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Merging all changes to the IMBG-refactoring to the main branch #4

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Merging all changes to the IMBG-refactoring to the main branch #4

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GennadiyZakharov
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d-goryslavets and others added 30 commits June 28, 2024 13:37
@d-goryslavets
add test data config and TODOs for steps 1.1-2.3
b9afcf9
@d-goryslavets
add test suite skeleton
1d2aabb
@d-goryslavets
add TODOs for steps 2.1-2.5 and update paths to point to test data
9ed44a1
@mkrooted256
minimal refactoring. add tmp_dir config. add mk43_ prefix to shared i…
117b2d1 
…ntermediate files and output files.
@mkrooted256
draft of a get_path util
df04bd0
@mkrooted256
successful 2.1. replace + with os.path.join. annotate hardcoded paths…
268affd 
…. add WES_CONFIG env var to specify config file programmatically. make header file optional.
@d-goryslavets
add test suite skeleton and test data
8354844
@d-goryslavets
Merge branch 'mk43/first-run' into imbg-refactoring. Refactor steps 1…
0023053 
….1 and 2.1
@d-goryslavets
add tmp_dir to test data configs
5890acd
@mkrooted256
cleanup 1.1
f77d107
@mkrooted256
first attempts
7bec087
@mkrooted256
steps 1.1-2.1: refactor config and move hardcoded values
2cdf407
@mkrooted256
add todo
68c2413
@lbombini
upload documentation
1412199
@d-goryslavets
change smoke test design and add unit test template
73a6373
@d-goryslavets
change string concat to os.path.join in steps 1-2, make some function…
efab22d 
…s in step 2 return mts and change spark init way
@d-goryslavets
add integration tests that run main() function of each step
e2cf204
@d-goryslavets
add unit tests for steps 1.1-2.2
261ac9b
@mkrooted256
add a snippet for new config system. research possible ways to refact…
052ee3d 
…or config.
@mkrooted256
add config utils and config ipynb playground
b5329a8
@mkrooted256
refactor path config for 1.1
1990d99
@mkrooted256
Finish config refactoring for 2.1.
f02b394 
Adopt path_spark. remove file:// paths from config. Add example cvar usage.
@lbombini
update the docs
e6c5f64
@lbombini
Merge branch 'imbg-refactoring' of https://github.com/wtsi-hgi/wes-qc …
10a28fa 
…into imbg-refactoring
@lbombini
fix the code blocks
835f77a
@d-goryslavets
refactor path concatenation in steps 2.3-2.5
6ee2fcb
@d-goryslavets
add unit and integration tests for steps 2.3-2.5
0de9822
@mkrooted256
Merge branch 'imbg-refactoring' into mk43/refactor-hardcoded-config/2.1
ffe66fd
@mkrooted256
add config tests. move config utils to a separate file.
3b8fb10
@mkrooted256
fix a probable config bug
adfc9c1
d-goryslavets and others added 30 commits September 20, 2024 18:38
@d-goryslavets
fix and improve integration tests config
d1ae745
@d-goryslavets
refactor step 4: move hardcoded params to config, add path type adapt…
09fee1e 
…ers, fix bugs
@d-goryslavets
add hail logs to gitignore
6d291b5
@lbombini
add step 3 integration tests
3bf274c
@d-goryslavets
allow to manually set run id in 3-train_rf
6df11c8
@d-goryslavets
add var_qc_rf_dir to config variables
b8f12f0
@d-goryslavets
switch to http-based test data downloading in unit tests; fix incorre…
ace32eb 
…ct input in test_2_3_5_predict_pops
@d-goryslavets
add updated integration tests template for step 3-variant_qc
afe7460
@d-goryslavets
Merge branch 'dh24/refactor-hardcoded-config/4' into imbg-refactoring
f2a98fe
@d-goryslavets
add missing path type adapters in 3.4
504d3a9
@d-goryslavets
upd example config and add script running all steps of QC
831f558
@d-goryslavets
improve helper script to run all steps
a47837a
@d-goryslavets
Merge branch 'mk43/parser/v2.0-pre' into imbg-refactoring
15d9742
@mkrooted256
Make parse_config_file return nested config and not flat. Add corresp…
3afeaa1 
…onding test cases
@d-goryslavets
Merge branch 'mk43/parser/v2.0-pre' into imbg-refactoring; fix bugs
8b0e7b5
@d-goryslavets
change dots to underscores in qc plot settings names
0f12c2f
@d-goryslavets
update config parsing function names in scripts
03cea82
@d-goryslavets
upd test suite to use new config system; add integration tests for 4-…
88f98ef 
…genotype_qc
@d-goryslavets
fix plot settings names in integration tests config template
c270e9b
@y-popov
adjust variant qc scripts
0613997
@y-popov
refactor evaluation script
2112dad
@y-popov
fix indentation and partition calcs
e720546
@y-popov
make giab sample optional for compare combinations
0a1defa
@d-goryslavets
add readme for the test suite
d802b70
@y-popov
more robust path join
c23ce27
@d-goryslavets
Merge pull request #2 from wtsi-hgi/ip13-1kg-trio-test
3793952 
Changes to run manual tests on 1kg data with trios
@d-goryslavets
add skeleton for the remaining regression tests
0bd3b8d
@d-goryslavets
add draft for downloading test data using list of files instead of an…
bd5bbe1 
… archive
@d-goryslavets
create plots dir if doesn't exist; refactor path joining for RF outdir
6a7e641
@d-goryslavets
switch to downloading unarchived test data; upd and refactor tests ac…
7fca5f9 
…cordingly
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5 participants
@GennadiyZakharov @d-goryslavets @mkrooted256 @lbombini @y-popov