WARNING None fewer variants in output compared to original file

Created by: amstilp

With pgscatalog-utils==1.4.1, I'm getting a new error running pgscatalog-combine with ~20 PGSCatalog scores. One example of a score that's newly causing an error is PGS003581.

Output from new version:

$ pip freeze | grep pgscatalog       
pgscatalog-utils==1.4.1
pgscatalog.calc==0.3.0
pgscatalog.core==0.3.1
pgscatalog.match==0.3.3

$ pgscatalog-download --pgs PGS003581 --build GRCh38 -o tmp/ 
100%|█████████████████████████████████████████████| 1/1 [04:35<00:00, 275.49s/it]

$ pgscatalog-combine -s tmp/PGS003581_hmPOS_GRCh38.txt.gz -t GRCh38 -o combined.txt.gz
pgscatalog.core.cli.combine_cli: 2024-10-16 09:21:14 WARNING  None fewer variants in output compared to original file
100%|█████████████████████████████████████████████| 1/1 [00:00<00:00,  3.57it/s]

Output from earlier version:

$ pip freeze | grep pgscatalog                                 
pgscatalog-utils==1.3.1
pgscatalog.calc==0.2.2
pgscatalog.core==0.2.2
pgscatalog.match==0.3.1

$ pgscatalog-combine -s tmp/PGS003581_hmPOS_GRCh38.txt.gz -t GRCh38 -o combined.txt.gz
  0%|                                                     | 0/1 [00:00<?, ?it/s]pgscatalog.core.lib._normalise: 2024-10-16 09:22:47 WARNING  2987 bad variants
pgscatalog.core.lib._normalise: 2024-10-16 09:22:47 WARNING  2979 of 4861398 variants are duplicated in: PGS003581_hmPOS_GRCh38
100%|█████████████████████████████████████████████| 1/1 [00:59<00:00, 59.07s/it]