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TASK-2478 #2239

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@pfurio pfurio commented Jan 18, 2023

TASK-2478

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pfurio commented Jan 18, 2023

Task linked: TASK-2478 RGA: Missing numHomAltCompHet stats

@pfurio pfurio requested a review from imedina January 18, 2023 10:41
pfurio and others added 24 commits January 24, 2023 16:52
@pfurio
analysis: calculate missing chPairVariantStats, #TASK-2478
99a25da
@pfurio
analysis: fix HOM_ALT filters with 2 pop freqs, #TASK-2478
7aeddf7
@pfurio
analysis: ensure RGA always have the same behaviour, #TASK-2478
d0f5eee 
When no KnockoutType filters are applied, we internally add all possible
values to the query to ensure we always get the same behaviour.
@pfurio
analysis: fix aux collection query parser, #TASK-2478
528b490
@pfurio
analysis: fix facet queries, #TASK-2478
b15d641
@pfurio
analysis: fix query parser options, #TASK-2478
35ae29a
@pfurio
analysis: fix ko filter, #TASK-2478
269f1b0
@pfurio
analysis: improve summary performance, #TASK-2478
24381c4
@pfurio
analysis: add cache for RGA, #TASK-1750
2ffd484
@pfurio
analysis: make map thread-safe, #TASK-1750
0567f68
@pfurio
analysis: remove static modifier, #TASK-1750
21d1033
@pfurio
analysis: cache only queries taking longer than 4 seconds, #TASK-1750
cac9f02
@pfurio
analysis: put if absent, #TASK-2478
40d3c1d
@pfurio
analysis: count CH variant stats properly, #TASK-2478
38fcd58
@pfurio
analysis: improve query parser with 2 pop freqs, #TASK-2478
822d012
@pfurio
analysis: store paired PFs to be able to filter, #TASK-2478
054d763
@pfurio
analysis: remove useless CH pair combinations, #TASK-2478
dbab096
@pfurio
analysis: fix queries with pop freq < 0.001
09aaaff
@pfurio
analysis: add collection suffix for RGA, #TASK-2478
4527509
@pfurio
analysis: check suffix is null, #TASK-2478
cd68009
@j-coll
storage: Fix trio serialization in CompoundHeterozygous variant query.
7293adc
@pfurio
analysis: remove limit to variant query, #TASK-2478
37d809a
@pfurio
analysis: reduce number of parallel tasks, #TASK-2478
2d95ee2
@pfurio
analysis: fix pop freq queries over CH variants, #TASK-2478
1a3c9a8
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@imedina imedina Awaiting requested review from imedina

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@pfurio @j-coll