Package picard.arrays.illumina
Class IlluminaManifest
- java.lang.Object
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- picard.arrays.illumina.IlluminaManifest
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- Direct Known Subclasses:
Build37ExtendedIlluminaManifest
public class IlluminaManifest extends Object
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
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Constructor Summary
Constructors Constructor Description IlluminaManifest(File manifestFile)
IlluminaManifest(File manifestFile, int numAssays)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description String[]
getAllPossibleHeaderNames()
String
getAssayFormat()
String[]
getAssayHeaderNames()
Map<String,Integer>
getAssayHeaderNameToIndex()
String
getDateManufactured()
String
getDescriptorFileName()
List<String[]>
getHeaderContents()
int
getLociCount()
File
getManifestFile()
String[]
getManifestFileHeaderNames()
CsvInputParser
getManifestFileParser()
int
getNumAssays()
Iterator<IlluminaManifestRecord>
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 Detail
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HG17
public static final String HG17
- See Also:
- Constant Field Values
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HG18
public static final String HG18
- See Also:
- Constant Field Values
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HG19
public static final String HG19
- See Also:
- Constant Field Values
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NCBI_35
public static final String NCBI_35
- See Also:
- Constant Field Values
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NCBI_36
public static final String NCBI_36
- See Also:
- Constant Field Values
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NCBI_37
public static final String NCBI_37
- See Also:
- Constant Field Values
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HG_TO_NCBI
public static final org.apache.commons.collections4.BidiMap HG_TO_NCBI
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ILLUMINA_ID_HEADER_NAME
public static final String ILLUMINA_ID_HEADER_NAME
- See Also:
- Constant Field Values
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NAME_HEADER_NAME
public static final String NAME_HEADER_NAME
- See Also:
- Constant Field Values
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ILLUMINA_STRAND_HEADER_NAME
public static final String ILLUMINA_STRAND_HEADER_NAME
- See Also:
- Constant Field Values
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SNP_HEADER_NAME
public static final String SNP_HEADER_NAME
- See Also:
- Constant Field Values
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ADDRESS_A_ID_HEADER_NAME
public static final String ADDRESS_A_ID_HEADER_NAME
- See Also:
- Constant Field Values
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ALLELE_A_PROBE_SEQ_HEADER_NAME
public static final String ALLELE_A_PROBE_SEQ_HEADER_NAME
- See Also:
- Constant Field Values
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ADDRESS_B_ID_HEADER_NAME
public static final String ADDRESS_B_ID_HEADER_NAME
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- Constant Field Values
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ALLELE_B_PROBE_SEQ_HEADER_NAME
public static final String ALLELE_B_PROBE_SEQ_HEADER_NAME
- See Also:
- Constant Field Values
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GENOME_BUILD_HEADER_NAME
public static final String GENOME_BUILD_HEADER_NAME
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- Constant Field Values
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CHROMOSOME_HEADER_NAME
public static final String CHROMOSOME_HEADER_NAME
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- Constant Field Values
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MAP_INFO_HEADER_NAME
public static final String MAP_INFO_HEADER_NAME
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- Constant Field Values
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PLOIDY_HEADER_NAME
public static final String PLOIDY_HEADER_NAME
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- Constant Field Values
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SPECIES_HEADER_NAME
public static final String SPECIES_HEADER_NAME
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- Constant Field Values
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SOURCE_HEADER_NAME
public static final String SOURCE_HEADER_NAME
- See Also:
- Constant Field Values
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SOURCE_VERSION_HEADER_NAME
public static final String SOURCE_VERSION_HEADER_NAME
- See Also:
- Constant Field Values
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SOURCE_STRAND_HEADER_NAME
public static final String SOURCE_STRAND_HEADER_NAME
- See Also:
- Constant Field Values
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SOURCE_SEQ_HEADER_NAME
public static final String SOURCE_SEQ_HEADER_NAME
- See Also:
- Constant Field Values
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TOP_GENOMIC_SEQ_HEADER_NAME
public static final String TOP_GENOMIC_SEQ_HEADER_NAME
- See Also:
- Constant Field Values
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BEAD_SET_ID_HEADER_NAME
public static final String BEAD_SET_ID_HEADER_NAME
- See Also:
- Constant Field Values
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EXP_CLUSTERS_HEADER_NAME
public static final String EXP_CLUSTERS_HEADER_NAME
- See Also:
- Constant Field Values
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REF_STRAND_HEADER_NAME
public static final String REF_STRAND_HEADER_NAME
- See Also:
- Constant Field Values
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INTENSITY_ONLY_HEADER_NAME
public static final String INTENSITY_ONLY_HEADER_NAME
- See Also:
- Constant Field Values
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MANIFEST_FILE_HEADER_NAMES
public static final String[] MANIFEST_FILE_HEADER_NAMES
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manifestFileParser
protected CsvInputParser manifestFileParser
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Constructor Detail
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IlluminaManifest
public IlluminaManifest(File manifestFile) throws IOException
- Throws:
IOException
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IlluminaManifest
public IlluminaManifest(File manifestFile, int numAssays) throws IOException
- Throws:
IOException
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Method Detail
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getAllPossibleHeaderNames
public String[] getAllPossibleHeaderNames()
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getAssayHeaderNames
public String[] getAssayHeaderNames()
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iterator
public Iterator<IlluminaManifestRecord> iterator()
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getManifestFileHeaderNames
public String[] getManifestFileHeaderNames()
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getManifestFile
public File getManifestFile()
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getManifestFileParser
public CsvInputParser getManifestFileParser()
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setManifestFileParser
public void setManifestFileParser(CsvInputParser manifestFileParser)
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getDescriptorFileName
public String getDescriptorFileName()
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setDescriptorFileName
public void setDescriptorFileName(String descriptorFileName)
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getAssayFormat
public String getAssayFormat()
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setAssayFormat
public void setAssayFormat(String assayFormat)
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getDateManufactured
public String getDateManufactured()
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setDateManufactured
public void setDateManufactured(String dateManufactured)
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setLociCount
public void setLociCount(int lociCount)
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getLociCount
public int getLociCount()
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getNumAssays
public int getNumAssays()
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setNumAssays
public void setNumAssays(int numAssays)
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