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);
}
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)));
}
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)));
}