef): Boolean

final def notify(): Unit

final def notifyAll(): Unit

val refseq: Option[String]

val species: Option[String]

def stripIndex: SequenceRecord

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

def toADAMReference: Reference

def toSAMSequenceRecord: SAMSequenceRecord

def toString(): String

val url: Option[String]

final def wait(): Unit

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

final def wait(arg0: Long): Unit

Inherited from Product

Inherited from Equals

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped