The two generatestatetrees commands

[ybta2957e]

Happy New Year! Thank you for developing DeCiFer. I found that there are two different generatestatetrees commands and I am not sure which one is appropriate. The one of this two commands got an error and another one worked.

Here are commands of generatestatetrees

(decifer_v2.0.4) [toby@nis test_input]$ generatestatetrees -help
Usage:
  generatestatetrees [--help|-h|-help] [-S str] [-SS str] [-maxCN int]
     [-maxXY int]
Where:
  --help|-h|-help
     Print a short help message
  -S str
     Input state tree file
  -SS str
     Output state tree file
  -maxCN int
     Maximum number of copy number events (default: 2)
  -maxXY int
     Maximum number of maternal/paternal copies (default: 2)
(decifer_v2.0.4) [toby@nis test_input]$ generatestatetrees -S CCLF-020_cn_states_unique.txt -SS CCLF-020_my_state_trees_unique.txt
Line: 4. Error: invalid copy number '1,1;2,2'
(decifer_v2.0.4) [toby@nis test_input]$ generatestatetrees CCLF-020_cn_states_unique.txt > CCLF-020_my_state_trees_unique.txt
(1,1)... Done.
(1,1) (2,0)... Done.
(1,1) (2,1)... Done.
(1,1) (2,2)... Done.
(1,1) (2,2) (5,1)... Done.
(1,1) (4,1)... Done.
Processed CCLF-020_cn_states_unique.txt...
(decifer_v2.0.4) [toby@nis test_input]$ 

Thank you Toby

[brian-arnold]

Thanks for catching this. For now please use generatestatetrees without the -S flag, i.e. the second way you've used it.

[melkebir]

Just to add to this, -S takes as input generatestatetrees output. That way you can build a comprehensive state trees file.