Examples of abra.NativeAssembler

  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");

  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;    
  }

Related Classes of abra.NativeAssembler

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