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