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Make ping mode default #323

Merged
merged 10 commits into from
May 29, 2024
Merged

Make ping mode default #323

merged 10 commits into from
May 29, 2024

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pbashyal-nmdp
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Fix ping mode for all

Fixes #321

  • When in ping mode, Alleles that were not already in lgx mode were not reduced properly. For those alleles educe to lgx first.

List of problematic alleles, their P group, the updated lgx reduction and the test to see if they match.

Allele P lgx P == lgx
DRB4*01:03 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:01 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:02 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:03 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:04 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:05 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:06 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:07 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:08 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:09 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:10 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:11 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:12 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:13 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:14 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:15 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:16 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:17 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:18 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:19 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:20 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:21 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:22 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:23 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:24 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:25 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:26 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:27 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:28 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:29 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:30 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:31 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:32 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:33 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:34 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:35 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:01:01 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:01:03 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:01:04 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:01:05 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:01:06 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:01:07 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:01:08 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:01:09 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:01:10 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:01:11 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:01:12 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:01:14 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:01:15 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:01:16 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:01:17 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:01:18 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:02:01 DRB4*01:01P DRB4*01:01 True
DRB4*01:03:02:02 DRB4*01:01P DRB4*01:01 True
C*02:10:02 C*02:02P C*02:02 True

@pbashyal-nmdp
Fix ping mode for all
e9bf6c5 
- When in `ping` mode, Alleles that were not already in `lgx` mode were not reduced properly. For those alleles educe to `lgx` first.
@pbashyal-nmdp
Bump version: 1.1.3 → 1.1.4
bb87b83
@pbashyal-nmdp pbashyal-nmdp added the bug Something isn't working label May 14, 2024
@pbashyal-nmdp pbashyal-nmdp self-assigned this May 14, 2024
@pbashyal-nmdp pbashyal-nmdp mentioned this pull request May 14, 2024
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@pbashyal-nmdp
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pbashyal-nmdp commented May 15, 2024 •
edited
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Lots of broken tests with making ping default. Working on fixing them. See
e.g.

       Expected: 'C*06:17'
           but: was 'C*06:02'

@pbashyal-nmdp pbashyal-nmdp changed the title Fix ping mode for all Draft: Fix ping mode for all May 16, 2024
@pbashyal-nmdp pbashyal-nmdp changed the title Draft: Fix ping mode for all **Draft**: Fix ping mode for all May 16, 2024
@pbashyal-nmdp pbashyal-nmdp changed the title **Draft**: Fix ping mode for all **Draft** : Fix ping mode for all May 16, 2024
@pbashyal-nmdp pbashyal-nmdp changed the title **Draft** : Fix ping mode for all Draft: Fix ping mode for all May 16, 2024
@pbashyal-nmdp
Fix tests to adjust for ping mode being the default.
87eece1 
 - Remove special ping ard object
 - Fix for `lg` (ARS) mode in `ping` mode
 - Remove duplicate tests in .json
@pbashyal-nmdp
Fix for Python 3.8
fba9222 
 - `removesuffix()` not available on str
@pbashyal-nmdp
Update README
a268b86
@pbashyal-nmdp
Bump version: 1.1.4 → 1.2.0
821862b
@pbashyal-nmdp
Add note for ping mode.
ed6d2cb
@pbashyal-nmdp pbashyal-nmdp changed the title Draft: Fix ping mode for all Make ping mode default May 21, 2024
@mmaiers-nmdp mmaiers-nmdp merged commit 4a7bb95 into nmdp-bioinformatics:master May 29, 2024
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@mmaiers-nmdp mmaiers-nmdp mmaiers-nmdp approved these changes

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bug Something isn't working
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Version 1.0.x - Bug fixes + Enhancements
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Successfully merging this pull request may close these issues.

g-group reduction for three-field alleles that aren't in a G-group is done incorrectly
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@pbashyal-nmdp @mmaiers-nmdp