Package picard.arrays.illumina
Class Build37ExtendedIlluminaManifest
- java.lang.Object
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- picard.arrays.illumina.IlluminaManifest
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- picard.arrays.illumina.Build37ExtendedIlluminaManifest
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public class Build37ExtendedIlluminaManifest extends IlluminaManifest
A class to represent an 'Extended' Illumina Manifest file. An Extended Illumina Manifest extends a 'standard' Illumina Manifest by adding seven new fields (columns) to the manifest These are currently specific to the reference NCBI Build 37 / HG38. The columns are: 'build37Chr' - the chromosome of the manifest entry, on build 37 'build37Pos' - the position of the manifest entry, on build 37 'build37RefAllele' - the reference allele of the manifest entry, on build 37 'build37AlleleA' - allele A of the manifest entry, on build 37 'build37AlleleB' - allele B of the manifest entry, on build 37 'build37Rsid' - The rsid the manifest entry, on build 37 'build37Flag' - A flag describing the validation status of the manifest entry Like the class IlluminaManifest which this class extends, this class reads the extended manifest header, stores the contents, and then provides an iterator to allow access to the ExtendedIlluminaManifestRecords (currently this only supports iterating over the assay records).
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Field Summary
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Fields inherited from class picard.arrays.illumina.IlluminaManifest
ADDRESS_A_ID_HEADER_NAME, ADDRESS_B_ID_HEADER_NAME, ALLELE_A_PROBE_SEQ_HEADER_NAME, ALLELE_B_PROBE_SEQ_HEADER_NAME, BEAD_SET_ID_HEADER_NAME, CHROMOSOME_HEADER_NAME, EXP_CLUSTERS_HEADER_NAME, GENOME_BUILD_HEADER_NAME, HEADER_NAMES, HG_TO_NCBI, HG17, HG18, HG19, ILLUMINA_ID_HEADER_NAME, ILLUMINA_STRAND_HEADER_NAME, INTENSITY_ONLY_HEADER_NAME, MANIFEST_FILE_HEADER_NAMES, manifestFileParser, MAP_INFO_HEADER_NAME, NAME_HEADER_NAME, NCBI_35, NCBI_36, NCBI_37, PLOIDY_HEADER_NAME, REF_STRAND_HEADER_NAME, SNP_HEADER_NAME, SOURCE_HEADER_NAME, SOURCE_SEQ_HEADER_NAME, SOURCE_STRAND_HEADER_NAME, SOURCE_VERSION_HEADER_NAME, SPECIES_HEADER_NAME, TOP_GENOMIC_SEQ_HEADER_NAME, VALID_ALLELES
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Constructor Summary
Constructors Constructor Description Build37ExtendedIlluminaManifest(File manifestFile)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description Iterator<Build37ExtendedIlluminaManifestRecord>
extendedIterator()
String[]
getAllPossibleHeaderNames()
String
getExtendedManifestVersion()
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Methods inherited from class picard.arrays.illumina.IlluminaManifest
getAssayFormat, getAssayHeaderNames, getAssayHeaderNameToIndex, getDateManufactured, getDescriptorFileName, getHeaderContents, getLociCount, getManifestFile, getManifestFileHeaderNames, getManifestFileParser, getNumAssays, iterator, setAssayFormat, setDateManufactured, setDescriptorFileName, setLociCount, setManifestFileParser, setNumAssays
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Constructor Detail
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Build37ExtendedIlluminaManifest
public Build37ExtendedIlluminaManifest(File manifestFile) throws IOException
- Throws:
IOException
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Method Detail
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getAllPossibleHeaderNames
public String[] getAllPossibleHeaderNames()
- Overrides:
getAllPossibleHeaderNames
in classIlluminaManifest
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extendedIterator
public Iterator<Build37ExtendedIlluminaManifestRecord> extendedIterator()
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getExtendedManifestVersion
public String getExtendedManifestVersion()
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