* samtools-0.1.5-27 (r443)

[samtools.git] / bam_import.c

diff --git a/bam_import.c b/bam_import.c
index 4c9395b7dccf6cc7adb071a8e93e5845a107690e..19cd75f4352f2d144b1d0a36ed0925cab6a50cc8 100644 (file)
--- a/bam_import.c
+++ b/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))