Class InfiniumGTCFile

java.lang.Object
picard.arrays.illumina.InfiniumDataFile
picard.arrays.illumina.InfiniumGTCFile
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.
  • Field Details

  • Constructor Details

    • InfiniumGTCFile

      public InfiniumGTCFile(File gtcFile, File bpmFile) throws IOException
      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.
  • Method Details

    • close

      public void close() throws IOException
      Specified by:
      close in interface AutoCloseable
      Throws:
      IOException
    • getRecord

      public InfiniumGTCRecord getRecord(int index)
    • getHetPercent

      public double getHetPercent()
    • getSampleName

      public String getSampleName()
    • getSamplePlate

      public String getSamplePlate()
    • getSampleWell

      public String getSampleWell()
    • getClusterFile

      public String getClusterFile()
    • getSnpManifest

      public String getSnpManifest()
    • getImagingDate

      public String getImagingDate()
    • getAutoCallDate

      public String getAutoCallDate()
    • getAutoCallVersion

      public String getAutoCallVersion()
    • getRawControlXIntensities

      public int[] getRawControlXIntensities()
    • getRawControlYIntensities

      public int[] getRawControlYIntensities()
    • getScannerName

      public String getScannerName()
    • getPmtGreen

      public int getPmtGreen()
    • getPmtRed

      public int getPmtRed()
    • getScannerVersion

      public String getScannerVersion()
    • getImagingUser

      public String getImagingUser()
    • getCallRate

      public double getCallRate()
    • getGender

      public String getGender()
    • 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

      public String getSentrixBarcode()
    • 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()