added pre-filter
split README
mod README
mod README
mod README
mod README
fixed bug in pre-filter
--cna-pen to --cna-pen-zero, new --cna-pen-diff, --cna-pen-norm
mod penalty options, mod README
mod README
mod .gitignore
fixed bug in SNV transition matrix
mod changelog
included Makefile.farm*
fixed bug in SNV trans mat, added test/data
removed test/ from git project
v1.17.4 commit
Merge branch 'develop'
removed test/ fully
Merge branch 'develop'