Package picard.arrays.illumina
Class InfiniumGTCFile
java.lang.Object
picard.arrays.illumina.InfiniumDataFile
picard.arrays.illumina.InfiniumGTCFile
- All Implemented Interfaces:
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
FieldsModifier and TypeFieldDescriptionstatic final byte
static final byte
static final byte
static final byte
Fields inherited from class picard.arrays.illumina.InfiniumDataFile
MAX_UNSIGNED_SHORT
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Constructor Summary
ConstructorsConstructorDescriptionInfiniumGTCFile
(File gtcFile, File bpmFile) Creates an InfiniumGTCFile object and parses the given input file. -
Method Summary
Modifier and TypeMethodDescriptionvoid
close()
long
int
float[]
byte[][]
long
double
int
getDx()
byte[]
float[]
double
float
float[]
float[]
float[]
int
int
int
int
int
int
float
getP10GC()
float
getP50GC()
int
int
int
int
int
int
int
int
int[]
int
getRawControlXIntensity
(int index) int[]
int
getRawControlYIntensity
(int index) int[]
int[]
getRecord
(int index) float[]
getRIlmn()
float[]
Methods inherited from class picard.arrays.illumina.InfiniumDataFile
byteArrayToCharArray, byteArrayToFloat, byteArrayToInt, floatToByteArray, getIdentifier, setIdentifier, shortToByteArray
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Field Details
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NO_CALL
public static final byte NO_CALL- See Also:
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AA_CALL
public static final byte AA_CALL- See Also:
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AB_CALL
public static final byte AB_CALL- See Also:
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BB_CALL
public static final byte BB_CALL- See Also:
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Constructor Details
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InfiniumGTCFile
Creates an InfiniumGTCFile object and parses the given input file.- Parameters:
gtcFile
- The gtc file.bpmFile
- The Illumina bead pool manifest (bpm) file- Throws:
IOException
- is thrown when there is a problem reading the files.
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Method Details
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close
- Specified by:
close
in interfaceAutoCloseable
- Throws:
IOException
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getRecord
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getHetPercent
public double getHetPercent() -
getSampleName
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getSamplePlate
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getSampleWell
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getClusterFile
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getSnpManifest
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getImagingDate
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getAutoCallDate
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getAutoCallVersion
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getRawControlXIntensities
public int[] getRawControlXIntensities() -
getRawControlYIntensities
public int[] getRawControlYIntensities() -
getScannerName
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getPmtGreen
public int getPmtGreen() -
getPmtRed
public int getPmtRed() -
getScannerVersion
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getImagingUser
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getCallRate
public double getCallRate() -
getGender
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getNumberOfSnps
public int getNumberOfSnps() -
getNumCalls
public int getNumCalls() -
getNumNoCalls
public int getNumNoCalls() -
getRawControlXIntensity
public int getRawControlXIntensity(int index) -
getRawControlYIntensity
public int getRawControlYIntensity(int index) -
getPloidy
public int getPloidy() -
getPloidyType
public int getPloidyType() -
getP05Red
public int getP05Red() -
getP50Red
public int getP50Red() -
getP95Red
public int getP95Red() -
getP05Green
public int getP05Green() -
getP50Green
public int getP50Green() -
getP95Green
public int getP95Green() -
getLogRDev
public float getLogRDev() -
getP10GC
public float getP10GC() -
getP50GC
public float getP50GC() -
getNumIntensityOnly
public int getNumIntensityOnly() -
getAaCalls
public long getAaCalls() -
getBbCalls
public long getBbCalls() -
getSentrixBarcode
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getDx
public int getDx() -
getBaseCalls
public byte[][] getBaseCalls() -
getAbCalls
public int getAbCalls() -
getRawXIntensities
public int[] getRawXIntensities() -
getRawYIntensities
public int[] getRawYIntensities() -
getNormalizedXIntensities
public float[] getNormalizedXIntensities() -
getNormalizedYIntensities
public float[] getNormalizedYIntensities() -
getbAlleleFreqs
public float[] getbAlleleFreqs() -
getLogRRatios
public float[] getLogRRatios() -
getRIlmn
public float[] getRIlmn() -
getThetaIlmn
public float[] getThetaIlmn() -
getGenotypeBytes
public byte[] getGenotypeBytes() -
getGenotypeScores
public float[] getGenotypeScores()
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