X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_md.c;h=d42aa8fc971fa627ccf34a781f0432214ac6f8e0;hp=17b0a4a4fa6943313be1b6d78b18c5255fe44982;hb=HEAD;hpb=cb12a866906ec4ac644de0e658679261c82ab098 diff --git a/bam_md.c b/bam_md.c index 17b0a4a..d42aa8f 100644 --- a/bam_md.c +++ b/bam_md.c @@ -2,42 +2,53 @@ #include #include #include +#include #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) +#define USE_EQUAL 1 +#define DROP_TAG 2 +#define BIN_QUAL 4 +#define UPDATE_NM 8 +#define UPDATE_MD 16 +#define HASH_QNM 32 + +char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 }; + +int bam_aux_drop_other(bam1_t *b, uint8_t *s); + +void bam_fillmd1_core(bam1_t *b, char *ref, int flag, 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) { + if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { 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; + if (flag&USE_EQUAL) seq[z/2] &= (z&1)? 0xf0 : 0x0f; ++u; } else { - ksprintf(str, "%d", u); - kputc(ref[x+j], str); + kputw(u, str); 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); + kputw(u, str); kputc('^', str); for (j = 0; j < l; ++j) { if (ref[x+j] == 0) break; kputc(ref[x+j], str); @@ -52,12 +63,12 @@ void bam_fillmd1_core(bam1_t *b, char *ref, int is_equal, int max_nm) x += l; } } - ksprintf(str, "%d", u); + kputw(u, str); // 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) { + if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) { for (j = 0; j < l; ++j) { int z = y + j; int c1 = bam1_seqi(seq, z), c2 = bam_nt16_table[(int)ref[x+j]]; @@ -74,58 +85,248 @@ void bam_fillmd1_core(bam1_t *b, char *ref, int is_equal, int max_nm) } } // 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); + if (flag & UPDATE_NM) { + uint8_t *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); + if (flag & UPDATE_MD) { + uint8_t *old_md = bam_aux_get(b, "MD"); + if (c->flag & BAM_FUNMAP) return; + 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); + } } } + // drop all tags but RG + if (flag&DROP_TAG) { + uint8_t *q = bam_aux_get(b, "RG"); + bam_aux_drop_other(b, q); + } + // reduce the resolution of base quality + if (flag&BIN_QUAL) { + uint8_t *qual = bam1_qual(b); + for (i = 0; i < b->core.l_qseq; ++i) + if (qual[i] >= 3) qual[i] = qual[i]/10*10 + 7; + } free(str->s); free(str); } -void bam_fillmd1(bam1_t *b, char *ref, int is_equal) +void bam_fillmd1(bam1_t *b, char *ref, int flag) { - bam_fillmd1_core(b, ref, is_equal, 0); + bam_fillmd1_core(b, ref, flag, 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 || op == BAM_CEQUAL || op == BAM_CDIFF) { + 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 flag) +{ + int k, i, bw, x, y, yb, ye, xb, xe, apply_baq = flag&1, extend_baq = flag>>1&1; + 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) || b->core.l_qseq == 0) 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 || op == BAM_CEQUAL || op == BAM_CDIFF) { + 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) { + if (ref[i] == 0) { xe = i; break; } + 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); + if (!extend_baq) { // in this block, bq[] is capped by base quality qual[] + 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 || op == BAM_CEQUAL || op == BAM_CDIFF) { + 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 + } else { // in this block, bq[] is BAQ that can be larger than qual[] (different from the above!) + uint8_t *left, *rght; + left = calloc(c->l_qseq, 1); rght = calloc(c->l_qseq, 1); + 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 || op == BAM_CEQUAL || op == BAM_CDIFF) { + for (i = y; i < y + l; ++i) + bq[i] = ((state[i]&3) != 0 || state[i]>>2 != x - xb + (i - y))? 0 : q[i]; + for (left[y] = bq[y], i = y + 1; i < y + l; ++i) + left[i] = bq[i] > left[i-1]? bq[i] : left[i-1]; + for (rght[y+l-1] = bq[y+l-1], i = y + l - 2; i >= y; --i) + rght[i] = bq[i] > rght[i+1]? bq[i] : rght[i+1]; + for (i = y; i < y + l; ++i) + bq[i] = left[i] < rght[i]? left[i] : rght[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] = 64 + (qual[i] <= bq[i]? 0 : qual[i] - bq[i]); // finalize BQ + free(left); free(rght); + } + 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 = 0, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm = 0; + int c, flt_flag, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm, is_realn, capQ, baq_flag; 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 = 0; + flt_flag = UPDATE_NM | UPDATE_MD; + is_bam_out = is_sam_in = is_uncompressed = is_realn = max_nm = capQ = baq_flag = 0; mode_w[0] = mode_r[0] = 0; strcpy(mode_r, "r"); strcpy(mode_w, "w"); - while ((c = getopt(argc, argv, "eubSn:")) >= 0) { + while ((c = getopt(argc, argv, "EqreuNhbSC:n:Ad")) >= 0) { switch (c) { - case 'e': is_equal = 1; break; + case 'r': is_realn = 1; break; + case 'e': flt_flag |= USE_EQUAL; break; + case 'd': flt_flag |= DROP_TAG; break; + case 'q': flt_flag |= BIN_QUAL; break; + case 'h': flt_flag |= HASH_QNM; break; + case 'N': flt_flag &= ~(UPDATE_MD|UPDATE_NM); 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': baq_flag |= 1; break; + case 'E': baq_flag |= 2; break; default: fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n", c); return 1; } } @@ -135,11 +336,14 @@ int bam_fillmd(int argc, char *argv[]) if (is_uncompressed) strcat(mode_w, "u"); if (optind + 1 >= argc) { fprintf(stderr, "\n"); - fprintf(stderr, "Usage: samtools fillmd [-eubS] \n\n"); + fprintf(stderr, "Usage: samtools fillmd [-eubrS] \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\n"); + fprintf(stderr, " -S the input is SAM with header\n"); + fprintf(stderr, " -A modify the quality string\n"); + fprintf(stderr, " -r compute the BQ tag (without -A) or cap baseQ by BAQ (with -A)\n"); + fprintf(stderr, " -E extended BAQ for better sensitivity but lower specificity\n\n"); return 1; } fp = samopen(argv[optind], mode_r, 0); @@ -162,7 +366,12 @@ int bam_fillmd(int argc, char *argv[]) fprintf(stderr, "[bam_fillmd] fail to find sequence '%s' in the reference.\n", fp->header->target_name[tid]); } - if (ref) bam_fillmd1_core(b, ref, is_equal, max_nm); + if (is_realn) bam_prob_realn_core(b, ref, baq_flag); + 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, flt_flag, max_nm); } samwrite(fpout, b); }