Package picard.arrays.illumina

## Class InfiniumVcfFields

- 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 class` | `InfiniumVcfFields.GENOTYPE_VALUES` |

  - ### Field Summary

    Fields
    Modifier and Type | Field | Description
    --- | --- | ---
    `static String` | `ALLELE_A` |
    `static String` | `ALLELE_B` |
    `static String` | `ANALYSIS_VERSION_NUMBER` |
    `static String` | `ARRAY_TYPE` |
    `static String` | `AUTOCALL_DATE` |
    `static String` | `AUTOCALL_GENDER` |
    `static String` | `AUTOCALL_VERSION` |
    `static String` | `BAF` |
    `static String` | `BEADSET_ID` |
    `static String` | `CHIP_WELL_BARCODE` |
    `static String` | `CLUSTER_FILE` |
    `static String[]` | `DEV_R` |
    `static String[]` | `DEV_THETA` |
    `static String[]` | `DEV_X` |
    `static String[]` | `DEV_Y` |
    `static String` | `DUPE` |
    `static String` | `EXPECTED_GENDER` |
    `static String` | `EXTENDED_ILLUMINA_MANIFEST_FILE` |
    `static String` | `EXTENDED_ILLUMINA_MANIFEST_VERSION` |
    `static String` | `FAIL_REF` |
    `static String` | `FINGERPRINT_GENDER` |
    `static String` | `GC_SCORE` |
    `static String` | `GTA` |
    `static String` | `GTC_CALL_RATE` |
    `static String` | `GTC_CALL_RATE_DETAIL` |
    `static String` | `GTZ` |
    `static String` | `IGC` |
    `static String` | `ILLUMINA_BUILD` |
    `static String` | `ILLUMINA_CHR` |
    `static String` | `ILLUMINA_POS` |
    `static String` | `ILLUMINA_STRAND` |
    `static String` | `IMAGING_DATE` |
    `static String` | `LRR` |
    `static String` | `MANIFEST_FILE` |
    `static String[]` | `MEAN_R` |
    `static String[]` | `MEAN_THETA` |
    `static String[]` | `MEAN_X` |
    `static String[]` | `MEAN_Y` |
    `static String[]` | `N` |
    `static String` | `NORMX` |
    `static String` | `NORMY` |
    `static String` | `P_95_GREEN` |
    `static String` | `P_95_RED` |
    `static String` | `PIPELINE_VERSION` |
    `static String` | `PROBE_A` |
    `static String` | `PROBE_B` |
    `static String` | `R` |
    `static String` | `RS_ID` |
    `static String` | `SAMPLE_ALIAS` |
    `static String` | `SCANNER_NAME` |
    `static String` | `SOURCE` |
    `static String` | `THETA` |
    `static String` | `TRIALLELIC` |
    `static String` | `X` |
    `static String` | `Y` |
    `static String` | `ZCALL_THRESHOLDS` |
    `static String` | `ZCALL_VERSION` |
    `static String` | `ZEROED_OUT_ASSAY` |
    `static String` | `ZTHRESH_X` |
    `static String` | `ZTHRESH_Y` |

  - ### Constructor Summary

    Constructors
    Constructor | Description
    --- | ---
    `InfiniumVcfFields()` |

  - ### Method Summary

    All Methods Static Methods Concrete Methods
    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 Detail

    - #### 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 Detail

    - #### InfiniumVcfFields

          public InfiniumVcfFields()

  - ### Method Detail

    - #### 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)