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bam_md.c

#include <unistd.h>
#include <assert.h>
#include <string.h>
#include <ctype.h>
#include <math.h>
#include "faidx.h"
#include "sam.h"
#include "kstring.h"
#include "kaln.h"
#include "kprobaln.h"

void bam_fillmd1_core(bam1_t *b, char *ref, int is_equal, int max_nm)
{
      uint8_t *seq = bam1_seq(b);
      uint32_t *cigar = bam1_cigar(b);
      bam1_core_t *c = &b->core;
      int i, x, y, u = 0;
      kstring_t *str;
      uint8_t *old_md, *old_nm;
      int32_t old_nm_i = -1, nm = 0;

      str = (kstring_t*)calloc(1, sizeof(kstring_t));
      for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
            int j, l = cigar[i]>>4, op = cigar[i]&0xf;
            if (op == BAM_CMATCH) {
                  for (j = 0; j < l; ++j) {
                        int z = y + j;
                        int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]];
                        if (ref[x+j] == 0) break; // out of boundary
                        if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match
                              if (is_equal) seq[z/2] &= (z&1)? 0xf0 : 0x0f;
                              ++u;
                        } else {
                              ksprintf(str, "%d", u);
                              kputc(ref[x+j], str);
                              u = 0; ++nm;
                        }
                  }
                  if (j < l) break;
                  x += l; y += l;
            } else if (op == BAM_CDEL) {
                  ksprintf(str, "%d", u);
                  kputc('^', str);
                  for (j = 0; j < l; ++j) {
                        if (ref[x+j] == 0) break;
                        kputc(ref[x+j], str);
                  }
                  u = 0;
                  if (j < l) break;
                  x += l; nm += l;
            } else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) {
                  y += l;
                  if (op == BAM_CINS) nm += l;
            } else if (op == BAM_CREF_SKIP) {
                  x += l;
            }
      }
      ksprintf(str, "%d", u);
      // apply max_nm
      if (max_nm > 0 && nm >= max_nm) {
            for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
                  int j, l = cigar[i]>>4, op = cigar[i]&0xf;
                  if (op == BAM_CMATCH) {
                        for (j = 0; j < l; ++j) {
                              int z = y + j;
                              int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]];
                              if (ref[x+j] == 0) break; // out of boundary
                              if ((c1 == c2 && c1 != 15 && c2 != 15) || c1 == 0) { // a match
                                    seq[z/2] |= (z&1)? 0x0f : 0xf0;
                                    bam1_qual(b)[z] = 0;
                              }
                        }
                        if (j < l) break;
                        x += l; y += l;
                  } else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += l;
                  else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
            }
      }
      // update NM
      old_nm = bam_aux_get(b, "NM");
      if (c->flag & BAM_FUNMAP) return;
      if (old_nm) old_nm_i = bam_aux2i(old_nm);
      if (!old_nm) bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
      else if (nm != old_nm_i) {
            fprintf(stderr, "[bam_fillmd1] different NM for read '%s': %d -> %d\n", bam1_qname(b), old_nm_i, nm);
            bam_aux_del(b, old_nm);
            bam_aux_append(b, "NM", 'i', 4, (uint8_t*)&nm);
      }
      // update MD
      old_md = bam_aux_get(b, "MD");
      if (!old_md) bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
      else {
            int is_diff = 0;
            if (strlen((char*)old_md+1) == str->l) {
                  for (i = 0; i < str->l; ++i)
                        if (toupper(old_md[i+1]) != toupper(str->s[i]))
                              break;
                  if (i < str->l) is_diff = 1;
            } else is_diff = 1;
            if (is_diff) {
                  fprintf(stderr, "[bam_fillmd1] different MD for read '%s': '%s' -> '%s'\n", bam1_qname(b), old_md+1, str->s);
                  bam_aux_del(b, old_md);
                  bam_aux_append(b, "MD", 'Z', str->l + 1, (uint8_t*)str->s);
            }
      }
      free(str->s); free(str);
}

void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
{
      bam_fillmd1_core(b, ref, is_equal, 0);
}

int bam_cap_mapQ(bam1_t *b, char *ref, int thres)
{
      uint8_t *seq = bam1_seq(b), *qual = bam1_qual(b);
      uint32_t *cigar = bam1_cigar(b);
      bam1_core_t *c = &b->core;
      int i, x, y, mm, q, len, clip_l, clip_q;
      double t;
      if (thres < 0) thres = 40; // set the default
      mm = q = len = clip_l = clip_q = 0;
      for (i = y = 0, x = c->pos; i < c->n_cigar; ++i) {
            int j, l = cigar[i]>>4, op = cigar[i]&0xf;
            if (op == BAM_CMATCH) {
                  for (j = 0; j < l; ++j) {
                        int z = y + j;
                        int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]];
                        if (ref[x+j] == 0) break; // out of boundary
                        if (c2 != 15 && c1 != 15 && qual[z] >= 13) { // not ambiguous
                              ++len;
                              if (c1 && c1 != c2 && qual[z] >= 13) { // mismatch
                                    ++mm;
                                    q += qual[z] > 33? 33 : qual[z];
                              }
                        }
                  }
                  if (j < l) break;
                  x += l; y += l; len += l;
            } else if (op == BAM_CDEL) {
                  for (j = 0; j < l; ++j)
                        if (ref[x+j] == 0) break;
                  if (j < l) break;
                  x += l;
            } else if (op == BAM_CSOFT_CLIP) {
                  for (j = 0; j < l; ++j) clip_q += qual[y+j];
                  clip_l += l;
                  y += l;
            } else if (op == BAM_CHARD_CLIP) {
                  clip_q += 13 * l;
                  clip_l += l;
            } else if (op == BAM_CINS) y += l;
            else if (op == BAM_CREF_SKIP) x += l;
      }
      for (i = 0, t = 1; i < mm; ++i)
            t *= (double)len / (i+1);
      t = q - 4.343 * log(t) + clip_q / 5.;
      if (t > thres) return -1;
      if (t < 0) t = 0;
      t = sqrt((thres - t) / thres) * thres;
//    fprintf(stderr, "%s %lf %d\n", bam1_qname(b), t, q);
      return (int)(t + .499);
}

int bam_prob_realn_core(bam1_t *b, const char *ref, int apply_baq)
{
      int k, i, bw, x, y, yb, ye, xb, xe;
      uint32_t *cigar = bam1_cigar(b);
      bam1_core_t *c = &b->core;
      kpa_par_t conf = kpa_par_def;
      uint8_t *bq = 0, *zq = 0, *qual = bam1_qual(b);
      if (c->flag & BAM_FUNMAP) return -1; // do nothing
      // test if BQ or ZQ is present
      if ((bq = bam_aux_get(b, "BQ")) != 0) ++bq;
      if ((zq = bam_aux_get(b, "ZQ")) != 0 && *zq == 'Z') ++zq;
      if (bq && zq) { // remove the ZQ tag
            bam_aux_del(b, zq-1);
            zq = 0;
      }
      if (bq || zq) {
            if ((apply_baq && zq) || (!apply_baq && bq)) return -3; // in both cases, do nothing
            if (bq && apply_baq) { // then convert BQ to ZQ
                  for (i = 0; i < c->l_qseq; ++i)
                        qual[i] = qual[i] + 64 < bq[i]? 0 : qual[i] - ((int)bq[i] - 64);
                  *(bq - 3) = 'Z';
            } else if (zq && !apply_baq) { // then convert ZQ to BQ
                  for (i = 0; i < c->l_qseq; ++i)
                        qual[i] += (int)zq[i] - 64;
                  *(zq - 3) = 'B';
            }
            return 0;
      }
      // find the start and end of the alignment      
      x = c->pos, y = 0, yb = ye = xb = xe = -1;
      for (k = 0; k < c->n_cigar; ++k) {
            int op, l;
            op = cigar[k]&0xf; l = cigar[k]>>4;
            if (op == BAM_CMATCH) {
                  if (yb < 0) yb = y;
                  if (xb < 0) xb = x;
                  ye = y + l; xe = x + l;
                  x += l; y += l;
            } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
            else if (op == BAM_CDEL) x += l;
            else if (op == BAM_CREF_SKIP) return -1; // do nothing if there is a reference skip
      }
      // set bandwidth and the start and the end
      bw = 7;
      if (abs((xe - xb) - (ye - yb)) > bw)
            bw = abs((xe - xb) - (ye - yb)) + 3;
      conf.bw = bw;
      xb -= yb + bw/2; if (xb < 0) xb = 0;
      xe += c->l_qseq - ye + bw/2;
      if (xe - xb - c->l_qseq > bw)
            xb += (xe - xb - c->l_qseq - bw) / 2, xe -= (xe - xb - c->l_qseq - bw) / 2;
      { // glocal
            uint8_t *s, *r, *q, *seq = bam1_seq(b), *bq;
            int *state;
            bq = calloc(c->l_qseq + 1, 1);
            memcpy(bq, qual, c->l_qseq);
            s = calloc(c->l_qseq, 1);
            for (i = 0; i < c->l_qseq; ++i) s[i] = bam_nt16_nt4_table[bam1_seqi(seq, i)];
            r = calloc(xe - xb, 1);
            for (i = xb; i < xe; ++i)
                  r[i-xb] = bam_nt16_nt4_table[bam_nt16_table[(int)ref[i]]];
            state = calloc(c->l_qseq, sizeof(int));
            q = calloc(c->l_qseq, 1);
            kpa_glocal(r, xe-xb, s, c->l_qseq, qual, &conf, state, q);
            for (k = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) {
                  int op = cigar[k]&0xf, l = cigar[k]>>4;
                  if (op == BAM_CMATCH) {
                        for (i = y; i < y + l; ++i) {
                              if ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y)) bq[i] = 0;
                              else bq[i] = bq[i] < q[i]? bq[i] : q[i];
                        }
                        x += l; y += l;
                  } else if (op == BAM_CSOFT_CLIP || op == BAM_CINS) y += l;
                  else if (op == BAM_CDEL) x += l;
            }
            for (i = 0; i < c->l_qseq; ++i) bq[i] = qual[i] - bq[i] + 64; // finalize BQ
            if (apply_baq) {
                  for (i = 0; i < c->l_qseq; ++i) qual[i] -= bq[i] - 64; // modify qual
                  bam_aux_append(b, "ZQ", 'Z', c->l_qseq + 1, bq);
            } else bam_aux_append(b, "BQ", 'Z', c->l_qseq + 1, bq);
            free(bq); free(s); free(r); free(q); free(state);
      }
      return 0;
}

int bam_prob_realn(bam1_t *b, const char *ref)
{
      return bam_prob_realn_core(b, ref, 1);
}

int bam_fillmd(int argc, char *argv[])
{
      int c, is_equal, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm, is_realn, capQ, apply_baq;
      samfile_t *fp, *fpout = 0;
      faidx_t *fai;
      char *ref = 0, mode_w[8], mode_r[8];
      bam1_t *b;

      is_equal = is_bam_out = is_sam_in = is_uncompressed = is_realn = max_nm = apply_baq = capQ = 0;
      mode_w[0] = mode_r[0] = 0;
      strcpy(mode_r, "r"); strcpy(mode_w, "w");
      while ((c = getopt(argc, argv, "reubSC:n:A")) >= 0) {
            switch (c) {
            case 'r': is_realn = 1; break;
            case 'e': is_equal = 1; break;
            case 'b': is_bam_out = 1; break;
            case 'u': is_uncompressed = is_bam_out = 1; break;
            case 'S': is_sam_in = 1; break;
            case 'n': max_nm = atoi(optarg); break;
            case 'C': capQ = atoi(optarg); break;
            case 'A': apply_baq = 1; break;
            default: fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n", c); return 1;
            }
      }
      if (!is_sam_in) strcat(mode_r, "b");
      if (is_bam_out) strcat(mode_w, "b");
      else strcat(mode_w, "h");
      if (is_uncompressed) strcat(mode_w, "u");
      if (optind + 1 >= argc) {
            fprintf(stderr, "\n");
            fprintf(stderr, "Usage:   samtools fillmd [-eubrS] <aln.bam> <ref.fasta>\n\n");
            fprintf(stderr, "Options: -e       change identical bases to '='\n");
            fprintf(stderr, "         -u       uncompressed BAM output (for piping)\n");
            fprintf(stderr, "         -b       compressed BAM output\n");
            fprintf(stderr, "         -S       the input is SAM with header\n");
            fprintf(stderr, "         -A       modify the quality string\n");
            fprintf(stderr, "         -r       read-independent local realignment\n\n");
            return 1;
      }
      fp = samopen(argv[optind], mode_r, 0);
      if (fp == 0) return 1;
      if (is_sam_in && (fp->header == 0 || fp->header->n_targets == 0)) {
            fprintf(stderr, "[bam_fillmd] input SAM does not have header. Abort!\n");
            return 1;
      }
      fpout = samopen("-", mode_w, fp->header);
      fai = fai_load(argv[optind+1]);

      b = bam_init1();
      while ((ret = samread(fp, b)) >= 0) {
            if (b->core.tid >= 0) {
                  if (tid != b->core.tid) {
                        free(ref);
                        ref = fai_fetch(fai, fp->header->target_name[b->core.tid], &len);
                        tid = b->core.tid;
                        if (ref == 0)
                              fprintf(stderr, "[bam_fillmd] fail to find sequence '%s' in the reference.\n",
                                          fp->header->target_name[tid]);
                  }
                  if (is_realn) bam_prob_realn_core(b, ref, apply_baq);
                  if (capQ > 10) {
                        int q = bam_cap_mapQ(b, ref, capQ);
                        if (b->core.qual > q) b->core.qual = q;
                  }
                  if (ref) bam_fillmd1_core(b, ref, is_equal, max_nm);
            }
            samwrite(fpout, b);
      }
      bam_destroy1(b);

      free(ref);
      fai_destroy(fai);
      samclose(fp); samclose(fpout);
      return 0;
}

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