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koadman / graphdeconvolution

deconvolution of species & strain genome mixtures in assembly graphs
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Invalid tag name for GFAv1 specification #2

Open cerebis opened 6 years ago

cerebis commented 6 years ago

https://github.com/koadman/graphdeconvolution/blob/32775c8141abecb32c10bc99024c8de8703199b1/external/gatb/convertToGFA.py#L74

This line introduces an optional field, using a tag which is non-compliant with respect to the GFAv1 specification. Tags are required to be a two characters long, with the pattern: [a-zA-Z][a-zA-Z0-9]

https://github.com/GFA-spec/GFA-spec/blob/master/GFA1.md#optional-fields

I would suggest km but it is already being used for Segment. However, there is no reason you cannot use the same tag on two different records, with different meanings. Perhaps this is confusing. Tags are also case-sensitive, so you could disambiguate it slightly with KM.

rchikhi commented 6 years ago

good catch! where do you see that KM is used? I see KC.

cerebis commented 6 years ago

It really depends on the what the assembled outputs I suppose. I might have been looking at a spades gfa, but I thought it was minia gfa that was using km in the Segment records as an optional field.

On Sun, 17 Dec 2017 at 8:08 am, Rayan Chikhi notifications@github.com wrote:

good catch! where do you see that KM is used? I see KC.

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rchikhi commented 6 years ago

minia only outputs GFA through this same script :) (it's based on GATB)