public void createIndex(File fn) throws Exception {
BlockCompressedInputStream fp = new BlockCompressedInputStream(fn);
makeIndex(fp);
fp.close();
File indexFile = new File(fn + ".tbi");
BlockCompressedOutputStream fpidx = new BlockCompressedOutputStream(indexFile);
saveIndex(fpidx);
fpidx.close();
}
private void saveIndex(BlockCompressedOutputStream fp) throws IOException {
fp.write("TBI\1".getBytes(LATIN1));
writeInt(fp, binningIndex.size());
// Write the ti_conf_t
writeInt(fp, mPreset);
writeInt(fp, mSc);
writeInt(fp, mBc);
writeInt(fp, mEc);
writeInt(fp, mMeta);
writeInt(fp, mSkip);
// Write sequence dictionary. Since mChr2tid is a LinkedHashmap, the keyset
// will be returned in insertion order.
int l = 0;
for (String k : mChr2tid.keySet()) {
l += k.length() + 1;
}
writeInt(fp, l);
for (String k : mChr2tid.keySet()) {
fp.write(k.getBytes(LATIN1));
fp.write(0);
}
for (int i = 0; i < mChr2tid.size(); i++) {
Map<Integer, List<TPair64>> binningForChr = binningIndex.get(i);
// Write the binning index.
writeInt(fp, binningForChr.size());
for (int k : binningForChr.keySet()) {
List<TPair64> p = binningForChr.get(k);
writeInt(fp, k);
writeInt(fp, p.size());
for (TPair64 bin : p) {
writeLong(fp, bin.u);
writeLong(fp, bin.v);
}
}
// Write the linear index.
List<Long> linearForChr = linearIndex.get(i);
writeInt(fp, linearForChr.size());
for (int x = 0; x < linearForChr.size(); x++) {
writeLong(fp, linearForChr.get(x));
}
}
}