Unitigger needs to cache the value of gkFragment_getIsNonRandom. During output, it loads all fragments in a chunk only to count the number of them that are non-random.
In AS_CGB_main.c, we make an initial pass through the gkpStore, to count the number of guides. At this time, we should save a bit for each fragment telling if it is non-random. Search for gkStore_getFragment.