Include reference genome or risk excluded locii mixup?

CPTR-ReSeqTB / UVP

Mycobacterium tuberculosis next generation sequence analysis

MIT License

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Closed tseemann closed 5 years ago

tseemann commented 5 years ago

It appears the user needs to supply the version 3 fasta file of H37Rv.

Are the masking coordinates excluded_locii.txt for version 3? Coliumin one of it does not have the version so it is unclear.

If a user accidently used V1 or V2 reference, the masking coordinates will be wrong.

mezewudo commented 5 years ago

Yes, the masking co-ordinates are in the Excluded_loci.txt file. Will include the version of the H37Rv reference file used to avoid mix-up.