rGFA

rGFA (https://github.com/lh3/gfatools/blob/master/doc/rGFA.md) is a subset of GFA1, in which only particular line types (S and L) are allowed, and the S lines are required to contain the tags SN (of type Z), SO and SR (of type i).

When working with rGFA files, it is convenient to use the dialect="rgfa" option in the constructor Gfa() and in func:Gfa.from_file().

This ensures that additional validations are performed: GFA version must be 1, only rGFA-compatible lines (S,L) are allowed and that the required tags are required (with the correct datatype). The validations can also be executed manually using Gfa.validate_rgfa().

Furthermore, the stable_sequence_names attribute of the GFA objects returns the set of stable sequence names contained in the SN tags of the segments.

>>> g = gfapy.Gfa("S\tS1\tCTGAA\tSN:Z:chr1\tSO:i:0\tSR:i:0", dialect="rgfa")
>>> g.segment_names
['S1']
>>> g.stable_sequence_names
['chr1']
>>> g.add_line("S\tS2\tACG\tSN:Z:chr1\tSO:i:5\tSR:i:0")