Open hyanwong opened 1 year ago
Over in https://github.com/tskit-dev/what-is-an-arg-paper/blob/main/argutils/convert.py we have some utilities to convert KwARG and ARGweaver files into ARG-format tree sequences. There is also a conversion-from-ARGweaver function associated with Guo and Rassmussen's SCAR which has simply lifted the code I wrote in https://github.com/mcveanlab/treeseq-inference/blob/master/src/ts_ARGweaver.py.
I think it would be useful, rather than reusing random bits of untested code, to have some of these in tsconvert. One question is whether we use the 2-RE-node representation (I guess yes, as this allows us to calculate the likelihood).
Over in https://github.com/tskit-dev/what-is-an-arg-paper/blob/main/argutils/convert.py we have some utilities to convert KwARG and ARGweaver files into ARG-format tree sequences. There is also a conversion-from-ARGweaver function associated with Guo and Rassmussen's SCAR which has simply lifted the code I wrote in https://github.com/mcveanlab/treeseq-inference/blob/master/src/ts_ARGweaver.py.
I think it would be useful, rather than reusing random bits of untested code, to have some of these in tsconvert. One question is whether we use the 2-RE-node representation (I guess yes, as this allows us to calculate the likelihood).