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
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.
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Instance Constructors
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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
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final
def
!=(arg0: Any): Boolean
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final
def
##(): Int
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final
def
==(arg0: Any): Boolean
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final
def
asInstanceOf[T0]: T0
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- val assembly: Option[String]
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def
clone(): AnyRef
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final
def
eq(arg0: AnyRef): Boolean
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def
equals(o: Any): Boolean
- Definition Classes
- SequenceRecord → Equals → AnyRef → Any
- val genbank: Option[String]
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final
def
getClass(): Class[_]
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- @native() @HotSpotIntrinsicCandidate()
- val index: Option[Int]
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final
def
isInstanceOf[T0]: Boolean
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- val length: Long
- val md5: Option[String]
- val name: String
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final
def
ne(arg0: AnyRef): Boolean
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final
def
notify(): Unit
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final
def
notifyAll(): Unit
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- @native() @HotSpotIntrinsicCandidate()
- val refseq: Option[String]
- val species: Option[String]
-
def
stripIndex: SequenceRecord
- returns
Returns a new sequence record with the index unset.
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final
def
synchronized[T0](arg0: ⇒ T0): T0
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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.
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def
toString(): String
- Definition Classes
- SequenceRecord → AnyRef → Any
- val url: Option[String]
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final
def
wait(arg0: Long, arg1: Int): Unit
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final
def
wait(arg0: Long): Unit
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final
def
wait(): Unit
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Deprecated Value Members
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def
finalize(): Unit
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- @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
- Deprecated
(Since version ) see corresponding Javadoc for more information.