Object/Class

org.bdgenomics.adam.models

SequenceRecord

Related Docs: class SequenceRecord | package models

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object SequenceRecord extends Serializable

Companion object for creating Sequence Records.

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  1. final def !=(arg0: Any): Boolean

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  2. final def ##(): Int

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  3. final def ==(arg0: Any): Boolean

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  4. def apply(name: String, length: Long, md5: String = null, url: String = null, refseq: String = null, genbank: String = null, assembly: String = null, species: String = null, index: Option[Int] = None): SequenceRecord

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    Java friendly apply method that wraps null strings.

    Java friendly apply method that wraps null strings.

    name

    The name of this reference in the assembly.

    length

    The length of the sequence for this reference.

    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).

    url

    If available, the URI from which the reference sequence was obtained.

    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.

    returns

    Returns a new SequenceRecord where all strings except for name are wrapped in Options to check for null values.

  5. final def asInstanceOf[T0]: T0

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  6. def clone(): AnyRef

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  7. final def eq(arg0: AnyRef): Boolean

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  8. def equals(arg0: Any): Boolean

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  9. def finalize(): Unit

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  10. def fromADAMContigFragment(fragment: NucleotideContigFragment): SequenceRecord

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    Extracts the contig metadata from a nucleotide fragment.

    Extracts the contig metadata from a nucleotide fragment.

    fragment

    The assembly fragment to extract a SequenceRecord from.

    returns

    The sequence record metadata from a single assembly fragment.

  11. def fromADAMReference(reference: Reference): SequenceRecord

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    Builds a sequence record from an Avro Contig.

    Builds a sequence record from an Avro Contig.

    returns

    This Contig record as a SequenceRecord.

  12. def fromSAMSequenceRecord(record: SAMSequenceRecord): SequenceRecord

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  13. final def getClass(): Class[_]

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  14. def hashCode(): Int

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  15. final def isInstanceOf[T0]: Boolean

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  16. final def ne(arg0: AnyRef): Boolean

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  17. final def notify(): Unit

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  18. final def notifyAll(): Unit

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

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  20. def toString(): String

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  21. final def wait(): Unit

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

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  23. final def wait(arg0: Long): Unit

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Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

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