VariantCallingAnnotations (Big Data Genomics: Avro Formats 0.15.0 API)

java.lang.Object
- org.apache.avro.specific.SpecificRecordBase
- - org.bdgenomics.formats.avro.VariantCallingAnnotations

All Implemented Interfaces:

Externalizable, Serializable, Comparable<org.apache.avro.specific.SpecificRecord>, org.apache.avro.generic.GenericContainer, org.apache.avro.generic.GenericRecord, org.apache.avro.generic.IndexedRecord, org.apache.avro.specific.SpecificRecord
```
public class VariantCallingAnnotations
extends org.apache.avro.specific.SpecificRecordBase
implements org.apache.avro.specific.SpecificRecord
```
See Also:

Serialized Form

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

static class VariantCallingAnnotations.Builder
RecordBuilder for VariantCallingAnnotations instances.

Nested Classes
Modifier and Type	Class and Description
`static class`	`VariantCallingAnnotations.Builder` RecordBuilder for VariantCallingAnnotations instances.

Field Summary

Fields
Modifier and Type	Field and Description
`Map<String,String>`	`attributes` Deprecated.
`Float`	`baseQRankSum` Deprecated.
`String`	`culprit` Deprecated.
`Boolean`	`downsampled` Deprecated.
`Boolean`	`filtersApplied` Deprecated.
`List<String>`	`filtersFailed` Deprecated.
`Boolean`	`filtersPassed` Deprecated.
`Float`	`fisherStrandBiasPValue` Deprecated.
`List<Float>`	`genotypePosteriors` Deprecated.
`List<Float>`	`genotypePriors` Deprecated.
`Integer`	`mapq0Reads` Deprecated.
`Float`	`mqRankSum` Deprecated.
`Float`	`readPositionRankSum` Deprecated.
`Float`	`rmsMapQ` Deprecated.
`static org.apache.avro.Schema`	`SCHEMA$`
`Float`	`vqslod` Deprecated.

Constructor Summary

Constructors
Constructor and Description
`VariantCallingAnnotations()` Default constructor.
`VariantCallingAnnotations(Boolean filtersApplied, Boolean filtersPassed, List<String> filtersFailed, Boolean downsampled, Float baseQRankSum, Float fisherStrandBiasPValue, Float rmsMapQ, Integer mapq0Reads, Float mqRankSum, Float readPositionRankSum, List<Float> genotypePriors, List<Float> genotypePosteriors, Float vqslod, String culprit, Map<String,String> attributes)` All-args constructor.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`static org.apache.avro.message.BinaryMessageDecoder<VariantCallingAnnotations>`	`createDecoder(org.apache.avro.message.SchemaStore resolver)` Create a new BinaryMessageDecoder instance for this class that uses the specified `SchemaStore`.
`static VariantCallingAnnotations`	`fromByteBuffer(ByteBuffer b)` Deserializes a VariantCallingAnnotations from a ByteBuffer.
`Object`	`get(int field$)`
`Map<String,String>`	`getAttributes()` Gets the value of the 'attributes' field.
`Float`	`getBaseQRankSum()` Gets the value of the 'baseQRankSum' field.
`static org.apache.avro.Schema`	`getClassSchema()`
`String`	`getCulprit()` Gets the value of the 'culprit' field.
`static org.apache.avro.message.BinaryMessageDecoder<VariantCallingAnnotations>`	`getDecoder()` Return the BinaryMessageDecoder instance used by this class.
`Boolean`	`getDownsampled()` Gets the value of the 'downsampled' field.
`Boolean`	`getFiltersApplied()` Gets the value of the 'filtersApplied' field.
`List<String>`	`getFiltersFailed()` Gets the value of the 'filtersFailed' field.
`Boolean`	`getFiltersPassed()` Gets the value of the 'filtersPassed' field.
`Float`	`getFisherStrandBiasPValue()` Gets the value of the 'fisherStrandBiasPValue' field.
`List<Float>`	`getGenotypePosteriors()` Gets the value of the 'genotypePosteriors' field.
`List<Float>`	`getGenotypePriors()` Gets the value of the 'genotypePriors' field.
`Integer`	`getMapq0Reads()` Gets the value of the 'mapq0Reads' field.
`Float`	`getMqRankSum()` Gets the value of the 'mqRankSum' field.
`Float`	`getReadPositionRankSum()` Gets the value of the 'readPositionRankSum' field.
`Float`	`getRmsMapQ()` Gets the value of the 'rmsMapQ' field.
`org.apache.avro.Schema`	`getSchema()`
`Float`	`getVqslod()` Gets the value of the 'vqslod' field.
`static VariantCallingAnnotations.Builder`	`newBuilder()` Creates a new VariantCallingAnnotations RecordBuilder.
`static VariantCallingAnnotations.Builder`	`newBuilder(VariantCallingAnnotations.Builder other)` Creates a new VariantCallingAnnotations RecordBuilder by copying an existing Builder.
`static VariantCallingAnnotations.Builder`	`newBuilder(VariantCallingAnnotations other)` Creates a new VariantCallingAnnotations RecordBuilder by copying an existing VariantCallingAnnotations instance.
`void`	`put(int field$, Object value$)`
`void`	`readExternal(ObjectInput in)`
`void`	`setAttributes(Map<String,String> value)` Sets the value of the 'attributes' field.
`void`	`setBaseQRankSum(Float value)` Sets the value of the 'baseQRankSum' field.
`void`	`setCulprit(String value)` Sets the value of the 'culprit' field.
`void`	`setDownsampled(Boolean value)` Sets the value of the 'downsampled' field.
`void`	`setFiltersApplied(Boolean value)` Sets the value of the 'filtersApplied' field.
`void`	`setFiltersFailed(List<String> value)` Sets the value of the 'filtersFailed' field.
`void`	`setFiltersPassed(Boolean value)` Sets the value of the 'filtersPassed' field.
`void`	`setFisherStrandBiasPValue(Float value)` Sets the value of the 'fisherStrandBiasPValue' field.
`void`	`setGenotypePosteriors(List<Float> value)` Sets the value of the 'genotypePosteriors' field.
`void`	`setGenotypePriors(List<Float> value)` Sets the value of the 'genotypePriors' field.
`void`	`setMapq0Reads(Integer value)` Sets the value of the 'mapq0Reads' field.
`void`	`setMqRankSum(Float value)` Sets the value of the 'mqRankSum' field.
`void`	`setReadPositionRankSum(Float value)` Sets the value of the 'readPositionRankSum' field.
`void`	`setRmsMapQ(Float value)` Sets the value of the 'rmsMapQ' field.
`void`	`setVqslod(Float value)` Sets the value of the 'vqslod' field.
`ByteBuffer`	`toByteBuffer()` Serializes this VariantCallingAnnotations to a ByteBuffer.
`void`	`writeExternal(ObjectOutput out)`

Methods inherited from class org.apache.avro.specific.SpecificRecordBase
compareTo, equals, get, getConverion, getConversion, getConversion, hashCode, put, toString

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

- Field Detail
  - SCHEMA$
```
public static final org.apache.avro.Schema SCHEMA$
```
  - filtersApplied
```
@Deprecated
public Boolean filtersApplied
```
    Deprecated.
    
    True if filters were applied for this genotype call. FORMAT field "FT" any value other than the missing value.
  - filtersPassed
```
@Deprecated
public Boolean filtersPassed
```
    Deprecated.
    
    True if all filters for this genotype call passed. FORMAT field "FT" value PASS.
  - filtersFailed
```
@Deprecated
public List<String> filtersFailed
```
    Deprecated.
    
    Zero or more filters that failed for this genotype call from FORMAT field "FT".
  - downsampled
```
@Deprecated
public Boolean downsampled
```
    Deprecated.
    
    True if the reads covering this site were randomly downsampled to reduce coverage.
  - baseQRankSum
```
@Deprecated
public Float baseQRankSum
```
    Deprecated.
    
    The Wilcoxon rank-sum test statistic of the base quality scores. The base quality scores are separated by whether or not the base supports the reference or the alternate allele.
  - fisherStrandBiasPValue
```
@Deprecated
public Float fisherStrandBiasPValue
```
    Deprecated.
    
    The Fisher's exact test score for the strand bias of the reference and alternate alleles. Stored as a phred scaled probability. Thus, if: a = The number of positive strand reads covering the reference allele b = The number of positive strand reads covering the alternate allele c = The number of negative strand reads covering the reference allele d = The number of negative strand reads covering the alternate allele This value takes the score: -10 log((a + b)! * (c + d)! * (a + c)! * (b + d)! / (a! b! c! d! n!) Where n = a + b + c + d.
  - rmsMapQ
```
@Deprecated
public Float rmsMapQ
```
    Deprecated.
    
    The root mean square of the mapping qualities of reads covering this site.
  - mapq0Reads
```
@Deprecated
public Integer mapq0Reads
```
    Deprecated.
    
    The number of reads at this site with mapping quality equal to 0.
  - mqRankSum
```
@Deprecated
public Float mqRankSum
```
    Deprecated.
    
    The Wilcoxon rank-sum test statistic of the mapping quality scores. The mapping quality scores are separated by whether or not the read supported the reference or the alternate allele.
  - readPositionRankSum
```
@Deprecated
public Float readPositionRankSum
```
    Deprecated.
    
    The Wilcoxon rank-sum test statistic of the position of the base in the read at this site. The positions are separated by whether or not the base supports the reference or the alternate allele.
  - genotypePriors
```
@Deprecated
public List<Float> genotypePriors
```
    Deprecated.
    
    The log scale prior probabilities of the various genotype states at this site. The number of elements in this array should be equal to the ploidy at this site, plus 1.
  - genotypePosteriors
```
@Deprecated
public List<Float> genotypePosteriors
```
    Deprecated.
    
    The log scaled posterior probabilities of the various genotype states at this site, in this sample. The number of elements in this array should be equal to the ploidy at this site, plus 1.
  - vqslod
```
@Deprecated
public Float vqslod
```
    Deprecated.
    
    The log-odds ratio of being a true vs. false variant under a trained statistical model. This model can be a multivariate Gaussian mixture, support vector machine, etc.
  - culprit
```
@Deprecated
public String culprit
```
    Deprecated.
    
    If known, the feature that contributed the most to this variant being classified as a false variant.
  - attributes
```
@Deprecated
public Map<String,String> attributes
```
    Deprecated.
    
    Additional feature info that doesn't fit into the standard fields above. They are all encoded as (string, string) key-value pairs.
- Constructor Detail
  - VariantCallingAnnotations
```
public VariantCallingAnnotations()
```
    Default constructor. Note that this does not initialize fields to their default values from the schema. If that is desired then one should use newBuilder().
  - VariantCallingAnnotations
```
public VariantCallingAnnotations(Boolean filtersApplied,
                                 Boolean filtersPassed,
                                 List<String> filtersFailed,
                                 Boolean downsampled,
                                 Float baseQRankSum,
                                 Float fisherStrandBiasPValue,
                                 Float rmsMapQ,
                                 Integer mapq0Reads,
                                 Float mqRankSum,
                                 Float readPositionRankSum,
                                 List<Float> genotypePriors,
                                 List<Float> genotypePosteriors,
                                 Float vqslod,
                                 String culprit,
                                 Map<String,String> attributes)
```
    All-args constructor.
    
    Parameters:
    
    filtersApplied - True if filters were applied for this genotype call. FORMAT field "FT" any value other than the missing value.
    
    filtersPassed - True if all filters for this genotype call passed. FORMAT field "FT" value PASS.
    
    filtersFailed - Zero or more filters that failed for this genotype call from FORMAT field "FT".
    
    downsampled - True if the reads covering this site were randomly downsampled to reduce coverage.
    
    baseQRankSum - The Wilcoxon rank-sum test statistic of the base quality scores. The base quality scores are separated by whether or not the base supports the reference or the alternate allele.
    
    fisherStrandBiasPValue - The Fisher's exact test score for the strand bias of the reference and alternate alleles. Stored as a phred scaled probability. Thus, if: a = The number of positive strand reads covering the reference allele b = The number of positive strand reads covering the alternate allele c = The number of negative strand reads covering the reference allele d = The number of negative strand reads covering the alternate allele This value takes the score: -10 log((a + b)! * (c + d)! * (a + c)! * (b + d)! / (a! b! c! d! n!) Where n = a + b + c + d.
    
    rmsMapQ - The root mean square of the mapping qualities of reads covering this site.
    
    mapq0Reads - The number of reads at this site with mapping quality equal to 0.
    
    mqRankSum - The Wilcoxon rank-sum test statistic of the mapping quality scores. The mapping quality scores are separated by whether or not the read supported the reference or the alternate allele.
    
    readPositionRankSum - The Wilcoxon rank-sum test statistic of the position of the base in the read at this site. The positions are separated by whether or not the base supports the reference or the alternate allele.
    
    genotypePriors - The log scale prior probabilities of the various genotype states at this site. The number of elements in this array should be equal to the ploidy at this site, plus 1.
    
    genotypePosteriors - The log scaled posterior probabilities of the various genotype states at this site, in this sample. The number of elements in this array should be equal to the ploidy at this site, plus 1.
    
    vqslod - The log-odds ratio of being a true vs. false variant under a trained statistical model. This model can be a multivariate Gaussian mixture, support vector machine, etc.
    
    culprit - If known, the feature that contributed the most to this variant being classified as a false variant.
    
    attributes - Additional feature info that doesn't fit into the standard fields above. They are all encoded as (string, string) key-value pairs.
- Method Detail
  - getClassSchema
```
public static org.apache.avro.Schema getClassSchema()
```
  - getDecoder
```
public static org.apache.avro.message.BinaryMessageDecoder<VariantCallingAnnotations> getDecoder()
```
    Return the BinaryMessageDecoder instance used by this class.
  - createDecoder
```
public static org.apache.avro.message.BinaryMessageDecoder<VariantCallingAnnotations> createDecoder(org.apache.avro.message.SchemaStore resolver)
```
    Create a new BinaryMessageDecoder instance for this class that uses the specified SchemaStore.
    
    Parameters:
    
    resolver - a SchemaStore used to find schemas by fingerprint
  - toByteBuffer
```
public ByteBuffer toByteBuffer()
                        throws IOException
```
    Serializes this VariantCallingAnnotations to a ByteBuffer.
    
    Throws:
    
    IOException
  - fromByteBuffer
```
public static VariantCallingAnnotations fromByteBuffer(ByteBuffer b)
                                                throws IOException
```
    Deserializes a VariantCallingAnnotations from a ByteBuffer.
    
    Throws:
    
    IOException
  - getSchema
```
public org.apache.avro.Schema getSchema()
```
    Specified by:
    
    getSchema in interface org.apache.avro.generic.GenericContainer
    
    Specified by:
    
    getSchema in class org.apache.avro.specific.SpecificRecordBase
  - get
```
public Object get(int field$)
```
    Specified by:
    
    get in interface org.apache.avro.generic.IndexedRecord
    
    Specified by:
    
    get in class org.apache.avro.specific.SpecificRecordBase
  - put
```
public void put(int field$,
                Object value$)
```
    Specified by:
    
    put in interface org.apache.avro.generic.IndexedRecord
    
    Specified by:
    
    put in class org.apache.avro.specific.SpecificRecordBase
  - getFiltersApplied
```
public Boolean getFiltersApplied()
```
    Gets the value of the 'filtersApplied' field.
    
    Returns:
    
    True if filters were applied for this genotype call. FORMAT field "FT" any value other than the missing value.
  - setFiltersApplied
```
public void setFiltersApplied(Boolean value)
```
    Sets the value of the 'filtersApplied' field. True if filters were applied for this genotype call. FORMAT field "FT" any value other than the missing value.
    
    Parameters:
    
    value - the value to set.
  - getFiltersPassed
```
public Boolean getFiltersPassed()
```
    Gets the value of the 'filtersPassed' field.
    
    Returns:
    
    True if all filters for this genotype call passed. FORMAT field "FT" value PASS.
  - setFiltersPassed
```
public void setFiltersPassed(Boolean value)
```
    Sets the value of the 'filtersPassed' field. True if all filters for this genotype call passed. FORMAT field "FT" value PASS.
    
    Parameters:
    
    value - the value to set.
  - getFiltersFailed
```
public List<String> getFiltersFailed()
```
    Gets the value of the 'filtersFailed' field.
    
    Returns:
    
    Zero or more filters that failed for this genotype call from FORMAT field "FT".
  - setFiltersFailed
```
public void setFiltersFailed(List<String> value)
```
    Sets the value of the 'filtersFailed' field. Zero or more filters that failed for this genotype call from FORMAT field "FT".
    
    Parameters:
    
    value - the value to set.
  - getDownsampled
```
public Boolean getDownsampled()
```
    Gets the value of the 'downsampled' field.
    
    Returns:
    
    True if the reads covering this site were randomly downsampled to reduce coverage.
  - setDownsampled
```
public void setDownsampled(Boolean value)
```
    Sets the value of the 'downsampled' field. True if the reads covering this site were randomly downsampled to reduce coverage.
    
    Parameters:
    
    value - the value to set.
  - getBaseQRankSum
```
public Float getBaseQRankSum()
```
    Gets the value of the 'baseQRankSum' field.
    
    Returns:
    
    The Wilcoxon rank-sum test statistic of the base quality scores. The base quality scores are separated by whether or not the base supports the reference or the alternate allele.
  - setBaseQRankSum
```
public void setBaseQRankSum(Float value)
```
    Sets the value of the 'baseQRankSum' field. The Wilcoxon rank-sum test statistic of the base quality scores. The base quality scores are separated by whether or not the base supports the reference or the alternate allele.
    
    Parameters:
    
    value - the value to set.
  - getFisherStrandBiasPValue
```
public Float getFisherStrandBiasPValue()
```
    Gets the value of the 'fisherStrandBiasPValue' field.
    
    Returns:
    
    The Fisher's exact test score for the strand bias of the reference and alternate alleles. Stored as a phred scaled probability. Thus, if: a = The number of positive strand reads covering the reference allele b = The number of positive strand reads covering the alternate allele c = The number of negative strand reads covering the reference allele d = The number of negative strand reads covering the alternate allele This value takes the score: -10 log((a + b)! * (c + d)! * (a + c)! * (b + d)! / (a! b! c! d! n!) Where n = a + b + c + d.
  - setFisherStrandBiasPValue
```
public void setFisherStrandBiasPValue(Float value)
```
    Sets the value of the 'fisherStrandBiasPValue' field. The Fisher's exact test score for the strand bias of the reference and alternate alleles. Stored as a phred scaled probability. Thus, if: a = The number of positive strand reads covering the reference allele b = The number of positive strand reads covering the alternate allele c = The number of negative strand reads covering the reference allele d = The number of negative strand reads covering the alternate allele This value takes the score: -10 log((a + b)! * (c + d)! * (a + c)! * (b + d)! / (a! b! c! d! n!) Where n = a + b + c + d.
    
    Parameters:
    
    value - the value to set.
  - getRmsMapQ
```
public Float getRmsMapQ()
```
    Gets the value of the 'rmsMapQ' field.
    
    Returns:
    
    The root mean square of the mapping qualities of reads covering this site.
  - setRmsMapQ
```
public void setRmsMapQ(Float value)
```
    Sets the value of the 'rmsMapQ' field. The root mean square of the mapping qualities of reads covering this site.
    
    Parameters:
    
    value - the value to set.
  - getMapq0Reads
```
public Integer getMapq0Reads()
```
    Gets the value of the 'mapq0Reads' field.
    
    Returns:
    
    The number of reads at this site with mapping quality equal to 0.
  - setMapq0Reads
```
public void setMapq0Reads(Integer value)
```
    Sets the value of the 'mapq0Reads' field. The number of reads at this site with mapping quality equal to 0.
    
    Parameters:
    
    value - the value to set.
  - getMqRankSum
```
public Float getMqRankSum()
```
    Gets the value of the 'mqRankSum' field.
    
    Returns:
    
    The Wilcoxon rank-sum test statistic of the mapping quality scores. The mapping quality scores are separated by whether or not the read supported the reference or the alternate allele.
  - setMqRankSum
```
public void setMqRankSum(Float value)
```
    Sets the value of the 'mqRankSum' field. The Wilcoxon rank-sum test statistic of the mapping quality scores. The mapping quality scores are separated by whether or not the read supported the reference or the alternate allele.
    
    Parameters:
    
    value - the value to set.
  - getReadPositionRankSum
```
public Float getReadPositionRankSum()
```
    Gets the value of the 'readPositionRankSum' field.
    
    Returns:
    
    The Wilcoxon rank-sum test statistic of the position of the base in the read at this site. The positions are separated by whether or not the base supports the reference or the alternate allele.
  - setReadPositionRankSum
```
public void setReadPositionRankSum(Float value)
```
    Sets the value of the 'readPositionRankSum' field. The Wilcoxon rank-sum test statistic of the position of the base in the read at this site. The positions are separated by whether or not the base supports the reference or the alternate allele.
    
    Parameters:
    
    value - the value to set.
  - getGenotypePriors
```
public List<Float> getGenotypePriors()
```
    Gets the value of the 'genotypePriors' field.
    
    Returns:
    
    The log scale prior probabilities of the various genotype states at this site. The number of elements in this array should be equal to the ploidy at this site, plus 1.
  - setGenotypePriors
```
public void setGenotypePriors(List<Float> value)
```
    Sets the value of the 'genotypePriors' field. The log scale prior probabilities of the various genotype states at this site. The number of elements in this array should be equal to the ploidy at this site, plus 1.
    
    Parameters:
    
    value - the value to set.
  - getGenotypePosteriors
```
public List<Float> getGenotypePosteriors()
```
    Gets the value of the 'genotypePosteriors' field.
    
    Returns:
    
    The log scaled posterior probabilities of the various genotype states at this site, in this sample. The number of elements in this array should be equal to the ploidy at this site, plus 1.
  - setGenotypePosteriors
```
public void setGenotypePosteriors(List<Float> value)
```
    Sets the value of the 'genotypePosteriors' field. The log scaled posterior probabilities of the various genotype states at this site, in this sample. The number of elements in this array should be equal to the ploidy at this site, plus 1.
    
    Parameters:
    
    value - the value to set.
  - getVqslod
```
public Float getVqslod()
```
    Gets the value of the 'vqslod' field.
    
    Returns:
    
    The log-odds ratio of being a true vs. false variant under a trained statistical model. This model can be a multivariate Gaussian mixture, support vector machine, etc.
  - setVqslod
```
public void setVqslod(Float value)
```
    Sets the value of the 'vqslod' field. The log-odds ratio of being a true vs. false variant under a trained statistical model. This model can be a multivariate Gaussian mixture, support vector machine, etc.
    
    Parameters:
    
    value - the value to set.
  - getCulprit
```
public String getCulprit()
```
    Gets the value of the 'culprit' field.
    
    Returns:
    
    If known, the feature that contributed the most to this variant being classified as a false variant.
  - setCulprit
```
public void setCulprit(String value)
```
    Sets the value of the 'culprit' field. If known, the feature that contributed the most to this variant being classified as a false variant.
    
    Parameters:
    
    value - the value to set.
  - getAttributes
```
public Map<String,String> getAttributes()
```
    Gets the value of the 'attributes' field.
    
    Returns:
    
    Additional feature info that doesn't fit into the standard fields above. They are all encoded as (string, string) key-value pairs.
  - setAttributes
```
public void setAttributes(Map<String,String> value)
```
    Sets the value of the 'attributes' field. Additional feature info that doesn't fit into the standard fields above. They are all encoded as (string, string) key-value pairs.
    
    Parameters:
    
    value - the value to set.
  - newBuilder
```
public static VariantCallingAnnotations.Builder newBuilder()
```
    Creates a new VariantCallingAnnotations RecordBuilder.
    
    Returns:
    
    A new VariantCallingAnnotations RecordBuilder
  - newBuilder
```
public static VariantCallingAnnotations.Builder newBuilder(VariantCallingAnnotations.Builder other)
```
    Creates a new VariantCallingAnnotations RecordBuilder by copying an existing Builder.
    
    Parameters:
    
    other - The existing builder to copy.
    
    Returns:
    
    A new VariantCallingAnnotations RecordBuilder
  - newBuilder
```
public static VariantCallingAnnotations.Builder newBuilder(VariantCallingAnnotations other)
```
    Creates a new VariantCallingAnnotations RecordBuilder by copying an existing VariantCallingAnnotations instance.
    
    Parameters:
    
    other - The existing instance to copy.
    
    Returns:
    
    A new VariantCallingAnnotations RecordBuilder
  - writeExternal
```
public void writeExternal(ObjectOutput out)
                   throws IOException
```
    Specified by:
    
    writeExternal in interface Externalizable
    
    Overrides:
    
    writeExternal in class org.apache.avro.specific.SpecificRecordBase
    
    Throws:
    
    IOException
  - readExternal
```
public void readExternal(ObjectInput in)
                  throws IOException
```
    Specified by:
    
    readExternal in interface Externalizable
    
    Overrides:
    
    readExternal in class org.apache.avro.specific.SpecificRecordBase
    
    Throws:
    
    IOException

Class VariantCallingAnnotations

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class org.apache.avro.specific.SpecificRecordBase

Methods inherited from class java.lang.Object

Field Detail

SCHEMA$

filtersApplied

filtersPassed

filtersFailed

downsampled

baseQRankSum

fisherStrandBiasPValue

rmsMapQ

mapq0Reads

mqRankSum

readPositionRankSum

genotypePriors

genotypePosteriors

vqslod

culprit

attributes

Constructor Detail

VariantCallingAnnotations

VariantCallingAnnotations

Method Detail

getClassSchema

getDecoder

createDecoder

toByteBuffer

fromByteBuffer

getSchema

get

put

getFiltersApplied

setFiltersApplied

getFiltersPassed

setFiltersPassed

getFiltersFailed

setFiltersFailed

getDownsampled

setDownsampled

getBaseQRankSum

setBaseQRankSum

getFisherStrandBiasPValue

setFisherStrandBiasPValue

getRmsMapQ

setRmsMapQ

getMapq0Reads

setMapq0Reads

getMqRankSum

setMqRankSum

getReadPositionRankSum

setReadPositionRankSum

getGenotypePriors

setGenotypePriors

getGenotypePosteriors

setGenotypePosteriors

getVqslod

setVqslod

getCulprit

setCulprit

getAttributes

setAttributes

newBuilder

newBuilder

newBuilder

writeExternal

readExternal