Merge discvr-23.7 to develop - #176

Merged

bbimber merged 61 commits into

fb_merge_23.7_to_develop

Aug 8, 2023

Commits on Jun 20, 2023

Correct ExtendedFuncotator arguments
bbimber
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cfa0442
Correct ExtendedFuncotator arguments
bbimber
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7b08af2

Commits on Jun 21, 2023

Correct ExtendedFuncotator arguments
bbimber
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7202897

Commits on Jun 22, 2023

Allow ExtendedFuncotator to skip MT
bbimber
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a2f2459

Commits on Jun 23, 2023

Add option to print missing fields for ExtendedFuncotator
bbimber
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09ded56

Commits on Jun 29, 2023

Specify the list of SnpSift fields to include
bbimber
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d031a26

Commits on Jun 30, 2023

Basic support for GroupCompare tool
bbimber
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67abe4d
Add more options for GroupCompareStep
bbimber
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04f1245
Update variant filter panel
bbimber
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0e7d3e4
Correct arguments for GroupCompareStep
bbimber
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192c305
Correct arguments for GroupCompareStep, missed with last commit
bbimber
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96cda11
Correct arguments for GroupCompareStep
bbimber
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f567aeb
Try to avoid test timing issues
bbimber
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4f7e3c8

Commits on Jul 3, 2023

Add initial pipelne job to cleanup extraneous MHC typing results
bbimber
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f7d146f
Add stubs for IDR study
bbimber
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6a413ab
Improved logging in MHC cleanup pipeline
bbimber
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71aca34
Allow more aspects of mGAP annotations to be driven using table (#113)
bbimber
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e76425a
Update field case
bbimber
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ce4dcc3
Add removal of low freq allele groups to MHC cleanup
bbimber
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e34b356
Add button to directly expose UpdateAnnotationsAction
bbimber
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b819d30
Fix button label
bbimber
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01a410c
UpdateAnnotationsAction: allow for source data with unequal line lengths
bbimber
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07cd1f0

Commits on Jul 4, 2023

Store annotation sourceField
bbimber
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2215b80
Rely on funcotator for clinvar annotation
bbimber
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8079599
Update field case
bbimber
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1b3c563
Allow for more missing values in annotations
bbimber
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a01eda2
Update code to load variant annotations
bbimber
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313d136
Improve MhcCleanupPipeline logging
bbimber
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5e45a28
Improve MhcCleanupPipeline logging
bbimber
committed
b6fe13d
Switch MhcCleanupPipeline to use transaction
bbimber
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858b2ab
Adjust logging thresholds for MhcCleanupPipeline
bbimber
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d39d0e9
Adjust logging thresholds for MhcCleanupPipeline
bbimber
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c20a471

Commits on Jul 5, 2023

Add additional MHC data collapse step
bbimber
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92caec5
Update location for MHC cleanup job
bbimber
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e87ebf6
Reduce logging for MHC cleanup job
bbimber
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c2b66c3

Commits on Jul 6, 2023

Fix error in MCC import
bbimber
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735b8e2
Improvements to MHC cleanup pipeline
bbimber
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f2f18c6

Commits on Jul 7, 2023

Commits on Jul 9, 2023

Misc improvements to variant annotation code
bbimber
committed
52f894b

Commits on Jul 19, 2023

Finalize implementation of fields/groups provider and add implementations in mGAP
bbimber
committed
345e67e

Commits on Jul 20, 2023

Make mGAP JBrowse fields data-driven (#116)
bbimber
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bbd31c6
mGAP UI updates
bbimber
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f434670
Allow mGAP redirect to also use variant search
bbimber
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bb4711c

Commits on Jul 21, 2023

Support both VCF and table selects for GroupCompare
bbimber
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f3f8c25

Commits on Jul 22, 2023

Misc improvements to JBrowse search
bbimber
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35370a8

Commits on Jul 23, 2023

Attempt to fix intermittent test failure
bbimber
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efd2488
Attempt to fix intermittent test failure
bbimber
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a72c769

Commits on Jul 25, 2023

Commits on Aug 3, 2023

Test fixes (#117)
bbimber
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b12940e

Commits on Aug 7, 2023

Correct study name in mGAP test
bbimber
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130edf4
Refactor mGAP study to folder export
bbimber
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6490e55
Refactor mGapReleaseGenerator to match new annotations
bbimber
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12da49b

Commits on Aug 8, 2023

Merge discvr-23.3 to discvr-23.7
bbimber
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25dd791
Merge pull request #118 from bimberlabinternal/23.7_fb_merge
bbimber
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c828500
Merge discvr-23.7 to develop
bbimber
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26eac1f