c_cpp/lib/htslib/realn.c

   1 /*  realn.c -- BAQ calculation and realignment.
   2
   3     Copyright (C) 2009-2011, 2014-2015 Genome Research Ltd.
   4     Portions copyright (C) 2009-2011 Broad Institute.
   5
   6     Author: Heng Li <lh3@sanger.ac.uk>
   7
   8 Permission is hereby granted, free of charge, to any person obtaining a copy
   9 of this software and associated documentation files (the "Software"), to deal
  10 in the Software without restriction, including without limitation the rights
  11 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  12 copies of the Software, and to permit persons to whom the Software is
  13 furnished to do so, subject to the following conditions:
  14
  15 The above copyright notice and this permission notice shall be included in
  16 all copies or substantial portions of the Software.
  17
  18 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  19 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  20 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
  21 THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  22 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
  23 FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
  24 DEALINGS IN THE SOFTWARE.  */
  25
  26 #include <config.h>
  27
  28 #include <stdlib.h>
  29 #include <string.h>
  30 #include <math.h>
  31 #include "htslib/hts.h"
  32 #include "htslib/sam.h"
  33
  34 int sam_cap_mapq(bam1_t *b, const char *ref, int ref_len, int thres)
  35 {
  36     uint8_t *seq = bam_get_seq(b), *qual = bam_get_qual(b);
  37     uint32_t *cigar = bam_get_cigar(b);
  38     bam1_core_t *c = &b->core;
  39     int i, x, y, mm, q, len, clip_l, clip_q;
  40     double t;
  41     if (thres < 0) thres = 40; // set the default
  42     mm = q = len = clip_l = clip_q = 0;
  43     for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
  44         int j, l = cigar[i]>>4, op = cigar[i]&0xf;
  45         if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
  46             for (j = 0; j < l; ++j) {
  47                 int c1, c2, z = y + j;
  48                 if (x+j >= ref_len || ref[x+j] == '\0') break; // out of bounds
  49                 c1 = bam_seqi(seq, z), c2 = seq_nt16_table[(int)ref[x+j]];
  50                 if (c2 != 15 && c1 != 15 && qual[z] >= 13) { // not ambiguous
  51                     ++len;
  52                     if (c1 && c1 != c2 && qual[z] >= 13) { // mismatch
  53                         ++mm;
  54                         q += qual[z] > 33? 33 : qual[z];
  55                     }
  56                 }
  57             }
  58             if (j < l) break;
  59             x += l; y += l; len += l;
  60         } else if (op == BAM_CDEL) {
  61             for (j = 0; j < l; ++j)
  62                 if (x+j >= ref_len || ref[x+j] == '\0') break;
  63             if (j < l) break;
  64             x += l;
  65         } else if (op == BAM_CSOFT_CLIP) {
  66             for (j = 0; j < l; ++j) clip_q += qual[y+j];
  67             clip_l += l;
  68             y += l;
  69         } else if (op == BAM_CHARD_CLIP) {
  70             clip_q += 13 * l;
  71             clip_l += l;
  72         } else if (op == BAM_CINS) y += l;
  73         else if (op == BAM_CREF_SKIP) x += l;
  74     }
  75     for (i = 0, t = 1; i < mm; ++i)
  76         t *= (double)len / (i+1);
  77     t = q - 4.343 * log(t) + clip_q / 5.;
  78     if (t > thres) return -1;
  79     if (t < 0) t = 0;
  80     t = sqrt((thres - t) / thres) * thres;
  81 //  fprintf(stderr, "%s %lf %d\n", bam_get_qname(b), t, q);
  82     return (int)(t + .499);
  83 }
  84
  85 int sam_prob_realn(bam1_t *b, const char *ref, int ref_len, int flag)
  86 {
  87     int k, i, bw, x, y, yb, ye, xb, xe, apply_baq = flag&1, extend_baq = flag>>1&1, redo_baq = flag&4;
  88     uint32_t *cigar = bam_get_cigar(b);
  89     bam1_core_t *c = &b->core;
  90     probaln_par_t conf = { 0.001, 0.1, 10 };
  91     uint8_t *bq = 0, *zq = 0, *qual = bam_get_qual(b);
  92     if ((c->flag & BAM_FUNMAP) || b->core.l_qseq == 0 || qual[0] == (uint8_t)-1)
  93         return -1; // do nothing
  94
  95     // test if BQ or ZQ is present
  96     if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq;
  97     if ((zq = bam_aux_get(b, "ZQ")) != 0 && *zq == 'Z') ++zq;
  98     if (bq && redo_baq)
  99     {
 100         bam_aux_del(b, bq-1);
 101         bq = 0;
 102     }
 103     if (bq && zq) { // remove the ZQ tag
 104         bam_aux_del(b, zq-1);
 105         zq = 0;
 106     }
 107     if (bq || zq) {
 108         if ((apply_baq && zq) || (!apply_baq && bq)) return -3; // in both cases, do nothing
 109         if (bq && apply_baq) { // then convert BQ to ZQ
 110             for (i = 0; i < c->l_qseq; ++i)
 111                 qual[i] = qual[i] + 64 < bq[i]? 0 : qual[i] - ((int)bq[i] - 64);
 112             *(bq - 3) = 'Z';
 113         } else if (zq && !apply_baq) { // then convert ZQ to BQ
 114             for (i = 0; i < c->l_qseq; ++i)
 115                 qual[i] += (int)zq[i] - 64;
 116             *(zq - 3) = 'B';
 117         }
 118         return 0;
 119     }
 120     // find the start and end of the alignment
 121     x = c->pos, y = 0, yb = ye = xb = xe = -1;
 122     for (k = 0; k < c->n_cigar; ++k) {
 123         int op, l;
 124         op = cigar[k]&0xf; l = cigar[k]>>4;
 125         if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
 126             if (yb < 0) yb = y;
 127             if (xb < 0) xb = x;
 128             ye = y + l; xe = x + l;
 129             x += l; y += l;
 130         } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
 131         else if (op == BAM_CDEL) x += l;
 132         else if (op == BAM_CREF_SKIP) return -1; // do nothing if there is a reference skip
 133     }
 134     // set bandwidth and the start and the end
 135     bw = 7;
 136     if (abs((xe - xb) - (ye - yb)) > bw)
 137         bw = abs((xe - xb) - (ye - yb)) + 3;
 138     conf.bw = bw;
 139     xb -= yb + bw/2; if (xb < 0) xb = 0;
 140     xe += c->l_qseq - ye + bw/2;
 141     if (xe - xb - c->l_qseq > bw)
 142         xb += (xe - xb - c->l_qseq - bw) / 2, xe -= (xe - xb - c->l_qseq - bw) / 2;
 143     { // glocal
 144         uint8_t *s, *r, *q, *seq = bam_get_seq(b), *bq;
 145         int *state;
 146         bq = calloc(c->l_qseq + 1, 1);
 147         memcpy(bq, qual, c->l_qseq);
 148         s = calloc(c->l_qseq, 1);
 149         for (i = 0; i < c->l_qseq; ++i) s[i] = seq_nt16_int[bam_seqi(seq, i)];
 150         r = calloc(xe - xb, 1);
 151         for (i = xb; i < xe; ++i) {
 152             if (i >= ref_len || ref[i] == '\0') { xe = i; break; }
 153             r[i-xb] = seq_nt16_int[seq_nt16_table[(int)ref[i]]];
 154         }
 155         state = calloc(c->l_qseq, sizeof(int));
 156         q = calloc(c->l_qseq, 1);
 157         probaln_glocal(r, xe-xb, s, c->l_qseq, qual, &conf, state, q);
 158         if (!extend_baq) { // in this block, bq[] is capped by base quality qual[]
 159             for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
 160                 int op = cigar[k]&0xf, l = cigar[k]>>4;
 161                 if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
 162                     for (i = y; i < y + l; ++i) {
 163                         if ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y)) bq[i] = 0;
 164                         else bq[i] = bq[i] < q[i]? bq[i] : q[i];
 165                     }
 166                     x += l; y += l;
 167                 } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
 168                 else if (op == BAM_CDEL) x += l;
 169             }
 170             for (i = 0; i < c->l_qseq; ++i) bq[i] = qual[i] - bq[i] + 64; // finalize BQ
 171         } else { // in this block, bq[] is BAQ that can be larger than qual[] (different from the above!)
 172             uint8_t *left, *rght;
 173             left = calloc(c->l_qseq, 1); rght = calloc(c->l_qseq, 1);
 174             for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
 175                 int op = cigar[k]&0xf, l = cigar[k]>>4;
 176                 if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
 177                     for (i = y; i < y + l; ++i)
 178                         bq[i] = ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y))? 0 : q[i];
 179                     for (left[y] = bq[y], i = y + 1; i < y + l; ++i)
 180                         left[i] = bq[i] > left[i-1]? bq[i] : left[i-1];
 181                     for (rght[y+l-1] = bq[y+l-1], i = y + l - 2; i >= y; --i)
 182                         rght[i] = bq[i] > rght[i+1]? bq[i] : rght[i+1];
 183                     for (i = y; i < y + l; ++i)
 184                         bq[i] = left[i] < rght[i]? left[i] : rght[i];
 185                     x += l; y += l;
 186                 } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
 187                 else if (op == BAM_CDEL) x += l;
 188             }
 189             for (i = 0; i < c->l_qseq; ++i) bq[i] = 64 + (qual[i] <= bq[i]? 0 : qual[i] - bq[i]); // finalize BQ
 190             free(left); free(rght);
 191         }
 192         if (apply_baq) {
 193             for (i = 0; i < c->l_qseq; ++i) qual[i] -= bq[i] - 64; // modify qual
 194             bam_aux_append(b, "ZQ", 'Z', c->l_qseq + 1, bq);
 195         } else bam_aux_append(b, "BQ", 'Z', c->l_qseq + 1, bq);
 196         free(bq); free(s); free(r); free(q); free(state);
 197     }
 198     return 0;
 199 }