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Added --trans_table (Diamond's --query-gencode, MMseqs2's --translation-table, Prodigal's -g/--trans-table) option, to specify a translation table for gene prediction and blastx searches.
Added --training_genome and --training_file options, to run Prodigal training mode.
Default search thresholds (pident, score, query and subject coverage) are set to None.
Both Diamond and MMseqs2 seed_orthologs file includes now percentage identity (pident), position of hits (qstart, qend, sstart, send) and query coverage (qcov) and subject coverage (scov).
Added --outfmt_short option for Diamond, to run it producing only query, subject, evalue and score as output. This option could be useful to obtain better performance when no thresholds for pident, and query and subject coverages are used (see Diamond docs about traceback). Of course, seed_orthologs file will contain only those 4 fields.
Added subject coverage (target_coverage) to gff output from blastx based gene predictions.