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jasperlinthorst / reveal

Graph based multi genome aligner
MIT License
46 stars 3 forks source link

revel convert --to maf #27

Closed fbemm closed 5 years ago

fbemm commented 6 years ago

Hey, guess the MAF converter was never really intended for production. Right now it only shows sequence segments but no separated blocks for subgraphs. Are you planning to do that? Cheers, F

jasperlinthorst commented 6 years ago

Hi Felix, Uhm, yes. I'm working on integrating everything with the transform part, which is a bit of work because of keeping the right offsets. To have a separate block for each of the subgraphs should be easy to fix, so if you need it I can see if I can give that some priority...

Cheers, Jasper

On Thu, Oct 4, 2018 at 1:58 PM Felix Bemm notifications@github.com wrote:

Hey, guess the MAF converter was never really intended for production. Right now it only shows sequence segments but no separated blocks for subgraphs. Are you planning to do that? Cheers, F

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fbemm commented 6 years ago

Hi Jasper, would be great but I don't want to mess up you roadmap. I just thought it would be great to see how a reveal derived GFA, converted to MAF, converted to HAL, might work in CAT or HomGenMapping (Augustus), especially with cross-chromosome duplications not being stacked into a single alignment block. Cheers, Felix

fbemm commented 5 years ago

I think reveal has grown so much that this is not necessary any more. vg and reveal can talk to each other well via the GFA file now.