Example #1
0
  private void merge(SingleHit[] hits, String prefix, int chrom) throws IOException {
    String postmp = getPositionsFname(prefix, chrom) + ".tmp";
    String weightstmp = getWeightsFname(prefix, chrom) + ".tmp";
    String lastmp = getLaSFname(prefix, chrom) + ".tmp";
    RandomAccessFile positionsRAF = new RandomAccessFile(postmp, "rw");
    RandomAccessFile weightsRAF = new RandomAccessFile(weightstmp, "rw");
    RandomAccessFile lasRAF = new RandomAccessFile(lastmp, "rw");
    int newsize = getPositionsBuffer().limit() + hits.length;
    IntBP posfile =
        new IntBP(positionsRAF.getChannel().map(FileChannel.MapMode.READ_WRITE, 0, newsize * 4));
    FloatBP weightfile =
        new FloatBP(weightsRAF.getChannel().map(FileChannel.MapMode.READ_WRITE, 0, newsize * 4));
    IntBP lasfile =
        new IntBP(lasRAF.getChannel().map(FileChannel.MapMode.READ_WRITE, 0, newsize * 4));

    int oldp = 0;
    int newp = 0;
    int pos = 0;
    IntBP oldpositions = getPositionsBuffer();
    FloatBP oldweights = getWeightsBuffer();
    IntBP oldlas = getLASBuffer();
    while (oldp < oldpositions.limit() || newp < hits.length) {
      while (newp < hits.length
          && (oldp == oldpositions.limit() || hits[newp].pos <= oldpositions.get(oldp))) {
        posfile.put(pos, hits[newp].pos);
        weightfile.put(pos, hits[newp].weight);
        lasfile.put(pos, Hits.makeLAS(hits[newp].length, hits[newp].strand));
        newp++;
        pos++;
      }
      while (oldp < oldpositions.limit()
          && (newp == hits.length || oldpositions.get(oldp) <= hits[newp].pos)) {
        posfile.put(pos, oldpositions.get(oldp));
        weightfile.put(pos, oldweights.get(oldp));
        lasfile.put(pos, oldlas.get(oldp));
        oldp++;
        pos++;
      }
      //            System.err.println(String.format("%d %d %d", pos, newp, oldp));
    }
    posfile = null;
    weightfile = null;
    lasfile = null;
    oldpositions = null;
    oldweights = null;
    oldlas = null;
    positionsRAF.close();
    weightsRAF.close();
    lasRAF.close();
    /* ideally this part with the renames would atomic... */
    (new File(postmp)).renameTo(new File(getPositionsFname(prefix, chrom)));
    (new File(weightstmp)).renameTo(new File(getWeightsFname(prefix, chrom)));
    (new File(lastmp)).renameTo(new File(getLaSFname(prefix, chrom)));
  }
Example #2
0
 public static void writeSingleHits(SingleHit[] hits, String prefix, int chrom)
     throws IOException {
   IntBP p = new IntBP(hits.length);
   FloatBP w = new FloatBP(hits.length);
   IntBP l = new IntBP(hits.length);
   for (int i = 0; i < hits.length; i++) {
     SingleHit h = hits[i];
     p.put(i, h.pos);
     w.put(i, h.weight);
     l.put(i, makeLAS(h.length, h.strand));
   }
   writeSingleHits(p, w, l, prefix, chrom);
 }
Example #3
0
  public void resort(String prefix, int chrom) throws IOException {
    IntBP positions = getPositionsBuffer();
    FloatBP weights = getWeightsBuffer();
    IntBP las = getLASBuffer();
    long indices[] = new long[positions.limit()];
    for (int i = 0; i < indices.length; i++) {
      long v = positions.get(i);
      v <<= 32;
      v |= i;
      indices[i] = v;
    }
    Arrays.sort(indices);

    String postmp = getPositionsFname(prefix, chrom) + ".tmp";
    String weightstmp = getWeightsFname(prefix, chrom) + ".tmp";
    String lastmp = getLaSFname(prefix, chrom) + ".tmp";
    RandomAccessFile positionsRAF = new RandomAccessFile(postmp, "rw");
    RandomAccessFile weightsRAF = new RandomAccessFile(weightstmp, "rw");
    RandomAccessFile lasRAF = new RandomAccessFile(lastmp, "rw");
    int newsize = getPositionsBuffer().limit();
    IntBP posfile =
        new IntBP(positionsRAF.getChannel().map(FileChannel.MapMode.READ_WRITE, 0, newsize * 4));
    FloatBP weightfile =
        new FloatBP(weightsRAF.getChannel().map(FileChannel.MapMode.READ_WRITE, 0, newsize * 4));
    IntBP lasfile =
        new IntBP(lasRAF.getChannel().map(FileChannel.MapMode.READ_WRITE, 0, newsize * 4));

    for (int i = 0; i < indices.length; i++) {
      int index = (int) (indices[i] & 0xffffffffL);
      int pos = (int) (indices[i] >> 32);
      posfile.put(i, pos);
      weightfile.put(i, weights.get(index));
      lasfile.put(i, las.get(index));
    }
    posfile = null;
    weightfile = null;
    lasfile = null;
    positionsRAF.close();
    weightsRAF.close();
    lasRAF.close();
    /* ideally this part with the renames would atomic... */
    (new File(postmp)).renameTo(new File(getPositionsFname(prefix, chrom)));
    (new File(weightstmp)).renameTo(new File(getWeightsFname(prefix, chrom)));
    (new File(lastmp)).renameTo(new File(getLaSFname(prefix, chrom)));
  }