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Fix missing groups for included strains #1000

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Jul 6, 2022
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Fix missing groups for included strains #1000

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5 changes: 5 additions & 0 deletions augur/filter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1547,6 +1547,11 @@ def run(args):
# during the first pass, but we want to minimize overall memory
# usage at the moment.
seq_keep = set(metadata.index.values) & valid_strains

# Prevent force-included strains from being considered in this
# second pass, as in the first pass.
seq_keep = seq_keep - all_sequences_to_include

group_by_strain, skipped_strains = get_groups_for_subsampling(
seq_keep,
metadata,
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21 changes: 21 additions & 0 deletions tests/functional/filter/cram/subsample-group-by-without-force-included-strains.t
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@@ -0,0 +1,21 @@
Setup

$ pushd "$TESTDIR" > /dev/null
$ source _setup.sh

Do not consider force-included strains for subsampling.
In this test, we force-include two old strains that are the only representatives of their month/year date group (December 2015).
We don't filter these strains, so they could be considered for subsampling, but Augur removes them from consideration because they have been force-included.

$ cat >$TMP/include_old_strains.txt <<~~
> PRVABC59
> COL/FLR_00008/2015
> ~~

$ ${AUGUR} filter \
> --metadata filter/data/metadata.tsv \
> --include $TMP/include_old_strains.txt \
> --group-by month year \
> --subsample-max-sequences 10 \
> --output-metadata $TMP/metadata-filtered.tsv > /dev/null
$ rm -f $TMP/metadata-filtered.tsv