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Cattle outbreak clock filter #110

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merged 2 commits into from
Dec 10, 2024
Merged

Cattle outbreak clock filter #110

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2fac740
update host map
jameshadfield Dec 9, 2024
871a0de
[cattle-outbreak] add genome clock filter
jameshadfield Dec 9, 2024
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4 changes: 3 additions & 1 deletion Snakefile
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Expand Up @@ -203,7 +203,9 @@ def refine_clock_rates(w):
return f"--clock-rate {info[w.segment][0]} --clock-std-dev {info[w.segment][1]}"

def refine_clock_filter(w):
filter = get_config('refine', 'clock_filter_iqd', w)
filter = get_config('refine', 'genome_clock_filter_iqd', w) \
if w.segment=='genome' \
else get_config('refine', 'clock_filter_iqd', w)
return f"--clock-filter-iqd {filter}" if filter else ""


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2 changes: 2 additions & 0 deletions config/h5n1-cattle-outbreak.yaml
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Expand Up @@ -75,6 +75,8 @@ refine:
coalescent: const
date_inference: marginal

genome_clock_filter_iqd:
FALLBACK: 3
clock_filter_iqd:
FALLBACK: false

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3 changes: 3 additions & 0 deletions ingest/build-configs/ncbi/defaults/host-map.tsv
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Expand Up @@ -92,3 +92,6 @@ western sandpiper Avian
Wild-Bird Avian
EMU Avian
Emu Avian
Dromaius novaehollandiae Avian
White-winged Dove Avian
Rock Pigeon Avian
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