Unit tests!

[ArtPoon]

We need 'em

[DBecker7]

Some unit tests/synthetic data started in 9eeaf51

[ArtPoon]

Eventually I think we'll need to simulate data for a comparison of pipelines against some ground truth

[DBecker7]

Proposal:

1. Select from sequences.fasta according to current estimates of relative frequencies (frequency and total count are known).
   • I.e. sample names from metadata then use seqtk subseq to extract from sequences.fasta (doesn't work with sequences.fasta.xz, must unzip first).
   • I've already created sequences_pangolin.fasta.xz, which only contains sequences with known pangolin lineages (data/get-sequences-with-pangolineage.sh, takes over an hour to run on Rei because of unzipping/zipping).
2. Extract amplicon regions from sampled fastas, output to a fastq with simulated Phred scores (or just fasta if the scores are not used).
   • Simulate coverage from our data.
   • At this step, we intentionally lose information about linkage across amplicons.
3. Randomly sample from this file (without replacement) to simulate degradation / incomplete sampling.
   • Assumed degradation will probably be arbitrary, but can help us demonstrate the effect of degradation on case count estimation.

A computationally faster method might be to calculate all mutations from sequences_pangolin (encode_diffs) ahead of time, sample amplicon regions, simulate coverage, then reconstruct the sequence within coverage regions from the reference.

[GopiGugan]

Unit test needed for #46

[ArtPoon]

Please focus on minimap2.py and estimate-freqs.R @SandeepThokala thanks

[GopiGugan]

@SandeepThokala to post coverage of unit tests