* samtools-0.1.2-24

[samtools.git] / bam_import.c

diff --git a/bam_import.c b/bam_import.c
index 404da01eb82841c48dd62fb03ec9d7bedff51865..746dc5bbbde0415911794b28d666a4a53ef86be8 100644 (file)
--- a/bam_import.c
+++ b/bam_import.c
@@ -102,7 +102,7 @@ bam_header_t *sam_header_read2(const char *fn)
        assert(fp);
        ks = ks_init(fp);
        str = (kstring_t*)calloc(1, sizeof(kstring_t));
-       while (ks_getuntil(ks, 0, str, &dret) >= 0) {
+       while (ks_getuntil(ks, 0, str, &dret) > 0) {
                char *s = strdup(str->s);
                int len, i;
                i = kh_size(hash);
@@ -227,10 +227,11 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
                for (i = 0; i < c->l_qseq; ++i)
                        p[i/2] |= bam_nt16_table[(int)str->s[i]] << 4*(1-i%2);
                if (ks_getuntil(ks, KS_SEP_TAB, str, &dret) < 0) return -6; // qual
-               if (c->l_qseq != strlen(str->s))
+               if (strcmp(str->s, "*") && c->l_qseq != strlen(str->s))
                        parse_error(fp->n_lines, "sequence and quality are inconsistent");
                p += (c->l_qseq+1)/2;
-               for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;
+               if (strcmp(str->s, "*") == 0) for (i = 0; i < c->l_qseq; ++i) p[i] = 0xff;
+               else for (i = 0; i < c->l_qseq; ++i) p[i] = str->s[i] - 33;
                doff += c->l_qseq + (c->l_qseq+1)/2;
        }
        doff0 = doff;
@@ -285,6 +286,11 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
                                *s++ = 'f';
                                *(float*)s = (float)atof(str->s + 5);
                                s += 4; doff += 5;
+                       } else if (type == 'd') {
+                               s = alloc_data(b, doff + 9) + doff;
+                               *s++ = 'd';
+                               *(float*)s = (float)atof(str->s + 9);
+                               s += 8; doff += 9;
                        } else if (type == 'Z' || type == 'H') {
                                int size = 1 + (str->l - 5) + 1;
                                if (type == 'H') { // check whether the hex string is valid