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isolateR 1.0.6

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@bdaisley bdaisley released this 04 Jan 21:41
  • Fixed get_db function stemming from same underlying taxonomy string parsing issue as #19. Custom database creation with "add_taxonomy=TRUE" will now output taxonomic ranks in the correct order in FASTA headers as follows: >Accession_no;d__Domain;p__Phylum;c__Class;o__Order;f__Family;g__Genus;s__Species (e.g., >NR_042817.1;d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiia;o__Verrucomicrobiales;f__Akkermansiaceae;g__Akkermansia;s__Akkermansia_muciniphila).
  • Patched sanger_assembly version error related to Issue #20 resulting in the following output: "Error in .call_fun_in_pwalign("pairwiseAlignment", ...) : pairwiseAlignment() has moved from Biostrings to the pwalign package, and is formally defunct in Biostrings >= 2.77.1. Please call pwalign::pairwiseAlignment() to get rid of this error." Function code updated to call pwalign instead of Biostrings where relevant.