TabixReader.java

/* The MIT License

   Copyright (c) 2010 Broad Institute.

   Permission is hereby granted, free of charge, to any person obtaining
   a copy of this software and associated documentation files (the
   "Software"), to deal in the Software without restriction, including
   without limitation the rights to use, copy, modify, merge, publish,
   distribute, sublicense, and/or sell copies of the Software, and to
   permit persons to whom the Software is furnished to do so, subject to
   the following conditions:

   The above copyright notice and this permission notice shall be
   included in all copies or substantial portions of the Software.

   THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
   EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
   MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
   NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
   BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
   ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
   CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
   SOFTWARE.
*/

/* Contact: Heng Li <hengli@broadinstitute.org> */

import net.sf.samtools.util.BlockCompressedInputStream;

import java.io.*;
import java.nio.*;
import java.util.HashMap;
import java.util.ArrayList;
import java.util.Arrays;
import java.lang.StringBuffer;

public class TabixReader
{
	private String mFn;
	private BlockCompressedInputStream mFp;

	private int mPreset;
	private int mSc;
	private int mBc;
	private int mEc;
	private int mMeta;
	private int mSkip;
	private String[] mSeq;

	private HashMap<String, Integer> mChr2tid;

	private static int MAX_BIN = 37450;
	private static int TAD_MIN_CHUNK_GAP = 32768;
	private static int TAD_LIDX_SHIFT = 14;

	private class TPair64 implements Comparable<TPair64> {
		long u, v;
		public TPair64(final long _u, final long _v) {
			u = _u; v = _v;
		}
		public TPair64(final TPair64 p) {
			u = p.u; v = p.v;
		}
		public int compareTo(final TPair64 p) {
			return u == p.u? 0 : ((u < p.u) ^ (u < 0) ^ (p.u < 0))? -1 : 1; // unsigned 64-bit comparison
		}
	};

	private class TIndex {
		HashMap<Integer, TPair64[]> b; // binning index
		long[] l; // linear index
	};
	private TIndex[] mIndex;

	private class TIntv {
		int tid, beg, end;
	};

	private static boolean less64(final long u, final long v) { // unsigned 64-bit comparison
		return (u < v) ^ (u < 0) ^ (v < 0);
	}

	/**
	 * The constructor
	 *
	 * @param fn File name of the data file
	 */
	public TabixReader(final String fn) throws IOException {
		mFn = fn;
		mFp = new BlockCompressedInputStream(new File(fn));
		readIndex();
	}

	private static int reg2bins(final int beg, final int _end, final int[] list) {
		int i = 0, k, end = _end;
		if (beg >= end) return 0;
		if (end >= 1<<29) end = 1<<29;
		--end;
		list[i++] = 0;
		for (k =    1 + (beg>>26); k <=    1 + (end>>26); ++k) list[i++] = k;
		for (k =    9 + (beg>>23); k <=    9 + (end>>23); ++k) list[i++] = k;
		for (k =   73 + (beg>>20); k <=   73 + (end>>20); ++k) list[i++] = k;
		for (k =  585 + (beg>>17); k <=  585 + (end>>17); ++k) list[i++] = k;
		for (k = 4681 + (beg>>14); k <= 4681 + (end>>14); ++k) list[i++] = k;
		return i;
	}

	public static int readInt(final InputStream is) throws IOException {
		byte[] buf = new byte[4];
		is.read(buf);
		return ByteBuffer.wrap(buf).order(ByteOrder.LITTLE_ENDIAN).getInt();
	}

	public static long readLong(final InputStream is) throws IOException {
		byte[] buf = new byte[8];
		is.read(buf);
		return ByteBuffer.wrap(buf).order(ByteOrder.LITTLE_ENDIAN).getLong();
	}

	public static String readLine(final InputStream is) throws IOException {
		StringBuffer buf = new StringBuffer();
		int c;
		while ((c = is.read()) >= 0 && c != '\n')
			buf.append((char)c);
		if (c < 0) return null;
		return buf.toString();
	}

	/**
	 * Read the Tabix index from a file
	 *
	 * @param fp File pointer
	 */
	public void readIndex(final File fp) throws IOException {
		if (fp == null) return;
		BlockCompressedInputStream is = new BlockCompressedInputStream(fp);
		byte[] buf = new byte[4];

		is.read(buf, 0, 4); // read "TBI\1"
		mSeq = new String[readInt(is)]; // # sequences
		mChr2tid = new HashMap<String, Integer>();
		mPreset = readInt(is);
		mSc = readInt(is);
		mBc = readInt(is);
		mEc = readInt(is);
		mMeta = readInt(is);
		mSkip = readInt(is);
		// read sequence dictionary
		int i, j, k, l = readInt(is);
		buf = new byte[l];
		is.read(buf);
		for (i = j = k = 0; i < buf.length; ++i) {
			if (buf[i] == 0) {
				byte[] b = new byte[i - j];
				System.arraycopy(buf, j, b, 0, b.length);
				String s = new String(b);
				mChr2tid.put(s, k);
				mSeq[k++] = s;
				j = i + 1;
			}
		}
		// read the index
		mIndex = new TIndex[mSeq.length];
		for (i = 0; i < mSeq.length; ++i) {
			// the binning index
			int n_bin = readInt(is);
			mIndex[i] = new TIndex();
			mIndex[i].b = new HashMap<Integer, TPair64[]>();
			for (j = 0; j < n_bin; ++j) {
				int bin = readInt(is);
				TPair64[] chunks = new TPair64[readInt(is)];
				for (k = 0; k < chunks.length; ++k) {
					long u = readLong(is);
					long v = readLong(is);
					chunks[k] = new TPair64(u, v); // in C, this is inefficient
				}
				mIndex[i].b.put(bin, chunks);
			}
			// the linear index
			mIndex[i].l = new long[readInt(is)];
			for (k = 0; k < mIndex[i].l.length; ++k)
				mIndex[i].l[k] = readLong(is);
		}
		// close
		is.close();
	}

	/**
	 * Read the Tabix index from the default file.
	 */
	public void readIndex() throws IOException {
		readIndex(new File(mFn + ".tbi"));
	}

	/**
	 * Read one line from the data file.
	 */
	public String readLine() throws IOException {
		return readLine(mFp);
	}

	private int chr2tid(final String chr) {
		if (mChr2tid.containsKey(chr)) return mChr2tid.get(chr);
		else return -1;
	}

	/**
	 * Parse a region in the format of "chr1", "chr1:100" or "chr1:100-1000"
	 *
	 * @param reg Region string
	 * @return An array where the three elements are sequence_id,
	 *         region_begin and region_end. On failure, sequence_id==-1.
	 */
	public int[] parseReg(final String reg) { // FIXME: NOT working when the sequence name contains : or -.
		String chr;
		int colon, hyphen;
		int[] ret = new int[3];
		colon = reg.indexOf(':'); hyphen = reg.indexOf('-');
		chr = colon >= 0? reg.substring(0, colon) : reg;
		ret[1] = colon >= 0? Integer.parseInt(reg.substring(colon+1, hyphen >= 0? hyphen : reg.length())) - 1 : 0;
		ret[2] = hyphen >= 0? Integer.parseInt(reg.substring(hyphen+1)) : 0x7fffffff;
		ret[0] = chr2tid(chr);
		return ret;
	}

	private TIntv getIntv(final String s) {
		TIntv intv = new TIntv();
		int col = 0, end = 0, beg = 0;
		while ((end = s.indexOf('\t', beg)) >= 0 || end == -1) {
			++col;
			if (col == mSc) {
				intv.tid = chr2tid(s.substring(beg, end));
			} else if (col == mBc) {
				intv.beg = intv.end = Integer.parseInt(s.substring(beg, end==-1?s.length():end));
				if ((mPreset&0x10000) != 0) ++intv.end;
				else --intv.beg;
				if (intv.beg < 0) intv.beg = 0;
				if (intv.end < 1) intv.end = 1;
			} else { // FIXME: SAM supports are not tested yet
				if ((mPreset&0xffff) == 0) { // generic
					if (col == mEc)
						intv.end = Integer.parseInt(s.substring(beg, end));
				} else if ((mPreset&0xffff) == 1) { // SAM
					if (col == 6) { // CIGAR
						int l = 0, i, j;
						String cigar = s.substring(beg, end);
						for (i = j = 0; i < cigar.length(); ++i) {
							if (cigar.charAt(i) > '9') {
								int op = cigar.charAt(i);
								if (op == 'M' || op == 'D' || op == 'N')
									l += Integer.parseInt(cigar.substring(j, i));
							}
						}
						intv.end = intv.beg + l;
					}
				} else if ((mPreset&0xffff) == 2) { // VCF
					String alt;
					alt = end >= 0? s.substring(beg, end) : s.substring(beg);
					if (col == 4) { // REF
						if (alt.length() > 0) intv.end = intv.beg + alt.length();
					} else if (col == 8) { // INFO
						int e_off = -1, i = alt.indexOf("END=");
						if (i == 0) e_off = 4;
						else if (i > 0) {
							i = alt.indexOf(";END=");
							if (i >= 0) e_off = i + 5;
						}
						if (e_off > 0) {
							i = alt.indexOf(";", e_off);
							intv.end = Integer.parseInt(i > e_off? alt.substring(e_off, i) : alt.substring(e_off));
						}
					}
				}
			}
			if (end == -1) break;
			beg = end + 1;
		}
		return intv;
	}

	public class Iterator {
		private int i, n_seeks;
		private int tid, beg, end;
		private TPair64[] off;
		private long curr_off;
		private boolean iseof;

		public Iterator(final int _tid, final int _beg, final int _end, final TPair64[] _off) {
			i = -1; n_seeks = 0; curr_off = 0; iseof = false;
			off = _off; tid = _tid; beg = _beg; end = _end;
		}

		public String next() throws IOException {
			if (iseof) return null;
			for (;;) {
				if (curr_off == 0 || !less64(curr_off, off[i].v)) { // then jump to the next chunk
					if (i == off.length - 1) break; // no more chunks
					if (i >= 0) assert(curr_off == off[i].v); // otherwise bug
					if (i < 0 || off[i].v != off[i+1].u) { // not adjacent chunks; then seek
						mFp.seek(off[i+1].u);
						curr_off = mFp.getFilePointer();
						++n_seeks;
					}
					++i;
				}
				String s;
				if ((s = readLine(mFp)) != null) {
					TIntv intv;
					char[] str = s.toCharArray();
					curr_off = mFp.getFilePointer();
					if (str.length == 0 || str[0] == mMeta) continue;
					intv = getIntv(s);
					if (intv.tid != tid || intv.beg >= end) break; // no need to proceed
					else if (intv.end > beg && intv.beg < end) return s; // overlap; return
				} else break; // end of file
			}
			iseof = true;
			return null;
		}
	};

	public Iterator query(final int tid, final int beg, final int end) {
		TPair64[] off, chunks;
		long min_off;
		TIndex idx = mIndex[tid];
		int[] bins = new int[MAX_BIN];
		int i, l, n_off, n_bins = reg2bins(beg, end, bins);
		if (idx.l.length > 0)
			min_off = (beg>>TAD_LIDX_SHIFT >= idx.l.length)? idx.l[idx.l.length-1] : idx.l[beg>>TAD_LIDX_SHIFT];
		else min_off = 0;
		for (i = n_off = 0; i < n_bins; ++i) {
			if ((chunks = idx.b.get(bins[i])) != null)
				n_off += chunks.length;
		}
		if (n_off == 0) return null;
		off = new TPair64[n_off];
		for (i = n_off = 0; i < n_bins; ++i)
			if ((chunks = idx.b.get(bins[i])) != null)
				for (int j = 0; j < chunks.length; ++j)
					if (less64(min_off, chunks[j].v))
						off[n_off++] = new TPair64(chunks[j]);
		if (n_off == 0) return null;
		Arrays.sort(off, 0, n_off);
		// resolve completely contained adjacent blocks
		for (i = 1, l = 0; i < n_off; ++i) {
			if (less64(off[l].v, off[i].v)) {
				++l;
				off[l].u = off[i].u; off[l].v = off[i].v;
			}
		}
		n_off = l + 1;
		// resolve overlaps between adjacent blocks; this may happen due to the merge in indexing
		for (i = 1; i < n_off; ++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 < n_off; ++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;
			}
		}
		n_off = l + 1;
		// return
		TPair64[] ret = new TPair64[n_off];
		for (i = 0; i < n_off; ++i) ret[i] = new TPair64(off[i].u, off[i].v); // in C, this is inefficient
		return new TabixReader.Iterator(tid, beg, end, ret);
	}
	
	public Iterator query(final String reg) {
		int[] x = parseReg(reg);
		return query(x[0], x[1], x[2]);
	}

	public static void main(String[] args) {
		if (args.length < 1) {
			System.out.println("Usage: java -cp .:sam.jar TabixReader <in.gz> [region]");
			System.exit(1);
		}
		try {
			TabixReader tr = new TabixReader(args[0]);
			String s;
			if (args.length == 1) { // no region is specified; print the whole file
				while ((s = tr.readLine()) != null)
					System.out.println(s);
			} else { // a region is specified; random access
				TabixReader.Iterator iter = tr.query(args[1]); // get the iterator
				while (iter != null && (s = iter.next()) != null)
					System.out.println(s);
			}
		} catch (IOException e) {
		}
	}
}