SequenceRecord

Metadata about a single reference contig.

name: The name of the contig.
length: The length of the contig.
url: If available, the URL the contig is accessible from.
md5: If available, the MD5 checksum for the contig.
refseq: If available, the REFSEQ ID for the contig.
genbank: If available, the Genbank ID for the contig.
assembly: If available, the assembly name for the assembly this contig is from.
species: If available, the species this contig was assembled from.
referenceIndex: If available, the number of this contig in a set of contigs.

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], referenceIndex: Option[Int])

name
The name of the contig.
length
The length of the contig.
url
If available, the URL the contig is accessible from.
md5
If available, the MD5 checksum for the contig.
refseq
If available, the REFSEQ ID for the contig.
genbank
If available, the Genbank ID for the contig.
assembly
If available, the assembly name for the assembly this contig is from.
species
If available, the species this contig was assembled from.
referenceIndex
If available, the number of this contig in a set of contigs.

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
val assembly: Option[String]

If available, the assembly name for the assembly this contig is from.
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 contig.
final def getClass(): Class[_]

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

Definition Classes
Any
val length: Long

The length of the contig.
val md5: Option[String]

If available, the MD5 checksum for the contig.
val name: String

The name of the contig.
final def ne(arg0: AnyRef): Boolean

Definition Classes
AnyRef
final def notify(): Unit

Definition Classes
AnyRef
final def notifyAll(): Unit

Definition Classes
AnyRef
val referenceIndex: Option[Int]

If available, the number of this contig in a set of contigs.
val refseq: Option[String]

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

If available, the species this contig was assembled from.
def stripIndex: SequenceRecord

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

Definition Classes
AnyRef
def toADAMContig: Contig

returns
Builds an Avro contig 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 URL the contig is accessible from.
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 SequenceRecord(name: String, length: Long, url: Option[String], md5: Option[String], refseq: Option[String], genbank: Option[String], assembly: Option[String], species: Option[String], referenceIndex: 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], referenceIndex: Option[Int])

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

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[_]

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 referenceIndex: Option[Int]

val refseq: Option[String]

val species: Option[String]

def stripIndex: SequenceRecord

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

def toADAMContig: Contig

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