- if (bc->ori_ref < 0) {
- kputc('N', &s); kputc('\0', &s);
- kputs("<INDEL>", &s); kputc('\0', &s);
- } else {
+ if (bc->ori_ref < 0) { // an indel
+ // write REF
+ kputc(ref[pos], &s);
+ for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+1+j], &s);
+ kputc('\0', &s);
+ // write ALT
+ kputc(ref[pos], &s);
+ for (i = 1; i < 4; ++i) {
+ if (bc->a[i] < 0) break;
+ if (i > 1) {
+ kputc(',', &s); kputc(ref[pos], &s);
+ }
+ if (bca->indel_types[bc->a[i]] < 0) { // deletion
+ for (j = -bca->indel_types[bc->a[i]]; j < bca->indelreg; ++j)
+ kputc(ref[pos+1+j], &s);
+ } else { // insertion; cannot be a reference unless a bug
+ char *inscns = &bca->inscns[bc->a[i] * bca->maxins];
+ for (j = 0; j < bca->indel_types[bc->a[i]]; ++j)
+ kputc("ACGTN"[(int)inscns[j]], &s);
+ for (j = 0; j < bca->indelreg; ++j) kputc(ref[pos+1+j], &s);
+ }
+ }
+ kputc('\0', &s);
+ } else { // a SNP