KeyError in `format_pileup.py`

[dfornika]

We've seen an error in format_pileup.py where a KeyError can be triggered here:

ncov-tools/workflow/scripts/format_pileup.py

Line 23 in 7a19778

freqs[b] += 1

Traceback (most recent call last):
  File "ncov-tools/workflow/rules/../scripts/format_pileup.py", line 23, in <module>
    freqs[b] += 1
KeyError: 'N'

...because the dict isn't initialized with an N key:

ncov-tools/workflow/scripts/format_pileup.py

Line 15 in 7a19778

freqs = {'A': 0, 'T': 0, 'G': 0, 'C': 0, '-': 0, 'R': 0 }

[dfornika]

The error appears to occur when a sample includes reads that have N bases. We ran into this issue when setting up some test data for a CI pipeline.

https://github.com/BCCDC-PHL/ncov-tools-nf/tree/9d10033fee0fb0fa75d4cc8d8c7ddedc51522e24/.github/data/fastqs

Sample SRR27503680-2-25x from the link above (derived from SRA sample SRR27503680 includes reads like this:

ATAACAACTTCTGTGGCCCTGATGGCTACCCTCTTGAGTGCATTAAAGACCTTCTAGCACGTGCTGGTANNNN

...which trigger the error.

[rdeborja]

Added N key in dictionary:

ncov-tools/workflow/scripts/format_pileup.py

Line 15 in 3028cc6

freqs = {'A': 0, 'T': 0, 'G': 0, 'C': 0, '-': 0, 'R': 0, 'N': 0 }

See branch fix/metadata-na. If you're happy with the results I'll merge the code and do a release.

[hgibling]

For what it's worth, the team I work with encountered this issue a while back, made the same change, and was able to run ncov-tools on the problematic sample with this solution.