X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_md.c;h=a4f4e01ce2672556746c399af379a325b61273af;hb=cd65d352809ab157b72524d8542e1ee66e5a09c6;hp=ead2346e4ec21f75b8ceb88a4b78690d2a3d3b39;hpb=030a404097c6f8b094eca03a8380b35ff81e6c70;p=samtools.git

diff --git a/bam_md.c b/bam_md.c
index ead2346..a4f4e01 100644
--- a/bam_md.c
+++ b/bam_md.c
@@ -5,8 +5,9 @@
 #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);
@@ -16,10 +17,6 @@ void bam_fillmd1(bam1_t *b, char *ref, int is_equal)
 	uint8_t *old_md, *old_nm;
 	int32_t old_nm_i = -1, nm = 0;
 
-	old_md = bam_aux_get(b, "MD");
-	old_nm = bam_aux_get(b, "NM");
-	if (c->flag & BAM_FUNMAP) return;
-	if (old_nm) old_nm_i = bam_aux2i(old_nm);
 	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;
@@ -57,12 +54,38 @@ 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) {
 		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;
@@ -81,23 +104,79 @@ 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);
+}
+
+// local realignment
+
+#define MIN_REF_LEN 10
+
+int bam_realn(bam1_t *b, const char *ref)
+{
+	int k, l_ref, score, n_cigar;
+	uint32_t *cigar = bam1_cigar(b);
+	uint8_t *s_ref = 0, *s_read = 0, *seq;
+	ka_param_t par;
+	bam1_core_t *c = &b->core;
+	// set S/W parameters
+	par = ka_param_blast; par.gap_open = 4; par.gap_ext = 1; par.gap_end_open = par.gap_end_ext = 0;
+	// calculate the length of the reference in the alignment
+	for (k = l_ref = 0; k < c->n_cigar; ++k) {
+		if ((cigar[k]&0xf) == BAM_CREF_SKIP) break; // do not do realignment if there is an `N' operation
+		if ((cigar[k]&0xf) == BAM_CMATCH || (cigar[k]&0xf) == BAM_CDEL)
+			l_ref += cigar[k]>>4;
+	}
+	if (k != c->n_cigar || l_ref < MIN_REF_LEN) return -1;
+	for (k = 0; k < l_ref; ++k)
+		if (ref[c->pos + k] == 0) return -1; // the read stands out of the reference
+	// allocate
+	s_ref = calloc(l_ref, 1);
+	s_read = calloc(c->l_qseq, 1);
+	for (k = 0, seq = bam1_seq(b); k < c->l_qseq; ++k)
+		s_read[k] = bam_nt16_nt4_table[bam1_seqi(seq, k)];
+	for (k = 0; k < l_ref; ++k)
+		s_ref[k] = bam_nt16_nt4_table[(int)bam_nt16_table[(int)ref[c->pos + k]]];
+	// do alignment
+	cigar = ka_global_core(s_ref, l_ref, s_read, c->l_qseq, &par, &score, &n_cigar);
+	if (score <= 0) { // realignment failed
+		free(cigar); free(s_ref); free(s_read);
+		return -1;
+	}
+	// 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_qseq - 4 * c->n_cigar);
+	memcpy(bam1_cigar(b), cigar, n_cigar * 4);
+	c->n_cigar = n_cigar;
+	free(s_ref); free(s_read); 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;
 	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 = 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, "reubSn:")) >= 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;
 		default: fprintf(stderr, "[bam_fillmd] unrecognized option '-%c'\n", c); return 1;
 		}
 	}
@@ -107,11 +186,12 @@ 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);
@@ -130,8 +210,12 @@ 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]);
 			}
-			bam_fillmd1(b, ref, is_equal);
+			if (is_realn) bam_realn(b, ref);
+			if (ref) bam_fillmd1_core(b, ref, is_equal, max_nm);
 		}
 		samwrite(fpout, b);
 	}