Class 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.
    • Constructor Detail

      • 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 Detail

      • 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()