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davidebolo1993 / VISOR

VarIant SimulatOR for short, long and linked reads
GNU Lesser General Public License v3.0
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HACk - Ignores index out of bounds #16

Closed vrohnie closed 3 years ago

vrohnie commented 3 years ago

Hi, thanks for your work.

We've automatically generated BED files for HACk, including some more complex Variants.

Due to a bug on our side, I've realized that HACk doesn't throw an error if the region given in the bed file is located after the chromosome length. It rather does nothing or inserts the sequence at the end.

I think this should be corrected to throwing something like an Index out of bounds, error.

Best regards, Veronika

BED examples :

NC_000913.3 2004441 2007026 translocation copy-paste h1:NC_000913.3:5642652:forward 0 NC_000913.3 5641652 5642652 deletion None 0

Tested with E.coli sequence from NCBI accession NC_000913.3, with VISOR HACk v1.1, provided through the latest docker image.

davidebolo1993 commented 3 years ago

Hi @vrohnie,

thanks for reporting. You are definitely right. I'll fix this asap.

Best,

Davide

davidebolo1993 commented 3 years ago

Hi @vrohnie,

this should be fixed through the latest master (and the latest docker image as well). Let me know if I missed something.

Thanks,

Davide