Package de.charite.compbio.jannovar.htsjdk

Class VariantContextAnnotator.Options

java.lang.Object

de.charite.compbio.jannovar.htsjdk.VariantContextAnnotator.Options

Enclosing class:

VariantContextAnnotator

public static class VariantContextAnnotator.Options
extends Object

Options class for VariantContextAnnotator.

Author:

Manuel Holtgrewe, Max Schubach

Constructor Summary

Constructors

Constructor	Description
Options()	Constructor
Options(boolean oneAnnotationOnly, de.charite.compbio.jannovar.hgvs.AminoAcidCode code, boolean escapeAnnField, boolean nt3PrimeShifting, boolean offTargetFilterEnabled, boolean offTargetFilterUtrIsOffTarget, boolean offTargetFilterIntronicSpliceIsOffTarget)	constructor using fields

Method Summary

Modifier and Type	Method	Description
boolean	isEscapeAnnField()
boolean	isNt3PrimeShifting()
boolean	isOffTargetFilterEnabled()
boolean	isOffTargetFilterIntronicSpliceIsOffTarget()
boolean	isOffTargetFilterUtrIsOffTarget()
boolean	isOneAnnotationOnly()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Options

public Options()

Constructor

Options

public Options(boolean oneAnnotationOnly,
               de.charite.compbio.jannovar.hgvs.AminoAcidCode code,
               boolean escapeAnnField,
               boolean nt3PrimeShifting,
               boolean offTargetFilterEnabled,
               boolean offTargetFilterUtrIsOffTarget,
               boolean offTargetFilterIntronicSpliceIsOffTarget)

constructor using fields

Parameters:

oneAnnotationOnly - Whether or not to trim each annotation list to the first (one with highest putative impact), defaults to true

code - HGVS protein output in three or one letter

escapeAnnField - whether or not to escape values in the ANN field (defaults to true)

nt3PrimeShifting - whether or not to perform shifting towards the 3' end of the transcript (defaults to true)

offTargetFilterEnabled - whether or not off target filter application is abled

offTargetFilterUtrIsOffTarget - whether or not to count UTR as off-target

offTargetFilterIntronicSpliceIsOffTarget - whether or not to to count non-consensus intronic splicing as off-target

Method Detail

isOneAnnotationOnly

public boolean isOneAnnotationOnly()

Returns:

if annotation list is trimmed to first.

isEscapeAnnField

public boolean isEscapeAnnField()

Returns:

Escape values in ANN field

isNt3PrimeShifting

public boolean isNt3PrimeShifting()

Returns:

perform shifting towards 3' end of the transcript

isOffTargetFilterEnabled

public boolean isOffTargetFilterEnabled()

isOffTargetFilterUtrIsOffTarget

public boolean isOffTargetFilterUtrIsOffTarget()

isOffTargetFilterIntronicSpliceIsOffTarget

public boolean isOffTargetFilterIntronicSpliceIsOffTarget()