switch to using gather exclusively, away from LCA methods.
#110
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ctb
changed the title
gather exclusively, away from LCA methods.
* add explicit moltype to config * add protein conf file * first full successful run * add gather_scaled to do faster searches * adjust thresholds for protein * use search rather than gather so we can look at GTDB 25k genomes * upd * refactor exact removal a bit * improve reporting * improve reporting * silence lineages file warnings * add gtdb conf * require provided lineage to remove exact match * flag identical matches removed * clean up reporting etc
* initial attempt to add snakemake tests * snakemake tests working * add test on protein side, too
* attempted refactor try 1 * look at many genomes at once * tentatively working? * start generating summaries * do progress elimination/reporting * add summarize rule * add provided lin to ibd2 * output CSV * recover comment * add f_major and f_ident to output * update for tara-delmont * remove lineage split * get protein working * fix provided lineage bug * fix self-matching * fix snakemake tests * write actual genome cleaning code * make min_f_ident and min_f_major configurable * swizzle f_match and f_ident rows to later; sort output by total_bad_bp * clean up imports a bit * 'fix' tests by commenting many of them out * pyflakes cleanup * refactor and cleanup * refactor and cleanup * refactor and cleanup * require genus-level match rank, for now. * eliminate match_rank as a configurable parameter * make use of gather threshold in contig classification * more refactoring and cleanup * rescue contigs that still have significant matches to correct lineage
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exploring #33.
This PR disables LCA-based decontamination, reasons 2 and 3.
It also includes #122 which switches to using
search --containmentinstead of gather, so as to enable decontamination of sequences that are in the search database. You'll need to rerun charcoal from scratch to make full use of this new feature.