tsinfer bug from latest msprime

[Yan Wong]

@jeromekelleher: has something changed recently with msprime? With the latest code I'm getting

ValueError: Error running '/usr/bin/python3 /home/yan/treeseq-inference/src/run_tsinfer.py dat.npy dat.pos.npy --length 5000 --recombination-rate 0.0005 --threads 8 /tmp/tmps1ji_28a': status=1:stderrb'Traceback (most recent call last):
  File "/home/yan/treeseq-inference/src/run_tsinfer.py", line 48, in <module>
    main()
  File "/home/yan/treeseq-inference/src/run_tsinfer.py", line 43, in main
    ts_new = panel.convert_records(P)
  File "/home/yan/treeseq-inference/src/tsinfer.py", line 131, in convert_records
    ll_ts.load_records(records)
TypeError: Required argument \'coalescence_records\' (pos 2) not found
Command exited with non-zero status '

with the array (dat.npy) and position (dat.pos.npy) data

array([[0, 0, 0, 1],
       [1, 0, 0, 1],
       [0, 0, 0, 1],
       [0, 0, 0, 1],
       [1, 0, 0, 1],
       [0, 1, 0, 1],
       [1, 0, 0, 1],
       [1, 0, 0, 1],
       [0, 0, 1, 0],
       [1, 1, 0, 1]], dtype=uint8)

and

array([ 2791.419188  ,  4276.1154304 ,  4665.81380159,  4692.31161638])

[Jerome Kelleher]

It's working for me using the tip of master.

>>> msprime.__version__
'0.4.1.dev198+ng535dffd'

Which version are you using?

[Yan Wong]

0.4.1.dev198+ng535dffd

[Yan Wong]

On holly, run

python3 ./src/run_tsinfer.py /tmp/dat.npy /tmp/dat.pos.npy --length 5000 --recombination-rate 0.0005 /tmp/out.hdf5

[Jerome Kelleher]

Should be fixed now.

[Yan Wong]

Yes, works, thanks