Package picard.arrays.illumina
Class InfiniumGTCFile
- java.lang.Object
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- picard.arrays.illumina.InfiniumDataFile
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- picard.arrays.illumina.InfiniumGTCFile
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- All Implemented Interfaces:
AutoCloseable
public class InfiniumGTCFile extends InfiniumDataFile implements AutoCloseable
A class to parse the contents of an Illumina Infinium genotype (GTC) file A GTC file is the output of Illumina's genotype calling software (either Autocall or Autoconvert) and contains genotype calls, confidence scores, basecalls and raw intensities for all calls made on the chip. This class will parse the binary GTC file format and allow access to the genotype, scores, basecalls and raw intensities.
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Field Summary
Fields Modifier and Type Field Description static byte
AA_CALL
static byte
AB_CALL
static byte
BB_CALL
static byte
NO_CALL
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Fields inherited from class picard.arrays.illumina.InfiniumDataFile
MAX_UNSIGNED_SHORT
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Constructor Summary
Constructors Constructor Description InfiniumGTCFile(DataInputStream gtcStream, InfiniumNormalizationManifest normalizationManifest)
Creates an InfiniumGTCFile object and parses the given input stream.
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Method Summary
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Methods inherited from class picard.arrays.illumina.InfiniumDataFile
byteArrayToCharArray, byteArrayToFloat, byteArrayToInt, floatToByteArray, getIdentifier, setIdentifier, shortToByteArray
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Field Detail
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NO_CALL
public static final byte NO_CALL
- See Also:
- Constant Field Values
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AA_CALL
public static final byte AA_CALL
- See Also:
- Constant Field Values
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AB_CALL
public static final byte AB_CALL
- See Also:
- Constant Field Values
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BB_CALL
public static final byte BB_CALL
- See Also:
- Constant Field Values
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Constructor Detail
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InfiniumGTCFile
public InfiniumGTCFile(DataInputStream gtcStream, InfiniumNormalizationManifest normalizationManifest) throws IOException
Creates an InfiniumGTCFile object and parses the given input stream.- Parameters:
gtcStream
- The gtc file input stream.- Throws:
IOException
- is thrown when there is a problem reading the stream.
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Method Detail
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close
public void close() throws IOException
- Specified by:
close
in interfaceAutoCloseable
- Throws:
IOException
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getRecord
public InfiniumGTCRecord getRecord(int index)
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getHetPercent
public double getHetPercent()
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getSampleName
public String getSampleName()
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getSamplePlate
public String getSamplePlate()
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getSampleWell
public String getSampleWell()
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getClusterFile
public String getClusterFile()
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getSnpManifest
public String getSnpManifest()
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getImagingDate
public String getImagingDate()
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getAutoCallDate
public String getAutoCallDate()
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getAutoCallVersion
public String getAutoCallVersion()
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getRawControlXIntensities
public int[] getRawControlXIntensities()
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getRawControlYIntensities
public int[] getRawControlYIntensities()
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getScannerName
public String getScannerName()
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getPmtGreen
public int getPmtGreen()
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getPmtRed
public int getPmtRed()
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getScannerVersion
public String getScannerVersion()
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getImagingUser
public String getImagingUser()
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getCallRate
public double getCallRate()
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getGender
public String getGender()
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getNumberOfSnps
public int getNumberOfSnps()
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getNumCalls
public int getNumCalls()
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getNumNoCalls
public int getNumNoCalls()
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getRawControlXIntensity
public int getRawControlXIntensity(int index)
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getRawControlYIntensity
public int getRawControlYIntensity(int index)
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getPloidy
public int getPloidy()
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getPloidyType
public int getPloidyType()
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getP05Red
public int getP05Red()
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getP50Red
public int getP50Red()
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getP95Red
public int getP95Red()
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getP05Green
public int getP05Green()
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getP50Green
public int getP50Green()
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getP95Green
public int getP95Green()
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getLogRDev
public float getLogRDev()
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getP10GC
public float getP10GC()
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getP50GC
public float getP50GC()
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getNumIntensityOnly
public int getNumIntensityOnly()
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getAaCalls
public long getAaCalls()
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getBbCalls
public long getBbCalls()
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getSentrixBarcode
public String getSentrixBarcode()
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getDx
public int getDx()
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getBaseCalls
public byte[][] getBaseCalls()
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getAbCalls
public int getAbCalls()
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getRawXIntensities
public int[] getRawXIntensities()
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getRawYIntensities
public int[] getRawYIntensities()
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getNormalizedXIntensities
public float[] getNormalizedXIntensities()
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getNormalizedYIntensities
public float[] getNormalizedYIntensities()
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getbAlleleFreqs
public float[] getbAlleleFreqs()
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getLogRRatios
public float[] getLogRRatios()
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getRIlmn
public float[] getRIlmn()
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getThetaIlmn
public float[] getThetaIlmn()
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getGenotypeBytes
public byte[] getGenotypeBytes()
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getGenotypeScores
public float[] getGenotypeScores()
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