X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_md.c;h=eee767e08fb290ab1ea8baae778201e797c923c3;hb=51f014165fb63b2b9b86db80ea4681f9351453a1;hp=c6c5a65b1a157fad71f9f8e2441b17f24429f9db;hpb=7c51db2e81d77efe6526803fa8d88fead5c82131;p=samtools.git diff --git a/bam_md.c b/bam_md.c index c6c5a65..eee767e 100644 --- a/bam_md.c +++ b/bam_md.c @@ -2,6 +2,7 @@ #include #include #include +#include #include "faidx.h" #include "sam.h" #include "kstring.h" @@ -109,6 +110,57 @@ 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) +{ + 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; + + 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 > 40) return -1; + if (t < 0) t = 0; + t = sqrt((40 - t) / 40) * 40; + fprintf(stderr, "%s %lf %d\n", bam1_qname(b), t, q); + return (int)(t + .499); +} + // local realignment #define MIN_REF_LEN 10 @@ -116,44 +168,83 @@ void bam_fillmd1(bam1_t *b, char *ref, int is_equal) int bam_realn(bam1_t *b, const char *ref) { - int k, l_ref, score, n_cigar; + int k, score, q[2], r[2], kk[2], kl[2], x, y, max, j, n_cigar, endx = -1; uint32_t *cigar = bam1_cigar(b); - uint8_t *s_ref = 0, *s_read = 0, *seq; - ka_param_t par; + uint8_t *seq = bam1_seq(b); bam1_core_t *c = &b->core; - // set S/W parameters - par = ka_param_blast; - par.gap_open = 4; par.gap_ext = 1; par.gap_end_open = par.gap_end_ext = 0; - if (c->n_cigar > 1) { // set band width - int sumi, sumd; - sumi = sumd = 0; - for (k = 0; k < c->n_cigar; ++k) - if ((cigar[k]&0xf) == BAM_CINS) sumi += cigar[k]>>4; - else if ((cigar[k]&0xf) == BAM_CDEL) sumd += cigar[k]>>4; - par.band_width = (sumi > sumd? sumi : sumd) + MIN_BAND_WIDTH; - } else par.band_width = MIN_BAND_WIDTH; - // calculate the length of the reference in the alignment - for (k = l_ref = 0; k < c->n_cigar; ++k) { - if ((cigar[k]&0xf) == BAM_CREF_SKIP) break; // do not do realignment if there is an `N' operation - if ((cigar[k]&0xf) == BAM_CMATCH || (cigar[k]&0xf) == BAM_CDEL) - l_ref += cigar[k]>>4; + q[0] = q[1] = r[0] = r[1] = kk[0] = kk[1] = kl[0] = kl[1] = -1; + // find the right boundary + for (k = 0, score = max = 0, x = c->pos, y = 0; k < c->n_cigar; ++k) { + int op = cigar[k]&0xf; + int ol = cigar[k]>>4; + if (op == BAM_CMATCH) { + for (j = 0; j < ol; ++j) { + int c1, c2, z = y + j; + c1 = bam_nt16_nt4_table[bam1_seqi(seq, z)]; + if (ref[x+j] == 0) return -1; + c2 = bam_nt16_nt4_table[(int)bam_nt16_table[(int)ref[x+j]]]; + if (c1 < 3 && c2 < 3) + score += c1 == c2? 5 : -4; + if (score < 0) score = 0; + if (score > max) max = score, q[1] = z, r[1] = x+j, kk[1] = k, kl[1] = j + 1; + } + x += ol; y += ol; + } else if (op == BAM_CINS) { + score -= 4 - ol * 3; + y += ol; + if (score < 0) score = 0; + } else if (op == BAM_CDEL) { + score -= 4 - ol * 3; + x += ol; + if (score < 0) score = 0; + } else if (op == BAM_CSOFT_CLIP) y += ol; + else if (op == BAM_CREF_SKIP) x += ol; + } + if (score < 0) return -1; // no high scoring segments + endx = x - 1; + // find the left boundary + for (k = c->n_cigar - 1, score = max = 0, x = x-1, y = y-1; k >= 0; --k) { + int op = cigar[k]&0xf; + int ol = cigar[k]>>4; + if (op == BAM_CMATCH) { + for (j = 0; j < ol; ++j) { + int c1, c2, z = y - j; + c1 = bam_nt16_nt4_table[bam1_seqi(seq, z)]; + if (ref[x+j] == 0) return -1; + c2 = bam_nt16_nt4_table[(int)bam_nt16_table[(int)ref[x-j]]]; + if (c1 < 3 && c2 < 3) + score += c1 == c2? 5 : -4; + if (score < 0) score = 0; + if (score > max) max = score, q[0] = z, r[0] = x-j, kk[0] = k, kl[0] = j + 1; + } + x -= ol; y -= ol; + } else if (op == BAM_CINS) { + score -= 4 - ol * 3; + y -= ol; + if (score < 0) score = 0; + } else if (op == BAM_CDEL) { + score -= 4 - ol * 3; + x -= ol; + if (score < 0) score = 0; + } else if (op == BAM_CSOFT_CLIP) y -= ol; + else if (op == BAM_CREF_SKIP) x -= ol; } - if (k != c->n_cigar || l_ref < MIN_REF_LEN) return -1; - for (k = 0; k < l_ref; ++k) - if (ref[c->pos + k] == 0) return -1; // the read stands out of the reference - // allocate - s_ref = calloc(l_ref, 1); - s_read = calloc(c->l_qseq, 1); - for (k = 0, seq = bam1_seq(b); k < c->l_qseq; ++k) - s_read[k] = bam_nt16_nt4_table[bam1_seqi(seq, k)]; - for (k = 0; k < l_ref; ++k) - s_ref[k] = bam_nt16_nt4_table[(int)bam_nt16_table[(int)ref[c->pos + k]]]; - // do alignment - cigar = ka_global_core(s_ref, l_ref, s_read, c->l_qseq, &par, &score, &n_cigar); - if (score <= 0) { // realignment failed - free(cigar); free(s_ref); free(s_read); - return -1; + if (q[1] - q[0] < 15) return -1; // the high-scoring segment is too short + // modify CIGAR + n_cigar = 0; + cigar = calloc(c->n_cigar + 4, 4); + if (q[0] != 0) cigar[n_cigar++] = (uint32_t)q[0]<<4 | BAM_CSOFT_CLIP; + if (r[0] != c->pos) cigar[n_cigar++] = (uint32_t)(r[0] - c->pos)<<4 | BAM_CREF_SKIP; + if (kk[0] == kk[1]) { + cigar[n_cigar++] = (uint32_t)(kl[0] + kl[1] - (bam1_cigar(b)[kk[0]]>>4))<<4 | BAM_CMATCH; + } else { + cigar[n_cigar++] = (uint32_t)kl[0]<<4 | BAM_CMATCH; + for (k = kk[0] + 1; k < kk[1]; ++k) + cigar[n_cigar++] = bam1_cigar(b)[k]; + cigar[n_cigar++] = (uint32_t)kl[1]<<4 | BAM_CMATCH; // FIXME: add ref_skip after this line } + if (q[1] + 1 != c->l_qseq) + cigar[n_cigar++] = (uint32_t)(c->l_qseq - q[1] - 1)<<4 | BAM_CSOFT_CLIP; // copy over the alignment if (4 * (n_cigar - (int)c->n_cigar) + b->data_len > b->m_data) { // enlarge b->data b->m_data = 4 * (n_cigar - (int)c->n_cigar) + b->data_len; @@ -166,22 +257,22 @@ int bam_realn(bam1_t *b, const char *ref) } memcpy(bam1_cigar(b), cigar, n_cigar * 4); c->n_cigar = n_cigar; - free(s_ref); free(s_read); free(cigar); + free(cigar); return 0; } int bam_fillmd(int argc, char *argv[]) { - int c, is_equal = 0, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm = 0, is_realn; + int c, is_equal = 0, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm = 0, is_realn, is_capQ; samfile_t *fp, *fpout = 0; faidx_t *fai; char *ref = 0, mode_w[8], mode_r[8]; bam1_t *b; - is_bam_out = is_sam_in = is_uncompressed = is_realn = 0; + is_bam_out = is_sam_in = is_uncompressed = is_realn = is_capQ = 0; mode_w[0] = mode_r[0] = 0; strcpy(mode_r, "r"); strcpy(mode_w, "w"); - while ((c = getopt(argc, argv, "reubSn:")) >= 0) { + while ((c = getopt(argc, argv, "reubSCn:")) >= 0) { switch (c) { case 'r': is_realn = 1; break; case 'e': is_equal = 1; break; @@ -189,6 +280,7 @@ int bam_fillmd(int argc, char *argv[]) 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': is_capQ = 1; break; default: fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n", c); return 1; } } @@ -227,6 +319,10 @@ int bam_fillmd(int argc, char *argv[]) fp->header->target_name[tid]); } if (is_realn) bam_realn(b, ref); + if (is_capQ) { + int q = bam_cap_mapQ(b, ref); + if (b->core.qual > q) b->core.qual = q; + } if (ref) bam_fillmd1_core(b, ref, is_equal, max_nm); } samwrite(fpout, b);