Package picard.arrays.illumina
Class InfiniumVcfFields
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- picard.arrays.illumina.InfiniumVcfFields
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public class InfiniumVcfFields extends Object
A class to store fields that are specific to a VCF generated from an Illumina GTC file.
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
InfiniumVcfFields.GENOTYPE_VALUES
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Field Summary
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Constructor Summary
Constructors Constructor Description InfiniumVcfFields()
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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)
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Field Detail
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ARRAY_TYPE
public static final String ARRAY_TYPE
- See Also:
- Constant Field Values
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EXTENDED_ILLUMINA_MANIFEST_VERSION
public static final String EXTENDED_ILLUMINA_MANIFEST_VERSION
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- Constant Field Values
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CHIP_WELL_BARCODE
public static final String CHIP_WELL_BARCODE
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- Constant Field Values
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ANALYSIS_VERSION_NUMBER
public static final String ANALYSIS_VERSION_NUMBER
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- Constant Field Values
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SAMPLE_ALIAS
public static final String SAMPLE_ALIAS
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- Constant Field Values
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EXPECTED_GENDER
public static final String EXPECTED_GENDER
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- Constant Field Values
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FINGERPRINT_GENDER
public static final String FINGERPRINT_GENDER
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- Constant Field Values
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GTC_CALL_RATE
public static final String GTC_CALL_RATE
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- Constant Field Values
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AUTOCALL_GENDER
public static final String AUTOCALL_GENDER
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- Constant Field Values
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AUTOCALL_DATE
public static final String AUTOCALL_DATE
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- Constant Field Values
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IMAGING_DATE
public static final String IMAGING_DATE
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- Constant Field Values
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CLUSTER_FILE
public static final String CLUSTER_FILE
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- Constant Field Values
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MANIFEST_FILE
public static final String MANIFEST_FILE
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- Constant Field Values
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EXTENDED_ILLUMINA_MANIFEST_FILE
public static final String EXTENDED_ILLUMINA_MANIFEST_FILE
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- Constant Field Values
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AUTOCALL_VERSION
public static final String AUTOCALL_VERSION
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- Constant Field Values
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ZCALL_VERSION
public static final String ZCALL_VERSION
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- Constant Field Values
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ZCALL_THRESHOLDS
public static final String ZCALL_THRESHOLDS
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- Constant Field Values
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P_95_RED
public static final String P_95_RED
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- Constant Field Values
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P_95_GREEN
public static final String P_95_GREEN
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- Constant Field Values
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SCANNER_NAME
public static final String SCANNER_NAME
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- Constant Field Values
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PIPELINE_VERSION
public static final String PIPELINE_VERSION
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- Constant Field Values
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X
public static final String X
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- Constant Field Values
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Y
public static final String Y
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- Constant Field Values
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NORMX
public static final String NORMX
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- Constant Field Values
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NORMY
public static final String NORMY
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- Constant Field Values
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R
public static final String R
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- Constant Field Values
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THETA
public static final String THETA
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- Constant Field Values
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BAF
public static final String BAF
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- Constant Field Values
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LRR
public static final String LRR
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- Constant Field Values
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IGC
public static final String IGC
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- Constant Field Values
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GTA
public static final String GTA
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- Constant Field Values
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GTZ
public static final String GTZ
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- Constant Field Values
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ALLELE_A
public static final String ALLELE_A
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- Constant Field Values
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ALLELE_B
public static final String ALLELE_B
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- Constant Field Values
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ILLUMINA_STRAND
public static final String ILLUMINA_STRAND
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- Constant Field Values
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PROBE_A
public static final String PROBE_A
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- Constant Field Values
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PROBE_B
public static final String PROBE_B
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- Constant Field Values
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BEADSET_ID
public static final String BEADSET_ID
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- Constant Field Values
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ILLUMINA_CHR
public static final String ILLUMINA_CHR
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- Constant Field Values
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ILLUMINA_POS
public static final String ILLUMINA_POS
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- Constant Field Values
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ILLUMINA_BUILD
public static final String ILLUMINA_BUILD
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- Constant Field Values
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SOURCE
public static final String SOURCE
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- Constant Field Values
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GC_SCORE
public static final String GC_SCORE
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- Constant Field Values
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N
public static final String[] N
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MEAN_R
public static final String[] MEAN_R
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DEV_R
public static final String[] DEV_R
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MEAN_THETA
public static final String[] MEAN_THETA
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DEV_THETA
public static final String[] DEV_THETA
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MEAN_X
public static final String[] MEAN_X
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DEV_X
public static final String[] DEV_X
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MEAN_Y
public static final String[] MEAN_Y
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DEV_Y
public static final String[] DEV_Y
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RS_ID
public static final String RS_ID
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- Constant Field Values
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ZTHRESH_X
public static final String ZTHRESH_X
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- Constant Field Values
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ZTHRESH_Y
public static final String ZTHRESH_Y
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- Constant Field Values
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TRIALLELIC
public static final String TRIALLELIC
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- Constant Field Values
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DUPE
public static final String DUPE
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- Constant Field Values
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FAIL_REF
public static final String FAIL_REF
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- Constant Field Values
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ZEROED_OUT_ASSAY
public static final String ZEROED_OUT_ASSAY
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- Constant Field Values
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Method Detail
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getValueFromVcfOtherHeaderLine
public static String getValueFromVcfOtherHeaderLine(htsjdk.variant.vcf.VCFHeader vcfHeader, String keyName)
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getDateFromVcfOtherHeaderLine
public static htsjdk.samtools.util.Iso8601Date getDateFromVcfOtherHeaderLine(htsjdk.variant.vcf.VCFHeader vcfHeader, String keyName, SimpleDateFormat dateformat)
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getOptionalDoubleFromVcfOtherHeaderLine
public static Double getOptionalDoubleFromVcfOtherHeaderLine(htsjdk.variant.vcf.VCFHeader vcfHeader, String keyName)
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getIntegerFromVcfOtherHeaderLine
public static Integer getIntegerFromVcfOtherHeaderLine(htsjdk.variant.vcf.VCFHeader vcfHeader, String keyName)
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getOptionalIntegerFromVcfOtherHeaderLine
public static Integer getOptionalIntegerFromVcfOtherHeaderLine(htsjdk.variant.vcf.VCFHeader vcfHeader, String keyName)
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