Fixing all paths #1200
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Fixing all paths #1200
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…uired of the browser
…the end freq_ht can be annotated with the fields inside the variant_qc struct
…ly avoid Hail errors. Also changing expected output path to be cohort prefix and not multicohort while issues in discrepancy between outputs is being investigated
…_and_popmax so that the gen_anc_faf_max_expr can pick up the correct population label
…point in Frequencies
…'oth' as we're using tenk10k
…ng InbreedingCoeff annotation to within the freq_ht.info struct so that prepare gnomad variants function works
…gnomad_v4_variants_helper to iterate through the .info field properly
…gnomad_v4_variants_helper to iterate through the .info field properly
…need to force some fields to be formatted correctly
…non-tmp bucket locations
… MakeSiteOnlyVcf outputs
… variant tables struct
… in the dataset being analysed instead of being hardcoded
…ed to speed up testing
…ogic that already exists in SampleQC
…nnotations() as it makes more sense there
…s using pop labels on mt itself rather than inferred_pop_ht
…t it was changed to for testing
…o that we can populate the 'filters' field of the freq_ht table output. This field is expected by the downstream PrepareBrowserTable functions that prepare the variants table for the browser
…g 'filters' field of sample qc ht to be an empty set
…quencies stage. This is because they are provided as StageInputs
…ead of the default 'pop'. Also propagating this change throughout the rest of Frequencies when calculating faf and popmax.
… needed. We will be saving all outputs to non-tmp storage
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #1200 +/- ##
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Coverage 26.46% 26.46%
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Files 9 9
Lines 1757 1757
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Hits 465 465
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