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nmdp-bioinformatics / py-ard

HLA ARD Reduction in Python
https://py-ard.org/
GNU Lesser General Public License v3.0
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Make `ping` mode default #323

Closed pbashyal-nmdp closed 6 months ago

pbashyal-nmdp commented 6 months ago

Fix ping mode for all

Fixes #321

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 commented 6 months ago

Lots of broken tests with making ping default. Working on fixing them. See e.g.

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