Package abra

Examples of abra.NativeAssembler$Position

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  void processReads(List<SAMRecord> reads) throws IOException {

    filterNbases(reads);
   
    if (reads.size() > 1) {
      NativeAssembler assem = newAssembler();
     
      String contigs = assem.simpleAssemble(reads);
     
      if (contigs.equals("<ERROR>") || contigs.equals("<REPEAT>")) {
       
        badRegionBed.write(getRegionEntry(reads) + "\n");
       
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  private synchronized void appendContigs(String contigs) throws IOException {
    contigWriter.write(contigs);
  }
 
  private NativeAssembler newAssembler() {
    NativeAssembler assem = new NativeAssembler();

    assem.setTruncateOutputOnRepeat(true);
    assem.setMaxContigs(100000);

    assem.setMaxPathsFromRoot(5000000);
    assem.setReadLength(75);
    assem.setKmer(new int[] { 17, 27, 37, 47 });
    assem.setMinKmerFrequency(2);
    assem.setMinBaseQuality(40);
   
    // The following params not used
    assem.setMinReadCandidateFraction(0);
    assem.setMaxAverageDepth(0);
    assem.setShouldSearchForSv(false);
    assem.setAverageDepthCeiling(0);

    return assem;   
  }
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  public Object extractCategoryTokenData(byte[] buffer, int offset, int length) {
    if (length == 0) {
      return null;
    }
    Integer i = Integer.valueOf(Vint8.decode(buffer, new Position(offset)));
    return i;
  }
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    if (!super.setdoc(docId)) {
      return false;
    }

    // read header - number of enhancements and their lengths
    Position position = new Position();
    nEnhancements = Vint8.decode(buffer, position);
    for (int i = 0; i < nEnhancements; i++) {
      enhancementLength[i] = Vint8.decode(buffer, position);
    }
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  public Object extractCategoryTokenData(byte[] buffer, int offset, int length) {
    if (length == 0) {
      return null;
    }
    Integer i = Integer.valueOf(Vint8.decode(buffer, new Position(offset)));
    return i;
  }
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Related Classes of abra.NativeAssembler$Position

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  • com.sun.tools.classfile.TypeAnnotation.Position.TypePathEntry
  • net.sf.samtools.SAMFileReader
  • net.sf.samtools.SAMRecord
  • org.apache.lucene.facet.enhancements.association.AssociationEnhancement
  • org.apache.lucene.facet.enhancements.EnhancementsPayloadIterator
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  • org.eclipse.wb.internal.core.utils.xml.DocumentElement
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