ENH: Add coverage to Nextclade output?

[tseemann]

Coverage is normally defined as number of valid called bases divided by length of the virus.

Does Nextclade have a column for this?

The only way I can seem to compute it is to use

• totalMissing
• totalNonACGTNs
• alignmentStart
• alignmentEnd along with the reference length.

But this seems error-prone and messy.

Is there an easier way?

[corneliusroemer]

Good point, we don't have a column for this (yet).

Given that coverage is a metric that may be of interest and involves 5 numbers we may want to add that to the tsv output.

I'll turn this into an enhancement proposal.

[corneliusroemer]

So right now we count:

• Ns
• ambiguous nucleotides
• inserted nucleotides
• deleted nucleotides

It would make sense to also count:

• sequenced nucleotides minus inserted nts plus deleted nucleotides

So that we know the total number of aligned bases. Coverage could then be calculated as that number divided by reference length.