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feat!: configurability + precomputed peaks #9

Merged
merged 106 commits into from
Jul 6, 2023
Merged

feat!: configurability + precomputed peaks #9

merged 106 commits into from
Jul 6, 2023

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davidlougheed
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@davidlougheed
lint: controls
c5d5936
@davidlougheed
fix: update ui if peak changes in url in PeakResults
adea46a
@davidlougheed
chore(config): add note on switching to hg38
072dbb9
@davidlougheed
chore: rm unused front end box plot component
2982525
@davidlougheed
chore: remove unused front end svg pattern
b16886b
@davidlougheed
refact: rewrite App as functional component
8e72434
@davidlougheed
lint
48db23e
@davidlougheed
lint: remove dead code & reformat
ea3cbd2
@davidlougheed
feat: configurable assembly/conditions/ethnicities
b55ed4a
@davidlougheed
feat: configurable gemini sample name extractor fn
72f98af
@davidlougheed
chore: dynamic conditions for p-values in db
52123ec 
chore: pre-filter peaks by p-value
@davidlougheed
refact: rewrite App component with more memoization
40e2a87
@davidlougheed
chore: add input-files subdirectory gitkeeps
4432c8d
@davidlougheed
feat: configurable static tracks file location
ea89b1d
@davidlougheed
feat: if ucsc static tracks not provided, show nothing instead of err…
400659a 
…oring
@davidlougheed
fix: missed handling of dynamic conditions for plot generation
022e64d
@davidlougheed
refact: configurable qtls input file path
dacf74c
@davidlougheed
refact: common constants for genotype states (ref/het/hom)
477cc5a
@davidlougheed
lint
4509c27
@davidlougheed
chore: consistent rna-seq default spelling
d6efb57
@davidlougheed
chore: prep work in tracks model for precomputed values
06366d2
@davidlougheed
feat: accept precomputed query arg for values/plot track endpoints
8a88682
@davidlougheed
fix: use different cache key for precomputed track values
2613fe5
@davidlougheed
refact: use plot size constants everywhere; add constant for track va…
2a06590 
…lue cache key
@davidlougheed
chore: add config path for point matrix file path template
2d2fcf0
@davidlougheed
chore: add points 2d array to schema for precomputed vals (opt)
569f2bd
@davidlougheed
chore!: change default config to use env vars for some directories/paths
3badc5e
@davidlougheed
docs: specify when notes are aracena-et-al specific
6385c59
@davidlougheed
feat: precomputed points import in import-peaks script
cb90c01
@davidlougheed
chore: optionally load qtls location template from env var
3477a36
@davidlougheed
chore: add runWithTransaction db method
5cdd071
@davidlougheed
fix: gene pre-processing to find top peaks
92776f3
@davidlougheed
fix(scripts): clear peak groups table on re run
52dc740
@davidlougheed
fix: pull chromosome sizes from assembly not manhattan config
2e3de7e
@davidlougheed
fix(client): overview page crash
795ff75
@davidlougheed
docs: notes on genes and gene-features files
96fc034
@davidlougheed
fix(scripts): import points with features from gene-peaks file
2997869
@davidlougheed
Merge remote-tracking branch 'origin/master' into feat/precomputed-peaks
f59e8e4 
# Conflicts:
#	client/package-lock.json
#	client/package.json
#	package-lock.json
#	package.json
@davidlougheed
fix: loading precomputed points for features in gene-peaks file
2e2165e
@davidlougheed
fix: consistent donor lookup array between plot + ingest
5a2bddc
@davidlougheed
docs: require metadata ingest before points ingest
55c9405
@davidlougheed
fix: script imports
f2e0e1a
@davidlougheed
fix: null handling for precomputed points
b86bc13
@davidlougheed
debug logging
2adcf0e
@davidlougheed
chore(client): re-enable checkbox for precomputed
34f66a5
@davidlougheed
lint: clean up debug logging
64b784b
@davidlougheed
chore(client): re-enable precomputed checkbox
3cdbfc6
@davidlougheed
chore(client): use precomputed points by default
ad40023
@davidlougheed
fix(client): properly include precomputed setting in value cache posts
d5cd0f9
@davidlougheed
docs: update wording around link to current instance
e7678f5
@davidlougheed
fix(client): missing usePrecomputed pass to cacheValues
d3c9d94
@davidlougheed davidlougheed changed the title [WIP]: feat!: configurability + precomputed peaks feat!: configurability + precomputed peaks Jul 6, 2023
@davidlougheed davidlougheed marked this pull request as ready for review July 6, 2023 13:35
@davidlougheed davidlougheed merged commit 6fa8f66 into master Jul 6, 2023
@davidlougheed davidlougheed deleted the feat/precomputed-peaks branch July 6, 2023 14:02
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@davidlougheed