public Iterator query()

in server/catgenome/src/main/java/com/epam/catgenome/util/feature/reader/TabixReader.java [558:631]
69 lines of code
22 McCabe index (conditional complexity)

    public Iterator query(final int tid, final int beg, final int end) {
        TPair64[] off, chunks;
        long minOff;
        if (tid < 0 || tid >= this.mIndex.length) {
            return EOF_ITERATOR;
        }
        TIndex idx = mIndex[tid];
        int[] bins = new int[MAX_BIN];
        int i, l, nOff, nBins = reg2bins(beg, end, bins);

        if (idx.l.length > 0) {
            minOff = (beg >> TAD_LIDX_SHIFT >= idx.l.length) ? idx.l[idx.l.length - 1] : idx.l[beg >> TAD_LIDX_SHIFT];
        } else {
            minOff = 0;
        }
        for (i = 0, nOff = 0; i < nBins; ++i) {
            chunks = idx.b.get(bins[i]);
            if (chunks != null) {
                nOff += chunks.length;
            }
        }
        if (nOff == 0) {
            return EOF_ITERATOR;
        }
        off = new TPair64[nOff];
        for (i = 0, nOff = 0; i < nBins; ++i) {
            chunks = idx.b.get(bins[i]);
            if (chunks != null) {
                for (int j = 0; j < chunks.length; ++j) {
                    if (less64(minOff, chunks[j].v)) {
                        off[nOff++] = new TPair64(chunks[j]);
                    }
                }
            }
        }
        Arrays.sort(off, 0, nOff);
        // resolve completely contained adjacent blocks
        for (i = 1, l = 0; i < nOff; ++i) {
            if (less64(off[l].v, off[i].v)) {
                ++l;
                off[l].u = off[i].u;
                off[l].v = off[i].v;
            }
        }
        nOff = l + 1;
        // resolve overlaps between adjacent blocks; this may happen due to the merge in indexing
        for (i = 1; i < nOff; ++i) {
            if (!less64(off[i - 1].v, off[i].u)) {
                off[i - 1].v = off[i].u;
            }
        }
        // merge adjacent blocks
        for (i = 1, l = 0; i < nOff; ++i) {
            if (off[l].v >> 16 == off[i].u >> 16) {
                off[l].v = off[i].v;
            } else {
                ++l;
                off[l].u = off[i].u;
                off[l].v = off[i].v;
            }
        }
        nOff = l + 1;
        // return
        TPair64[] ret = new TPair64[nOff];
        for (i = 0; i < nOff; ++i) {
            if (off[i] != null) {
                ret[i] = new TPair64(off[i].u, off[i].v); // in C, this is inefficient
            }
        }
        if (ret.length == 0 || (ret.length == 1 && ret[0] == null)) {
            return EOF_ITERATOR;
        }
        return new TabixReader.IteratorImpl(tid, beg, end, ret);
    }