Package picard.arrays.illumina
Class IlluminaManifest
java.lang.Object
picard.arrays.illumina.IlluminaManifest
- Direct Known Subclasses:
Build37ExtendedIlluminaManifest
A class to represent an Illumina Manifest file.
Reads the header, stores the contents, and then provides an iterator to allow
access to the IlluminaManifestRecords (currently this only supports iterating over the assay records).
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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 org.apache.commons.collections4.BidiMap
static final String
static final String
static final String
static final String
static final String
static final String
static final String[]
protected CsvInputParser
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
ConstructorsConstructorDescriptionIlluminaManifest
(File manifestFile) IlluminaManifest
(File manifestFile, int numAssays) -
Method Summary
Modifier and TypeMethodDescriptionString[]
String[]
int
String[]
int
iterator()
void
setAssayFormat
(String assayFormat) void
setDateManufactured
(String dateManufactured) void
setDescriptorFileName
(String descriptorFileName) void
setLociCount
(int lociCount) void
setManifestFileParser
(CsvInputParser manifestFileParser) void
setNumAssays
(int numAssays)
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Field Details
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HG17
- See Also:
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HG18
- See Also:
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HG19
- See Also:
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NCBI_35
- See Also:
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NCBI_36
- See Also:
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NCBI_37
- See Also:
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HG_TO_NCBI
public static final org.apache.commons.collections4.BidiMap HG_TO_NCBI -
VALID_ALLELES
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ILLUMINA_ID_HEADER_NAME
- See Also:
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NAME_HEADER_NAME
- See Also:
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ILLUMINA_STRAND_HEADER_NAME
- See Also:
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SNP_HEADER_NAME
- See Also:
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ADDRESS_A_ID_HEADER_NAME
- See Also:
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ALLELE_A_PROBE_SEQ_HEADER_NAME
- See Also:
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ADDRESS_B_ID_HEADER_NAME
- See Also:
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ALLELE_B_PROBE_SEQ_HEADER_NAME
- See Also:
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GENOME_BUILD_HEADER_NAME
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CHROMOSOME_HEADER_NAME
- See Also:
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MAP_INFO_HEADER_NAME
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PLOIDY_HEADER_NAME
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SPECIES_HEADER_NAME
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SOURCE_HEADER_NAME
- See Also:
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SOURCE_VERSION_HEADER_NAME
- See Also:
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SOURCE_STRAND_HEADER_NAME
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SOURCE_SEQ_HEADER_NAME
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TOP_GENOMIC_SEQ_HEADER_NAME
- See Also:
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BEAD_SET_ID_HEADER_NAME
- See Also:
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EXP_CLUSTERS_HEADER_NAME
- See Also:
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REF_STRAND_HEADER_NAME
- See Also:
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INTENSITY_ONLY_HEADER_NAME
- See Also:
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MANIFEST_FILE_HEADER_NAMES
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HEADER_NAMES
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manifestFileParser
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Constructor Details
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IlluminaManifest
- Throws:
IOException
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IlluminaManifest
- Throws:
IOException
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Method Details
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getAllPossibleHeaderNames
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getAssayHeaderNames
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getAssayHeaderNameToIndex
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iterator
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getManifestFileHeaderNames
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getManifestFile
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getManifestFileParser
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setManifestFileParser
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getDescriptorFileName
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setDescriptorFileName
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getAssayFormat
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setAssayFormat
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getDateManufactured
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setDateManufactured
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setLociCount
public void setLociCount(int lociCount) -
getLociCount
public int getLociCount() -
getNumAssays
public int getNumAssays() -
setNumAssays
public void setNumAssays(int numAssays) -
getHeaderContents
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