Package org.snpeff.fileIterator

Class MarkerFileIterator<M extends Marker>

java.lang.Object
org.snpeff.fileIterator.FileIterator<M>
org.snpeff.fileIterator.MarkerFileIterator<M>
All Implemented Interfaces:
Iterable<M>, Iterator<M>
Direct Known Subclasses:
GenericMarkerFileIterator, Gff3FileIterator, MotifFileIterator, RegulationFileIterator, VariantFileIterator, VcfFileIterator, VcfHapMapFileIterator
public abstract class MarkerFileIterator<M extends Marker> extends FileIterator<M>
Opens a Marker file and iterates over all markers
Author:
pcingola

  • Field Details

    • createChromos

      protected boolean createChromos

    • genome

      protected Genome genome

    • ignoreChromosomeErrors

      protected boolean ignoreChromosomeErrors

    • inOffset

      protected int inOffset

  • Constructor Details

    • MarkerFileIterator

      public MarkerFileIterator(BufferedReader reader, int inOffset)

    • MarkerFileIterator

      public MarkerFileIterator(String fileName, Genome genome, int inOffset)

    • MarkerFileIterator

      public MarkerFileIterator(String fileName, int inOffset)

  • Method Details

    • getChromosome

      public Chromosome getChromosome(String chromoName)
      Find chromosome 'chromoName'. If it does not exists and 'createChromos' is true, the chromosome is created

    • getGenome

      public Genome getGenome()

    • init

      protected void init(String fileName, int inOffset)
      Initialize
      Overrides:
      init in class FileIterator<M extends Marker>
      Parameters:
      fileName - : Can be null (no file is opened)

    • isIgnoreChromosomeErrors

      public boolean isIgnoreChromosomeErrors()

    • loadMarkers

      public Markers loadMarkers()

    • parsePosition

      public int parsePosition(String posStr)
      Parse a string as a 'position'. Note: It subtracts 'inOffset' so that all coordinates are zero-based

    • sanityCheckChromo

      public void sanityCheckChromo(String chromoName, Chromosome chromo)
      Sanity check

    • setCreateChromos

      public void setCreateChromos(boolean createChromos)

    • setIgnoreChromosomeErrors

      public void setIgnoreChromosomeErrors(boolean ignoreChromosomeErrors)

    • setInOffset

      public void setInOffset(int inOffset)