Completely overhauls the mapping module of wfmash to use MashMap3
No more spaced seeds, minimizers, or world minimizers
New CLI options for the MashMap3 hypergeometric filter, --no-hg-filter, --hg-filter-ani-diff, and --hg-filter-conf.
New CLI option to filter out low complexity mappings --kmer-complexity
--no-merge now implemented
--sketch-size is now used to specify indexing seed density as opposed to --window-size. If no option is provided, --sketch-size uses MashMap3's --dense sketch size calculation.
-L lower triangular option now uses the sequence's index in a file to compute lower triangular as opposed to the length of the sequence. This way, the output of -L is a subset of the full matrix. It yields a 2x speedup in mapping time.
The filesystem.hpp module has been removed in favor of std::filesystem.
GitHub actions now ran on PRs in addition to all master branch updates.
Completely overhauls the mapping module of wfmash to use MashMap3
--no-hg-filter,--hg-filter-ani-diff, and--hg-filter-conf.--kmer-complexity--no-mergenow implemented--sketch-sizeis now used to specify indexing seed density as opposed to--window-size. If no option is provided,--sketch-sizeuses MashMap3's--densesketch size calculation.-Llower triangular option now uses the sequence's index in a file to compute lower triangular as opposed to the length of the sequence. This way, the output of-Lis a subset of the full matrix. It yields a 2x speedup in mapping time.filesystem.hppmodule has been removed in favor ofstd::filesystem.To merge MashMap updates in the future: