left = pos > INDEL_WINDOW_SIZE? pos - INDEL_WINDOW_SIZE : 0;
right = pos + INDEL_WINDOW_SIZE;
if (types[0] < 0) right -= types[0];
+ // in case the alignments stand out the reference
+ for (i = pos; i < right; ++i)
+ if (ref[i] == 0) break;
+ right = i;
}
{ // the core part
char *ref2, *rs, *inscns = 0;