add new pp params
add unfiltered file accessor
indent
modify snvindel access
update generate sciclonees
update sciclone step
add prefix calculation
update filter column
whitespace
skip clustering if too few sites
use different way to estimate size
make some ips optional
add newer params to TF
wait for snvindel to complete
refactor createmutspec 1
update mutation-spectrum calling
update mutation spectrum to handle special cases
fix tsv reader header
move parse_qualities to Utils
update processing profile param