John Lees

Add ambiguous genotypes in VCF output

1

Currently any non-ACGT IUPAC codes are written as an 'N'. It would be possible to keep the information by writing out multiple output genotypes for a sample, with equal probabilities....

issues with assigning GPSCs

4

I am also having issues with assigning GPSCs -- the external clustering file labels every strain as "NA" even though the GPSC of most of these strains have been previously...

Possible faster bloom filter

1

See: https://github.com/rockset/rocksdb-cloud/blob/master/util/bloom_impl.h#L94-L142 May also be useful in sparrowhawk

Add M1 builds for PopPUNK

7

Have add arm64 for pp-sketchlib and mandrake, looks like rapidnj supported too ---- Please read the [guidelines for Bioconda recipes](https://bioconda.github.io/contributor/guidelines.html) before opening a pull request (PR). ### General instructions *...

Fixes #321

The square coremat call uses a lot of memory when it probably needn't -- let's just regenerate the distances for small numbers of samples.

See https://github.com/conda-forge/conda-forge.github.io/issues/1963

Build kite broken

2

The docker image is no longer working. I replaced the graph-tool installation with the apt package (the old hack would have been very painful to fix here), that seems ok....

Some functions e.g. fast assign #322 don't yet work with cugraph. In general, a tidyup of network.py with this in mind would be useful