I reworked coverage quite a bit, and moved some parts around. It now handles heterozygosity correctly, target/discard beds (needs more testing...), single ploid and multiple, short and longish references (tested up to ecoli length), N-masking (as in the human reference genome) and softmasking. I need to go through and do final cleanup in develop, then it will be ready.
I reworked coverage quite a bit, and moved some parts around. It now handles heterozygosity correctly, target/discard beds (needs more testing...), single ploid and multiple, short and longish references (tested up to ecoli length), N-masking (as in the human reference genome) and softmasking. I need to go through and do final cleanup in develop, then it will be ready.