/* The MIT License Copyright (C) 2003-2006, 2008-2010 by Heng Li 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. */ #include #include #include #include #include #include #include #include #include "htslib/hts.h" /***************************************** * Probabilistic banded glocal alignment * *****************************************/ #define EI .25 #define EM .33333333333 static float g_qual2prob[256]; #define set_u(u, b, i, k) { int x=(i)-(b); x=x>0?x:0; (u)=((k)-x+1)*3; } /* The topology of the profile HMM: /\ /\ /\ /\ I[1] I[k-1] I[k] I[L] ^ \ \ ^ \ ^ \ \ ^ | \ \ | \ | \ \ | M[0] M[1] -> ... -> M[k-1] -> M[k] -> ... -> M[L] M[L+1] \ \/ \/ \/ / \ /\ /\ /\ / -> D[k-1] -> D[k] -> M[0] points to every {M,I}[k] and every {M,I}[k] points to M[L+1]. On input, ref is the reference sequence and query is the query sequence. Both are sequences of 0/1/2/3/4 where 4 stands for an ambiguous residue. iqual is the base quality. c sets the gap open probability, gap extension probability and band width. On output, state and q are arrays of length l_query. The higher 30 bits give the reference position the query base is matched to and the lower two bits can be 0 (an alignment match) or 1 (an insertion). q[i] gives the phred scaled posterior probability of state[i] being wrong. Returns phred-scaled likelihood score, or INT_MIN on failure. */ int probaln_glocal(const uint8_t *ref, int l_ref, const uint8_t *query, int l_query, const uint8_t *iqual, const probaln_par_t *c, int *state, uint8_t *q) { double *f = NULL, *b = NULL, *s = NULL, m[9], sI, sM, bI, bM; float *qual = NULL; int bw, bw2, i, k, is_backward = 1, Pr; if ( l_ref<0 || l_query<0 || l_query >= INT_MAX - 2) { errno = EINVAL; return INT_MIN; } if (l_ref==0 || l_query==0) return 0; // Is this actually invalid?? /*** initialization ***/ is_backward = state && q? 1 : 0; bw = l_ref > l_query? l_ref : l_query; if (bw > c->bw) bw = c->bw; if (bw < abs(l_ref - l_query)) bw = abs(l_ref - l_query); bw2 = bw * 2 + 1; size_t i_dim = bw2 < l_ref ? (size_t) bw2*3+6 : (size_t) l_ref*3+6; // allocate the forward and backward matrices f[][] and b[][] and the scaling array s[] // Ideally these callocs would be mallocs + initialisation of the few bits needed. if (SIZE_MAX / (l_query+1) / i_dim < sizeof(double)) { errno = ENOMEM; // Allocation would fail return INT_MIN; } f = calloc((l_query+1)*i_dim, sizeof(double)); if (!f) goto fail; if (is_backward) { b = calloc((l_query+1)*i_dim, sizeof(double)); if (!b) goto fail; } s = malloc((l_query+2) * sizeof(double)); // s[] is the scaling factor to avoid underflow if (!s) goto fail; // initialize qual qual = malloc(l_query * sizeof(float)); if (!qual) goto fail; if (g_qual2prob[0] == 0) for (i = 0; i < 256; ++i) g_qual2prob[i] = pow(10, -i/10.); qual[0] = 0.0; // Should be unused for (i = 0; i < l_query; ++i) qual[i] = g_qual2prob[iqual? iqual[i] : 30]; // initialize transition probability sM = sI = 1. / (2 * l_query + 2); // the value here seems not to affect results; FIXME: need proof m[0*3+0] = (1 - c->d - c->d) * (1 - sM); m[0*3+1] = m[0*3+2] = c->d * (1 - sM); m[1*3+0] = (1 - c->e) * (1 - sI); m[1*3+1] = c->e * (1 - sI); m[1*3+2] = 0.; m[2*3+0] = 1 - c->e; m[2*3+1] = 0.; m[2*3+2] = c->e; bM = (1 - c->d) / l_ref; bI = c->d / l_ref; // (bM+bI)*l_ref==1 /*** forward ***/ // f[0] set_u(k, bw, 0, 0); f[0*i_dim+k] = s[0] = 1.; { // f[1] double *fi = &f[1*i_dim], sum; int beg = 1, end = l_ref < bw + 1? l_ref : bw + 1; for (k = beg, sum = 0.; k <= end; ++k) { int u; double e = (ref[k - 1] > 3 || query[0] > 3)? 1. : ref[k - 1] == query[0]? 1. - qual[0] : qual[0] * EM; set_u(u, bw, 1, k); fi[u+0] = e * bM; fi[u+1] = EI * bI; sum += fi[u] + fi[u+1]; } s[1] = sum; } // f[2..l_query] for (i = 2; i <= l_query; ++i) { double *fi = &f[i*i_dim], *fi1 = &f[(i-1)*i_dim], sum, qli = qual[i-1]; int beg = 1, end = l_ref, x; uint8_t qyi = query[i - 1]; x = i - bw; beg = beg > x? beg : x; // band start x = i + bw; end = end < x? end : x; // band end double E[] = { qli * EM, // 00 1. - qli, // 01 1., // 10 1., // 11 }; double M = 1./s[i-1]; for (k = beg, sum = 0.; k <= end; ++k) { int u, v11, v01, v10; double e; e = E[(ref[k - 1] > 3 || qyi > 3)*2 + (ref[k - 1] == qyi)]; set_u(u, bw, i, k); set_u(v11, bw, i-1, k-1); set_u(v10, bw, i-1, k); set_u(v01, bw, i, k-1); fi[u+0] = e * (m[0] * M*fi1[v11+0] + m[3] * M*fi1[v11+1] + m[6] * M*fi1[v11+2]); fi[u+1] = EI * (m[1] * M*fi1[v10+0] + m[4] * M*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]; // fprintf(stderr, "F (%d,%d;%d): %lg,%lg,%lg\n", i, k, u, fi[u], fi[u+1], fi[u+2]); // DEBUG } s[i] = sum; } { // f[l_query+1] double sum; double M = 1./s[l_query]; for (k = 1, sum = 0.; k <= l_ref; ++k) { int u; set_u(u, bw, l_query, k); if (u < 3 || u >= i_dim - 3) continue; sum += M*f[l_query*i_dim + u+0] * sM + M*f[l_query*i_dim + u+1] * sI; } s[l_query+1] = sum; // the last scaling factor } { // compute likelihood double p = 1., Pr1 = 0.; for (i = 0; i <= l_query + 1; ++i) { p *= s[i]; if (p < 1e-100) Pr1 += -4.343 * log(p), p = 1.; } Pr1 += -4.343 * log(p * l_ref * l_query); Pr = (int)(Pr1 + .499); if (!is_backward) { // skip backward and MAP free(f); free(s); free(qual); return Pr; } } /*** 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; double *bi = &b[l_query*i_dim]; set_u(u, bw, l_query, k); if (u < 3 || u >= i_dim - 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*i_dim], *bi1 = &b[(i+1)*i_dim], y = (i > 1), qli1 = qual[i]; uint8_t qyi1 = query[i]; x = i - bw; beg = beg > x? beg : x; x = i + bw; end = end < x? end : x; double E[] = { qli1 * EM, //000 1. - qli1, //001 1., //010 1., //011 //0,0,0,0 //1xx }; for (k = end; k >= beg; --k) { int u, v11, v01, v10; double e; set_u(u, bw, i, k); set_u(v11, bw, i+1, k+1); set_u(v10, bw, i+1, k); set_u(v01, bw, i, k+1); e = (k>=l_ref)?0 :E[(ref[k] > 3 || qyi1 > 3)*2 + (ref[k] == qyi1)] * bi1[v11]; bi[u+0] = e * m[0] + EI * m[1] * bi1[v10+1] + m[2] * bi[v01+2]; // bi1[v11] has been foled into e. bi[u+1] = e * m[3] + EI * m[4] * bi1[v10+1]; bi[u+2] = (e * m[6] + m[8] * bi[v01+2]) * y; // fprintf(stderr, "B (%d,%d;%d): %lg,%lg,%lg\n", i, k, u, bi[u], bi[u+1], bi[u+2]); // DEBUG } // rescale set_u(_beg, bw, i, beg); set_u(_end, bw, i, end); _end += 2; for (k = _beg, y = 1./s[i]; k <= _end; ++k) bi[k] *= y; } { // 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; double e = (ref[k - 1] > 3 || query[0] > 3)? 1. : ref[k - 1] == query[0]? 1. - qual[0] : qual[0] * EM; set_u(u, bw, 1, k); if (u < 3 || u >= i_dim - 3) continue; sum += e * b[1*i_dim + u+0] * bM + EI * b[1*i_dim + u+1] * bI; } set_u(k, bw, 0, 0); b[0*i_dim + k] = sum / s[0]; // if everything works as is expected, b[0][k] == 1.0 } /*** MAP ***/ for (i = 1; i <= l_query; ++i) { double sum = 0., *fi = &f[i*i_dim], *bi = &b[i*i_dim], max = 0.; 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; double M = 1./s[i]; for (k = beg; k <= end; ++k) { int u; double z; set_u(u, bw, i, k); z = M*fi[u+0] * bi[u+0]; if (z > max) max = z, max_k = (k-1)<<2 | 0; sum += z; z = M*fi[u+1] * bi[u+1]; if (z > max) max = z, max_k = (k-1)<<2 | 1; sum += z; } max /= sum; sum *= s[i]; // if everything works as is expected, sum == 1.0 if (state) state[i-1] = max_k; if (q) k = (int)(-4.343 * log(1. - max) + .499), q[i-1] = k > 100? 99 : k; #ifdef _MAIN k = 0; set_u(k, bw, 0, 0); fprintf(stderr, "(%.10lg,%.10lg) (%d,%d:%c,%c:%d) %lg\n", b[0][k], sum, i-1, max_k>>2, "ACGT"[query[i - 1]], "ACGT"[ref[(max_k>>2)]], max_k&3, max); // DEBUG #endif } /*** free ***/ free(f); free(b); free(s); free(qual); return Pr; fail: free(f); free(b); free(s); free(qual); return INT_MIN; } #ifdef _MAIN #include int main(int argc, char *argv[]) { uint8_t conv[256], *iqual, *ref, *query; probaln_par_t par = { 0.001, 0.1, 10 }; int c, l_ref, l_query, i, q = 30, b = 10, P; while ((c = getopt(argc, argv, "b:q:")) >= 0) { switch (c) { case 'b': b = atoi(optarg); break; case 'q': q = atoi(optarg); break; } } if (optind + 2 > argc) { fprintf(stderr, "Usage: %s [-q %d] [-b %d] \n", argv[0], q, b); // example: acttc attc return 1; } memset(conv, 4, 256); conv['a'] = conv['A'] = 0; conv['c'] = conv['C'] = 1; conv['g'] = conv['G'] = 2; conv['t'] = conv['T'] = 3; ref = (uint8_t*)argv[optind]; query = (uint8_t*)argv[optind+1]; l_ref = strlen((char*)ref); l_query = strlen((char*)query); for (i = 0; i < l_ref; ++i) ref[i] = conv[ref[i]]; for (i = 0; i < l_query; ++i) query[i] = conv[query[i]]; iqual = malloc(l_query); memset(iqual, q, l_query); par.bw = b; P = probaln_glocal(ref, l_ref, query, l_query, iqual, &par, 0, 0); fprintf(stderr, "%d\n", P); free(iqual); return 0; } #endif