Package picard.arrays.illumina
Class Build37ExtendedIlluminaManifest
java.lang.Object
picard.arrays.illumina.IlluminaManifest
picard.arrays.illumina.Build37ExtendedIlluminaManifest
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
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 -
Method Summary
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 Details
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Build37ExtendedIlluminaManifest
- Throws:
IOException
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Method Details
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getAllPossibleHeaderNames
- Overrides:
getAllPossibleHeaderNames
in classIlluminaManifest
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extendedIterator
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getExtendedManifestVersion
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