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Split chrPloidy into its own CTE in the CNV gene query #230

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Split chrPloidy into its own CTE in the CNV gene query #230

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29 changes: 21 additions & 8 deletions Model/lib/wdk/model/questions/queries/geneQueries.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -5482,23 +5482,36 @@ select distinct ta.gene_source_id
<column name="median_gene_dose_hits"/>
<sql>
<![CDATA[
WITH bySample AS (
-- chrPloidy is split out of bySample, and the sample filter is repeated in
-- both, deliberately. Collapsing them back into one join costs ~30%: with the
-- chromosome side pre-filtered the planner parallelises the GeneCopyNumbers
-- scan (2 workers, bySample 4.3s instead of 7.2s single-threaded). Repeating
-- the filter is what lets it - the gene side gets its own restriction rather
-- than inheriting one through the join.
WITH chrPloidy AS (
SELECT c.eda_sample_stable_id
, c.na_sequence_id
, c.ploidy
FROM apidbtuning.ChrCopyNumbers c
WHERE c.organism = '$$organismSinglePick$$'
AND c.eda_sample_stable_id IN ($$cnv_sample_meta$$)
)
, bySample AS (
SELECT DISTINCT g.project_id
, g.source_id
, g.gene_source_id
, g.eda_sample_stable_id AS strain
, g.raw_estimate
, g.ref_cn
, g.haploid_number
, c.ploidy
, cp.ploidy
, g.chromosome
FROM apidbtuning.GeneCopyNumbers g
, apidbtuning.ChrCopyNumbers c
WHERE c.eda_sample_stable_id IN ($$cnv_sample_meta$$)
AND g.eda_sample_stable_id = c.eda_sample_stable_id
AND g.na_sequence_id = c.na_sequence_id
AND g.organism = '$$organismSinglePick$$'
AND c.organism = '$$organismSinglePick$$'
JOIN chrPloidy cp
ON g.eda_sample_stable_id = cp.eda_sample_stable_id
AND g.na_sequence_id = cp.na_sequence_id
WHERE g.organism = '$$organismSinglePick$$'
AND g.eda_sample_stable_id IN ($$cnv_sample_meta$$)
)
, medians AS (
SELECT s.gene_source_id
Expand Down