search

WGLab / LinkedSV

MIT License
20 stars 8 forks source link

Handle case were zero large SVs are called #18

Closed pontushojer closed 3 years ago

pontushojer commented 3 years ago

Thank you for creating this wonderful tool!

I have been running LinkedSV a while and started running into this error (see excerpt in log below). 

[12/07/2020 14:50:41 (243.913 MB)] number of retained SVs: 0
Traceback (most recent call last):
  File "/Users/pontus.hojer/miniconda3/envs/blr-latest/bin/linkedsv.py", line 313, in <module>
    main()
  File "/Users/pontus.hojer/miniconda3/envs/blr-latest/bin/linkedsv.py", line 59, in main
    filter_calls.filter_calls(args, dbo_args, endpoint_args)
  File "/Users/pontus.hojer/projects/LinkedSV/scripts/filter_calls.py", line 137, in filter_calls
    n_digit = int(math.log10(n_svcall) + 2)
ValueError: math domain error

The error happens when I run on a single chromosome the number of large SV is sometimes 0. This causes this fatal error. However there are ofter small_deletions and/or large_cnv called for the same chromsome. With this edit the tool will continue to call small_deletions and large_cnv.

fangli80 commented 3 years ago

Thanks for the editing! Best, Li