X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_md.c;h=eee767e08fb290ab1ea8baae778201e797c923c3;hb=51f014165fb63b2b9b86db80ea4681f9351453a1;hp=e2fdff801aebf4cf8e28d8e620434ec21a48ac69;hpb=140d53dfdfe32bfa3ae4b24f1f33d071f366054f;p=samtools.git

diff --git a/bam_md.c b/bam_md.c
index e2fdff8..eee767e 100644
--- a/bam_md.c
+++ b/bam_md.c
@@ -2,11 +2,13 @@
 #include <assert.h>
 #include <string.h>
 #include <ctype.h>
+#include <math.h>
 #include "faidx.h"
 #include "sam.h"
 #include "kstring.h"
+#include "kaln.h"
 
-void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
+void bam_fillmd1_core(bam1_t *b, char *ref, int is_equal, int max_nm)
 {
 	uint8_t *seq = bam1_seq(b);
 	uint32_t *cigar = bam1_cigar(b);
@@ -53,13 +55,32 @@ void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
 		}
 	}
 	ksprintf(str, "%d", u);
+	// 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) {
+				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
+						seq[z/2] |= (z&1)? 0x0f : 0xf0;
+						bam1_qual(b)[z] = 0;
+					}
+				}
+				if (j < l) break;
+				x += l; y += l;
+			} else if (op == BAM_CDEL || op == BAM_CREF_SKIP) x += l;
+			else if (op == BAM_CINS || op == BAM_CSOFT_CLIP) y += l;
+		}
+	}
 	// 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) {
-		uint8_t *old_data = b->data;
 		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);
@@ -84,23 +105,182 @@ void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
 	free(str->s); free(str);
 }
 
+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
+#define MIN_BAND_WIDTH 11
+
+int bam_realn(bam1_t *b, const char *ref)
+{
+	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 *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;
+	}
+	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;
+		kroundup32(b->m_data);
+		b->data = realloc(b->data, b->m_data);
+	}
+	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);
+	}
+	memcpy(bam1_cigar(b), cigar, n_cigar * 4);
+	c->n_cigar = n_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;
+	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 = 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, "eubS")) >= 0) {
+	while ((c = getopt(argc, argv, "reubSCn:")) >= 0) {
 		switch (c) {
+		case 'r': is_realn = 1; break;
 		case 'e': is_equal = 1; 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': is_capQ = 1; break;
 		default: fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n", c); return 1;
 		}
 	}
@@ -110,11 +290,12 @@ 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] <aln.bam> <ref.fasta>\n\n");
+		fprintf(stderr, "Usage:   samtools fillmd [-eubrS] <aln.bam> <ref.fasta>\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, "         -r       read-independent local realignment\n\n");
 		return 1;
 	}
 	fp = samopen(argv[optind], mode_r, 0);
@@ -133,8 +314,16 @@ int bam_fillmd(int argc, char *argv[])
 				free(ref);
 				ref = fai_fetch(fai, fp->header->target_name[b->core.tid], &len);
 				tid = b->core.tid;
+				if (ref == 0)
+					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);
+				if (b->core.qual > q) b->core.qual = q;
 			}
-			bam_fillmd1(b, ref, is_equal);
+			if (ref) bam_fillmd1_core(b, ref, is_equal, max_nm);
 		}
 		samwrite(fpout, b);
 	}