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Population-scale genomics
Is there a method when simplifying a tree sequence to remove all unary nodes except the recombination nodes (a middle ground between ts.simplify(keep_unary=False) versus ts.simplify(keep_unary=True))? We are working with the...
## Description Pull out the logic that iterates over trees and variants into a single base class, and allow this class to return a length. Also allows left, right, copy...
As I've been implementing tree traversal methods, I've commonly wanted to go up the chain of parents for a node. I think there's a good argument for a `tree.parents(u)` (or...
It seems that the ALT field being produce by `write_vcf()` is an integer. The VCF v4.2 spec indicates that the ALT field should be a nucleotide, a star, or a...
When I try to construct a tree sequence through a mutation table, - time must either be UNKNOWN_TIME (a NAN value which indicates the time is unknown) or be a...
It's useful to have a summary of the average arity of nodes in the trees. Here's a function that computes it: ```python def nodes_mean_arity(ts): weighted_arity = np.zeros(ts.num_nodes) span_in_tree = np.zeros(ts.num_nodes)...
Hi, When I try to convert a tree file to a vcf file, I get some error message as following. How do I solve this problem? ##############Error message **Traceback (most...
This issue tracks what needs to be done to eliminate the need to sort the edges associated with new births. The method has been used in [fwdpy11](https://github.com/molpopgen/fwpdy11) for about 3...
These should be seen as analogous to the ``start`` and ``stop`` arguments to Python's builtin ``range``, and be specified in tree sequence coordinates. We should initially ensure that start <...
A useful extension to the ``keep_rows`` functions added in #2700 would be a way to remap all the node ID values in a TableCollection using a given id_map (i.e., the...