Merge commit 'upstream/0.1.17'

[samtools.git] / bam_import.c

diff --git a/bam_import.c b/bam_import.c
index 9d84328bdbdafb5f4e76a19e7edf176121aca5b4..29516c92ff42593313caf2833c38213d62ebdc52 100644 (file)
--- a/bam_import.c
+++ b/bam_import.c
@@ -427,6 +427,27 @@ int sam_read1(tamFile fp, bam_header_t *header, bam1_t *b)
                                memcpy(s, str->s + 5, str->l - 5);
                                s[str->l - 5] = 0;
                                doff += size;
+                       } else if (type == 'B') {
+                               int32_t n = 0, Bsize, k = 0, size;
+                               char *p;
+                               if (str->l < 8) parse_error(fp->n_lines, "too few values in aux type B");
+                               Bsize = bam_aux_type2size(str->s[5]); // the size of each element
+                               for (p = (char*)str->s + 6; *p; ++p) // count the number of elements in the array
+                                       if (*p == ',') ++n;
+                               p = str->s + 7; // now p points to the first number in the array
+                               size = 6 + Bsize * n; // total number of bytes allocated to this tag
+                               s = alloc_data(b, doff + 6 * Bsize * n) + doff; // allocate memory
+                               *s++ = 'B'; *s++ = str->s[5];
+                               memcpy(s, &n, 4); s += 4; // write the number of elements
+                               if (str->s[5] == 'c')      while (p < str->s + str->l) ((int8_t*)s)[k++]   = (int8_t)strtol(p, &p, 0),   ++p;
+                               else if (str->s[5] == 'C') while (p < str->s + str->l) ((uint8_t*)s)[k++]  = (uint8_t)strtol(p, &p, 0),  ++p;
+                               else if (str->s[5] == 's') while (p < str->s + str->l) ((int16_t*)s)[k++]  = (int16_t)strtol(p, &p, 0),  ++p; // FIXME: avoid unaligned memory
+                               else if (str->s[5] == 'S') while (p < str->s + str->l) ((uint16_t*)s)[k++] = (uint16_t)strtol(p, &p, 0), ++p;
+                               else if (str->s[5] == 'i') while (p < str->s + str->l) ((int32_t*)s)[k++]  = (int32_t)strtol(p, &p, 0),  ++p;
+                               else if (str->s[5] == 'I') while (p < str->s + str->l) ((uint32_t*)s)[k++] = (uint32_t)strtol(p, &p, 0), ++p;
+                               else if (str->s[5] == 'f') while (p < str->s + str->l) ((float*)s)[k++]    = (float)strtod(p, &p),       ++p;
+                               else parse_error(fp->n_lines, "unrecognized array type");
+                               s += Bsize * n; doff += size;
                        } else parse_error(fp->n_lines, "unrecognized type");
                        if (dret == '\n' || dret == '\r') break;
                }