public final class TranscriptSequenceChangeHelper extends Object
Constructor and Description |
---|
TranscriptSequenceChangeHelper(TranscriptModel transcript)
Construct helper with the given
TranscriptModel |
Modifier and Type | Method and Description |
---|---|
String |
getCDSWithGenomeVariant(GenomeVariant change)
Similar to
getTranscriptWithChange(de.charite.compbio.jannovar.reference.GenomeVariant) but starting at the CDS begin position. |
String |
getTranscriptWithChange(GenomeVariant change)
Return modified transcript after applying a
GenomeVariant . |
public TranscriptSequenceChangeHelper(TranscriptModel transcript)
TranscriptModel
transcript
- with position and sequence informationpublic String getTranscriptWithChange(GenomeVariant change)
GenomeVariant
.change
- GenomeVariant
to apply to the transcriptGenomeVariant
public String getCDSWithGenomeVariant(GenomeVariant change)
getTranscriptWithChange(de.charite.compbio.jannovar.reference.GenomeVariant)
but starting at the CDS begin position.
We extend the CDS transcript to the right so that the changed protein sequence can be computed for
frameshift changes.change
- GenomeVariant
to apply to the CDS region of the transcriptGenomeVariant
Copyright © 2016. All rights reserved.