Changelog

MetaScope 1.3.7 (Bioc 3.19)

Identified the Rbowtie2 parameter k as being doubled when specified for bowtie filter or align steps.
Added another call to taxize in convert_animalcules() to catch any accessions that were not mapped to a UID in metascope_id(), in addition to another call in metascope_id() itself

Altered bt2_params objects to reflect 98% identity (16S), 95% identity (metagenomics) and added a parameter for when the origin genome is thought to not be present in the reference database.
Added SILVA species_headers object called internally in convert_animalcules_silva
Added convert_animalcules_silva function

Fixed taxonomy table function to output correctly formatted table
Fixed examples for various functions that were calling genomes with download_refseq but genomes were not able to be found.
Fixed plot generation for metascope_id()
Fixed premature stopping of download_refseq for strains labeled as “no rank” in NCBI.
Fixed identification of reads as unknown genomes (due to outdated reference databases that identify genomes now removed from NCBI). The unknown genomes will now be distinctly identified based on NCBI accession ID, which will separate them in the final results. IDs can also be looked up manually (on NCBI website) to see what the reads were aligning to.
Incorporated unknown taxa (removed from NCBI databases) into output of convert_animalcules()

Added ability to identify reads from databases other than NCBI (known to work for Silva and Greengenes2)

Fixed check error message about data.table::fread for reading .gz files by adding R.utils to imports.