X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_md.c;h=20b1913efa09ce796392885b0f4b831c8c759f4a;hb=7251efa37992752a8cf62ff363da0ad5099937bd;hp=d2c84dcccd084c3399bf94ac6085af8902eb8532;hpb=6cda28b3a4c6afcf8c739a478b6bcf1e514f96e9;p=samtools.git

diff --git a/bam_md.c b/bam_md.c
index d2c84dc..20b1913 100644
--- a/bam_md.c
+++ b/bam_md.c
@@ -7,6 +7,9 @@
 #include "sam.h"
 #include "kstring.h"
 #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)
 {
@@ -161,118 +164,132 @@ int bam_cap_mapQ(bam1_t *b, char *ref, int thres)
 	return (int)(t + .499);
 }
 
-// local realignment
-
-#define MIN_REF_LEN 10
-#define MIN_BAND_WIDTH 11
-
-int bam_realn(bam1_t *b, const char *ref)
+int bam_prob_realn_core(bam1_t *b, const char *ref, int flag)
 {
-	int k, score, q[2], r[2], kk[2], kl[2], x, y, max, j, n_cigar, endx = -1;
+	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);
-	uint8_t *seq = bam1_seq(b);
 	bam1_core_t *c = &b->core;
-	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;
+	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 (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 (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;
 	}
-	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;
-		kroundup32(b->m_data);
-		b->data = realloc(b->data, b->m_data);
+	// 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
 	}
-	if (n_cigar != (int)c->n_cigar) { // move data
-		memmove(b->data + c->l_qname + 4 * n_cigar, bam1_seq(b), b->data_len - c->l_qname - 4 * c->n_cigar);
-		b->data_len += 4 * (n_cigar - (int)c->n_cigar);
+	// 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) {
+					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);
+		}
+		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);
 	}
-	memcpy(bam1_cigar(b), cigar, n_cigar * 4);
-	c->n_cigar = n_cigar;
-	free(cigar);
 	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, is_realn, is_capQ;
+	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_bam_out = is_sam_in = is_uncompressed = is_realn = is_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, "reubSCn:")) >= 0) {
+	while ((c = getopt(argc, argv, "EreubSC:n:A")) >= 0) {
 		switch (c) {
 		case 'r': is_realn = 1; break;
 		case 'e': is_equal = 1; break;
@@ -280,7 +297,9 @@ 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;
+		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;
 		}
 	}
@@ -295,7 +314,9 @@ int bam_fillmd(int argc, char *argv[])
 		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, "         -r       read-independent local realignment\n\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);
@@ -318,9 +339,9 @@ 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_realn(b, ref);
-			if (is_capQ) {
-				int q = bam_cap_mapQ(b, ref, 40);
+			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, is_equal, max_nm);