@Deprecated public class GeliTextFeature extends java.lang.Object implements Feature
Constructor and Description |
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GeliTextFeature(java.lang.String contig,
long position,
char refBase,
int depthOfCoverage,
int maximumMappingQual,
DiploidGenotype genotype,
double LODBestToReference,
double LODBestToNext,
double[] likelihoods)
Deprecated.
Create a geli text feature, given:
|
Modifier and Type | Method and Description |
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boolean |
equals(java.lang.Object o)
Deprecated.
|
java.lang.String |
getContig()
Deprecated.
Gets the contig name for the contig this is mapped to.
|
int |
getDepthOfCoverage()
Deprecated.
|
int |
getEnd()
Deprecated.
Return the end position following 1-based fully closed conventions.
|
DiploidGenotype |
getGenotype()
Deprecated.
|
double[] |
getLikelihoods()
Deprecated.
|
double |
getLODBestToNext()
Deprecated.
|
double |
getLODBestToReference()
Deprecated.
|
int |
getMaximumMappingQual()
Deprecated.
|
char |
getRefBase()
Deprecated.
|
int |
getStart()
Deprecated.
Return the start position in 1-based coordinates (first base is 1)
|
public GeliTextFeature(java.lang.String contig, long position, char refBase, int depthOfCoverage, int maximumMappingQual, DiploidGenotype genotype, double LODBestToReference, double LODBestToNext, double[] likelihoods)
contig
- the contigposition
- the position on the contigrefBase
- the reference basedepthOfCoverage
- the depth of coverage at this positionmaximumMappingQual
- the maximum mapping quality of a read at this positiongenotype
- the called genotypeLODBestToReference
- the LOD score of the best to the referenceLODBestToNext
- the LOD score of the best to the next best genotypelikelihoods
- the array of all genotype likelihoods, in ordinal orderingpublic java.lang.String getContig()
Locatable
public int getStart()
public int getEnd()
public char getRefBase()
public int getDepthOfCoverage()
public int getMaximumMappingQual()
public DiploidGenotype getGenotype()
public double getLODBestToNext()
public double getLODBestToReference()
public double[] getLikelihoods()
public boolean equals(java.lang.Object o)
equals
in class java.lang.Object