Related Issues (20)
- handle ? and U characters in GISAID format files HOT 1
- dereplicate context sequences in sample_diversity HOT 1
- filter context sequences with ids that are not in metadata
- summarize-selections improvements
- generalize label_seqs input type HOT 1
- Add MRCA to neighbor selection
- add action to support vcf-based masking
- update mask format and parser
- add documentation section on running in parallel
- illustrate sampling of focal sequences in tutorial
- illustrate alignment, masking, and tree building in tutorial
- add pangolin action for lineage assignment
- running the tutorial yields a KeyError. HOT 3
- Add GitHub issue templates
- update install instructions in docs
- allow user to define target size for subsampled collection of sequences
- move overridable configuration parameters from Snakefile to YAML file HOT 1
- Allow sample-random to take a proportion to be randomly sampled
- Stochastic test failure in TestSubsampleNeighbors.test_sample_cluster_missing_locales HOT 3
- Error in rule view_context_seqs
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from genome-sampler.