feat: add translation of alignment

[gordonkoehn]

This PR tackles the long dreaded issue of skipping the realignment when using nextclade for translation.

[gordonkoehn]

It appears nextclade has two functions that do the alignment. Within the nextclade/run/nextclade_run_one.rs there is a function called align_nuc() which does the alignment via Smith-Waterman. It returns the qry_seq aligned qry_seq so has inserted Gaps into it, but astonishingly leaves the inserts in. Then the next function comes along called insertions_strip which returns qry_seq and insertions which is the main output nextclade works on with. Here the insertions_strip now holds the cleartext sequence with Gaps inserted to match the reference, and insertions stopped. insertions_strip does this by comparing the output of the aligment qry_seq and the reference.

Bottom line: I can indeed just input insertions_strip output <StripInsertionsResult> and run nextclade from there. In order to do that, I need to get clear text reads, with insretions stripped and the reference.

This sounds doable.

[gordonkoehn]

sr2silo side is read. I can now produce a cleartext file with reads aligned to the reference with gaps and padding such that the string has the same length as the actual reference and also have the inserts with position put out.

This is what I have to feed to nextclade.

[gordonkoehn]

Hurray - half way there !!

[gordonkoehn]

Translation works now. Next update the Python side to do the translation and create the ndjson.