SRST2 & groot parsers #9
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- CIGAR string could be used to calculate some standardised metrics e.g. %ID, not implemented - Certain databases contain information related to other fields in their gene name (e.g. groot run with ARG-ANNOT has an accession and genomic location for the AMR gene) but not all databases - Databases pre-prepared by groot also contain the `reference_database_id` in the `gene_name` but this isn't guaranteed depending on how the database has been prepared for indexing.
- Parser assumes the "fullgenes" gene typing output file from srst2 - Occasionally, the annotation field contains more information depending on the database but not in a consistent format across dbs used.
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Looks great @fmaguire are you planning on doing any more work on this before we merge? The CI setup still needs some work so we don't expect to get green checkmarks there. |
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I was planning on adding a couple more but won't get around to it until next week. So merge away! |
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See a5e6d39 for caveats of groot parser and 674f14d for srst2 caveats