Alignment |
An anchor-based alignment, optimized for small-ish alignments where linear search in the gap
anchor is fast or even faster than binary search.
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AminoAcidChange |
Representation of a change in amino acids.
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AminoAcidChangeNormalizer |
Helper for normalizing changes in amino acid sequences.
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Anchor |
An anchor in an Alignment .
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Anchors |
Helper class for working with Anchor -based alignments.
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CDSInterval |
Interval on a transcript.
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CDSPosition |
Position on a transcript.
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DuplicationChecker |
Helper class for checking whether an insertion in a string is a duplication.
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GenomeInterval |
Representation of a genomic interval (chromsome, begin, end).
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GenomePosition |
Representation of a position on a genome (chromosome, position).
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GenomeVariant |
Denote a change with a "REF" and an "ALT" string using genome coordinates.
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GenomeVariantNormalizer |
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HG19RefDictBuilder |
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NucleotidePointLocationBuilder |
Helper class that allows easy building of NucleotidePointLocation s.
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SVBreakend |
Breakend.
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SVCopyNumberVariant |
Represents an SV deletion.
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SVDeletion |
Deletion relative to the reference.
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SVDuplication |
Region of elevated copy number relative to the reference.
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SVGenomeVariant |
Representation of a structural variant on the genome level as defined in VCF.
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SVInsertion |
Insertion of novel sequence relative to the reference.
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SVInversion |
Inversion of reference sequence
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SVMobileElementDeletion |
Deletion of mobile element relative to the reference.
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SVMobileElementInsertion |
Insertion of mobile element relative to the reference.
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SVTandemDuplication |
Tandem duplication.
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SVUnknown |
Unknown structural variant.
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TranscriptInterval |
Interval on a transcript.
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TranscriptIntervalEndExtractor |
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TranscriptModel |
The information representing a transcript model.
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TranscriptModelBuilder |
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TranscriptModelBuilder.AlignmentPart |
Describe a part of an alignment, e.g., as parsed from RefSeq.
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TranscriptPosition |
Position on a transcript.
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TranscriptProjectionDecorator |
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TranscriptSequenceChangeHelper |
Helper class for getting updated transcript sequence for deletions and block substitutions.
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TranscriptSequenceDecorator |
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TranscriptSequenceOntologyDecorator |
Functionality for finding out about certain points/regions of TranscriptModel using genomic
positions.
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