Should check for sample abundance rather than sample_alt_id

[timothyjlaurent]

Problem

must use --reload to re-run samples that whose runs have failed for some reason.

Proposed solution

--reload should still 'rerun' a sample but you could check for existence of sample_alt_id joined with the abundance table and not require reload to 'rerun' these. This could enable batching of sample runs and without the risk of re analyzing data.

select sample_alt_id from abundances join samples on abundances.sample_id =
 samples.sample_id and sample_alt_id = $sample;