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HmmGlocal.java

import java.io.*;
import java.lang.*;

public class HmmGlocal
{
      private double[] qual2prob;
      private double cd, ce; // gap open probility [1e-3], gap extension probability [0.1]
      private int cb; // band width [7]

      public HmmGlocal(final double d, final double e, final int b) {
            cd = d; ce = e; cb = b;
            qual2prob = new double[256];
            for (int i = 0; i < 256; ++i)
                  qual2prob[i] = Math.pow(10, -i/10.);
      }
      private static int set_u(final int b, final int i, final int k) {
            int x = i - b;
            x = x > 0? x : 0;
            return (k + 1 - x) * 3;
      }
      public int hmm_glocal(final byte[] _ref, final byte[] _query, final byte[] _iqual, int[] state, byte[] q) {
            int i, k;
            /*** initialization ***/
            // change coordinates
            int l_ref = _ref.length;
            byte[] ref = new byte[l_ref+1];
            for (i = 0; i < l_ref; ++i) ref[i+1] = _ref[i]; // FIXME: this is silly...
            int l_query = _query.length;
            byte[] query = new byte[l_query+1];
            double[] qual = new double[l_query+1];
            for (i = 0; i < l_query; ++i) {
                  query[i+1] = _query[i];
                  qual[i+1] = qual2prob[_iqual[i]];
            }
            // set band width
            int bw2, bw = l_ref > l_query? l_ref : l_query;
            if (bw > cb) bw = cb;
            if (bw < Math.abs(l_ref - l_query)) bw = Math.abs(l_ref - l_query);
            bw2 = bw * 2 + 1;
            // allocate the forward and backward matrices f[][] and b[][] and the scaling array s[]
            double[][] f = new double[l_query+1][bw2*3 + 6];
            double[][] b = new double[l_query+1][bw2*3 + 6];
            double[] s = new double[l_query+2];
            // initialize transition probabilities
            double sM, sI, bM, bI;
            sM = sI = 1. / (2 * l_query + 2);
            bM = (1 - cd) / l_query; bI = cd / l_query; // (bM+bI)*l_query==1
            double[] m = new double[9];
            m[0*3+0] = (1 - cd - cd) * (1 - sM); m[0*3+1] = m[0*3+2] = cd * (1 - sM);
            m[1*3+0] = (1 - ce) * (1 - sI); m[1*3+1] = ce * (1 - sI); m[1*3+2] = 0.;
            m[2*3+0] = 1 - ce; m[2*3+1] = 0.; m[2*3+2] = ce;
            /*** forward ***/
            // f[0]
            f[0][set_u(bw, 0, 0)] = s[0] = 1.;
            { // f[1]
                  double[] fi = f[1];
                  double sum;
                  int beg = 1, end = l_ref < bw + 1? l_ref : bw + 1, _beg, _end;
                  for (k = beg, sum = 0.; k <= end; ++k) {
                        int u;
                        double e = (ref[k] > 3 || query[1] > 3)? 1. : ref[k] == query[1]? 1. - qual[1] : qual[1] / 3.;
                        u = set_u(bw, 1, k);
                        fi[u+0] = e * bM; fi[u+1] = .25 * bI;
                        sum += fi[u] + fi[u+1];
                  }
                  // rescale
                  s[1] = sum;
                  _beg = set_u(bw, 1, beg); _end = set_u(bw, 1, end); _end += 2;
                  for (k = _beg; k <= _end; ++k) fi[k] /= sum;
            }
            // f[2..l_query]
            for (i = 2; i <= l_query; ++i) {
                  double[] fi = f[i], fi1 = f[i-1];
                  double sum, qli = qual[i];
                  int beg = 1, end = l_ref, x, _beg, _end;
                  byte qyi = query[i];
                  x = i - bw; beg = beg > x? beg : x; // band start
                  x = i + bw; end = end < x? end : x; // band end
                  for (k = beg, sum = 0.; k <= end; ++k) {
                        int u, v11, v01, v10;
                        double e;
                        e = (ref[k] > 3 || qyi > 3)? 1. : ref[k] == qyi? 1. - qli : qli / 3.;
                        u = set_u(bw, i, k); v11 = set_u(bw, i-1, k-1); v10 = set_u(bw, i-1, k); v01 = set_u(bw, i, k-1);
                        fi[u+0] = e * (m[0] * fi1[v11+0] + m[3] * fi1[v11+1] + m[6] * fi1[v11+2]);
                        fi[u+1] = .25 * (m[1] * fi1[v10+0] + m[4] * fi1[v10+1]);
                        fi[u+2] = m[2] * fi[v01+0] + m[8] * fi[v01+2];
                        sum += fi[u] + fi[u+1] + fi[u+2];
                        //System.out.println("("+i+","+k+";"+u+"): "+fi[u]+","+fi[u+1]+","+fi[u+2]);
                  }
                  // rescale
                  s[i] = sum;
                  _beg = set_u(bw, i, beg); _end = set_u(bw, i, end); _end += 2;
                  for (k = _beg, sum = 1./sum; k <= _end; ++k) fi[k] *= sum;
            }
            { // f[l_query+1]
                  double sum;
                  for (k = 1, sum = 0.; k <= l_ref; ++k) {
                        int u = set_u(bw, l_query, k);
                        if (u < 3 || u >= bw2*3+3) continue;
                        sum += f[l_query][u+0] * sM + f[l_query][u+1] * sI;
                  }
                  s[l_query+1] = sum; // the last scaling factor
            }
            /*** backward ***/
            // b[l_query] (b[l_query+1][0]=1 and thus \tilde{b}[][]=1/s[l_query+1]; this is where s[l_query+1] comes from)
            for (k = 1; k <= l_ref; ++k) {
                  int u = set_u(bw, l_query, k);
                  double[] bi = b[l_query];
                  if (u < 3 || u >= bw2*3+3) continue;
                  bi[u+0] = sM / s[l_query] / s[l_query+1]; bi[u+1] = sI / s[l_query] / s[l_query+1];
            }
            // b[l_query-1..1]
            for (i = l_query - 1; i >= 1; --i) {
                  int beg = 1, end = l_ref, x, _beg, _end;
                  double[] bi = b[i], bi1 = b[i+1];
                  double y = (i > 1)? 1. : 0., qli1 = qual[i+1];
                  byte qyi1 = query[i+1];
                  x = i - bw; beg = beg > x? beg : x;
                  x = i + bw; end = end < x? end : x;
                  for (k = end; k >= beg; --k) {
                        int u, v11, v01, v10;
                        double e;
                        u = set_u(bw, i, k); v11 = set_u(bw, i+1, k+1); v10 = set_u(bw, i+1, k); v01 = set_u(bw, i, k+1);
                        e = (k >= l_ref? 0 : (ref[k+1] > 3 || qyi1 > 3)? 1. : ref[k+1] == qyi1? 1. - qli1 : qli1 / 3.) * bi1[v11];
                        bi[u+0] = e * m[0] + .25 * m[1] * bi1[v10+1] + m[2] * bi[v01+2]; // bi1[v11] has been foled into e.
                        bi[u+1] = e * m[3] + .25 * m[4] * bi1[v10+1];
                        bi[u+2] = (e * m[6] + m[8] * bi[v01+2]) * y;
                  }
                  // rescale
                  _beg = set_u(bw, i, beg); _end = set_u(bw, i, end); _end += 2;
                  for (k = _beg, y = 1./s[i]; k <= _end; ++k) bi[k] *= y;
            }
            double pb;
            { // b[0]
                  int beg = 1, end = l_ref < bw + 1? l_ref : bw + 1;
                  double sum = 0.;
                  for (k = end; k >= beg; --k) {
                        int u = set_u(bw, 1, k);
                        double e = (ref[k] > 3 || query[1] > 3)? 1. : ref[k] == query[1]? 1. - qual[1] : qual[1] / 3.;
                        if (u < 3 || u >= bw2*3+3) continue;
                        sum += e * b[1][u+0] * bM + .25 * b[1][u+1] * bI;
                  }
                  pb = b[0][set_u(bw, 0, 0)] = sum / s[0]; // if everything works as is expected, pb == 1.0
            }
            int is_diff = Math.abs(pb - 1.) > 1e-7? 1 : 0;
            /*** MAP ***/
            for (i = 1; i <= l_query; ++i) {
                  double sum = 0., max = 0.;
                  double[] fi = f[i], bi = b[i];
                  int beg = 1, end = l_ref, x, max_k = -1;
                  x = i - bw; beg = beg > x? beg : x;
                  x = i + bw; end = end < x? end : x;
                  for (k = beg; k <= end; ++k) {
                        int u = set_u(bw, i, k);
                        double z;
                        sum += (z = fi[u+0] * bi[u+0]); if (z > max) { max = z; max_k = (k-1)<<2 | 0; }
                        sum += (z = fi[u+1] * bi[u+1]); if (z > max) { max = z; max_k = (k-1)<<2 | 1; }
                  }
                  max /= sum; sum *= s[i]; // if everything works as is expected, sum == 1.0
                  if (state != null) state[i-1] = max_k;
                  if (q != null) {
                        k = (int)(-4.343 * Math.log(1. - max) + .499);
                        q[i-1] = (byte)(k > 100? 99 : k);
                  }
                  //System.out.println("("+pb+","+sum+")"+" ("+(i-1)+","+(max_k>>2)+","+(max_k&3)+","+max+")");
            }
            return 0;
      }

      public static void main(String[] args) {
            byte[] ref = {'\0', '\1', '\3', '\3', '\1'};
            byte[] query = {'\0', '\3', '\3', '\1'};
            byte[] qual = new byte[4];
            qual[0] = qual[1] = qual[2] = qual[3] = (byte)20;
            HmmGlocal hg = new HmmGlocal(1e-3, 0.1, 7);
            hg.hmm_glocal(ref, query, qual, null, null);
      }
}

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