java.lang.Object
- htsjdk.samtools.metrics.MetricBase
- - picard.analysis.MergeableMetricBase
  - - picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
    - - picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics

Enclosing class:: CollectArraysVariantCallingMetrics

public static class CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics
extends CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics

Nested Class Summary
- Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase
  MergeableMetricBase.MergeByAdding, MergeableMetricBase.MergeByAssertEquals, MergeableMetricBase.MergingIsManual, MergeableMetricBase.NoMergingIsDerived, MergeableMetricBase.NoMergingKeepsValue

Field Summary

Fields
Modifier and Type	Field	Description
`Integer`	`ANALYSIS_VERSION`	The version number of the analysis run
`htsjdk.samtools.util.Iso8601Date`	`AUTOCALL_DATE`	The date this sample was autocalled
`String`	`AUTOCALL_GENDER`	The sex, as determined by Autocall
`Boolean`	`AUTOCALL_PF`	Whether the sample passes QC based on call rate threshold
`String`	`AUTOCALL_VERSION`	The version of autocall used for calling this sample
`String`	`CHIP_TYPE`	The chip type name
`String`	`CHIP_WELL_BARCODE`	The chip well barcode of the Illumina array being assayed
`String`	`CLUSTER_FILE_NAME`	The name of the cluster file used
`String`	`EXTENDED_MANIFEST_VERSION`	The version of the Extended Illumina Manifest used for calling this sample
`String`	`FP_GENDER`	The sex, as reported for the fingerprinted sample
`Boolean`	`GENDER_CONCORDANCE_PF`	Whether or not the three sexs agree
`Double`	`GTC_CALL_RATE`	The call rate as determined by Autocall/IAAP (and stored in the GTC File)
`double`	`HET_HOMVAR_RATIO`	(count of hets)/(count of homozygous non-ref) for this sample
`double`	`HET_PCT`	100 * (count of hets) / (total calls) for this sample
`htsjdk.samtools.util.Iso8601Date`	`IMAGING_DATE`	The date that this sample was imaged
`Boolean`	`IS_ZCALLED`	Whether the sample was zcalled
`Integer`	`P95_GREEN`	The 95th Intensity Percentile for the green color channel for this sample
`Integer`	`P95_RED`	The 95th Intensity Percentile for the red color channel for this sample
`String`	`PIPELINE_VERSION`	The version of the pipeline used for this sample
`String`	`REPORTED_GENDER`	The sex, as reported by the collaborator
`String`	`SAMPLE_ALIAS`	The name of the sample
`String`	`SCANNER_NAME`	The name of the scanner used for this sample
`String`	`ZCALL_VERSION`	The version of ZCall used for calling this sample

Fields inherited from class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
AUTOCALL_CALL_RATE, CALL_RATE, NOVEL_SNPS, NUM_ASSAYS, NUM_AUTOCALL_CALLS, NUM_CALLS, NUM_FILTERED_ASSAYS, NUM_IN_DB_SNP, NUM_INDELS, NUM_NO_CALLS, NUM_NON_FILTERED_ASSAYS, NUM_SINGLETONS, NUM_SNPS, NUM_ZEROED_OUT_ASSAYS, PCT_DBSNP

Constructor Summary

Constructors
Constructor Description

ArraysVariantCallingDetailMetrics()

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`calculateDerivedFields()`	Placeholder method that will calculate the derived fields from the other ones.
`static String`	`getFileExtension()`

Methods inherited from class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
foldInto

Methods inherited from class picard.analysis.MergeableMetricBase
canMerge, merge, merge, mergeIfCan

Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString

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

- Field Detail
  - CHIP_WELL_BARCODE
```
public String CHIP_WELL_BARCODE
```
    The chip well barcode of the Illumina array being assayed
  - SAMPLE_ALIAS
```
public String SAMPLE_ALIAS
```
    The name of the sample
  - ANALYSIS_VERSION
```
public Integer ANALYSIS_VERSION
```
    The version number of the analysis run
  - CHIP_TYPE
```
public String CHIP_TYPE
```
    The chip type name
  - AUTOCALL_PF
```
public Boolean AUTOCALL_PF
```
    Whether the sample passes QC based on call rate threshold
  - AUTOCALL_DATE
```
public htsjdk.samtools.util.Iso8601Date AUTOCALL_DATE
```
    The date this sample was autocalled
  - IMAGING_DATE
```
public htsjdk.samtools.util.Iso8601Date IMAGING_DATE
```
    The date that this sample was imaged
  - IS_ZCALLED
```
public Boolean IS_ZCALLED
```
    Whether the sample was zcalled
  - GTC_CALL_RATE
```
public Double GTC_CALL_RATE
```
    The call rate as determined by Autocall/IAAP (and stored in the GTC File)
  - AUTOCALL_GENDER
```
public String AUTOCALL_GENDER
```
    The sex, as determined by Autocall
  - FP_GENDER
```
public String FP_GENDER
```
    The sex, as reported for the fingerprinted sample
  - REPORTED_GENDER
```
public String REPORTED_GENDER
```
    The sex, as reported by the collaborator
  - GENDER_CONCORDANCE_PF
```
public Boolean GENDER_CONCORDANCE_PF
```
    Whether or not the three sexs agree
  - HET_PCT
```
public double HET_PCT
```
    100 * (count of hets) / (total calls) for this sample
  - CLUSTER_FILE_NAME
```
public String CLUSTER_FILE_NAME
```
    The name of the cluster file used
  - P95_GREEN
```
public Integer P95_GREEN
```
    The 95th Intensity Percentile for the green color channel for this sample
  - P95_RED
```
public Integer P95_RED
```
    The 95th Intensity Percentile for the red color channel for this sample
  - AUTOCALL_VERSION
```
public String AUTOCALL_VERSION
```
    The version of autocall used for calling this sample
  - ZCALL_VERSION
```
public String ZCALL_VERSION
```
    The version of ZCall used for calling this sample
  - EXTENDED_MANIFEST_VERSION
```
public String EXTENDED_MANIFEST_VERSION
```
    The version of the Extended Illumina Manifest used for calling this sample
  - HET_HOMVAR_RATIO
```
public double HET_HOMVAR_RATIO
```
    (count of hets)/(count of homozygous non-ref) for this sample
  - SCANNER_NAME
```
public String SCANNER_NAME
```
    The name of the scanner used for this sample
  - PIPELINE_VERSION
```
public String PIPELINE_VERSION
```
    The version of the pipeline used for this sample
- Constructor Detail
  - ArraysVariantCallingDetailMetrics
```
public ArraysVariantCallingDetailMetrics()
```
- Method Detail
  - calculateDerivedFields
```
public void calculateDerivedFields()
```
    Description copied from class: MergeableMetricBase
    
    Placeholder method that will calculate the derived fields from the other ones. Classes that are derived from non-trivial derived classes should consider calling super.calculateDerivedFields() as well. Fields whose value will change due to this method should be annotated with NoMergingKeepsValue.
    
    Overrides:
    
    calculateDerivedFields in class CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics
  - getFileExtension
```
public static String getFileExtension()
```

Class CollectArraysVariantCallingMetrics.ArraysVariantCallingDetailMetrics

Nested Class Summary

Nested classes/interfaces inherited from class picard.analysis.MergeableMetricBase

Field Summary

Fields inherited from class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics

Constructor Summary

Method Summary

Methods inherited from class picard.arrays.CollectArraysVariantCallingMetrics.ArraysVariantCallingSummaryMetrics

Methods inherited from class picard.analysis.MergeableMetricBase

Methods inherited from class htsjdk.samtools.metrics.MetricBase

Methods inherited from class java.lang.Object

Field Detail

CHIP_WELL_BARCODE

SAMPLE_ALIAS

ANALYSIS_VERSION

CHIP_TYPE

AUTOCALL_PF

AUTOCALL_DATE

IMAGING_DATE

IS_ZCALLED

GTC_CALL_RATE

AUTOCALL_GENDER

FP_GENDER

REPORTED_GENDER

GENDER_CONCORDANCE_PF

HET_PCT

CLUSTER_FILE_NAME

P95_GREEN

P95_RED

AUTOCALL_VERSION

ZCALL_VERSION

EXTENDED_MANIFEST_VERSION

HET_HOMVAR_RATIO

SCANNER_NAME

PIPELINE_VERSION

Constructor Detail

ArraysVariantCallingDetailMetrics

Method Detail

calculateDerivedFields

getFileExtension