X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=bam_md.c;h=20b1913efa09ce796392885b0f4b831c8c759f4a;hp=44d46a492438beecae74fc648c9564a566565be7;hb=e2bd290b8643f0a728c282a8b825392307750210;hpb=016b50ab60e879a0b8f81cb76ce11ea360a03d4a diff --git a/bam_md.c b/bam_md.c index 44d46a4..20b1913 100644 --- a/bam_md.c +++ b/bam_md.c @@ -9,6 +9,8 @@ #include "kaln.h" #include "kprobaln.h" +char bam_nt16_nt4_table[] = { 4, 0, 1, 4, 2, 4, 4, 4, 3, 4, 4, 4, 4, 4, 4, 4 }; + void bam_fillmd1_core(bam1_t *b, char *ref, int is_equal, int max_nm) { uint8_t *seq = bam1_seq(b); @@ -162,14 +164,14 @@ int bam_cap_mapQ(bam1_t *b, char *ref, int thres) return (int)(t + .499); } -int bam_prob_realn_core(bam1_t *b, const char *ref, int apply_baq) +int bam_prob_realn_core(bam1_t *b, const char *ref, int flag) { - int k, i, bw, x, y, yb, ye, xb, xe; + 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) return -1; // do nothing + 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; @@ -221,23 +223,47 @@ int bam_prob_realn_core(bam1_t *b, const char *ref, int apply_baq) 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) + 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); - 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; + 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) { + 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) { + 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); } - 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); @@ -254,16 +280,16 @@ int bam_prob_realn(bam1_t *b, const char *ref) 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; + int c, is_equal, 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_equal = is_bam_out = is_sam_in = is_uncompressed = is_realn = max_nm = apply_baq = capQ = 0; + is_equal = 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, "reubSC:n:A")) >= 0) { + while ((c = getopt(argc, argv, "EreubSC:n:A")) >= 0) { switch (c) { case 'r': is_realn = 1; break; case 'e': is_equal = 1; break; @@ -272,7 +298,8 @@ int bam_fillmd(int argc, char *argv[]) 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; + case 'A': baq_flag |= 1; break; + case 'E': baq_flag |= 2; break; default: fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n", c); return 1; } } @@ -288,7 +315,8 @@ int bam_fillmd(int argc, char *argv[]) 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"); + 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); @@ -311,7 +339,7 @@ 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 (is_realn) bam_prob_realn_core(b, ref, apply_baq); + 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;