* samtools-0.1.5-27 (r443)

 * SEQ and QUAL can be "*"
 * parse CIGAR "=" and "X" as "M"

bam.c

@@ -271,10 +271,12 @@ char *bam_format1_core(const bam_header_t *header, const bam1_t *b, int of)
 	else if (c->mtid == c->tid) kputs("=\t", &str);
 	else ksprintf(&str, "%s\t", header->target_name[c->mtid]);
 	ksprintf(&str, "%d\t%d\t", c->mpos + 1, c->isize);
-	for (i = 0; i < c->l_qseq; ++i) kputc(bam_nt16_rev_table[bam1_seqi(s, i)], &str);
-	kputc('\t', &str);
-	if (t[0] == 0xff) kputc('*', &str);
-	else for (i = 0; i < c->l_qseq; ++i) kputc(t[i] + 33, &str);
+	if (c->l_qseq) {
+		for (i = 0; i < c->l_qseq; ++i) kputc(bam_nt16_rev_table[bam1_seqi(s, i)], &str);
+		kputc('\t', &str);
+		if (t[0] == 0xff) kputc('*', &str);
+		else for (i = 0; i < c->l_qseq; ++i) kputc(t[i] + 33, &str);
+	} else ksprintf(&str, "*\t*");
 	s = bam1_aux(b);
 	while (s < b->data + b->data_len) {
 		uint8_t type, key[2];

bam_import.c

@@ -359,7 +359,7 @@ 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 +373,10 @@ 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)) parse_error(fp->n_lines, "mapped sequence without CIGAR");
+			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 +389,18 @@ 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))

bamtk.c

@@ -9,7 +9,7 @@
 #endif
 
 #ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.5-26 (r442)"
+#define PACKAGE_VERSION "0.1.5-27 (r443)"
 #endif
 
 int bam_taf2baf(int argc, char *argv[]);