object SequenceDictionary extends Serializable
Singleton object for creating SequenceDictionaries.
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def
apply(header: SAMFileHeader): SequenceDictionary
Makes a SequenceDictionary from a SAMFileHeader.
Makes a SequenceDictionary from a SAMFileHeader.
- header
htsjdk SAMFileHeader to extract sequences from.
- returns
A SequenceDictionary with populated sequence records.
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def
apply(dict: SAMSequenceDictionary): SequenceDictionary
Builds a sequence dictionary from an htsjdk SAMSequenceDictionary.
Builds a sequence dictionary from an htsjdk SAMSequenceDictionary.
- dict
Htsjdk sequence dictionary to build from.
- returns
A SequenceDictionary with populated sequence records.
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def
apply(records: SequenceRecord*): SequenceDictionary
Builds a sequence dictionary for a variable length collection of records.
Builds a sequence dictionary for a variable length collection of records.
- records
Records to include in the dictionary.
- returns
A sequence dictionary containing these records.
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def
empty: SequenceDictionary
- returns
Creates a new, empty SequenceDictionary.
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def
fromAvro(references: Seq[Reference]): SequenceDictionary
Creates a sequence dictionary from a sequence of Avro References.
Creates a sequence dictionary from a sequence of Avro References.
- references
Seq of Reference records.
- returns
Returns a sequence dictionary.
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def
fromSAMSequenceDictionary(samDict: SAMSequenceDictionary): SequenceDictionary
Converts a picard/samtools SAMSequenceDictionary into an ADAM sequence dictionary.
Converts a picard/samtools SAMSequenceDictionary into an ADAM sequence dictionary.
- samDict
SAM style sequence dictionary.
- returns
Returns an ADAM style sequence dictionary.
- See also
fromSAMHeader
fromVCFHeader
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def
fromVCFHeader(header: VCFHeader): SequenceDictionary
Extracts a SAM sequence dictionary from a VCF header and returns an ADAM sequence dictionary.
Extracts a SAM sequence dictionary from a VCF header and returns an ADAM sequence dictionary.
- header
VCF file header.
- returns
Returns an ADAM style sequence dictionary.
- See also
fromSAMHeader
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