private void makeIndex(BlockCompressedInputStream fp) throws Exception {
int last_bin, save_bin;
int last_coor, last_tid, save_tid;
long save_off, last_off, lineno = 0, offset0 = (long) -1;
String str;
save_bin = save_tid = last_tid = last_bin = 0xffffffff; // Was unsigned in C implementation.
save_off = last_off = 0;
last_coor = 0xffffffff; // Should be unsigned.
while ((str = readLine(fp)) != null) {
++lineno;
if (lineno <= mSkip || str.charAt(0) == mMeta) {
last_off = fp.getFilePointer();
continue;
}
TIntv intv = getIntv(str);
if (intv.beg < 0 || intv.end < 0) {
throw new Exception("The indexes overlap or are out of bounds.");
}
if (last_tid != intv.tid) { // change of chromosomes
if (last_tid > intv.tid) {
throw new Exception(
String.format(
"The chromosome blocks are not continuous at line %d, is the file sorted? [pos %d].",
lineno, intv.beg + 1));
}
last_tid = intv.tid;
last_bin = 0xffffffff;
} else if (last_coor > intv.beg) {
throw new Exception(String.format("File out of order at line %d.", lineno));
}
long tmp = insertLinear(linearIndex.get(intv.tid), intv.beg, intv.end, last_off);
if (last_off == 0) offset0 = tmp;
if (intv.bin != last_bin) { // then possibly write the binning index
if (save_bin != 0xffffffff) { // save_bin==0xffffffffu only happens to the first record
insertBinning(binningIndex.get(save_tid), save_bin, save_off, last_off);
}
save_off = last_off;
save_bin = last_bin = intv.bin;
save_tid = intv.tid;
if (save_tid < 0) break;
}
if (fp.getFilePointer() <= last_off) {
throw new Exception(String.format("Bug in BGZF: %x < %x.", fp.getFilePointer(), last_off));
}
last_off = fp.getFilePointer();
last_coor = intv.beg;
}
if (save_tid >= 0)
insertBinning(binningIndex.get(save_tid), save_bin, save_off, fp.getFilePointer());
mergeChunks();
fillMissing();
if (offset0 != (long) -1 && !linearIndex.isEmpty() && linearIndex.get(0) != null) {
int beg = (int) (offset0 >> 32), end = (int) (offset0 & 0xffffffff);
for (int i = beg; i <= end; ++i) {
linearIndex.get(0).set(i, 0L);
}
}
}
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();
}