X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=bam_import.c;h=eaa9452080e2624bc38a131265171bd2b53d4d11;hb=d410ecbf60b5aed90ee20c6ba40637ca50241edd;hp=4c9395b7dccf6cc7adb071a8e93e5845a107690e;hpb=70e923225f586027ab0954d23cb03a8ea0bfdbc5;p=samtools.git

diff --git a/bam_import.c b/bam_import.c
index 4c9395b..eaa9452 100644
--- a/bam_import.c
+++ b/bam_import.c
@@ -211,7 +211,6 @@ int sam_header_parse_rg(bam_header_t *h)
 			break;
 		}
 		if (r < p) r = p;
-		s = r + 3;
 	}
 	if (rgid->l && rglib->l) {
 		bam_strmap_put(h->rg2lib, rgid->s, rglib->s);
@@ -359,7 +358,7 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 			for (i = 0, s = str->s; i != c->n_cigar; ++i) {
 				x = strtol(s, &t, 10);
 				op = toupper(*t);
-				if (op == 'M') op = BAM_CMATCH;
+				if (op == 'M' || op == '=' || op == 'X') op = BAM_CMATCH;
 				else if (op == 'I') op = BAM_CINS;
 				else if (op == 'D') op = BAM_CDEL;
 				else if (op == 'N') op = BAM_CREF_SKIP;
@@ -373,7 +372,13 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 			if (*s) parse_error(fp->n_lines, "unmatched CIGAR operation");
 			c->bin = bam_reg2bin(c->pos, bam_calend(c, bam1_cigar(b)));
 			doff += c->n_cigar * 4;
-		} else c->bin = bam_reg2bin(c->pos, c->pos + 1);
+		} else {
+			if (!(c->flag&BAM_FUNMAP)) {
+				fprintf(stderr, "Parse warning at line %lld: mapped sequence without CIGAR\n", (long long)fp->n_lines);
+				c->flag |= BAM_FUNMAP;
+			}
+			c->bin = bam_reg2bin(c->pos, c->pos + 1);
+		}
 	}
 	{ // mtid, mpos, isize
 		ret = ks_getuntil(ks, KS_SEP_TAB, str, &dret); z += str->l + 1;
@@ -386,16 +391,18 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
 	}
 	{ // seq and qual
 		int i;
-		uint8_t *p;
+		uint8_t *p = 0;
 		if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -5; // seq
 		z += str->l + 1;
-		c->l_qseq = strlen(str->s);
-		if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
-			parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
-		p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
-		memset(p, 0, (c->l_qseq+1)/2);
-		for (i = 0; i < c->l_qseq; ++i)
-			p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
+		if (strcmp(str->s, "*")) {
+			c->l_qseq = strlen(str->s);
+			if (c->n_cigar && c->l_qseq != (int32_t)bam_cigar2qlen(c, bam1_cigar(b)))
+				parse_error(fp->n_lines, "CIGAR and sequence length are inconsistent");
+			p = (uint8_t*)alloc_data(b, doff + c->l_qseq + (c->l_qseq+1)/2) + doff;
+			memset(p, 0, (c->l_qseq+1)/2);
+			for (i = 0; i < c->l_qseq; ++i)
+				p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
+		} else c->l_qseq = 0;
 		if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -6; // qual
 		z += str->l + 1;
 		if (strcmp(str->s, "*") && c->l_qseq != strlen(str->s))