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marschall-lab / gaftools

General purpose utility related to GAF files
https://gaftools.readthedocs.io/
MIT License
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Possible to use GFA 1.0 as input to gaftools index? #19

Closed adadiehl closed 6 months ago

adadiehl commented 8 months ago

I would like to use this toolkit within an analysis workflow I am developing. The nature of the analysis requires the graph be in GFA 1.0 format for reasons I won't go into. However, supplying a GFA 1.0 as input to gaftools index causes a crash, and looking into the code shows that rGFA is, indeed, baked in, as it were.

I am wondering if there are technical reasons rGFA is used and GFA 1.0 is not supported. This constraint prevents applying gaftools to any genomics analyses that require haplotype information, which is a pretty big limitation. Any thoughts?

asylvz commented 8 months ago

Hi @adadiehl , currently gaftools is dependent on rGFA and I'm not sure if we have plans to make it compatible with GFA format in the near future.

Thanks for your interest.