java.lang.Object

picard.arrays.illumina.InfiniumVcfFields

public class InfiniumVcfFields extends Object

A class to store fields that are specific to a VCF generated from an Illumina GTC file.

Nested Class Summary

Nested Classes

Modifier and Type

Class

Description

static enum

InfiniumVcfFields.GENOTYPE_VALUES
Field Summary

Fields

Modifier and Type

Field

Description

static final String

ALLELE_A

static final String

ALLELE_B

static final String

ANALYSIS_VERSION_NUMBER

static final String

ARRAY_TYPE

static final String

AUTOCALL_DATE

static final String

AUTOCALL_GENDER

static final String

AUTOCALL_VERSION

static final String

BAF

static final String

BEADSET_ID

static final String

CHIP_WELL_BARCODE

static final String

CLUSTER_FILE

static final String[]

DEV_R

static final String[]

DEV_THETA

static final String[]

DEV_X

static final String[]

DEV_Y

static final String

DUPE

static final String

EXPECTED_GENDER

static final String

EXTENDED_ILLUMINA_MANIFEST_FILE

static final String

EXTENDED_ILLUMINA_MANIFEST_VERSION

static final String

FAIL_REF

static final String

FINGERPRINT_GENDER

static final String

GC_SCORE

static final String

GTA

static final String

GTC_CALL_RATE

static final String

GTC_CALL_RATE_DETAIL

static final String

GTZ

static final String

IGC

static final String

ILLUMINA_BUILD

static final String

ILLUMINA_CHR

static final String

ILLUMINA_POS

static final String

ILLUMINA_STRAND

static final String

IMAGING_DATE

static final String

LRR

static final String

MANIFEST_FILE

static final String[]

MEAN_R

static final String[]

MEAN_THETA

static final String[]

MEAN_X

static final String[]

MEAN_Y

static final String[]

N

static final String

NORMX

static final String

NORMY

static final String

P_95_GREEN

static final String

P_95_RED

static final String

PIPELINE_VERSION

static final String

PROBE_A

static final String

PROBE_B

static final String

R

static final String

RS_ID

static final String

SAMPLE_ALIAS

static final String

SCANNER_NAME

static final String

SOURCE

static final String

THETA

static final String

TRIALLELIC

static final String

X

static final String

Y

static final String

ZCALL_THRESHOLDS

static final String

ZCALL_VERSION

static final String

ZEROED_OUT_ASSAY

static final String

ZTHRESH_X

static final String

ZTHRESH_Y
Constructor Summary

Constructors

Constructor

Description

InfiniumVcfFields()
Method Summary

Modifier and Type

Method

Description

static htsjdk.samtools.util.Iso8601Date

getDateFromVcfOtherHeaderLine(htsjdk.variant.vcf.VCFHeader vcfHeader, String keyName, SimpleDateFormat dateformat)

static Integer

getIntegerFromVcfOtherHeaderLine(htsjdk.variant.vcf.VCFHeader vcfHeader, String keyName)

static Double

getOptionalDoubleFromVcfOtherHeaderLine(htsjdk.variant.vcf.VCFHeader vcfHeader, String keyName)

static Integer

getOptionalIntegerFromVcfOtherHeaderLine(htsjdk.variant.vcf.VCFHeader vcfHeader, String keyName)

static String

getOptionalValueFromVcfOtherHeaderLine(htsjdk.variant.vcf.VCFHeader vcfHeader, String keyName)

static String

getValueFromVcfOtherHeaderLine(htsjdk.variant.vcf.VCFHeader vcfHeader, String keyName)

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

Field Details
- ARRAY_TYPE
  
  public static final String ARRAY_TYPE
  See Also:
  
  Constant Field Values
- EXTENDED_ILLUMINA_MANIFEST_VERSION
  
  public static final String EXTENDED_ILLUMINA_MANIFEST_VERSION
  See Also:
  
  Constant Field Values
- CHIP_WELL_BARCODE
  
  public static final String CHIP_WELL_BARCODE
  See Also:
  
  Constant Field Values
- ANALYSIS_VERSION_NUMBER
  
  public static final String ANALYSIS_VERSION_NUMBER
  See Also:
  
  Constant Field Values
- SAMPLE_ALIAS
  
  public static final String SAMPLE_ALIAS
  See Also:
  
  Constant Field Values
- EXPECTED_GENDER
  
  public static final String EXPECTED_GENDER
  See Also:
  
  Constant Field Values
- FINGERPRINT_GENDER
  
  public static final String FINGERPRINT_GENDER
  See Also:
  
  Constant Field Values
- GTC_CALL_RATE
  
  public static final String GTC_CALL_RATE
  See Also:
  
  Constant Field Values
- GTC_CALL_RATE_DETAIL
  
  public static final String GTC_CALL_RATE_DETAIL
  See Also:
  
  Constant Field Values
- AUTOCALL_GENDER
  
  public static final String AUTOCALL_GENDER
  See Also:
  
  Constant Field Values
- AUTOCALL_DATE
  
  public static final String AUTOCALL_DATE
  See Also:
  
  Constant Field Values
- IMAGING_DATE
  
  public static final String IMAGING_DATE
  See Also:
  
  Constant Field Values
- CLUSTER_FILE
  
  public static final String CLUSTER_FILE
  See Also:
  
  Constant Field Values
- MANIFEST_FILE
  
  public static final String MANIFEST_FILE
  See Also:
  
  Constant Field Values
- EXTENDED_ILLUMINA_MANIFEST_FILE
  
  public static final String EXTENDED_ILLUMINA_MANIFEST_FILE
  See Also:
  
  Constant Field Values
- AUTOCALL_VERSION
  
  public static final String AUTOCALL_VERSION
  See Also:
  
  Constant Field Values
- ZCALL_VERSION
  
  public static final String ZCALL_VERSION
  See Also:
  
  Constant Field Values
- ZCALL_THRESHOLDS
  
  public static final String ZCALL_THRESHOLDS
  See Also:
  
  Constant Field Values
- P_95_RED
  
  public static final String P_95_RED
  See Also:
  
  Constant Field Values
- P_95_GREEN
  
  public static final String P_95_GREEN
  See Also:
  
  Constant Field Values
- SCANNER_NAME
  
  public static final String SCANNER_NAME
  See Also:
  
  Constant Field Values
- PIPELINE_VERSION
  
  public static final String PIPELINE_VERSION
  See Also:
  
  Constant Field Values
- X
  
  public static final String X
  See Also:
  
  Constant Field Values
- Y
  
  public static final String Y
  See Also:
  
  Constant Field Values
- NORMX
  
  public static final String NORMX
  See Also:
  
  Constant Field Values
- NORMY
  
  public static final String NORMY
  See Also:
  
  Constant Field Values
- R
  
  public static final String R
  See Also:
  
  Constant Field Values
- THETA
  
  public static final String THETA
  See Also:
  
  Constant Field Values
- BAF
  
  public static final String BAF
  See Also:
  
  Constant Field Values
- LRR
  
  public static final String LRR
  See Also:
  
  Constant Field Values
- IGC
  
  public static final String IGC
  See Also:
  
  Constant Field Values
- GTA
  
  public static final String GTA
  See Also:
  
  Constant Field Values
- GTZ
  
  public static final String GTZ
  See Also:
  
  Constant Field Values
- ALLELE_A
  
  public static final String ALLELE_A
  See Also:
  
  Constant Field Values
- ALLELE_B
  
  public static final String ALLELE_B
  See Also:
  
  Constant Field Values
- ILLUMINA_STRAND
  
  public static final String ILLUMINA_STRAND
  See Also:
  
  Constant Field Values
- PROBE_A
  
  public static final String PROBE_A
  See Also:
  
  Constant Field Values
- PROBE_B
  
  public static final String PROBE_B
  See Also:
  
  Constant Field Values
- BEADSET_ID
  
  public static final String BEADSET_ID
  See Also:
  
  Constant Field Values
- ILLUMINA_CHR
  
  public static final String ILLUMINA_CHR
  See Also:
  
  Constant Field Values
- ILLUMINA_POS
  
  public static final String ILLUMINA_POS
  See Also:
  
  Constant Field Values
- ILLUMINA_BUILD
  
  public static final String ILLUMINA_BUILD
  See Also:
  
  Constant Field Values
- SOURCE
  
  public static final String SOURCE
  See Also:
  
  Constant Field Values
- GC_SCORE
  
  public static final String GC_SCORE
  See Also:
  
  Constant Field Values
- N
  
  public static final String[] N
- MEAN_R
  
  public static final String[] MEAN_R
- DEV_R
  
  public static final String[] DEV_R
- MEAN_THETA
  
  public static final String[] MEAN_THETA
- DEV_THETA
  
  public static final String[] DEV_THETA
- MEAN_X
  
  public static final String[] MEAN_X
- DEV_X
  
  public static final String[] DEV_X
- MEAN_Y
  
  public static final String[] MEAN_Y
- DEV_Y
  
  public static final String[] DEV_Y
- RS_ID
  
  public static final String RS_ID
  See Also:
  
  Constant Field Values
- ZTHRESH_X
  
  public static final String ZTHRESH_X
  See Also:
  
  Constant Field Values
- ZTHRESH_Y
  
  public static final String ZTHRESH_Y
  See Also:
  
  Constant Field Values
- TRIALLELIC
  
  public static final String TRIALLELIC
  See Also:
  
  Constant Field Values
- DUPE
  
  public static final String DUPE
  See Also:
  
  Constant Field Values
- FAIL_REF
  
  public static final String FAIL_REF
  See Also:
  
  Constant Field Values
- ZEROED_OUT_ASSAY
  
  public static final String ZEROED_OUT_ASSAY
  See Also:
  
  Constant Field Values
Constructor Details
- InfiniumVcfFields
  
  public InfiniumVcfFields()
Method Details
- getValueFromVcfOtherHeaderLine
  
  public static String getValueFromVcfOtherHeaderLine(htsjdk.variant.vcf.VCFHeader vcfHeader, String keyName)
- getDateFromVcfOtherHeaderLine
  
  public static htsjdk.samtools.util.Iso8601Date getDateFromVcfOtherHeaderLine(htsjdk.variant.vcf.VCFHeader vcfHeader, String keyName, SimpleDateFormat dateformat)
- getOptionalDoubleFromVcfOtherHeaderLine
  
  public static Double getOptionalDoubleFromVcfOtherHeaderLine(htsjdk.variant.vcf.VCFHeader vcfHeader, String keyName)
- getIntegerFromVcfOtherHeaderLine
  
  public static Integer getIntegerFromVcfOtherHeaderLine(htsjdk.variant.vcf.VCFHeader vcfHeader, String keyName)
- getOptionalIntegerFromVcfOtherHeaderLine
  
  public static Integer getOptionalIntegerFromVcfOtherHeaderLine(htsjdk.variant.vcf.VCFHeader vcfHeader, String keyName)
- getOptionalValueFromVcfOtherHeaderLine
  
  public static String getOptionalValueFromVcfOtherHeaderLine(htsjdk.variant.vcf.VCFHeader vcfHeader, String keyName)

Class InfiniumVcfFields

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

ARRAY_TYPE

EXTENDED_ILLUMINA_MANIFEST_VERSION

CHIP_WELL_BARCODE

ANALYSIS_VERSION_NUMBER

SAMPLE_ALIAS

EXPECTED_GENDER

FINGERPRINT_GENDER

GTC_CALL_RATE

GTC_CALL_RATE_DETAIL

AUTOCALL_GENDER

AUTOCALL_DATE

IMAGING_DATE

CLUSTER_FILE

MANIFEST_FILE

EXTENDED_ILLUMINA_MANIFEST_FILE

AUTOCALL_VERSION

ZCALL_VERSION

ZCALL_THRESHOLDS

P_95_RED

P_95_GREEN

SCANNER_NAME

PIPELINE_VERSION

X

Y

NORMX

NORMY

R

THETA

BAF

LRR

IGC

GTA

GTZ

ALLELE_A

ALLELE_B

ILLUMINA_STRAND

PROBE_A

PROBE_B

BEADSET_ID

ILLUMINA_CHR

ILLUMINA_POS

ILLUMINA_BUILD

SOURCE

GC_SCORE

N

MEAN_R

DEV_R

MEAN_THETA

DEV_THETA

MEAN_X

DEV_X

MEAN_Y

DEV_Y

RS_ID

ZTHRESH_X

ZTHRESH_Y

TRIALLELIC

DUPE

FAIL_REF

ZEROED_OUT_ASSAY

Constructor Details

InfiniumVcfFields

Method Details

getValueFromVcfOtherHeaderLine

getDateFromVcfOtherHeaderLine

getOptionalDoubleFromVcfOtherHeaderLine

getIntegerFromVcfOtherHeaderLine

getOptionalIntegerFromVcfOtherHeaderLine

getOptionalValueFromVcfOtherHeaderLine