object SequenceRecord extends Serializable
Companion object for creating Sequence Records.
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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
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.
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def
fromADAMReference(reference: Reference): SequenceRecord
Builds a sequence record from an Avro Reference.
Builds a sequence record from an Avro Reference.
- reference
Reference record to build from.
- returns
This Reference record as a SequenceRecord.
- def fromSAMSequenceRecord(record: SAMSequenceRecord): SequenceRecord
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def
fromSequence(sequence: Sequence): SequenceRecord
Builds a sequence record from a sequence.
Builds a sequence record from a sequence.
- sequence
Sequence to build from.
- returns
The specified sequence as a SequenceRecord.
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def
fromSlice(slice: Slice): SequenceRecord
Builds a sequence record from a slice.
Builds a sequence record from a slice.
- slice
Slice to build from.
- returns
The specified slice as a SequenceRecord.
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