store encseq to disk from EncseqBuilder about genometools

[satta]

It should be possible to implement this by writing a new class implementing the GtSequenceBuffer interface using a GtEncseq as a storage backend and adding an additional GtEncseqEncoder function gt_encseq_encoder_encode_from_seqbuffer() which bypasses file input and directly accepts a GtSequenceBuffer. Might require moving around some code internally in the GtEncseq code, but I cannot see why this can and should not be done.
With that new code in place, one could create an in-memory uncompressed GtEncseq with the builder, then create a sequence buffer based on it, which can then be used to feed sequence data into the encoder.

[Garonenur]

ass this is of concern right now for me:
looking at gt_inputfiles2sequencekeyvalues() in encseq.c this would be a lot of moving code around.

[satta]

Are you sure? Because gt_inputfiles2sequencekeyvalues() uses a GtSequenceBuffer internally anyway, so isn't it possible passing one in to this function and move the plainformat check out of this function?

[Garonenur]

I will have a closer look at the end of the week.