Improve IBD documentation and IdentitySegments docs #3330
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I made the changes above and did some more here. I think it could of course be better but is good enough to go unless someone sees typos/errors. |
petrelharp
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petrelharp
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These are all changes I implemented in my commit, but some of these comments have explanation so I'm putting them in still.
docs/ibd.md
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| segments returned are the longest possible ones: for a fixed pair | ||
| ``(u, v)`` we follow the ancestral paths from ``u`` and ``v`` up the | ||
| trees and merge together adjacent genomic intervals whenever both the | ||
| MRCA ``a`` and the full ancestral paths from ``u`` and ``v`` to ``a`` | ||
| are identical. |
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TODO: double-check this is true. I suspect this might need some nuance at least.
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None of the things I checked that might be "merged" are merged - even if I split an edge, that also splits the IBD segment.
docs/ibd.md
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| by genealogical path) the IBD segments are obtained by merging together | ||
| adjacent MRCA intervals that share the same ancestor and paths to that |
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| by genealogical path) the IBD segments are obtained by merging together | |
| adjacent MRCA intervals that share the same ancestor and paths to that | |
| by genealogical path) the IBD segments are those | |
| that share the same ancestor and paths to that |
docs/ibd.md
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| - Passing an empty list, e.g. ``within=[]``, is allowed and simply | ||
| yields a result with zero pairs and zero segments. |
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Unnecessary detail.
| - Passing an empty list, e.g. ``within=[]``, is allowed and simply | |
| yields a result with zero pairs and zero segments. |
docs/ibd.md
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| no greater than ``max_time`` are returned. The time is measured in | ||
| the same units as the node times in the tree sequence (e.g., generations). |
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What else would it be measured in?
| no greater than ``max_time`` are returned. The time is measured in | |
| the same units as the node times in the tree sequence (e.g., generations). | |
| no greater than ``max_time`` are returned. |
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Extracted from #3329