class TwoBitFile extends ReferenceFile
Represents a set of reference sequences backed by a .2bit file.
See http://genome.ucsc.edu/FAQ/FAQformat.html#format7 for the spec.
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new
TwoBitFile(byteAccess: ByteAccess)
- byteAccess
ByteAccess pointing to a .2bit file.
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def
extract(region: ReferenceRegion): String
Extract reference sequence from the .2bit data.
Extract reference sequence from the .2bit data. Do not apply masks.
- region
The desired ReferenceRegion to extract.
- returns
The reference sequence at the desired locus.
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- TwoBitFile → ReferenceFile
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def
extract(region: ReferenceRegion, mask: Boolean): String
Extract reference sequence from the .2bit data.
Extract reference sequence from the .2bit data.
- region
The desired ReferenceRegion to extract.
- mask
Whether to apply masks (with lowercase letters)
- returns
The reference sequence at the desired locus.
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val
references: SequenceDictionary
The sequence dictionary corresponding to the reference sequences in this two bit file.
The sequence dictionary corresponding to the reference sequences in this two bit file.
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- TwoBitFile → ReferenceFile
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