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tseemann / mlst

:id: Scan contig files against PubMLST typing schemes
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Added check for subsequence exact matches #64

Open kriskiil opened 6 years ago

kriskiil commented 6 years ago

Additional exact matches are checked whether they are subsequences of previous matches. If that is the case, they are ignored. Example: aroC 807 and 819 are subsequences of aroC 5.

tseemann commented 6 years ago

@kriskiil i think this can be resolved by just adding -culling_limit 1 to the blastn search command, like I do in abricate.

I thought I used to have this, but it isn't there. Some erroneous subsequence alleles were recently added (accidently) to pubMLST and I discovered this problem too.

I am going to add it back in 2.13

mjsull commented 1 year ago

Hi Torsten, was this re-added, I seem to be having the same problem