make assembly and sequence names separate fields

[diekhans]

MAF made a big mistake in combining the assembly name and sequence name into a single string. Worse yet, a dot was chosen as the separator, which was used as a separator in assembly accession and versions.

The Browser group has to hack around this in multiple places. Oddly, it is not in the library function that splits assembly and sequence IDs. So it seems that it is so 'simple' to parse; it is done in many places. Once more, seemingly 'simple' makes things complex for the user.

Assembly and sequence should be made into separate taffy fields for it to achieve world domination

[glennhickey]

Yeah, the dot separator is a disaster. A good case could also be made for breaking haplotype into its own field (as we do in some pangenome formats).

Failing adding new fields, then switching to (and somewhat strictly enforcing) PanSN (sample#hap#contig) could also be an improvement.

[diekhans]

Having flexibility to add fields would be great rather than requiring parsing. I have several enhancements, that I will make issues for, From my first real use of Taffy; many related to metadata. MAF is becoming unusable as thing grow with nothing to replace it. Taffy could/should become a defacto standard... Maybe I can get a rotation in the lab? Glenn Hickey ***@***.***> writes:

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Yeah, the dot separator is a disaster. A good case could also be made for breaking haplotype into its own field (as we do in some pangenome formats). Failing adding new fields, then switching to (and somewhat strictly enforcing) PanSN (`sample#hap#contig`) could also be an improvement. -- Reply to this email directly or view it on GitHub: #71 (comment) You are receiving this because you authored the thread. Message ID: ***@***.***>