Field Detail

• ILLUMINA_FLAGGED_BAD_CHR

  public static final String ILLUMINA_FLAGGED_BAD_CHR

  See Also:

  Constant Field Values

Method Detail

• getLine

  public String getLine()

• getIlmnId

  public String getIlmnId()

• getName

  public String getName()

• getIlmnStrand

  public IlluminaManifestRecord.IlluminaStrand getIlmnStrand()

• getSnp

  public String getSnp()

• isIndel

  public boolean isIndel()

• isAmbiguous

  public boolean isAmbiguous()

• isSnp

  public boolean isSnp()

• getAddressAId

  public String getAddressAId()

• getAlleleAProbeSeq

  public String getAlleleAProbeSeq()

• getAddressBId

  public String getAddressBId()

• getAlleleBProbeSeq

  public String getAlleleBProbeSeq()

• getGenomeBuild

  public String getGenomeBuild()

• getMajorGenomeBuild

  public String getMajorGenomeBuild()

• getHgGenomeBuild

  public String getHgGenomeBuild()

• setHgGenomeBuild

  public void setHgGenomeBuild​(String hgGenomeBuild)

• getChr

  public String getChr()

• getPosition

  public int getPosition()

• getPloidy

  public String getPloidy()

• getSpecies

  public String getSpecies()

• getSource

  public String getSource()

• getSourceVersion

  public String getSourceVersion()

• getSourceStrand

  public IlluminaManifestRecord.IlluminaStrand getSourceStrand()

• getSourceSeq

  public String getSourceSeq()

• getTopGenomicSeq

  public String getTopGenomicSeq()

• getBeadSetId

  public int getBeadSetId()

• getExpClusters

  public String getExpClusters()

• getRefStrand

  public htsjdk.tribble.annotation.Strand getRefStrand()

• getIntensityOnly

  public boolean getIntensityOnly()

• getIndex

  public int getIndex()