X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_md.c;h=7023046b87748de170de994a2565ec0b7a8172a2;hb=4c8358db36b9d83a4aaa176a8f2c072ef5cc534d;hp=f3f7e228a62c18e5d1beba2686cb2095da385002;hpb=cdfe59776873444748f34af06bed3ade0bd2aee2;p=samtools.git

diff --git a/bam_md.c b/bam_md.c
index f3f7e22..7023046 100644
--- a/bam_md.c
+++ b/bam_md.c
@@ -261,18 +261,75 @@ int bam_realn(bam1_t *b, const char *ref)
 	return 0;
 }
 
+int bam_prob_realn(bam1_t *b, const char *ref)
+{
+	int k, i, bw, x, y, yb, ye, xb, xe;
+	uint32_t *cigar = bam1_cigar(b);
+	bam1_core_t *c = &b->core;
+	ka_probpar_t conf = ka_probpar_def;
+	// find the start and end of the alignment
+	if (c->flag & BAM_FUNMAP) return -1;
+	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;
+	}
+	// 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), *qual = bam1_qual(b);
+		int *state;
+		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);
+		ka_prob_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)) qual[i] = 0;
+					else qual[i] = qual[i] < q[i]? qual[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;
+		}
+		free(s); free(r); free(q); free(state);
+	}
+	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, is_capQ;
+	int c, is_equal = 0, tid = -2, ret, len, is_bam_out, is_sam_in, is_uncompressed, max_nm = 0, is_realn, capQ = 0;
 	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_bam_out = is_sam_in = is_uncompressed = is_realn = 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, "reubSC:n:")) >= 0) {
 		switch (c) {
 		case 'r': is_realn = 1; break;
 		case 'e': is_equal = 1; break;
@@ -280,7 +337,7 @@ 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;
+		case 'C': capQ = atoi(optarg); break;
 		default: fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n", c); return 1;
 		}
 	}
@@ -318,9 +375,10 @@ 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_realn(b, ref);
+			if (is_realn) bam_prob_realn(b, ref);
+			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);