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hcdenbakker / sepia

taxonomic classifier based on the kraken2 algorithms and more

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Error checking

lskatz opened this issue · comments

commented

Hi, I'd recommend some error checking on the accession string in src/build_index.rs. This seemed to work for me around line 600:

        if ! lookup.contains_key(&accession_plus_root) {
            panic!("Could not find {} in lookup hash", &accession_plus_root);
        }
        let accession_lineage = lookup[&accession_plus_root]; //now a u32, original when we have complete taxonomy_string
commented

Yes, writing informative error messages throughout sepia is on my to do list! I will look into this and may add your suggested error check.

commented

I'll change line 600 in src/build_index.rs to:

let accession_lineage = lookup.get(&accession_plus_root).expect(&format!("Could not find {} in lookup hash", &accession_plus_root));

That should have the same result. Do you have the files to recreate the error? I tried to mess up my reference file with empty tax strings/lineages, but that didn't do the trick (probably another thing to 'error' check, because no taxonomy information does not give an error, but may have bigger consequences)

commented

Sounds good! It was when we had the wrong bacillus