TODO list

[shenwei356]

• Search: supporting specifying TaxID, e.g., only searching from a species or a genus.
  • No need to rebuild the index. Just filter matches in the seed-matching step .
  • Existing information:
    • genomes.map.bin stores genome id - internal id pairs.
  • File needed:
    • a genome accession -> taxid mapping file
    • taxdump files from NCBI or created by TaxonKit
  • Relationship: internal id -> taxid
  • Check: isAChild = LCA(taxid_target, taxid_test) == taxid_target.
  • implemented: https://github.com/shenwei356/LexicMap/tree/search-by-taxid
• Create a table to explain the changes and compatibility of the index format.
• Add a daemon process for searching via RESTful API.
• Add a utility tool to edit genome names in the index via a regular expression, which only needs to edit the file genomes.map.bin.
• utils subseq: accept search result as input, for batch sequence extraction.
  • parallelise it.
• add a new command to combine multiple indexes (dozens)