Invalid tag name for GFAv1 specification

[cerebis]

graphdeconvolution/external/gatb/convertToGFA.py

Line 74 in 32775c8

g.write('H\tVN:Z:1.0\t k:i:%d\n' %k) # includes the k-mer size

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]

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

[cerebis]

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 ***@***.***> wrote: good catch! where do you see that KM is used? I see KC. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#2 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFuni_XoAMVlqnK59xqqYpQqjl5srwLsks5tBDFTgaJpZM4REP4m> .

[rchikhi]

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