picard.arrays.illumina.IlluminaManifest

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).

Field Summary

Fields

Modifier and Type

Field

Description

static final String

ADDRESS_A_ID_HEADER_NAME

static final String

ADDRESS_B_ID_HEADER_NAME

static final String

ALLELE_A_PROBE_SEQ_HEADER_NAME

static final String

ALLELE_B_PROBE_SEQ_HEADER_NAME

static final String

BEAD_SET_ID_HEADER_NAME

static final String

CHROMOSOME_HEADER_NAME

static final String

EXP_CLUSTERS_HEADER_NAME

static final String

GENOME_BUILD_HEADER_NAME

static final HashSet<String>

HEADER_NAMES

static final org.apache.commons.collections4.BidiMap

HG_TO_NCBI

static final String

HG17

static final String

HG18

static final String

HG19

static final String

ILLUMINA_ID_HEADER_NAME

static final String

ILLUMINA_STRAND_HEADER_NAME

static final String

INTENSITY_ONLY_HEADER_NAME

static final String[]

MANIFEST_FILE_HEADER_NAMES

protected CsvInputParser

manifestFileParser

static final String

MAP_INFO_HEADER_NAME

static final String

NAME_HEADER_NAME

static final String

NCBI_35

static final String

NCBI_36

static final String

NCBI_37

static final String

PLOIDY_HEADER_NAME

static final String

REF_STRAND_HEADER_NAME

static final String

SNP_HEADER_NAME

static final String

SOURCE_HEADER_NAME

static final String

SOURCE_SEQ_HEADER_NAME

static final String

SOURCE_STRAND_HEADER_NAME

static final String

SOURCE_VERSION_HEADER_NAME

static final String

SPECIES_HEADER_NAME

static final String

TOP_GENOMIC_SEQ_HEADER_NAME

static final HashSet<String>

VALID_ALLELES
Constructor Summary

Constructors

Constructor

Description

IlluminaManifest(File manifestFile)

IlluminaManifest(File manifestFile, int numAssays)
Method Summary

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)

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- HG17
  
  public static final String HG17
  See Also:
  
  Constant Field Values
- HG18
  
  public static final String HG18
  See Also:
  
  Constant Field Values
- HG19
  
  public static final String HG19
  See Also:
  
  Constant Field Values
- NCBI_35
  
  public static final String NCBI_35
  See Also:
  
  Constant Field Values
- NCBI_36
  
  public static final String NCBI_36
  See Also:
  
  Constant Field Values
- NCBI_37
  
  public static final String NCBI_37
  See Also:
  
  Constant Field Values
- HG_TO_NCBI
  
  public static final org.apache.commons.collections4.BidiMap HG_TO_NCBI
- VALID_ALLELES
  
  public static final HashSet<String> VALID_ALLELES
- ILLUMINA_ID_HEADER_NAME
  
  public static final String ILLUMINA_ID_HEADER_NAME
  See Also:
  
  Constant Field Values
- NAME_HEADER_NAME
  
  public static final String NAME_HEADER_NAME
  See Also:
  
  Constant Field Values
- ILLUMINA_STRAND_HEADER_NAME
  
  public static final String ILLUMINA_STRAND_HEADER_NAME
  See Also:
  
  Constant Field Values
- SNP_HEADER_NAME
  
  public static final String SNP_HEADER_NAME
  See Also:
  
  Constant Field Values
- ADDRESS_A_ID_HEADER_NAME
  
  public static final String ADDRESS_A_ID_HEADER_NAME
  See Also:
  
  Constant Field Values
- ALLELE_A_PROBE_SEQ_HEADER_NAME
  
  public static final String ALLELE_A_PROBE_SEQ_HEADER_NAME
  See Also:
  
  Constant Field Values
- ADDRESS_B_ID_HEADER_NAME
  
  public static final String ADDRESS_B_ID_HEADER_NAME
  See Also:
  
  Constant Field Values
- ALLELE_B_PROBE_SEQ_HEADER_NAME
  
  public static final String ALLELE_B_PROBE_SEQ_HEADER_NAME
  See Also:
  
  Constant Field Values
- GENOME_BUILD_HEADER_NAME
  
  public static final String GENOME_BUILD_HEADER_NAME
  See Also:
  
  Constant Field Values
- CHROMOSOME_HEADER_NAME
  
  public static final String CHROMOSOME_HEADER_NAME
  See Also:
  
  Constant Field Values
- MAP_INFO_HEADER_NAME
  
  public static final String MAP_INFO_HEADER_NAME
  See Also:
  
  Constant Field Values
- PLOIDY_HEADER_NAME
  
  public static final String PLOIDY_HEADER_NAME
  See Also:
  
  Constant Field Values
- SPECIES_HEADER_NAME
  
  public static final String SPECIES_HEADER_NAME
  See Also:
  
  Constant Field Values
- SOURCE_HEADER_NAME
  
  public static final String SOURCE_HEADER_NAME
  See Also:
  
  Constant Field Values
- SOURCE_VERSION_HEADER_NAME
  
  public static final String SOURCE_VERSION_HEADER_NAME
  See Also:
  
  Constant Field Values
- SOURCE_STRAND_HEADER_NAME
  
  public static final String SOURCE_STRAND_HEADER_NAME
  See Also:
  
  Constant Field Values
- SOURCE_SEQ_HEADER_NAME
  
  public static final String SOURCE_SEQ_HEADER_NAME
  See Also:
  
  Constant Field Values
- TOP_GENOMIC_SEQ_HEADER_NAME
  
  public static final String TOP_GENOMIC_SEQ_HEADER_NAME
  See Also:
  
  Constant Field Values
- BEAD_SET_ID_HEADER_NAME
  
  public static final String BEAD_SET_ID_HEADER_NAME
  See Also:
  
  Constant Field Values
- EXP_CLUSTERS_HEADER_NAME
  
  public static final String EXP_CLUSTERS_HEADER_NAME
  See Also:
  
  Constant Field Values
- REF_STRAND_HEADER_NAME
  
  public static final String REF_STRAND_HEADER_NAME
  See Also:
  
  Constant Field Values
- INTENSITY_ONLY_HEADER_NAME
  
  public static final String INTENSITY_ONLY_HEADER_NAME
  See Also:
  
  Constant Field Values
- MANIFEST_FILE_HEADER_NAMES
  
  public static final String[] MANIFEST_FILE_HEADER_NAMES
- HEADER_NAMES
  
  public static final HashSet<String> HEADER_NAMES
- manifestFileParser
  
  protected CsvInputParser manifestFileParser
Constructor Details
- IlluminaManifest
  
  public IlluminaManifest(File manifestFile) throws IOException
  
  Throws:
  
  IOException
- IlluminaManifest
  
  public IlluminaManifest(File manifestFile, int numAssays) throws IOException
  
  Throws:
  
  IOException
Method Details
- getAllPossibleHeaderNames
  
  public String[] getAllPossibleHeaderNames()
- getAssayHeaderNames
  
  public String[] getAssayHeaderNames()
- getAssayHeaderNameToIndex
  
  public Map<String,Integer> getAssayHeaderNameToIndex()
- iterator
  
  public Iterator<IlluminaManifestRecord> iterator()
- getManifestFileHeaderNames
  
  public String[] getManifestFileHeaderNames()
- getManifestFile
  
  public File getManifestFile()
- getManifestFileParser
  
  public CsvInputParser getManifestFileParser()
- setManifestFileParser
  
  public void setManifestFileParser(CsvInputParser manifestFileParser)
- getDescriptorFileName
  
  public String getDescriptorFileName()
- setDescriptorFileName
  
  public void setDescriptorFileName(String descriptorFileName)
- getAssayFormat
  
  public String getAssayFormat()
- setAssayFormat
  
  public void setAssayFormat(String assayFormat)
- getDateManufactured
  
  public String getDateManufactured()
- setDateManufactured
  
  public void setDateManufactured(String dateManufactured)
- setLociCount
  
  public void setLociCount(int lociCount)
- getLociCount
  
  public int getLociCount()
- getNumAssays
  
  public int getNumAssays()
- setNumAssays
  
  public void setNumAssays(int numAssays)
- getHeaderContents
  
  public List<String[]> getHeaderContents()

Class IlluminaManifest

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

HG17

HG18

HG19

NCBI_35

NCBI_36

NCBI_37

HG_TO_NCBI

VALID_ALLELES

ILLUMINA_ID_HEADER_NAME

NAME_HEADER_NAME

ILLUMINA_STRAND_HEADER_NAME

SNP_HEADER_NAME

ADDRESS_A_ID_HEADER_NAME

ALLELE_A_PROBE_SEQ_HEADER_NAME

ADDRESS_B_ID_HEADER_NAME

ALLELE_B_PROBE_SEQ_HEADER_NAME

GENOME_BUILD_HEADER_NAME

CHROMOSOME_HEADER_NAME

MAP_INFO_HEADER_NAME

PLOIDY_HEADER_NAME

SPECIES_HEADER_NAME

SOURCE_HEADER_NAME

SOURCE_VERSION_HEADER_NAME

SOURCE_STRAND_HEADER_NAME

SOURCE_SEQ_HEADER_NAME

TOP_GENOMIC_SEQ_HEADER_NAME

BEAD_SET_ID_HEADER_NAME

EXP_CLUSTERS_HEADER_NAME

REF_STRAND_HEADER_NAME

INTENSITY_ONLY_HEADER_NAME

MANIFEST_FILE_HEADER_NAMES

HEADER_NAMES

manifestFileParser

Constructor Details

IlluminaManifest

IlluminaManifest

Method Details

getAllPossibleHeaderNames

getAssayHeaderNames

getAssayHeaderNameToIndex

iterator

getManifestFileHeaderNames

getManifestFile

getManifestFileParser

setManifestFileParser

getDescriptorFileName

setDescriptorFileName

getAssayFormat

setAssayFormat

getDateManufactured

setDateManufactured

setLociCount

getLociCount

getNumAssays

setNumAssays

getHeaderContents