v3.3.0 Cenote-Taker 3: Sauceman's grotto

Changes from v3.2.1:

1. redoing read coverage parsing from samtools coverage table to sequin comment files: make_sequin_cmts.py

2. Adding read coverage to summary table. Adding virus gcode to virus summary table: virus_summary.py

3. Fixing minor error/warning when trying to create a directory that exists: assess_virus_genes1.py

4. adding sequencing tech argument--seqtech

5. Added/integrated a new taxonomy database hallmark. This database is compiled from: 1) genbank nr clustered -> extracting virus proteins with taxonomical labels for genus, family, and class -> filtering to seqs with CT3 hallmark gene hits -> reclustering at 90% AAI with cd-hit and 2) refseq virus -> filtering to seqs with CT3 hallmark gene hits.

• a) I've found this new hallmark taxdb returns better or identical taxonomical calls to the original refseq without size/memory increase
• b) Zenodo files have been update to include this database. Zenodo DB v4.1
• c) users can choose original refseq taxdb or new hallmark db with the --taxdb flag
• d) To add the hallmark taxdb, run get_ct3_dbs -o ct3_DBs --hallmark_tax T

What's Changed

• Update3 (v3.3.0 updates) by @mtisza1 in #5

Full Changelog: v3.2.1...v3.3.0