Package abra

Examples of abra.ThreadManager


  public void run(String input, String output, String temp, int numThreads, String badRegionBedFile) throws IOException, InterruptedException {
   
    init(temp);
   
    this.threadManager = new ThreadManager(numThreads);
   
    contigWriter = new BufferedWriter(new FileWriter(output, false));
    badRegionBed = new BufferedWriter(new FileWriter(badRegionBedFile, false));
   
//    reads1 = new BufferedWriter(new FileWriter(readsFile + "1.fa", false));
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      dir.mkdir();
    }
   
    SAMFileReader rdr = new SAMFileReader(new File(filename));
   
    ThreadManager threads = new ThreadManager(numThreads);
   
    Map<String, SAMFileWriter> outputWriterMap = new HashMap<String, SAMFileWriter>();
   
    SAMFileWriterFactory writerFactory = new SAMFileWriterFactory();
    writerFactory.setUseAsyncIo(false);
   
    // Farm each chromosome out to its own thread.
    for (SAMSequenceRecord chr : rdr.getFileHeader().getSequenceDictionary().getSequences()) {   
      SAMFileWriter writer = writerFactory.makeSAMOrBAMWriter(
          rdr.getFileHeader(), false, new File(outputDirectory + "/" + chr.getSequenceName() + ".bam"));
     
      outputWriterMap.put(chr.getSequenceName(), writer);
     
      BamSplitterThread thread = new BamSplitterThread(threads, filename, chr.getSequenceName(), writer);
      threads.spawnThread(thread);
    }
    threads.waitForAllThreadsToComplete();
   
    // Now go back and retrieve the unmapped reads.
    System.err.println("Processing unmapped reads");
    Iterator<SAMRecord> iter = rdr.queryUnmapped();
    while (iter.hasNext()) {
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