TypeError: '<' not supported between instances of 'RecombinationEvent' and 'RecombinationEvent'

[PengJia6]

Hi !

I report an error when I use whatshap phase command.

• whatshap 1.1
• Python 3.7.10
• command

  whatshap phase  --recombination-list  child.phased.vcf.gz.rec.list --indels -r GRCh38_full_analysis_set_plus_decoy_hla.fa --ped Quartet.ped  -o  Quartet.child.phased.vcf.gz  Quartet.minimap2.dv.pass.vcf.gz ChineseQuartet.LCL5.GRCh38.minimap2.bam ChineseQuartet.LCL6.GRCh38.minimap2.bam
  

• Note:
  The vcf file includes a family of four samples, two daughters and their biological parents.
• Error:

Cost accounted for by recombination events: 432
Traceback (most recent call last):
  File "/data/home/pengjia/miniconda3/envs/default/bin/whatshap", line 10, in <module>
    sys.exit(main())
  File "/data/home/pengjia/miniconda3/envs/default/lib/python3.7/site-packages/whatshap/__main__.py", line 83, in main
    module.main(args)
  File "/data/home/pengjia/miniconda3/envs/default/lib/python3.7/site-packages/whatshap/cli/phase.py", line 1107, in main
    run_whatshap(**vars(args))
  File "/data/home/pengjia/miniconda3/envs/default/lib/python3.7/site-packages/whatshap/cli/phase.py", line 565, in run_whatshap
    trios,
  File "/data/home/pengjia/miniconda3/envs/default/lib/python3.7/site-packages/whatshap/cli/phase.py", line 923, in write_recombination_list
    recombination_costs,
  File "/data/home/pengjia/miniconda3/envs/default/lib/python3.7/site-packages/whatshap/pedigree.py", line 160, in find_recombination
    event_list.sort()
TypeError: '<' not supported between instances of 'RecombinationEvent' and 'RecombinationEvent'

Thanks!

Peng Jia

[marcelm]

Do you think you can make the data available somewhere so we can reproduce this more easily? The full dataset is fine, but even better would be a reduced dataset that still shows the error.

[marcelm]

Hi again and thanks for the report. I have found the problem and fixed it in the development version of WhatsHap. I will release version 1.5 that contains the fix.

[PengJia6]

Thanks！